Comparative Transcriptome Analysis of Resistant and Susceptible Tomato Lines in Response to Infection by Xanthomonas perforans Race T3
Identifieur interne : 000019 ( Pmc/Corpus ); précédent : 000018; suivant : 000020Comparative Transcriptome Analysis of Resistant and Susceptible Tomato Lines in Response to Infection by Xanthomonas perforans Race T3
Auteurs : Heshan Du ; Yuqing Wang ; Jingjing Yang ; Wencai YangSource :
- Frontiers in Plant Science [ 1664-462X ] ; 2015.
Abstract
Bacterial spot, incited by several
Url:
DOI: 10.3389/fpls.2015.01173
PubMed: 26734053
PubMed Central: 4689867
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Comparative Transcriptome Analysis of Resistant and Susceptible Tomato Lines in Response to Infection by <italic>Xanthomonas perforans</italic> Race T3</title><author><name sortKey="Du, Heshan" sort="Du, Heshan" uniqKey="Du H" first="Heshan" last="Du">Heshan Du</name></author><author><name sortKey="Wang, Yuqing" sort="Wang, Yuqing" uniqKey="Wang Y" first="Yuqing" last="Wang">Yuqing Wang</name></author><author><name sortKey="Yang, Jingjing" sort="Yang, Jingjing" uniqKey="Yang J" first="Jingjing" last="Yang">Jingjing Yang</name></author><author><name sortKey="Yang, Wencai" sort="Yang, Wencai" uniqKey="Yang W" first="Wencai" last="Yang">Wencai Yang</name></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">26734053</idno><idno type="pmc">4689867</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4689867</idno><idno type="RBID">PMC:4689867</idno><idno type="doi">10.3389/fpls.2015.01173</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000019</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000019</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Comparative Transcriptome Analysis of Resistant and Susceptible Tomato Lines in Response to Infection by <italic>Xanthomonas perforans</italic> Race T3</title><author><name sortKey="Du, Heshan" sort="Du, Heshan" uniqKey="Du H" first="Heshan" last="Du">Heshan Du</name></author><author><name sortKey="Wang, Yuqing" sort="Wang, Yuqing" uniqKey="Wang Y" first="Yuqing" last="Wang">Yuqing Wang</name></author><author><name sortKey="Yang, Jingjing" sort="Yang, Jingjing" uniqKey="Yang J" first="Jingjing" last="Yang">Jingjing Yang</name></author><author><name sortKey="Yang, Wencai" sort="Yang, Wencai" uniqKey="Yang W" first="Wencai" last="Yang">Wencai Yang</name></author></analytic><series><title level="j">Frontiers in Plant Science</title><idno type="eISSN">1664-462X</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Bacterial spot, incited by several <italic>Xanthomonas</italic> sp., is a serious disease in tomato (<italic>Solanum lycopersicum</italic> L.). Although genetics of resistance has been widely investigated, the interactions between the pathogen and tomato plants remain unclear. In this study, tanscriptomes of <italic>X. perforans</italic> race T3 infected tomato lines were compared to those of controls. An average of 7 million reads were generated with approximately 21,526 genes mapped in each sample post-inoculation at 6 h (6 HPI) and 6 days (6 DPI) using RNA-sequencing technology. Overall, the numbers of differentially expressed genes (DEGs) were higher in the resistant tomato line PI 114490 than in the susceptible line OH 88119, and the numbers of DEGs were higher at 6 DPI than at 6 HPI. Fewer genes (78 in PI 114490 and 15 in OH 88119) were up-regulated and most DEGs were down-regulated, suggesting that the inducible defense response might not be fully activated at 6 HPI. Accumulation expression levels of 326 co-up regulated genes in both tomato lines at 6 DPI might be involved in basal defense, while the specific and strongly induced genes at 6 DPI might be correlated with the resistance in PI 114490. Most DEGs were involved in plant hormone signal transduction, plant-pathogen interaction and phenylalanine metabolism, and the genes significantly up-regulated in PI 114490 at 6 DPI were associated with defense response pathways. DEGs containing NBS-LRR domain or defense-related WRKY transcription factors were also identified. The results will provide a valuable resource for understanding the interactions between <italic>X. perforans</italic> and tomato plants.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Asai, T" uniqKey="Asai T">T. Asai</name></author><author><name sortKey="Tena, G" uniqKey="Tena G">G. Tena</name></author><author><name sortKey="Plotnikova, J" uniqKey="Plotnikova J">J. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Front Plant Sci</journal-id><journal-id journal-id-type="iso-abbrev">Front Plant Sci</journal-id><journal-id journal-id-type="publisher-id">Front. Plant Sci.</journal-id><journal-title-group><journal-title>Frontiers in Plant Science</journal-title></journal-title-group><issn pub-type="epub">1664-462X</issn><publisher><publisher-name>Frontiers Media S.A.</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">26734053</article-id><article-id pub-id-type="pmc">4689867</article-id><article-id pub-id-type="doi">10.3389/fpls.2015.01173</article-id><article-categories><subj-group subj-group-type="heading"><subject>Plant Science</subject><subj-group><subject>Original Research</subject></subj-group></subj-group></article-categories><title-group><article-title>Comparative Transcriptome Analysis of Resistant and Susceptible Tomato Lines in Response to Infection by <italic>Xanthomonas perforans</italic> Race T3</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Du</surname><given-names>Heshan</given-names></name><uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/288915/overview"></uri></contrib><contrib contrib-type="author"><name><surname>Wang</surname><given-names>Yuqing</given-names></name><xref ref-type="author-notes" rid="fn001"><sup>*</sup></xref><uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/300016/overview"></uri></contrib><contrib contrib-type="author"><name><surname>Yang</surname><given-names>Jingjing</given-names></name><uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/302980/overview"></uri></contrib><contrib contrib-type="author"><name><surname>Yang</surname><given-names>Wencai</given-names></name><xref ref-type="author-notes" rid="fn002"><sup>*</sup></xref><uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/266801/overview"></uri></contrib></contrib-group><aff><institution>Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, China Agricultural University</institution><country>Beijing, China</country></aff><author-notes><fn fn-type="edited-by"><p>Edited by: Vasileios Fotopoulos, Cyprus University of Technology, Cyprus</p></fn><fn fn-type="edited-by"><p>Reviewed by: Jaime Auger, Universidad de Chile, Chile; Hao Peng, Washington State University, USA</p></fn><corresp id="fn001">*Correspondence: Yuqing Wang <email xlink:type="simple">wyq@cau.edu.cn</email>;</corresp><corresp id="fn002">Wencai Yang <email xlink:type="simple">yangwencai@cau.edu.cn</email></corresp><fn fn-type="other" id="fn003"><p>This article was submitted to Crop Science and Horticulture, a section of the journal Frontiers in Plant Science</p></fn></author-notes><pub-date pub-type="epub"><day>24</day><month>12</month><year>2015</year></pub-date><pub-date pub-type="collection"><year>2015</year></pub-date><volume>6</volume><elocation-id>1173</elocation-id><history><date date-type="received"><day>21</day><month>8</month><year>2015</year></date><date date-type="accepted"><day>07</day><month>12</month><year>2015</year></date></history><permissions><copyright-statement>Copyright © 2015 Du, Wang, Yang and Yang.</copyright-statement><copyright-year>2015</copyright-year><copyright-holder>Du, Wang, Yang and Yang</copyright-holder><license xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.</license-p></license></permissions><abstract><p>Bacterial spot, incited by several <italic>Xanthomonas</italic> sp., is a serious disease in tomato (<italic>Solanum lycopersicum</italic> L.). Although genetics of resistance has been widely investigated, the interactions between the pathogen and tomato plants remain unclear. In this study, tanscriptomes of <italic>X. perforans</italic> race T3 infected tomato lines were compared to those of controls. An average of 7 million reads were generated with approximately 21,526 genes mapped in each sample post-inoculation at 6 h (6 HPI) and 6 days (6 DPI) using RNA-sequencing technology. Overall, the numbers of differentially expressed genes (DEGs) were higher in the resistant tomato line PI 114490 than in the susceptible line OH 88119, and the numbers of DEGs were higher at 6 DPI than at 6 HPI. Fewer genes (78 in PI 114490 and 15 in OH 88119) were up-regulated and most DEGs were down-regulated, suggesting that the inducible defense response might not be fully activated at 6 HPI. Accumulation expression levels of 326 co-up regulated genes in both tomato lines at 6 DPI might be involved in basal defense, while the specific and strongly induced genes at 6 DPI might be correlated with the resistance in PI 114490. Most DEGs were involved in plant hormone signal transduction, plant-pathogen interaction and phenylalanine metabolism, and the genes significantly up-regulated in PI 114490 at 6 DPI were associated with defense response pathways. DEGs containing NBS-LRR domain or defense-related WRKY transcription factors were also identified. The results will provide a valuable resource for understanding the interactions between <italic>X. perforans</italic> and tomato plants.</p></abstract><kwd-group><kwd><italic>Solanum lycopersicum</italic></kwd><kwd><italic>Xanthomonas perforans</italic></kwd><kwd>compatible and incompatible interactions</kwd><kwd>transcriptome analysis</kwd><kwd>RNA sequencing</kwd></kwd-group><funding-group><award-group><funding-source id="cn001">National Natural Science Foundation of China<named-content content-type="fundref-id">10.13039/501100001809</named-content></funding-source><award-id rid="cn001">31372073</award-id></award-group></funding-group><counts><fig-count count="6"></fig-count><table-count count="5"></table-count><equation-count count="0"></equation-count><ref-count count="51"></ref-count><page-count count="14"></page-count><word-count count="9660"></word-count></counts></article-meta></front><body><sec sec-type="intro" id="s1"><title>Introduction</title><p>Bacterial spot caused by at least four distinct species of <italic>Xanthomonas</italic> (<italic>X. euvesicatoria, X. vesicatoria, X. perforans</italic>, and <italic>X. gardneri</italic>), severely affects marketability of both fresh-market and processing tomato (Jones et al., <xref rid="B17" ref-type="bibr">2000</xref>; Stall et al., <xref rid="B39" ref-type="bibr">2009</xref>). Based on their virulence on a group of tomato genotypes, the causative agents of bacterial spot can be classified into five physiological races T1–T5 (Jones et al., <xref rid="B18" ref-type="bibr">2005</xref>). It is difficult to manage the disease once the outbreak occurs (Yang et al., <xref rid="B50" ref-type="bibr">2007</xref>; Stall et al., <xref rid="B39" ref-type="bibr">2009</xref>). Identification and characterization of the host resistance as well as regulatory genes can provide insights into understanding the mechanisms of host resistance and the use of host resistance to develop new cultivars with durable resistance.</p><p>The resistance to <italic>X. perforans</italic> race T3 in tomato can be classified into two types, hypersensitive response (HR) and field resistance. HR is usually conditioned by single dominant genes, while field resistance is generally controlled by multiple genes (Yang, <xref rid="B49" ref-type="bibr">2013</xref>). To date, four major dominant genes, <italic>Rx4</italic> in <italic>Solanum pimpinellifolium</italic> accession PI 128216 (Robbins et al., <xref rid="B33" ref-type="bibr">2009</xref>; Pei et al., <xref rid="B32" ref-type="bibr">2012</xref>), <italic>Xv3</italic> in an unimproved breeding line Hawaii 7981 (Wang et al., <xref rid="B47" ref-type="bibr">2011</xref>), <italic>Rx</italic><sub><italic>LA</italic>1589</sub> in <italic>S. pimpinellifolium</italic> accession LA 1589 (Sun et al., <xref rid="B41" ref-type="bibr">2011a</xref>), and <italic>RXopJ4</italic> in <italic>S. pennellii</italic> accession LA 716 (Sharlach et al., <xref rid="B38" ref-type="bibr">2013</xref>), conferring HR to <italic>X. perforans</italic> race T3 have been identified and mapped. A recent study suggests that <italic>Rx4, Xv3</italic>, and <italic>Rx</italic><sub><italic>LA</italic>1589</sub> are possibly the same gene (Zhao et al., <xref rid="B51" ref-type="bibr">2015</xref>). Although these genes also confer field resistance to race T3, they need modifiers and may be affected by genetic background (Scott et al., <xref rid="B37" ref-type="bibr">2001</xref>; Robbins et al., <xref rid="B33" ref-type="bibr">2009</xref>; Wang et al., <xref rid="B47" ref-type="bibr">2011</xref>; Sharlach et al., <xref rid="B38" ref-type="bibr">2013</xref>). Therefore, the tomato lines with HR usually show partial resistance to race T3 in the field. On the contrary, the <italic>S. lycopersicum</italic> var. <italic>cerasiforme</italic> accession PI 114490 shows no HR but high resistance to race T3 conditioned by at least five quantitative trait loci (QTL) in the field (Sun et al., <xref rid="B43" ref-type="bibr">2011b</xref>, <xref rid="B42" ref-type="bibr">2014</xref>; Scott et al., <xref rid="B36" ref-type="bibr">2015</xref>). In addition to identification and genetic mapping of genes or QTLs, efforts have also been making on discovery of genes participating in a complex molecular network of regulation during the time-course of HR to race T3 in the unimproved tomato line Hawaii 7981 using microarray analysis approach (Gibly et al., <xref rid="B13" ref-type="bibr">2004</xref>; Balaji et al., <xref rid="B2" ref-type="bibr">2007</xref>), and identification of genes differentially expressed in the resistant line PI 114490 and a susceptible line OH 88119 during the time-course of the race T3 infection using cDNA-AFLP techniques (Du et al., <xref rid="B10" ref-type="bibr">2014</xref>). Comparison of genes differentially expressed in PI 114490 and OH 88119 provides us some information to understand the mechanism of resistance to bacterial spot race T3 in tomato during the process of symptom development at the 3, 4, and 5 days post spray-inoculation stages (Du et al., <xref rid="B10" ref-type="bibr">2014</xref>). However, both microarray and cDNA-AFLP can only identify part of the genes involved in resistance or defense processes due to their low throughput limitation. To fully unravel the mechanisms of field resistance to race T3 of bacterial spot, it is necessary to identify more genes differentially expressed during different infection times in tomato.</p><p>With the availability of a high-quality tomato genome sequence and second-generation sequencing, RNA-seq technology has rapidly become a popular tool for genome-wide expression profiling, providing the potential to better understanding the comprehensive host-pathogen interactions. Many studies have, therefore, tried to elucidate a nearly complete picture of inducible defense response pathways using RNA-seq analysis (Kim et al., <xref rid="B21" ref-type="bibr">2011</xref>; Li et al., <xref rid="B25" ref-type="bibr">2012</xref>; Gao et al., <xref rid="B12" ref-type="bibr">2013</xref>; Tan et al., <xref rid="B44" ref-type="bibr">2015</xref>). Through comparing the different RNA-seq data about hosts and pathogens interactions, similar or specific sets of genes activated in different plant pathosystems have been discovered. Meanwhile, using the expression pattern regulated by pathogen infection, it is also possible to identify the known defense gene family member involved in the tomato immune response. For example, some plant R genes, such as pepper <italic>Bs3</italic> and rice <italic>Xa27</italic> belonging to NBS-LRR gene family, are transcriptionally activated by corresponding transcription activator-like effector (TALE) protein (Gu et al., <xref rid="B15" ref-type="bibr">2005</xref>; Röemer et al., <xref rid="B34" ref-type="bibr">2007</xref>). Taking advantage of the TALE-induced expression pattern, a <italic>Xanthomonas</italic> TAL-effector activated resistance gene <italic>Bs4C</italic> has been identified using RNA-seq (Strauss et al., <xref rid="B40" ref-type="bibr">2012</xref>). Therefore, RNA-seq technology can be used as a tool to isolate pathogen induced R gene, which could avoid laborious positional cloning and investigate the expression pattern of different defense signaling genes family members as well as identify novel defense related genes.</p><p>In the current study, it is first time using RNA-seq to investigate transcript dynamics of the field resistant line PI 114490 and the susceptible line OH 88119 in response to <italic>X. perforans</italic> race T3 at 6 h and 6 days post-infection. Large-scale expression profiling identified both common and specific differentially expressed genes in two tomato lines at different time points after inoculation. In addition, 8 induced genes were validated by quantitative real-time PCR (qRT-PCR) experiments. Our results may provide a subset of potential candidate defense-related genes in tomato-<italic>X. perforans</italic> interaction, which will help in better understanding the molecular basis of field resistance to bacterial spot in tomato.</p></sec><sec sec-type="materials and methods" id="s2"><title>Materials and methods</title><sec><title>Plant materials and <italic>X. perforans</italic> race T3 inoculation</title><p>Two tomato lines, a cherry tomato line PI 114490 with high level of field resistance and an elite processing breeding line OH 88119 with susceptibility to <italic>X. perforans</italic> race T3 (Sun et al., <xref rid="B43" ref-type="bibr">2011b</xref>), were used in this study. For inoculation with <italic>X. perforans</italic> race T3, tomato seedlings were grown in a growth room at 28°C/25°C (light/dark), with a 14-h photoperiod. The race T3 strain <italic>Xv829</italic> was cultured on yeast, dextrose, calcium carbonate (YDC) agar medium (Lelliot and Stead, <xref rid="B24" ref-type="bibr">1987</xref>) at 28°C for 48–72 h prior to inoculation. Bacterial cultures were diluted to a concentration of approximately 3 × 10<sup>8</sup> colony forming units per ml using sterile solution containing 10 mM MgSO<sub>4</sub>·7H<sub>2</sub>O and 0.025% (v/v) Silwet L77. Six-week-old plants were spray-inoculated with the bacterial suspension, and plants sprayed with the sterile solution containing 10 mM MgSO<sub>4</sub>·7H<sub>2</sub>O and 0.025% (v/v) Silwet L77 were used as controls (mock-treatment). The plants were misted with water twice a day (9:00 a.m. and 5:00 p.m.) from 1 day before inoculation to 6 days after inoculation to increase humidity and prolong leaf wetness for disease development.</p></sec><sec><title>RNA isolation, RNA-seq library preparation, and sequencing</title><p>Total RNA was isolated from leaf samples collected at started point (mock-treatment), 6 h-post-inoculation (HPI) and 6 day-post-inoculation (DPI) using the TRIzol reagent (Invitrogen, USA) following to the manufacturer's protocol. The concentration of total RNA was determined by NanoDrop 2000 Spectrophotometer (Thermo Fisher Scientific, USA), and the RNA integrity value (RIN) was checked using RNA 6000 Pico LabChip of Agilent 2100 Bioanalyzer (Agilent, USA).</p><p>Three libraries (mock-treatment, race T3 treatment at 6 HPI and 6 DPI) for each tomato line were constructed for RNA-seq analysis. Two hundred micro-grams total RNA was incubated with 10 units DNase I (Ambion, USA) at 37°C for 1 h, and then nuclease-free water was added to bring the sample volume to 250 μl. The MicroPoly(A)Purist™ Kit (Ambion) was used to enrich mRNA according to the manufacture's protocol. The enriched mRNA was dissolved in 100 μl RNA storage solution and the final concentration was determined by NanoDrop 2000 Spectrophotometer. Double-stranded cDNA was synthesized from the mRNA according to the method described previously (Ng et al., <xref rid="B29" ref-type="bibr">2005</xref>) with some modifications. First-strand cDNA was synthesized from 10 μg mRNA with Gsul-oligo dT primers using 1000 units of superscript II reverse transcriptase (Invitrogen). After incubation at 42°C for 1 h, the 5′-CAP structure of mRNA was oxidized by NalO<sub>4</sub> (Sigma, USA) and ligated to biotin hydrazide, which was used to select complete mRNA/cDNA by binding Dynal M280 beads (Invitrogen). The second-strand cDNA synthesis was subsequently performed using Ex Taq polymerase (TaKaRa, Japan). The polyA and 5′ adaptor were removed by GsuI digestion. The double-strand cDNA was ultrasonically fractioned with a cDNA size fractionation column at a range of 300–500 bp, and then purified using Agencourt Ampure beads (Agencourt, USA). Sequencing libraries were generated using TruSeqTM DNA Sample Prep Kit—Set A (Illumina, USA). Libraries were clustered using TruSeq PE Cluster Kit (Illumina) according to manufacturer's instructions. After cluster generation, the libraries were sequenced with an Illumina HiSeq™ 2000 platform by Hanyu Bio-Tech Co., Ltd (Shanghai, China).</p></sec><sec><title>Analysis of illumina reads and identification of differentially expressed genes</title><p>Raw reads were firstly cleaned by removing adaptor sequences and unreliable low quality sequences (reads with unknown sequences “N”). The filtered clean reads were then mapped to <italic>S. lycopersicum</italic> reference genome sequence (SL2.40 version) and related annotation was obtained from the International Tomato Annotation Group (ITAG) Release 2.3 Predicted CDS (<ext-link ext-link-type="uri" xlink:href="https://www.sgn.cornell.edu/">https://www.sgn.cornell.edu/</ext-link>) using Bowtie2 with default settings (Langmead et al., <xref rid="B22" ref-type="bibr">2009</xref>). Clean reads mapped to reference genome sequence with multiple genes were filtered. Reads per kilo bases per million uniquely mapped reads (RPKM) values per sample for all genes were calculated based on both the total number of reads that mapped to the tomato reference CDS database and corresponding genes length (Mortazavi et al., <xref rid="B28" ref-type="bibr">2008</xref>). Differentially expressed genes (DEG) were identified by DEG-seq package using the MA-plot-based method with Random Sampling model (MARS) (Wang et al., <xref rid="B48" ref-type="bibr">2010</xref>). The <italic>q</italic>-value was adjusted using the method described in Benjamini and Hochberg (<xref rid="B3" ref-type="bibr">1995</xref>). “False Discovery Rate (FDR) ≤ 0.001 and the absolute value of Log2fold-change ≥ 2” were used as the threshold to determine the significance of gene expression difference.</p></sec><sec><title>Gene ontology and KEGG pathway analysis</title><p>Gene ontology analysis for DEGs was performed using GoPipe (Chen et al., <xref rid="B6" ref-type="bibr">2005</xref>) through BLASTP against Swiss-Prot and TrEMBL database. The metabolic pathway was constructed based on Kyoto Encyclopedia of Genes and Genomes (KEGG) database using BBH (bi-directional best hit) method (Kanehisa et al., <xref rid="B20" ref-type="bibr">2010</xref>). The KO number was obtained for each protein and used for constructing metabolic pathways.</p></sec><sec><title>RT-PCR and qRT-PCR validation</title><p>To verify the results of RNA-seq analysis, 8 differentially expressed genes (Receptor like kinase, Polyphenol oxidase, Harpin-induced protein-like, LRR receptor-like serine/threonine-protein kinase, 1-aminocyclopropane-1-carboxylate oxidase, Calmodulin 2, Universal stress protein family protein, and WRKY transcription factor 16) were selected for semi-quantitative RT-PCR and qRT-PCR analysis. First strand cDNA was synthesized by M-MLV reverse transcriptase (TaKaRa) with the same batch of RNA samples used in RNA-seq analysis. The specificity of primers for each gene (Table <xref ref-type="supplementary-material" rid="SM1">S1</xref>) was confirmed by analyzing PCR products on agarose gel and melting curve during real-time PCR. RT-PCR and qRT-PCR was conducted according to the previous protocols (Pei et al., <xref rid="B32" ref-type="bibr">2012</xref>; Du et al., <xref rid="B10" ref-type="bibr">2014</xref>).</p></sec></sec><sec sec-type="results" id="s3"><title>Results</title><sec><title>Analysis of RNA-seq libraries and reads alignment</title><p>Approximately 43 million Illumina raw reads were generated from six libraries with an average of 7 million 100 bp raw reads in each individual library. The raw reads were deposited in the National Center for Biotechnology Information Sequence Read Archive under the accession number <ext-link ext-link-type="DDBJ/EMBL/GenBank" xlink:href="SRP065597">SRP065597</ext-link>. In the six libraries, 97.9–99.3% of raw reads were clean. Of the clean reads, 46.5–77.3% could be mapped uniquely to one location within the tomato reference genome, 8.4–40.3% could be aligned to highly conserved domain sequences shared by different annotated genes, and 9.6–21.3% failed to map to the tomato genome sequence (Table <xref ref-type="table" rid="T1">1</xref>). The uniquely mapped clean reads matched 21,168–21,993 with an average of 21,526 genes (approximately 62%) to the tomato annotated genes for the six libraries (Table <xref ref-type="table" rid="T1">1</xref>). Approximately 20,000 genes were mapped at both mock- and T3-treatment samples (Image <xref ref-type="supplementary-material" rid="SM6">S1</xref>). The number of specific matched genes was higher in the PT6d library (890) than in other five libraries (Image <xref ref-type="supplementary-material" rid="SM6">S1</xref>).</p><table-wrap id="T1" position="float"><label>Table 1</label><caption><p><bold>Summary of RNA-seq data</bold>.</p></caption><table frame="hsides" rules="groups"><thead><tr><th valign="top" align="left" rowspan="1" colspan="1"><bold>Sample ID<xref ref-type="table-fn" rid="TN1"><sup>a</sup></xref></bold></th><th valign="top" align="center" rowspan="1" colspan="1"><bold>No. of raw reads</bold></th><th valign="top" align="center" colspan="4" style="border-bottom: thin solid #000000;" rowspan="1"><bold>No. of clean reads</bold></th><th valign="top" align="center" rowspan="1" colspan="1"><bold>No. of matched genes</bold></th></tr><tr><th rowspan="1" colspan="1"></th><th rowspan="1" colspan="1"></th><th valign="top" align="center" rowspan="1" colspan="1"><bold>Total</bold></th><th valign="top" align="center" rowspan="1" colspan="1"><bold>Mapped to unique genes</bold></th><th valign="top" align="center" rowspan="1" colspan="1"><bold>Mapped to multiple genes</bold></th><th valign="top" align="center" rowspan="1" colspan="1"><bold>Unmapped</bold></th><th rowspan="1" colspan="1"></th></tr></thead><tbody><tr><td valign="top" align="left" rowspan="1" colspan="1">PM</td><td valign="top" align="center" rowspan="1" colspan="1">10,937,043</td><td valign="top" align="center" rowspan="1" colspan="1">10,783,924</td><td valign="top" align="center" rowspan="1" colspan="1">5,402,226</td><td valign="top" align="center" rowspan="1" colspan="1">4,347,202</td><td valign="top" align="center" rowspan="1" colspan="1">1,034,496</td><td valign="top" align="center" rowspan="1" colspan="1">21,776</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">PT6h</td><td valign="top" align="center" rowspan="1" colspan="1">6,707,580</td><td valign="top" align="center" rowspan="1" colspan="1">6,603,613</td><td valign="top" align="center" rowspan="1" colspan="1">4,852,118</td><td valign="top" align="center" rowspan="1" colspan="1">556,598</td><td valign="top" align="center" rowspan="1" colspan="1">1,194,897</td><td valign="top" align="center" rowspan="1" colspan="1">21,345</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">PT6d</td><td valign="top" align="center" rowspan="1" colspan="1">7,148,378</td><td valign="top" align="center" rowspan="1" colspan="1">7,096,195</td><td valign="top" align="center" rowspan="1" colspan="1">5,421,494</td><td valign="top" align="center" rowspan="1" colspan="1">548,184</td><td valign="top" align="center" rowspan="1" colspan="1">1,126,517</td><td valign="top" align="center" rowspan="1" colspan="1">21,993</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">OM</td><td valign="top" align="center" rowspan="1" colspan="1">6,154,320</td><td valign="top" align="center" rowspan="1" colspan="1">6,094,623</td><td valign="top" align="center" rowspan="1" colspan="1">4,710,354</td><td valign="top" align="center" rowspan="1" colspan="1">476,999</td><td valign="top" align="center" rowspan="1" colspan="1">907,270</td><td valign="top" align="center" rowspan="1" colspan="1">21,708</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">OT6h</td><td valign="top" align="center" rowspan="1" colspan="1">5,381,872</td><td valign="top" align="center" rowspan="1" colspan="1">5,316,213</td><td valign="top" align="center" rowspan="1" colspan="1">3,927,090</td><td valign="top" align="center" rowspan="1" colspan="1">399,894</td><td valign="top" align="center" rowspan="1" colspan="1">989,229</td><td valign="top" align="center" rowspan="1" colspan="1">21,168</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">OT6d</td><td valign="top" align="center" rowspan="1" colspan="1">6,921,528</td><td valign="top" align="center" rowspan="1" colspan="1">6,773,407</td><td valign="top" align="center" rowspan="1" colspan="1">3,148,353</td><td valign="top" align="center" rowspan="1" colspan="1">2,181,678</td><td valign="top" align="center" rowspan="1" colspan="1">1,443,376</td><td valign="top" align="center" rowspan="1" colspan="1">21,168</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Average</td><td valign="top" align="center" rowspan="1" colspan="1">7,208,454</td><td valign="top" align="center" rowspan="1" colspan="1">7,111,329</td><td valign="top" align="center" rowspan="1" colspan="1">4,576,939</td><td valign="top" align="center" rowspan="1" colspan="1">1,418,426</td><td valign="top" align="center" rowspan="1" colspan="1">1,115,964</td><td valign="top" align="center" rowspan="1" colspan="1">21,526</td></tr></tbody></table><table-wrap-foot><fn id="TN1"><label>a</label><p><italic>PM and OM: PI 114490 and OH 88119 respectively mock-treatment with the sterile solution containing 10 mM MgSO<sub>4</sub>. 7H<sub>2</sub>O and 0.025%(v/v) Silwet L77. PT and OT: PI 114490 and OH 88119 respectively inoculated with bacterial spot race T3</italic>.</p></fn></table-wrap-foot></table-wrap><p>The genes RPKM values were calculated only for those uniquely mapped reads. The number of genes with RPKM values of 0 varied from 12,734 to 13,559, with an average of 13,200 in the six libraries (Table <xref ref-type="supplementary-material" rid="SM2">S2</xref>). Of which 10,117 were common in all libraries, indicating a very low level or no expression of those genes in the six samples. The numbers of genes with RPKM value of 0 were slightly higher in the three libraries of the susceptible line OH 88119 than the corresponding samples in the resistant line PI 114490. Based on the expression analysis using RT-PCR and qRT-PCR, genes with RPKM value less than 2.28 needed more amount of cDNA and genes with RPLM value greater than 10.7 needed less amount of cDNA for obtaining clear bands (data not shown). Therefore, genes with RPKM values of 0–3 were considered as at low level of expression, while genes with RPKM values beyond 10 were considered to be expressed at high level. The number of highly expressed genes was less in PT6h library compared to OT6h, but more in PT6d than OT6d (Table <xref ref-type="supplementary-material" rid="SM2">S2</xref>).</p></sec><sec><title>Differentially expressed genes in response to <italic>X. perforans</italic> race T3</title><p>More stringent criteria with smaller FDR (≤ 0.001) and higher fold-change value (absolute value of Log<sub>2</sub>fold-change ≥ 2) were used to analyze the global transcriptome dynamics of both resistant line PI 114490 and susceptible line OH 88119 in response to race T3 during 6 h and 6 days post-inoculation. Overall, the number of differentially expressed genes (DEGs) was higher in PI 114490 than in OH 88119 at both infection stages, and the number of DEGs was considerably higher at 6 DPI than at 6 HPI in both tomato lines (Figure <xref ref-type="fig" rid="F1">1</xref>). At the 6 HPI, there were 591 and 299 genes were differentially expressed in PI 114490 and OH 88119, respectively. Most DEGs showed down-regulations in both tomato lines, whereas only 78 and 15 genes were up-regulated in PI 114490 and OH 88119, respectively (Figure <xref ref-type="fig" rid="F1">1</xref>). However, the numbers of DEGs dramatically increased to 1656 and 1154 at 6 DPI in PI 114490 and OH 88119, respectively, and the numbers of up-regulated genes were obviously greater than that of down-regulated genes (Figure <xref ref-type="fig" rid="F1">1</xref>). Consideration of numbers and fold changes of these DEGs, resistant tomato line PI 114490 had a higher frequency and stronger fold changes of DEGs at 6 DPI, compared to PI 114490 at 6 HPI and OH 88119 at both time points (Figure <xref ref-type="fig" rid="F1">1</xref>).</p><fig id="F1" position="float"><label>Figure 1</label><caption><p><bold>Numbers of differentially expressed genes (DEGs) identified in tomato lines PI 114490 and OH 88119 at 6 h and 6 days post-inoculation of <italic>Xanthomonas perforans</italic> race T3</bold>. The DEGs were identified using FDR ≤ 0.001 and the absolute value of Log<sub>2</sub> fold-change ≥ 2 as the threshold for the significance of genes expression difference. PM and OM: PI 114490 and OH 88119 respectively mock-inoculated with the sterile solution containing 10 mM MgSO<sub>4</sub>·7H<sub>2</sub>O and 0.025% (v/v) Silwet L77. PT and OT: PI 114490 and OH 88119 respectively inoculated with T3.</p></caption><graphic xlink:href="fpls-06-01173-g0001"></graphic></fig></sec><sec><title>Genes with differentially expressed patterns in two tomato lines during infection with race T3</title><p>In order to gain comprehensive insights into understanding molecular mechanisms of resistance induced by <italic>X. perforans</italic> race T3, the overlap differentially expressed patterns of DEGs between PI 114490 and OH 88119 at two infection stages were analyzed using a Venn diagram (Figure <xref ref-type="fig" rid="F2">2</xref>). For tomato line PI 114490, 282 genes (8 up-regulated and 274 down-regulated) were co-modulated in both 6 HPI and 6 DPI compared to mock-treatment (Figure <xref ref-type="fig" rid="F2">2A</xref>), while 86 genes (6 up-regulated and 80 down-regulated) were co-modulated in both 6 HPI and 6 DPI compared to mock-treatment in line OH 88119 (Figure <xref ref-type="fig" rid="F2">2B</xref>). Comparison between the two tomato lines discovered 51 and 344 DEGs co-regulated at 6 HPI and 6 DPI, respectively (Figures <xref ref-type="fig" rid="F2">2C,D</xref>). Among the 51 co-regulated DEGs at 6 HPI, 50 were co-down-regulated, and only 1 (Solyc03g114530.2.1) encoding Strictosidine synthase family protein was co-up-regulated. The expression of Strictosidine synthase (Str), the key gene of terpenoid indole alkaloid (TIA) biosynthetic pathway, has been found to be induced by fungal elicitor (Pasquali et al., <xref rid="B31" ref-type="bibr">1992</xref>) and salinity stress in <italic>Catharanthus roseus</italic> (Dutta et al., <xref rid="B11" ref-type="bibr">2013</xref>). Go classification analysis of the 50 down-regulated genes, showed that the dominant subcategories in biological process were response to stimulus (Table <xref ref-type="supplementary-material" rid="SM3">S3</xref>). Among the 344 DEGs co-regulated at 6 DPI, 326 genes were commonly up-regulated, and 18 genes were commonly down-regulated (Figure <xref ref-type="fig" rid="F2">2D</xref>). In the face of a large number of commonly up-regulated genes, particular emphasis was placed on the highly up-regulated genes resulting in 32 DEGs with the Log<sub>2</sub> fold-change ≥ 5 in both lines at 6 DPI (Table <xref ref-type="table" rid="T2">2</xref>), of which a large proportion (40.6%) were assigned to Go term “response to stimulus.” For example, marker genes of stress signaling such as pathogen-related genes (PR) and osmotin-like protein were intensely induced, and PR proteins are inducible by infection with various types of pathogens in many plant families (van Loon et al., <xref rid="B46" ref-type="bibr">2006</xref>). In addition to these stimulus genes, other genes also have been clarified related to defense response.</p><fig id="F2" position="float"><label>Figure 2</label><caption><p><bold>Venn diagram showing the number of up/down-regulated genes between tomato lines PI 114490 and OH 88119 at 6 h and 6 days post-inoculation with <italic>Xanthomonas perforans</italic> race T3</bold>. PM and OM: PI 114490 and OH 88119 respectively mock-inoculated with the sterile solution containing 10 mM MgSO<sub>4</sub>·7H<sub>2</sub>O and 0.025% (v/v) Silwet L77. PT and OT: PI 114490 and OH 88119 respectively inoculated with race T3. <bold>(A,B)</bold> Comparison of co-DEGs between 6 HPI and 6 DPI in PI 114490 and OH 88119, respectively. <bold>(C,D)</bold> Comparison of co-DEGs between two tomato lines at 6 HPI and 6 DPI, respectively. Overlapping portion indicates co-regulated genes.</p></caption><graphic xlink:href="fpls-06-01173-g0002"></graphic></fig><table-wrap id="T2" position="float"><label>Table 2</label><caption><p><bold>RPKM for common highly up-regulated (Log<sub>2</sub>fold-change ≥ 5) genes in tomato lines P I114490 and OH 88119 at 6 days post-inoculation (DPI)</bold>.</p></caption><table frame="hsides" rules="groups"><thead><tr><th valign="top" align="left" rowspan="1" colspan="1"><bold>Gene</bold></th><th valign="top" align="left" rowspan="1" colspan="1"><bold>Function description</bold></th><th valign="top" align="center" colspan="3" style="border-bottom: thin solid #000000;" rowspan="1"><bold>PI 114490</bold></th><th valign="top" align="center" colspan="3" style="border-bottom: thin solid #000000;" rowspan="1"><bold>OH 88119</bold></th></tr><tr><th rowspan="1" colspan="1"></th><th rowspan="1" colspan="1"></th><th valign="top" align="center" rowspan="1" colspan="1"><bold>Mock<xref ref-type="table-fn" rid="TN3"><sup>b</sup></xref></bold></th><th valign="top" align="center" rowspan="1" colspan="1"><bold>6 DPI<xref ref-type="table-fn" rid="TN3"><sup>b</sup></xref></bold></th><th valign="top" align="center" rowspan="1" colspan="1"><bold>Fold value<xref ref-type="table-fn" rid="TN4"><sup>c</sup></xref></bold></th><th valign="top" align="center" rowspan="1" colspan="1"><bold>Mock<xref ref-type="table-fn" rid="TN3"><sup>b</sup></xref></bold></th><th valign="top" align="center" rowspan="1" colspan="1"><bold>6 DPI<xref ref-type="table-fn" rid="TN3"><sup>b</sup></xref></bold></th><th valign="top" align="center" rowspan="1" colspan="1"><bold>Fold-change<xref ref-type="table-fn" rid="TN4"><sup>c</sup></xref></bold></th></tr></thead><tbody><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc00g174330.2.1</td><td valign="top" align="left" rowspan="1" colspan="1">Pathogenesis related protein<xref ref-type="table-fn" rid="TN2"><sup>a</sup></xref></td><td valign="top" align="char" char="." rowspan="1" colspan="1">6.37</td><td valign="top" align="char" char="." rowspan="1" colspan="1">11.43</td><td valign="top" align="char" char="." rowspan="1" colspan="1">5.06</td><td valign="top" align="char" char="." rowspan="1" colspan="1">2.88</td><td valign="top" align="char" char="." rowspan="1" colspan="1">9.42</td><td valign="top" align="char" char="." rowspan="1" colspan="1">6.54</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc09g007010.1.1</td><td valign="top" align="left" rowspan="1" colspan="1">Pathogenesis related protein<xref ref-type="table-fn" rid="TN2"><sup>a</sup></xref></td><td valign="top" align="char" char="." rowspan="1" colspan="1">4.69</td><td valign="top" align="char" char="." rowspan="1" colspan="1">10.02</td><td valign="top" align="char" char="." rowspan="1" colspan="1">5.33</td><td valign="top" align="char" char="." rowspan="1" colspan="1">2.63</td><td valign="top" align="char" char="." rowspan="1" colspan="1">9.17</td><td valign="top" align="char" char="." rowspan="1" colspan="1">6.54</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc00g174340.1.1</td><td valign="top" align="left" rowspan="1" colspan="1">Pathogenesis-related protein<xref ref-type="table-fn" rid="TN2"><sup>a</sup></xref></td><td valign="top" align="char" char="." rowspan="1" colspan="1">8.88</td><td valign="top" align="char" char="." rowspan="1" colspan="1">14.31</td><td valign="top" align="char" char="." rowspan="1" colspan="1">5.43</td><td valign="top" align="char" char="." rowspan="1" colspan="1">5.50</td><td valign="top" align="char" char="." rowspan="1" colspan="1">12.42</td><td valign="top" align="char" char="." rowspan="1" colspan="1">6.93</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc01g106620.2.1</td><td valign="top" align="left" rowspan="1" colspan="1">Pathogenesis-related protein<xref ref-type="table-fn" rid="TN2"><sup>a</sup></xref></td><td valign="top" align="char" char="." rowspan="1" colspan="1">4.49</td><td valign="top" align="char" char="." rowspan="1" colspan="1">10.20</td><td valign="top" align="char" char="." rowspan="1" colspan="1">5.71</td><td valign="top" align="char" char="." rowspan="1" colspan="1">1.62</td><td valign="top" align="char" char="." rowspan="1" colspan="1">9.27</td><td valign="top" align="char" char="." rowspan="1" colspan="1">7.65</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc08g080620.1.1</td><td valign="top" align="left" rowspan="1" colspan="1">Osmotin-like protein<xref ref-type="table-fn" rid="TN2"><sup>a</sup></xref></td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">5.38</td><td valign="top" align="char" char="." rowspan="1" colspan="1">7.26</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">5.05</td><td valign="top" align="char" char="." rowspan="1" colspan="1">6.73</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc08g080650.1.1</td><td valign="top" align="left" rowspan="1" colspan="1">Osmotin-like protein<xref ref-type="table-fn" rid="TN2"><sup>a</sup></xref></td><td valign="top" align="char" char="." rowspan="1" colspan="1">6.43</td><td valign="top" align="char" char="." rowspan="1" colspan="1">11.47</td><td valign="top" align="char" char="." rowspan="1" colspan="1">5.03</td><td valign="top" align="char" char="." rowspan="1" colspan="1">4.39</td><td valign="top" align="char" char="." rowspan="1" colspan="1">9.75</td><td valign="top" align="char" char="." rowspan="1" colspan="1">5.36</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc08g080670.1.1</td><td valign="top" align="left" rowspan="1" colspan="1">Osmotin-like protein<xref ref-type="table-fn" rid="TN2"><sup>a</sup></xref></td><td valign="top" align="char" char="." rowspan="1" colspan="1">2.62</td><td valign="top" align="char" char="." rowspan="1" colspan="1">7.77</td><td valign="top" align="char" char="." rowspan="1" colspan="1">5.15</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">8.14</td><td valign="top" align="char" char="." rowspan="1" colspan="1">8.38</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc02g082960.2.1</td><td valign="top" align="left" rowspan="1" colspan="1">Endochitinase<xref ref-type="table-fn" rid="TN2"><sup>a</sup></xref></td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">3.30</td><td valign="top" align="char" char="." rowspan="1" colspan="1">6.67</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">4.37</td><td valign="top" align="char" char="." rowspan="1" colspan="1">7.54</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc02g086700.2.1</td><td valign="top" align="left" rowspan="1" colspan="1">Beta-1 3-glucanase<xref ref-type="table-fn" rid="TN2"><sup>a</sup></xref></td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">5.82</td><td valign="top" align="char" char="." rowspan="1" colspan="1">7.62</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">6.43</td><td valign="top" align="char" char="." rowspan="1" colspan="1">10.04</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc01g060020.2.1</td><td valign="top" align="left" rowspan="1" colspan="1">Beta-glucanase<xref ref-type="table-fn" rid="TN2"><sup>a</sup></xref></td><td valign="top" align="char" char="." rowspan="1" colspan="1">4.12</td><td valign="top" align="char" char="." rowspan="1" colspan="1">9.30</td><td valign="top" align="char" char="." rowspan="1" colspan="1">5.18</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">7.27</td><td valign="top" align="char" char="." rowspan="1" colspan="1">7.70</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc07g056510.2.1</td><td valign="top" align="left" rowspan="1" colspan="1">Glutathione S-transferase<xref ref-type="table-fn" rid="TN2"><sup>a</sup></xref></td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">5.57</td><td valign="top" align="char" char="." rowspan="1" colspan="1">5.46</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">2.11</td><td valign="top" align="char" char="." rowspan="1" colspan="1">5.39</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc07g066330.2.1</td><td valign="top" align="left" rowspan="1" colspan="1">NAC domain protein<xref ref-type="table-fn" rid="TN2"><sup>a</sup></xref></td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">4.77</td><td valign="top" align="char" char="." rowspan="1" colspan="1">6.59</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">1.67</td><td valign="top" align="char" char="." rowspan="1" colspan="1">5.28</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc01g106630.2.1</td><td valign="top" align="left" rowspan="1" colspan="1">Unknown Protein<xref ref-type="table-fn" rid="TN2"><sup>a</sup></xref></td><td valign="top" align="char" char="." rowspan="1" colspan="1">4.31</td><td valign="top" align="char" char="." rowspan="1" colspan="1">9.83</td><td valign="top" align="char" char="." rowspan="1" colspan="1">5.51</td><td valign="top" align="char" char="." rowspan="1" colspan="1">1.39</td><td valign="top" align="char" char="." rowspan="1" colspan="1">8.91</td><td valign="top" align="char" char="." rowspan="1" colspan="1">7.53</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc12g011150.1.1</td><td valign="top" align="left" rowspan="1" colspan="1">Unknown Protein</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">5.52</td><td valign="top" align="char" char="." rowspan="1" colspan="1">7.02</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">3.87</td><td valign="top" align="char" char="." rowspan="1" colspan="1">5.17</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc03g098760.1.1</td><td valign="top" align="left" rowspan="1" colspan="1">Kunitz-type protease inhibitor protein<xref ref-type="table-fn" rid="TN2"><sup>a</sup></xref></td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">2.44</td><td valign="top" align="char" char="." rowspan="1" colspan="1">5.16</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">4.70</td><td valign="top" align="char" char="." rowspan="1" colspan="1">5.23</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc07g052150.2.1</td><td valign="top" align="left" rowspan="1" colspan="1">Sesquiterpene synthase</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">6.84</td><td valign="top" align="char" char="." rowspan="1" colspan="1">8.65</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">4.83</td><td valign="top" align="char" char="." rowspan="1" colspan="1">6.44</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc02g093580.2.1</td><td valign="top" align="left" rowspan="1" colspan="1">Pectate lyase</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">2.14</td><td valign="top" align="char" char="." rowspan="1" colspan="1">6.16</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">1.84</td><td valign="top" align="char" char="." rowspan="1" colspan="1">5.67</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc01g059990.2.1</td><td valign="top" align="left" rowspan="1" colspan="1">Serine/threonine-protein phosphatase 7</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">5.81</td><td valign="top" align="char" char="." rowspan="1" colspan="1">5.06</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">3.99</td><td valign="top" align="char" char="." rowspan="1" colspan="1">6.36</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc02g090970.1.1</td><td valign="top" align="left" rowspan="1" colspan="1">Serine/threonine-protein kinase 24</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">3.28</td><td valign="top" align="char" char="." rowspan="1" colspan="1">5.83</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">2.93</td><td valign="top" align="char" char="." rowspan="1" colspan="1">5.28</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc04g074000.2.1</td><td valign="top" align="left" rowspan="1" colspan="1">Receptor like kinase, RLK</td><td valign="top" align="char" char="." rowspan="1" colspan="1">1.66</td><td valign="top" align="char" char="." rowspan="1" colspan="1">6.80</td><td valign="top" align="char" char="." rowspan="1" colspan="1">5.14</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">2.19</td><td valign="top" align="char" char="." rowspan="1" colspan="1">6.20</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc02g071470.2.1</td><td valign="top" align="left" rowspan="1" colspan="1">1-aminocyclopropane-1-carboxylate oxidase 1</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">4.71</td><td valign="top" align="char" char="." rowspan="1" colspan="1">7.55</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">2.40</td><td valign="top" align="char" char="." rowspan="1" colspan="1">6.04</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc07g049530.2.1</td><td valign="top" align="char" char="." rowspan="1" colspan="1">1-aminocyclopropane-1-carboxylate oxidase</td><td valign="top" align="char" char="." rowspan="1" colspan="1">4.43</td><td valign="top" align="char" char="." rowspan="1" colspan="1">9.62</td><td valign="top" align="char" char="." rowspan="1" colspan="1">5.19</td><td valign="top" align="char" char="." rowspan="1" colspan="1">1.97</td><td valign="top" align="char" char="." rowspan="1" colspan="1">7.44</td><td valign="top" align="char" char="." rowspan="1" colspan="1">5.47</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc01g109140.2.1</td><td valign="top" align="left" rowspan="1" colspan="1">Cytochrome P450</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">5.41</td><td valign="top" align="char" char="." rowspan="1" colspan="1">8.60</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">1.17</td><td valign="top" align="char" char="." rowspan="1" colspan="1">5.17</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc11g068940.1.1</td><td valign="top" align="left" rowspan="1" colspan="1">U-box domain-containing 24</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">3.36</td><td valign="top" align="char" char="." rowspan="1" colspan="1">7.14</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">2.17</td><td valign="top" align="char" char="." rowspan="1" colspan="1">5.75</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc04g008100.1.1</td><td valign="top" align="left" rowspan="1" colspan="1">U-box domain-containing</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">3.38</td><td valign="top" align="char" char="." rowspan="1" colspan="1">5.22</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">2.46</td><td valign="top" align="char" char="." rowspan="1" colspan="1">5.10</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc06g062330.1.1</td><td valign="top" align="left" rowspan="1" colspan="1">UDP-glucosyltransferase</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">4.63</td><td valign="top" align="char" char="." rowspan="1" colspan="1">5.34</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">3.61</td><td valign="top" align="char" char="." rowspan="1" colspan="1">6.71</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc07g052120.2.1</td><td valign="top" align="left" rowspan="1" colspan="1">(−)-germacrene D synthase</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">4.08</td><td valign="top" align="char" char="." rowspan="1" colspan="1">6.99</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">3.04</td><td valign="top" align="char" char="." rowspan="1" colspan="1">5.75</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc07g052140.2.1</td><td valign="top" align="left" rowspan="1" colspan="1">(−)-germacrene D synthase</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">7.61</td><td valign="top" align="char" char="." rowspan="1" colspan="1">7.71</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">6.45</td><td valign="top" align="char" char="." rowspan="1" colspan="1">7.66</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc08g029000.2.1</td><td valign="top" align="left" rowspan="1" colspan="1">Lipoxygenase</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">6.19</td><td valign="top" align="char" char="." rowspan="1" colspan="1">6.70</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">1.96</td><td valign="top" align="char" char="." rowspan="1" colspan="1">5.58</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc08g068870.2.1</td><td valign="top" align="left" rowspan="1" colspan="1">Aspartic proteinase nepenthesin-1</td><td valign="top" align="char" char="." rowspan="1" colspan="1">2.28</td><td valign="top" align="char" char="." rowspan="1" colspan="1">7.35</td><td valign="top" align="char" char="." rowspan="1" colspan="1">5.07</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">5.31</td><td valign="top" align="char" char="." rowspan="1" colspan="1">5.38</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc12g044950.1.1</td><td valign="top" align="left" rowspan="1" colspan="1">Omega-6 fatty acid desaturase</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">2.68</td><td valign="top" align="char" char="." rowspan="1" colspan="1">5.04</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">3.46</td><td valign="top" align="char" char="." rowspan="1" colspan="1">6.63</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc12g049030.1.1</td><td valign="top" align="left" rowspan="1" colspan="1">Fatty acid desaturase</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">5.04</td><td valign="top" align="char" char="." rowspan="1" colspan="1">5.68</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">3.04</td><td valign="top" align="char" char="." rowspan="1" colspan="1">6.49</td></tr></tbody></table><table-wrap-foot><fn id="TN2"><label>a</label><p><italic>The representative genes are associated with “response to stimulus” according to Gene Ontology classification</italic>.</p></fn><fn id="TN3"><label>b</label><p><italic>the value of RPKM</italic>.</p></fn><fn id="TN4"><label>c</label><p><italic>the value of Log<sub>2</sub>(fold-change)</italic>.</p></fn></table-wrap-foot></table-wrap><p>Clustering analysis of DEGs among the four comparison groups resulted in 37 clusters (Figure <xref ref-type="fig" rid="F3">3</xref>). Despite there were substantial number of DEGs, none of these genes was commonly up-regulated at four comparison groups. Cluster 10 was the largest with 711 DEGs, followed by cluster 8 representing 223 common up-regulated genes in PI 114490 and OH 88119 at 6 DPI. Common up-regulated genes in cluster 8 indicated that both PI114490 and OH88119 used some same sets of genes to response to race T3 infection but the induced intensity of transcriptional levels were different between two genotypes. Cluster 10 and cluster 20 consisting of the DEGs were only up-regulated (compared to mock-inoculated) in PI 114490 and OH 88119 at 6 DPI response to race T3. These specific DEGs in PI 114490 from cluster 10 (Table <xref ref-type="table" rid="T3">3</xref>) were promising candidates for revealing the resistance response mechanism. Cluster 32 comprised only one unknown function gene Solyc02g084850.2.1 with strongly down-regulated in both PI 114490 and OH 88119 at two infection stages (Table <xref ref-type="table" rid="T3">3</xref>). Cluster 27 contained 7 genes strongly down-regulated at 6 HPI but strongly up-regulated at 6 DPI (Table <xref ref-type="table" rid="T3">3</xref>), with three genes annotated for pathogenesis-related (Solyc00g174330.2.1, Solyc00g174340.1.1, and Solyc06g009140.2.1). Cluster 13 exhibited that 8 genes were up-regulated in PI 114490 but down-regulated in OH 88119 (Table <xref ref-type="table" rid="T3">3</xref>).</p><fig id="F3" position="float"><label>Figure 3</label><caption><p><bold>Hierarchical clustering of differentially expressed genes (DEGs) among four groups</bold>. Up-regulation and down-regulation is represented by red shading and green shading, respectively. Gray shading indicates non-modulated. PT: PI 114490 inoculated with race T3. OT: OH 88119 inoculated with race T3.</p></caption><graphic xlink:href="fpls-06-01173-g0003"></graphic></fig><table-wrap id="T3" position="float"><label>Table 3</label><caption><p><bold>Part of significantly altered expression genes from Hierarchical clustering analysis</bold>.</p></caption><table frame="hsides" rules="groups"><thead><tr><th valign="top" align="left" rowspan="1" colspan="1"><bold>Gene</bold></th><th valign="top" align="left" rowspan="1" colspan="1"><bold>Function description</bold></th><th valign="top" align="center" colspan="4" style="border-bottom: thin solid #000000;" rowspan="1"><bold>Log</bold><sub><bold>2</bold></sub><bold>Fold-change value</bold><xref ref-type="table-fn" rid="TN6"><sup><bold>b</bold></sup></xref></th></tr><tr><th rowspan="1" colspan="1"></th><th rowspan="1" colspan="1"></th><th valign="top" align="center" colspan="2" style="border-bottom: thin solid #000000;" rowspan="1"><bold>PI 114490</bold></th><th valign="top" align="center" colspan="2" style="border-bottom: thin solid #000000;" rowspan="1"><bold>OH 88119</bold></th></tr><tr><th rowspan="1" colspan="1"></th><th rowspan="1" colspan="1"></th><th valign="top" align="center" rowspan="1" colspan="1"><bold>6 HPI</bold></th><th valign="top" align="center" rowspan="1" colspan="1"><bold>6 DPI</bold></th><th valign="top" align="center" rowspan="1" colspan="1"><bold>6 HPI</bold></th><th valign="top" align="center" rowspan="1" colspan="1"><bold>6 DPI</bold></th></tr></thead><tbody><tr><td valign="top" align="left" colspan="6" style="background-color:#bbbdc0" rowspan="1"><bold>CLUSTER 10 (SPECIFIC UP-REGULATED IN PT6d)</bold><xref ref-type="table-fn" rid="TN5"><sup>a</sup></xref></td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc02g087070.2.1</td><td valign="top" align="left" rowspan="1" colspan="1">Peroxidase family protein</td><td valign="top" align="center" rowspan="1" colspan="1">No</td><td valign="top" align="char" char="." rowspan="1" colspan="1">7.6</td><td valign="top" align="center" rowspan="1" colspan="1">No</td><td valign="top" align="center" rowspan="1" colspan="1">No</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc03g020050.2.1</td><td valign="top" align="left" rowspan="1" colspan="1">Proteinase inhibitor II</td><td valign="top" align="center" rowspan="1" colspan="1">No</td><td valign="top" align="char" char="." rowspan="1" colspan="1">8.72</td><td valign="top" align="center" rowspan="1" colspan="1">No</td><td valign="top" align="center" rowspan="1" colspan="1">No</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc06g065060.1.1</td><td valign="top" align="left" rowspan="1" colspan="1">FAD-binding domain protein</td><td valign="top" align="center" rowspan="1" colspan="1">No</td><td valign="top" align="char" char="." rowspan="1" colspan="1">7.4</td><td valign="top" align="center" rowspan="1" colspan="1">No</td><td valign="top" align="center" rowspan="1" colspan="1">No</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc07g008600.1.1</td><td valign="top" align="left" rowspan="1" colspan="1">LRR receptor-like serine/threonine-protein kinase</td><td valign="top" align="center" rowspan="1" colspan="1">No</td><td valign="top" align="char" char="." rowspan="1" colspan="1">7.14</td><td valign="top" align="center" rowspan="1" colspan="1">No</td><td valign="top" align="center" rowspan="1" colspan="1">No</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc07g009500.1.1</td><td valign="top" align="left" rowspan="1" colspan="1">Chitinase</td><td valign="top" align="center" rowspan="1" colspan="1">No</td><td valign="top" align="char" char="." rowspan="1" colspan="1">7.33</td><td valign="top" align="center" rowspan="1" colspan="1">No</td><td valign="top" align="center" rowspan="1" colspan="1">No</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc08g079230.1.1</td><td valign="top" align="left" rowspan="1" colspan="1">Cortical cell-delineating protein</td><td valign="top" align="center" rowspan="1" colspan="1">No</td><td valign="top" align="char" char="." rowspan="1" colspan="1">7.32</td><td valign="top" align="center" rowspan="1" colspan="1">No</td><td valign="top" align="center" rowspan="1" colspan="1">No</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc08g080610.1.1</td><td valign="top" align="left" rowspan="1" colspan="1">Osmotin-like protein</td><td valign="top" align="center" rowspan="1" colspan="1">No</td><td valign="top" align="char" char="." rowspan="1" colspan="1">7.35</td><td valign="top" align="center" rowspan="1" colspan="1">No</td><td valign="top" align="center" rowspan="1" colspan="1">No</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc12g005720.1.1</td><td valign="top" align="left" rowspan="1" colspan="1">Cysteine-rich receptor-like kinase</td><td valign="top" align="center" rowspan="1" colspan="1">No</td><td valign="top" align="char" char="." rowspan="1" colspan="1">7.9</td><td valign="top" align="center" rowspan="1" colspan="1">No</td><td valign="top" align="center" rowspan="1" colspan="1">No</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc12g100250.1.1</td><td valign="top" align="left" rowspan="1" colspan="1">Fatty acid desaturase</td><td valign="top" align="center" rowspan="1" colspan="1">No</td><td valign="top" align="char" char="." rowspan="1" colspan="1">7.6</td><td valign="top" align="center" rowspan="1" colspan="1">No</td><td valign="top" align="center" rowspan="1" colspan="1">No</td></tr><tr><td valign="top" align="left" colspan="6" style="background-color:#bbbdc0" rowspan="1"><bold>CLUSTER 13 (UP-REGULATED IN PT6d; DOWN-REGULATED IN OT6h AND OT6d)</bold><xref ref-type="table-fn" rid="TN5"><sup>a</sup></xref></td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc01g057000.2.1</td><td valign="top" align="left" rowspan="1" colspan="1">Universal stress protein</td><td valign="top" align="center" rowspan="1" colspan="1">No</td><td valign="top" align="char" char="." rowspan="1" colspan="1">6.35</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−6.87</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−3.96</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc03g013440.2.1</td><td valign="top" align="left" rowspan="1" colspan="1">Amino acid transporter</td><td valign="top" align="center" rowspan="1" colspan="1">No</td><td valign="top" align="char" char="." rowspan="1" colspan="1">2.90</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−2.91</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−2.85</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc03g096670.2.1</td><td valign="top" align="left" rowspan="1" colspan="1">Integrin-linked kinase-associated serine/threonine phosphatase 2C</td><td valign="top" align="center" rowspan="1" colspan="1">No</td><td valign="top" align="char" char="." rowspan="1" colspan="1">2.46</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−7.00</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−4.22</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc04g063350.2.1</td><td valign="top" align="left" rowspan="1" colspan="1">3-methyl-2-oxobutanoate dehydrogenase</td><td valign="top" align="center" rowspan="1" colspan="1">No</td><td valign="top" align="char" char="." rowspan="1" colspan="1">2.16</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−2.40</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−2.33</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc06g007180.2.1</td><td valign="top" align="left" rowspan="1" colspan="1">Asparagine synthase</td><td valign="top" align="center" rowspan="1" colspan="1">No</td><td valign="top" align="char" char="." rowspan="1" colspan="1">3.77</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−4.52</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−2.56</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc07g006500.2.1</td><td valign="top" align="left" rowspan="1" colspan="1">Alpha alpha-trehalose-phosphate</td><td valign="top" align="center" rowspan="1" colspan="1">No</td><td valign="top" align="char" char="." rowspan="1" colspan="1">2.52</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−2.21</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−2.31</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc08g077900.2.1</td><td valign="top" align="left" rowspan="1" colspan="1">Expansin-like protein</td><td valign="top" align="center" rowspan="1" colspan="1">No</td><td valign="top" align="char" char="." rowspan="1" colspan="1">3.49</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−5.73</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−4.06</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc12g006230.1.1</td><td valign="top" align="left" rowspan="1" colspan="1">RING-H2 finger protein</td><td valign="top" align="center" rowspan="1" colspan="1">No</td><td valign="top" align="char" char="." rowspan="1" colspan="1">2.05</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−4.02</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−3.12</td></tr><tr><td valign="top" align="left" colspan="6" style="background-color:#bbbdc0" rowspan="1"><bold>CLUSTER 27 (DOWN-REGULATED IN PT6h AND OT6h; UP-REGULATED IN PT6d AND OT6d)</bold><xref ref-type="table-fn" rid="TN5"><sup>a</sup></xref></td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc00g174330.2.1</td><td valign="top" align="left" rowspan="1" colspan="1">Pathogenesis related protein PR-1</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−8.49</td><td valign="top" align="char" char="." rowspan="1" colspan="1">5.06</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−5.7</td><td valign="top" align="char" char="." rowspan="1" colspan="1">6.54</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc00g174340.1.1</td><td valign="top" align="left" rowspan="1" colspan="1">Pathogenesis-related protein 1b</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−9.1</td><td valign="top" align="char" char="." rowspan="1" colspan="1">5.43</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−5.41</td><td valign="top" align="char" char="." rowspan="1" colspan="1">6.93</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc03g025670.2.1</td><td valign="top" align="left" rowspan="1" colspan="1">PAR-1c protein</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−2.43</td><td valign="top" align="char" char="." rowspan="1" colspan="1">4.23</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−2.5</td><td valign="top" align="char" char="." rowspan="1" colspan="1">2.46</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc04g077980.1.1</td><td valign="top" align="left" rowspan="1" colspan="1">Zinc-finger protein</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−3.75</td><td valign="top" align="char" char="." rowspan="1" colspan="1">2.06</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−3.2</td><td valign="top" align="char" char="." rowspan="1" colspan="1">3.41</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc06g009140.2.1</td><td valign="top" align="left" rowspan="1" colspan="1">Late embryogenesis abundant 3</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−5.78</td><td valign="top" align="char" char="." rowspan="1" colspan="1">2.73</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−4.74</td><td valign="top" align="char" char="." rowspan="1" colspan="1">2.38</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc07g049530.2.1</td><td valign="top" align="left" rowspan="1" colspan="1">1-aminocyclopropane-1-carboxylate oxidase</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−4.14</td><td valign="top" align="char" char="." rowspan="1" colspan="1">5.19</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−4.54</td><td valign="top" align="char" char="." rowspan="1" colspan="1">5.47</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc10g085030.1.1</td><td valign="top" align="left" rowspan="1" colspan="1">Soul heme-binding family protein</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−3.19</td><td valign="top" align="char" char="." rowspan="1" colspan="1">2.29</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−2.2</td><td valign="top" align="char" char="." rowspan="1" colspan="1">2.39</td></tr><tr><td valign="top" align="left" colspan="6" style="background-color:#bbbdc0" rowspan="1"><bold>CLUSTER 32 (DOWN-REGULATED IN PT6h, PT6d, OT6h, AND OT6d)</bold><xref ref-type="table-fn" rid="TN5"><sup>a</sup></xref></td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc02g084850.2.1</td><td valign="top" align="left" rowspan="1" colspan="1">Unknown Protein</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−4.12</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−4.86</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−12.62</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−9.72</td></tr></tbody></table><table-wrap-foot><fn id="TN5"><label>a</label><p><italic>PT6h: 6 h after inoculation with bacterial spot race T3 in PI 114490. PT6d: 6 day after inoculation with bacterial spot race T3 in PI 114490. OH6h: 6 h after inoculation with bacterial spot race T3 in OH 88119. OH6d: 6 day after inoculation with bacterial spot race T3 in OH 88119</italic>.</p></fn><fn id="TN6"><label>b</label><p><italic>“NO” indicates that the expression level of the genes after infection with race T3 is not significant difference as relative to that of mock-treatment</italic>.</p></fn></table-wrap-foot></table-wrap></sec><sec><title>Gene ontology classification analysis of DEGs</title><p>Go enrichment categorized for 52.5, 54.2, 50.5, and 51.2% of DEGs into functional groups from PT6h, OT6h, PT6d, and OT6d, respectively. More assigned function of DEGs was covered in biological process and molecular function categories than in cellular component categories (Image <xref ref-type="supplementary-material" rid="SM7">S2</xref>). The dominant subcategories of both PI 114490 and OH 88119 at 6 HPI and 6 DPI in each main category were cellular process, cell and catalytic activity, respectively (Image <xref ref-type="supplementary-material" rid="SM7">S2</xref>). Despite these enrichment subcategories were similar in both tomato lines, the individual genes contributing to the common enriched subcategories were substantial diversified between the two tomato lines.</p><p>The most significantly enriched GO terms in biological process in the OT6d library included “response to wounding (Go:0009611),” “response to external stimulus (GO:0009605),” “oxidation reduction (GO:0055114),” “response to stress (GO:0006950),” and “response to biotic stimulus (GO:0009607),” For the library of PT6d, the most significantly enriched GO terms were “cell wall macromolecule metabolic process (GO:0044036)” and “response to water (GO:0009415)” (Table <xref ref-type="supplementary-material" rid="SM4">S4</xref>).</p></sec><sec><title>Metabolic pathway by KEGG analysis of DEGs</title><p>To characterize the pathway enrichment of the identified DEGs, gene classification was performed on the basis of KEGG analysis (Kanehisa et al., <xref rid="B20" ref-type="bibr">2010</xref>). Only significant pathway categories among four comparisons were selected and listed in Table <xref ref-type="table" rid="T4">4</xref>. Genes involved in photosynthesis and oxidative phosphorylation pathways were mainly up-regulated in OH 88119 at 6 DPI, but down-regulated in PI114490 at 6 HPI and 6 DPI (Table <xref ref-type="table" rid="T4">4</xref>). It was obvious that genes associated with defense response pathways (labeled in bold in Table <xref ref-type="table" rid="T4">4</xref>) were significantly up-regulated in PI114490 at 6 DPI. The defense-related pathways with most representation by DEGs were plant hormone signal transduction, plant-pathogen interaction and phenylalanine metabolism. A total of 16 defense response genes in KEGG pathway “plant-pathogen interaction” (KO: 04626) exhibited significant differences between PI 114490 and OH 88119 in response to T3 infection (Table <xref ref-type="table" rid="T5">5</xref>). Of which, 5 and 3 were down-regulated at 6 HPI in PI 114490 and OH 88119, respectively. However, the numbers of DEGs increased in both tomato lines at 6 DPI. A total of 15 (14 up-regulated and 1 down-regulated) in PI 114490 and 8 (6 up-regulated and 2 down-regulated) gens in OH 88119 was detected. It was noteworthy that 5 DEGs (Solyc05g050350.1.1, Solyc10g079420.1.1, Solyc11g071740.1.1, Solyc09g014990.2.1, and Solyc12g009220.1.1) had the similar expression pattern between two tomato lines at both 6 HPI and 6 DPI (Table <xref ref-type="table" rid="T5">5</xref>).</p><table-wrap id="T4" position="float"><label>Table 4</label><caption><p><bold>Significantly enriched KEGG pathways of differentially expressed genes by <italic>Xanthomonas perforans</italic> race T3 infection</bold>.</p></caption><table frame="hsides" rules="groups"><thead><tr><th rowspan="1" colspan="1"></th><th valign="top" align="left" rowspan="1" colspan="1"><bold>Pathway</bold></th><th valign="top" align="center" rowspan="1" colspan="1"><bold>No. of up-regulated genes</bold></th><th valign="top" align="center" rowspan="1" colspan="1"><bold>No. of down-regulated genes</bold></th><th valign="top" align="center" rowspan="1" colspan="1"><bold>Pathway ID</bold></th></tr></thead><tbody><tr><td valign="top" align="left" rowspan="1" colspan="1">PT6h vs. PM</td><td valign="top" align="left" rowspan="1" colspan="1">Photosynthesis</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="center" rowspan="1" colspan="1">23</td><td valign="top" align="center" rowspan="1" colspan="1">Ko 00195</td></tr><tr><td rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1">Oxidative phosphorylation</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="center" rowspan="1" colspan="1">27</td><td valign="top" align="center" rowspan="1" colspan="1">Ko 00190</td></tr><tr><td style="border-bottom: thin solid #000000;" rowspan="1" colspan="1"></td><td valign="top" align="left" style="border-bottom: thin solid #000000;" rowspan="1" colspan="1">Ribosome</td><td valign="top" align="center" style="border-bottom: thin solid #000000;" rowspan="1" colspan="1">0</td><td valign="top" align="center" style="border-bottom: thin solid #000000;" rowspan="1" colspan="1">13</td><td valign="top" align="center" style="border-bottom: thin solid #000000;" rowspan="1" colspan="1">Ko 03010</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">PT6d vs. PM</td><td valign="top" align="left" rowspan="1" colspan="1">Photosynthesis</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="center" rowspan="1" colspan="1">23</td><td valign="top" align="center" rowspan="1" colspan="1">Ko 00195</td></tr><tr><td rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1">Oxidative phosphorylation</td><td valign="top" align="center" rowspan="1" colspan="1">1</td><td valign="top" align="center" rowspan="1" colspan="1">28</td><td valign="top" align="center" rowspan="1" colspan="1">Ko 00190</td></tr><tr><td rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1">Phenylalanine metabolism</td><td valign="top" align="center" rowspan="1" colspan="1">9</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="center" rowspan="1" colspan="1">Ko 00360</td></tr><tr><td rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1">Glutathione metabolism</td><td valign="top" align="center" rowspan="1" colspan="1">10</td><td valign="top" align="center" rowspan="1" colspan="1">1</td><td valign="top" align="center" rowspan="1" colspan="1">Ko 00480</td></tr><tr><td rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1">Phenylpropanoid biosynthesis</td><td valign="top" align="center" rowspan="1" colspan="1">11</td><td valign="top" align="center" rowspan="1" colspan="1">2</td><td valign="top" align="center" rowspan="1" colspan="1">Ko 00940</td></tr><tr><td rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1">Ribosome</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="center" rowspan="1" colspan="1">14</td><td valign="top" align="center" rowspan="1" colspan="1">Ko 03010</td></tr><tr><td rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1">Plant hormone signal transduction</td><td valign="top" align="center" rowspan="1" colspan="1">15</td><td valign="top" align="center" rowspan="1" colspan="1">3</td><td valign="top" align="center" rowspan="1" colspan="1">Ko 04075</td></tr><tr><td style="border-bottom: thin solid #000000;" rowspan="1" colspan="1"></td><td valign="top" align="left" style="border-bottom: thin solid #000000;" rowspan="1" colspan="1">Plant-pathogen interaction</td><td valign="top" align="center" style="border-bottom: thin solid #000000;" rowspan="1" colspan="1">14</td><td valign="top" align="center" style="border-bottom: thin solid #000000;" rowspan="1" colspan="1">1</td><td valign="top" align="center" style="border-bottom: thin solid #000000;" rowspan="1" colspan="1">Ko 04626</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">OT6h vs. OM</td><td valign="top" align="left" rowspan="1" colspan="1">Protein processing in endoplasmic reticulum</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="center" rowspan="1" colspan="1">10</td><td valign="top" align="center" rowspan="1" colspan="1">Ko 04141</td></tr><tr><td rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1">MAPK signaling pathway</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="center" rowspan="1" colspan="1">4</td><td valign="top" align="center" rowspan="1" colspan="1">Ko 04010</td></tr><tr><td style="border-bottom: thin solid #000000;" rowspan="1" colspan="1"></td><td valign="top" align="left" style="border-bottom: thin solid #000000;" rowspan="1" colspan="1">Plant hormone signal transduction</td><td valign="top" align="center" style="border-bottom: thin solid #000000;" rowspan="1" colspan="1">0</td><td valign="top" align="center" style="border-bottom: thin solid #000000;" rowspan="1" colspan="1">9</td><td valign="top" align="center" style="border-bottom: thin solid #000000;" rowspan="1" colspan="1">Ko 04075</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">OT6d vs. OM</td><td valign="top" align="left" rowspan="1" colspan="1">Oxidative phosphorylation</td><td valign="top" align="center" rowspan="1" colspan="1">25</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="center" rowspan="1" colspan="1">Ko 00190</td></tr><tr><td rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1">Photosynthesis</td><td valign="top" align="center" rowspan="1" colspan="1">19</td><td valign="top" align="center" rowspan="1" colspan="1">1</td><td valign="top" align="center" rowspan="1" colspan="1">Ko 00195</td></tr><tr><td rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1">Ribosome</td><td valign="top" align="center" rowspan="1" colspan="1">11</td><td valign="top" align="center" rowspan="1" colspan="1">1</td><td valign="top" align="center" rowspan="1" colspan="1">Ko 03010</td></tr><tr><td rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1">Phenylalanine metabolism</td><td valign="top" align="center" rowspan="1" colspan="1">7</td><td valign="top" align="center" rowspan="1" colspan="1">1</td><td valign="top" align="center" rowspan="1" colspan="1">Ko 00360</td></tr><tr><td rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1">Metabolism of xenobiotics by cytochrome P450</td><td valign="top" align="center" rowspan="1" colspan="1">9</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="center" rowspan="1" colspan="1">Ko 00980</td></tr></tbody></table><table-wrap-foot><p><italic>PM and OM: PI 114490 and OH 88119 respective mock-treatment with the sterile solution containing 10 mM MgSO<sub>4</sub>.7H<sub>2</sub>O and 0.025%(v/v) Silwet L77. PT and OT: inoculation with bacterial spot race T3 in PI 114490 and OH 99119, respectively</italic>.</p></table-wrap-foot></table-wrap><table-wrap id="T5" position="float"><label>Table 5</label><caption><p><bold>Differentially expressed genes in the common enriched KEGG pathway “Plant-pathogen interaction”(ko 04626) in tomato lines PI 114490 and OH 88119 at 6 h post-inoculation (HPI) and 6 days post-inoculation (DPI)</bold>.</p></caption><table frame="hsides" rules="groups"><thead><tr><th valign="top" align="left" rowspan="1" colspan="1"><bold>Gene</bold></th><th valign="top" align="left" rowspan="1" colspan="1"><bold>Homologous protein in KEGG</bold></th><th valign="top" align="center" colspan="5" style="border-bottom: thin solid #000000;" rowspan="1"><bold>PI 11449</bold></th><th valign="top" align="center" colspan="5" style="border-bottom: thin solid #000000;" rowspan="1"><bold>OH 88119</bold></th></tr><tr><th rowspan="1" colspan="1"></th><th rowspan="1" colspan="1"></th><th valign="top" align="center" colspan="3" style="border-bottom: thin solid #000000;" rowspan="1"><bold>RPKM</bold></th><th valign="top" align="center" colspan="2" style="border-bottom: thin solid #000000;" rowspan="1"><bold>Log</bold><sub><bold>2</bold></sub><bold>Fold-change</bold><xref ref-type="table-fn" rid="TN7"><sup><bold>a</bold></sup></xref></th><th valign="top" align="center" colspan="3" style="border-bottom: thin solid #000000;" rowspan="1"><bold>RPKM</bold></th><th valign="top" align="center" colspan="2" style="border-bottom: thin solid #000000;" rowspan="1"><bold>Log</bold><sub><bold>2</bold></sub><bold>Fold-change</bold><xref ref-type="table-fn" rid="TN7"><sup><bold>a</bold></sup></xref></th></tr><tr><th rowspan="1" colspan="1"></th><th rowspan="1" colspan="1"></th><th valign="top" align="center" rowspan="1" colspan="1"><bold>Mock</bold></th><th valign="top" align="center" rowspan="1" colspan="1"><bold>6 HPI</bold></th><th valign="top" align="center" rowspan="1" colspan="1"><bold>6 DPI</bold></th><th valign="top" align="center" rowspan="1" colspan="1"><bold>6 HPI vs. Mock</bold></th><th valign="top" align="center" rowspan="1" colspan="1"><bold>6 DPI vs. Mock</bold></th><th valign="top" align="center" rowspan="1" colspan="1"><bold>Mock</bold></th><th valign="top" align="center" rowspan="1" colspan="1"><bold>6 HPI</bold></th><th valign="top" align="center" rowspan="1" colspan="1"><bold>6 DPI</bold></th><th valign="top" align="center" rowspan="1" colspan="1"><bold>6 HPI vs. Mock</bold></th><th valign="top" align="center" rowspan="1" colspan="1"><bold>6 DPI vs. Mock</bold></th></tr></thead><tbody><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc03g113390.2.1</td><td valign="top" align="left" rowspan="1" colspan="1">CPK</td><td valign="top" align="char" char="." rowspan="1" colspan="1">7.25</td><td valign="top" align="char" char="." rowspan="1" colspan="1">7.21</td><td valign="top" align="char" char="." rowspan="1" colspan="1">38.92</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−0.008</td><td valign="top" align="char" char="." rowspan="1" colspan="1"><bold>2.42</bold></td><td valign="top" align="char" char="." rowspan="1" colspan="1">8.62</td><td valign="top" align="char" char="." rowspan="1" colspan="1">6.89</td><td valign="top" align="char" char="." rowspan="1" colspan="1">16.01</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−0.32</td><td valign="top" align="char" char="." rowspan="1" colspan="1">0.89</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc06g065380.2.1</td><td valign="top" align="left" rowspan="1" colspan="1">CPK</td><td valign="top" align="char" char="." rowspan="1" colspan="1">3.06</td><td valign="top" align="char" char="." rowspan="1" colspan="1">4.83</td><td valign="top" align="char" char="." rowspan="1" colspan="1">0.68</td><td valign="top" align="char" char="." rowspan="1" colspan="1">0.66</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−<bold>2.15</bold></td><td valign="top" align="char" char="." rowspan="1" colspan="1">3.17</td><td valign="top" align="char" char="." rowspan="1" colspan="1">5.97</td><td valign="top" align="char" char="." rowspan="1" colspan="1">1.86</td><td valign="top" align="char" char="." rowspan="1" colspan="1">0.91</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−0.76</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc05g050350.1.1</td><td valign="top" align="left" rowspan="1" colspan="1">CNGF</td><td valign="top" align="char" char="." rowspan="1" colspan="1">0.25</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">2.74</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1"><bold>3.41</bold></td><td valign="top" align="char" char="." rowspan="1" colspan="1">0.09</td><td valign="top" align="char" char="." rowspan="1" colspan="1">0.11</td><td valign="top" align="char" char="." rowspan="1" colspan="1">0.88</td><td valign="top" align="char" char="." rowspan="1" colspan="1">0.26</td><td valign="top" align="char" char="." rowspan="1" colspan="1"><bold>3.16</bold></td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc10g081170.1.1</td><td valign="top" align="left" rowspan="1" colspan="1">CALM</td><td valign="top" align="char" char="." rowspan="1" colspan="1">336.89</td><td valign="top" align="char" char="." rowspan="1" colspan="1">336.1</td><td valign="top" align="char" char="." rowspan="1" colspan="1">1391.1</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−0.003</td><td valign="top" align="char" char="." rowspan="1" colspan="1"><bold>2.05</bold></td><td valign="top" align="char" char="." rowspan="1" colspan="1">189.18</td><td valign="top" align="char" char="." rowspan="1" colspan="1">336.69</td><td valign="top" align="char" char="." rowspan="1" colspan="1">387.5<xref ref-type="table-fn" rid="TN7"><sup>a</sup></xref></td><td valign="top" align="char" char="." rowspan="1" colspan="1">0.83</td><td valign="top" align="char" char="." rowspan="1" colspan="1">1.03</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc03g118810.1.1</td><td valign="top" align="left" rowspan="1" colspan="1">CML</td><td valign="top" align="char" char="." rowspan="1" colspan="1">83.01</td><td valign="top" align="char" char="." rowspan="1" colspan="1">14.98</td><td valign="top" align="char" char="." rowspan="1" colspan="1">235.87</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−<bold>2.46</bold></td><td valign="top" align="char" char="." rowspan="1" colspan="1">1.51</td><td valign="top" align="char" char="." rowspan="1" colspan="1">14.15</td><td valign="top" align="char" char="." rowspan="1" colspan="1">8.74</td><td valign="top" align="char" char="." rowspan="1" colspan="1">96.89<xref ref-type="table-fn" rid="TN7"><sup>a</sup></xref></td><td valign="top" align="char" char="." rowspan="1" colspan="1">−0.69</td><td valign="top" align="char" char="." rowspan="1" colspan="1"><bold>2.77</bold></td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc06g068960.1.1</td><td valign="top" align="left" rowspan="1" colspan="1">CML</td><td valign="top" align="char" char="." rowspan="1" colspan="1">31.84</td><td valign="top" align="char" char="." rowspan="1" colspan="1">30.13</td><td valign="top" align="char" char="." rowspan="1" colspan="1">161.84</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−0.07</td><td valign="top" align="char" char="." rowspan="1" colspan="1"><bold>2.35</bold></td><td valign="top" align="char" char="." rowspan="1" colspan="1">13.69</td><td valign="top" align="char" char="." rowspan="1" colspan="1">18.07</td><td valign="top" align="char" char="." rowspan="1" colspan="1">21.85</td><td valign="top" align="char" char="." rowspan="1" colspan="1">0.39</td><td valign="top" align="char" char="." rowspan="1" colspan="1">0.67</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc10g079420.1.1</td><td valign="top" align="left" rowspan="1" colspan="1">CML</td><td valign="top" align="char" char="." rowspan="1" colspan="1">41.93</td><td valign="top" align="char" char="." rowspan="1" colspan="1">25.34</td><td valign="top" align="char" char="." rowspan="1" colspan="1">257.87</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−0.72</td><td valign="top" align="char" char="." rowspan="1" colspan="1"><bold>2.62</bold></td><td valign="top" align="char" char="." rowspan="1" colspan="1">19.58</td><td valign="top" align="char" char="." rowspan="1" colspan="1">23.48</td><td valign="top" align="char" char="." rowspan="1" colspan="1">131.57<xref ref-type="table-fn" rid="TN7"><sup>a</sup></xref></td><td valign="top" align="char" char="." rowspan="1" colspan="1">0.26</td><td valign="top" align="char" char="." rowspan="1" colspan="1"><bold>2.75</bold></td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc02g094000.1.1</td><td valign="top" align="left" rowspan="1" colspan="1">CML</td><td valign="top" align="char" char="." rowspan="1" colspan="1">3.04</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">32.47</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−<bold>3.65</bold></td><td valign="top" align="char" char="." rowspan="1" colspan="1"><bold>3.42</bold></td><td valign="top" align="char" char="." rowspan="1" colspan="1">0.49</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">11.18<xref ref-type="table-fn" rid="TN7"><sup>a</sup></xref></td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1"><bold>4.49</bold></td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc03g044900.2.1</td><td valign="top" align="left" rowspan="1" colspan="1">CML</td><td valign="top" align="char" char="." rowspan="1" colspan="1">5.19</td><td valign="top" align="char" char="." rowspan="1" colspan="1">6.71</td><td valign="top" align="char" char="." rowspan="1" colspan="1">25.07</td><td valign="top" align="char" char="." rowspan="1" colspan="1">0.36</td><td valign="top" align="char" char="." rowspan="1" colspan="1"><bold>2.27</bold></td><td valign="top" align="char" char="." rowspan="1" colspan="1">8.34</td><td valign="top" align="char" char="." rowspan="1" colspan="1">10.58</td><td valign="top" align="char" char="." rowspan="1" colspan="1">6.06</td><td valign="top" align="char" char="." rowspan="1" colspan="1">0.34</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−0.46</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc06g073830.1.1</td><td valign="top" align="left" rowspan="1" colspan="1">CML</td><td valign="top" align="char" char="." rowspan="1" colspan="1">0.66</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">19.27</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1"><bold>4.85</bold></td><td valign="top" align="char" char="." rowspan="1" colspan="1">1.147</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">1.71</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">0.58</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc11g071740.1.1</td><td valign="top" align="left" rowspan="1" colspan="1">CML</td><td valign="top" align="char" char="." rowspan="1" colspan="1">5.19</td><td valign="top" align="char" char="." rowspan="1" colspan="1">0.34</td><td valign="top" align="char" char="." rowspan="1" colspan="1">74.57</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−<bold>3.93</bold></td><td valign="top" align="char" char="." rowspan="1" colspan="1"><bold>3.84</bold></td><td valign="top" align="char" char="." rowspan="1" colspan="1">4.20</td><td valign="top" align="char" char="." rowspan="1" colspan="1">10.42</td><td valign="top" align="char" char="." rowspan="1" colspan="1">18.34</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−<bold>3.32</bold></td><td valign="top" align="char" char="." rowspan="1" colspan="1"><bold>2.13</bold></td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc11g071760.1.1</td><td valign="top" align="left" rowspan="1" colspan="1">CML</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">8.34</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1"><bold>5.75</bold></td><td valign="top" align="char" char="." rowspan="1" colspan="1">1.42</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">2.66</td><td valign="top" align="center" rowspan="1" colspan="1">0</td><td valign="top" align="char" char="." rowspan="1" colspan="1">0.90</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc09g014990.2.1</td><td valign="top" align="left" rowspan="1" colspan="1">WRKY33</td><td valign="top" align="char" char="." rowspan="1" colspan="1">2.52</td><td valign="top" align="char" char="." rowspan="1" colspan="1">0.11</td><td valign="top" align="char" char="." rowspan="1" colspan="1">28.48</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−<bold>4.43</bold></td><td valign="top" align="char" char="." rowspan="1" colspan="1"><bold>3.50</bold></td><td valign="top" align="char" char="." rowspan="1" colspan="1">0.84</td><td valign="top" align="char" char="." rowspan="1" colspan="1">0.14</td><td valign="top" align="char" char="." rowspan="1" colspan="1">12.26</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−<bold>2.54</bold></td><td valign="top" align="char" char="." rowspan="1" colspan="1"><bold>3.86</bold></td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc06g036290.2.1</td><td valign="top" align="left" rowspan="1" colspan="1">HSP90</td><td valign="top" align="char" char="." rowspan="1" colspan="1">16.45</td><td valign="top" align="char" char="." rowspan="1" colspan="1">2.76</td><td valign="top" align="char" char="." rowspan="1" colspan="1">70.45</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−<bold>2.57</bold></td><td valign="top" align="char" char="." rowspan="1" colspan="1"><bold>2.09</bold></td><td valign="top" align="char" char="." rowspan="1" colspan="1">32.76</td><td valign="top" align="char" char="." rowspan="1" colspan="1">2.02</td><td valign="top" align="char" char="." rowspan="1" colspan="1">18.11</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−<bold>4.0</bold></td><td valign="top" align="char" char="." rowspan="1" colspan="1">−0.85</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc07g042170.2.1</td><td valign="top" align="left" rowspan="1" colspan="1">JAZ</td><td valign="top" align="char" char="." rowspan="1" colspan="1">15.32</td><td valign="top" align="char" char="." rowspan="1" colspan="1">10.98</td><td valign="top" align="char" char="." rowspan="1" colspan="1">69.14</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−0.48</td><td valign="top" align="char" char="." rowspan="1" colspan="1"><bold>2.17</bold></td><td valign="top" align="char" char="." rowspan="1" colspan="1">15.35</td><td valign="top" align="char" char="." rowspan="1" colspan="1">13.32</td><td valign="top" align="char" char="." rowspan="1" colspan="1">60.44</td><td valign="top" align="char" char="." rowspan="1" colspan="1">−0.20</td><td valign="top" align="char" char="." rowspan="1" colspan="1">1.98</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Solyc12g009220.1.1</td><td valign="top" align="left" rowspan="1" colspan="1">JAZ</td><td valign="top" align="char" char="." rowspan="1" colspan="1">3.41</td><td valign="top" align="char" char="." rowspan="1" colspan="1">7.33</td><td valign="top" align="char" char="." rowspan="1" colspan="1">75.82</td><td valign="top" align="char" char="." rowspan="1" colspan="1">1.10</td><td valign="top" align="char" char="." rowspan="1" colspan="1"><bold>4.47</bold></td><td valign="top" align="char" char="." rowspan="1" colspan="1">6.43</td><td valign="top" align="char" char="." rowspan="1" colspan="1">7.71</td><td valign="top" align="char" char="." rowspan="1" colspan="1">33.47</td><td valign="top" align="char" char="." rowspan="1" colspan="1">0.26</td><td valign="top" align="char" char="." rowspan="1" colspan="1"><bold>2.38</bold></td></tr></tbody></table><table-wrap-foot><fn id="TN7"><label>a</label><p><italic>Significant difference (FDR ≤ 0.001 and the absolute value of Log<sub>2</sub> fold-change ≥ 2) were shown in boldface</italic>.</p></fn></table-wrap-foot></table-wrap></sec><sec><title>Validation of RNA-seq data for selected genes by RT-PCR and qRT-PCR</title><p>To evaluate the validity of RNA-seq analysis, transcriptional levels of selected 8 DEGs representing a wide range of expression levels and patterns were determined by RT-PCR and qRT-PCR analysis. Based on the functional annotation in literatures, majority of these DEGs were associated with massive defense response processes including ethylene biosynthesis (Solyc07g049530.2.1), defense-related enzymes (Solyc02g072470.2.1, Solyc07g008600.1.1, Solyc01g057000.2.1, Solyc02g036480.1.1, Solyc04g072070.2.1 and Solyc10g081170.1.1), and second metabolite biosynthesis (Solyc08g074630.1.1). In general, the expression data provided by qRT-PCR were almost consistent with profiles detected by RNA-seq at all time-points (Figure <xref ref-type="fig" rid="F4">4</xref>), confirming the trends of up- or down-regulation of all the analyzed genes. The differences in the magnitudes of changes observed between the qRT-PCR and RNA-seq results might be caused by different algorithms.</p><fig id="F4" position="float"><label>Figure 4</label><caption><p><bold>RT-PCR and qRT-PCR validation of differentially expressed 8 genes related to defense response at 6 h post-inoculation (6 HPI) and 6 days post-inoculation (6 DPI)</bold>. Expression levels of each sample were normalized on the basis of transcript amounts of <italic>EF1</italic>-α. Relative expression values for qRT-PCR analysis were determined against the average value of mock sample with PI 114490. Each experiment determined in three technical replicates and standard deviation (<italic>n</italic> = 3) is represented by error bars. The asterisk above the bars indicates statistically significant differences between the infected samples and corresponding mock samples.</p></caption><graphic xlink:href="fpls-06-01173-g0004"></graphic></fig><p>It was validated by qRT-PCR that four genes Solyc02g072470.2.1, Solyc02g036480.1.1, Solyc08g074630.1.1, and Solyc07g008600.1.1 were steadily up-regulated during two time-points infection in both PI 114490 and OH 88119, differing in their induced strength. Solyc07g049530.2.1 and Solyc04g072070.2.1 initially displayed down-regulated at 6 HPI but significantly reinforced at 6DPI in both tomato lines, and the up-regulated fold-change was higher in PI 114490. The expression pattern of Solyc01g057000.2.1 was opposite between two tomato lines, which was up-regulated in the resistant line PI 114490 while down-regulated in the susceptible line OH 88119 (Figure <xref ref-type="fig" rid="F4">4</xref>).</p></sec></sec><sec id="s4"><title>Disscussion</title><p>The <italic>S. lycopersicum</italic> var. <italic>cerasiforme</italic> accession PI 114490 has been considered as a durable source for resistance to bacterial spot due to its high level of quantitative field resistance to four races T1–T4 (Yang, <xref rid="B49" ref-type="bibr">2013</xref>). There is no or few lesions on PI 114490, but the bacterial population of race T3 in its leaves is not significantly different from that in the susceptible line OH 88119 (Sun et al., <xref rid="B42" ref-type="bibr">2014</xref>). So considering on the aspect of phenotype, PI 114490 shows higher tolerant response to avoid the development of symptoms. But the difference of global inducible defense response against <italic>X. perforance</italic> race T3 infection between PI 114490 and OH 88119 were not clear.</p><p>In this study, RNA-seq technique was adapted to detect the DEGs during the race T3 infection in PI 114490 and OH 88119. Our previous study using cDNA-AFLP techniques has already identified DEGs between the two tomato lines (Du et al., <xref rid="B10" ref-type="bibr">2014</xref>). Therefore, we started with one biological replication for RNA-seq analysis. An average of 7 million sequence reads were obtained from RNA-seq and the clean reads could match approximately 62% of reference genes (Table <xref ref-type="table" rid="T1">1</xref>), which was closed to previous tomato RNA-seq data with 20 million sequence reads (Tang et al., <xref rid="B45" ref-type="bibr">2013</xref>), indicating that the sequencing depth was sufficient for the transcriptome coverage. The well correlation between qRT-PCR and RNA-seq data (Figure <xref ref-type="fig" rid="F4">4</xref>) also demonstrated the reliability of RNA-seq analysis. Of course, more replicates should provide more reliable information for understanding the genes involved in the process of resistance/defense to the pathogen of bacterial spot race T3 in tomato.</p><sec><title>Inducible defense response to <italic>X. perforans</italic> interfered at 6 HPI but activated at 6 DPI in both resistant and susceptible tomato lines</title><p>Despite PI 114490 and OH 88119 have different responses to race T3 infection (Sun et al., <xref rid="B42" ref-type="bibr">2014</xref>), lots of common DEGs were regulated in both two tomato lines. At 6 HPI, 50 common down-regulated genes existed in both two tomato lines (Figure <xref ref-type="fig" rid="F2">2C</xref>) suggested that the inducible defense response pathways were not completely activated at 6 HPI. Meanwhile, down-regulation of the minority of pathogen-related genes in cluster 27 (Figure <xref ref-type="fig" rid="F3">3</xref>) indicated that at least some defense response had been interfered by pathogen infection as early as 6 HPI.</p><p>Among the 344 common DEGs at 6 DPI, a majority of 326 genes were commonly up-regulated (Figure <xref ref-type="fig" rid="F2">2D</xref>) in both tomato lines. The dominant subcategories in biological process were cellular process, macromolecule metabolism and response to stimulus (data not shown). Six up-regulated genes in plant-pathogen interaction pathway were shared by the two tomato lines at 6 DPI (Table <xref ref-type="table" rid="T5">5</xref>). Previous studies have proven that the function of these regulated genes plays important role in bacterial spot defense response (Cui et al., <xref rid="B8" ref-type="bibr">2015</xref>). Therefore, defense response of tomato lines was activated 6 days after infection by race T3. Accumulation expression levels of those co-regulated genes were likely to increase basal defense response and improve the disease resistance to race T3 infection in both resistant and susceptible tomato. So the susceptible line OH 88119 also succeeded to properly activate the expression of many defense-related genes.</p></sec><sec><title>Resistant and susceptible tomato lines displayed differentially expressed patterns in photosynthesis pathway</title><p>Plant-pathogen interaction response usually alters the expressional level of genes associated with photosynthesis (Major et al., <xref rid="B26" ref-type="bibr">2010</xref>). Many photosynthesis-related genes including chlorophyII a/b binding proteins and photosynthetic reaction center proteins were strongly repressed in susceptible hybrid poplar leaves at 9 days inoculated with <italic>Melampsora medusa</italic> (Miranda et al., <xref rid="B27" ref-type="bibr">2007</xref>). However, our RNA-seq data showed that race T3 pathogen caused opposite impact on photosynthesis between resistance and susceptible tomato lines. Genes involved in photosynthesis pathway were mainly up-regulated in the susceptible tomato line OH 88119 at 6 DPI, but down-regulated in the resistant line PI 114490 at 6 HPI and 6 DPI (Table <xref ref-type="table" rid="T4">4</xref>). To the best of our knowledge, the reason of this divergent response between resistant and susceptible plants in photosynthesis pathway has not previously been known in plant-pathogen interactions.</p></sec><sec><title>Analysis of differentially expressed genes involved in plant immune response pathways</title><p>Plants possess different sophisticated defense strategies which are usually accompanied by transcriptional changes to protect themselves against pathogen attacks. The plant immune response pathway can be mainly divided into two branches (Jones and Dangl, <xref rid="B19" ref-type="bibr">2006</xref>). The first branch and initial defense response is usually activated by pathogen-associated molecular patterns (PAMP) whose presence is recognized by plant plasma membrane-localized pattern recognition receptors (PRRs), which results in PAMP-triggered immunity (PTI). The second branch is activated by nucleotide-binding leucine-rich repeat (NB-LRR) resistance gene, which directly or indirectly interacts with virulence factor, and results in activation of effector-triggered immunity (ETI). Since the plant-pathogen interaction pathways (KEGG: 04626) summarized the genes involved in defense network of PTI and ETI, so we focused on the transcript dynamics of this KEGG pathways and enumerated the DEGs imparting the plant immune response (Table <xref ref-type="table" rid="T5">5</xref>).</p><p>Several PAMPs have been identified from bacteria. Flagellin is one of important and well-characterized PAMPs that can be recognized by the LRR receptor-like serine/threonine-protein kinase (FLS2) (Gómez-Gómez and Boller, <xref rid="B14" ref-type="bibr">2000</xref>). In our study, RLK protein Solyc02g070890.2.1 with the highest amino acid similarity (54%) to FLS2 protein from <italic>Arabidopsis thaliana</italic> than other tomato RLK genes was down-regulated at 6 HPI, and slightly up-regulated at 6 DPI in PI 114490, but this gene was not differentially expressed in OH 88119 upon race T3 infection. RLK protein Solyc02g072470.2.1 was the highest induced member of RLK family in our RNA-seq data. qRT-PCR validated that Solyc02g072470.2.1 were significantly induced in both tomato lines at 6 DPI, which displayed more than 35- and 18-fold-induction in PI 114490 and OH 88119, respectively (Figure <xref ref-type="fig" rid="F4">4</xref>). The highest induced member of LRR receptor-like serine/threonine-protein kinase was Solyc07g008600.1.1 in RNA-seq analysis, which was verified up-regulated in both two tomato lines (Figure <xref ref-type="fig" rid="F4">4</xref>).</p><p>Recognition of PAMPs initiates downstream signaling pathways involving WRKY transcription factors to confer defense response against bacterial, fungal pathogens and nematodes (Asai et al., <xref rid="B1" ref-type="bibr">2002</xref>; Bhattarai et al., <xref rid="B4" ref-type="bibr">2010</xref>). Based on KEGG analysis, WRKY transcription factor Solyc09g014990.2.1 homologous to WRKY33 was down-regulated at 6 HPI but highly up-regulated at 6 DPI in both genotypes (Table <xref ref-type="table" rid="T5">5</xref>). Since members of WRKY families are thought to play important role in defense response, we further investigated the expression patterns of all 85 WRKY families genes annotated in the International Tomato Annotation Group (ITAG) Release 2.3 Predicted CDS. A total of 29 WRKY genes were differentially expressed. Among them, none was significantly up-regulated at 6 HPI but 17 (58.6%) were up-regulated in both tomato lines at 6 DPI (Figure <xref ref-type="fig" rid="F5">5</xref>). Previous study indicated that the expression levels of SlWRKY8 (Solyc02g093050.2.1), SlWRKY23 (Solyc01g079260.2.1), SlWRKY39 (Solyc03g116890.2.1), SlWRKY53 (Solyc08g008280.2.1), SlWRKY80 (Solyc03g095770.2.1), and SlWRKY81 (Solyc09g015770.2.1) were enhanced in <italic>S. lycopersicum</italic> cultivar Alisa Craig under the invasion of <italic>Pseudomonas syringae</italic> (Huang et al., <xref rid="B16" ref-type="bibr">2012</xref>). In the current study, none of these WRKY genes were detected at 6 HPI, but SlWRKY39/53/80/81 were significantly induced in both tomato lines, and SlWRKY8/23 were specific up-regulated in PI 114490 at 6 DPI. SlWRKY72b are transcriptionally up-regulated during disease resistance mediated by the R gene <italic>Mi-1</italic>, and virus-induced gene silencing of this gene in tomato resulted in a clear reduction of <italic>Mi-1</italic>-mediated resistance as well as basal defense against root-knot nematodes and potato aphids (Bhattarai et al., <xref rid="B4" ref-type="bibr">2010</xref>). WRKY gene Solyc06g070990.2.1, the highest identity with SlWRKY72b than other WRKY protein in tomato, were significantly induced at 6 DPI in PI 114490 (Figure <xref ref-type="fig" rid="F5">5</xref>).</p><fig id="F5" position="float"><label>Figure 5</label><caption><p><bold>Differentially expressed WRKY genes in tomato lines PI 1144490 and OH 88119 at 6 h and 6 days post-inoculation with <italic>Xanthomonas perforans</italic> race T3</bold>. PM and OM: PI 114490 and OH 88119 respectively mock-inoculated with the sterile solution containing 10 mM MgSO<sub>4</sub>·7H<sub>2</sub>O and 0.025% (v/v) Silwet L77. PT and OT: PI 114490 and OH 88119 respectively inoculated with race T3.</p></caption><graphic xlink:href="fpls-06-01173-g0005"></graphic></fig><p>Intracellular Ca<sup>2+</sup> influxes have also long been recognized as essential and early events downstream of multiple PAMP perception, leading to local and systemic acquired resistance (Lecourieux et al., <xref rid="B23" ref-type="bibr">2005</xref>; Boudsocq et al., <xref rid="B5" ref-type="bibr">2010</xref>). In the process of Ca<sup>2+</sup> signaling, some members of Calcium-dependent protein kinase (CDPK) family was immediately induced by flg22 and Avr-Cf9 interaction (Romeis et al., <xref rid="B35" ref-type="bibr">2000</xref>; Boudsocq et al., <xref rid="B5" ref-type="bibr">2010</xref>). Unexpectedly, none of CDPK genes was induced as early as 6 HPI in both tomato lines. Calmodulin (CALM or CaM), a major Ca<sup>2+</sup> sensor, play positive regulatory resistance roles in different host-pathogen interaction (Park et al., <xref rid="B30" ref-type="bibr">2004</xref>; Choi et al., <xref rid="B7" ref-type="bibr">2009</xref>). Only one CALM gene Solyc10g081170.1.1 was specifically up-regulated at 6 DPI in PI 114490 (Table <xref ref-type="table" rid="T5">5</xref>), which was also validated by qRT-PCR analysis (Figure <xref ref-type="fig" rid="F4">4</xref>).</p><p>In the process of plant and pathogen interaction, bacterial type III effectors which are directly delivered into the host cells via the type III secretion system can bypass or disrupt host first line of PAMP-triggered immunity. But resistant plants contain R proteins belonging to the nucleotide -binding site-leucine-rich repeat (NBS-LRR) family to directly or indirectly detect bacterial effectors, which will activate downstream signaling and lead to pathogen resistance (DeYoung and Innes, <xref rid="B9" ref-type="bibr">2006</xref>). Previous papers have evidence that some R genes can be activated by the specific effectors, which are displayed by the accumulation of R genes expression levels. Therefore, we paid attention to those putative R genes containing NBS-LRR domain that could possibly be induced by the <italic>X. perforans</italic> infection. A total of 298 genes were annotated as NBS-LRR proteins for tomato in SGN database, and the RPKM values of most genes were low in the six sequenced samples, indicating the expression level of most putative R genes was low in tomato plant. The RNA-seq data showed that none of putative R genes were up-regulated in both tomato lines at 6 HPI. But the number of up-regulated putative R genes in PI 114490 at 6 DPI was more than that of in OH 881119 (Figure <xref ref-type="fig" rid="F6">6</xref>). Six putative R genes were commonly up-regulated in both tomato lines. Among these genes, Solyc07g056190.2.1 displayed the highest fold-change (Figure <xref ref-type="fig" rid="F6">6</xref>). In addition, there were 11 and 1 putative R genes were specifically up-regulated in P I114490 and OH88119, respectively (Figure <xref ref-type="fig" rid="F6">6</xref>).</p><fig id="F6" position="float"><label>Figure 6</label><caption><p><bold>Differentially expressed putative R genes containing NBS-LRR domain in tomato lines PI 1144490 and OH 88119 at 6 h and 6 days post-inoculation</bold>. PM and OM: PI 114490 and OH 88119 respectively mock-inoculated with the sterile solution containing 10 mM MgSO<sub>4</sub>·7H<sub>2</sub>O and 0.025% (v/v) Silwet L77. PT and OT: PI 114490 and OH 88119 respectively inoculated with race T3.</p></caption><graphic xlink:href="fpls-06-01173-g0006"></graphic></fig></sec><sec><title>Enumerate of significant <italic>X. perforans</italic> up-regulated genes</title><p>Previously, we used cDNA-AFLP technique to identify differential expression genes in tomato lines PI 114490 and OH 88119 in response to race T3 infection at 3, 4, and 5 days. A total of 60 genes were commonly up-regulated at different levels in two tomato lines (Du et al., <xref rid="B10" ref-type="bibr">2014</xref>). Among these genes, 14 genes were also up-regulated in this study (Table <xref ref-type="supplementary-material" rid="SM5">S5</xref>). Based on the functional annotation in literatures, majority of these genes were associated with massive defense response process including jasmonic acid biosynthesis pathways (Solyc03g122190.2.1 and Solyc04g079730.1.1), ethylene biosynthesis (Solyc07g049530.2.1), defense-related enzymes (Solyc10g055800.1.1, Solyc00g071180.2.1, Solyc03g007240.2.1, and Solyc04g015970.2.1), and cell death related (Solyc03g006700.2.1, Solyc01g105070.2.1, Solyc08g074680.2.1, and Solyc11g068940.1.1). The remaining (Solyc05g050120.2.1, Solyc08g068710.1.1, and Solyc04g010250.2.1) did not match any known defense response genes. Similar expression pattern in different expression profile techniques indicates that these well-validated and reproducible 14 up-regulated genes may play important role in tomato-<italic>X. perforans</italic> interaction.</p></sec></sec><sec sec-type="conclusions" id="s5"><title>Conclusion</title><p>In this study, high-throughput sequencing data was used to identify <italic>X. perforans</italic> responsive modules, which were enriched for differentially expressed genes between resistant line PI 114490 and susceptible line OH 88119 at different time point after spray-inoculation of race T3. The data provided a whole view on the variation tendency of genes involved in tomato-<italic>X. perforans</italic> interaction. A large number of candidate genes involved in tomato-<italic>X. perforans</italic> interaction were identified. Comparison of RNA-seq data with our previous cDNA-AFLP data revealed common up-regulated genes, and some of them were involved in jasmonic acid and ethylene biosynthesis.</p></sec><sec id="s6"><title>Author contributions</title><p>Conceived and designed the experiments: YW, WY. Performed the experiments: HD. Analyzed the data: HD, JY, WY. Contributed reagents/materials/analysis tools: YW, JY, WY. Wrote the paper: HD, WY.</p><sec><title>Conflict of interest statement</title><p>The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.</p></sec></sec></body><back><ack><p>The authors would like to thank Dr. David M. Francis in the Department of Horticulture and Crop Science at the Ohio State University for providing the seeds of tomato lines and Dr. Jeffrey B. Jones in the Department of Plant Pathology at the University of Florida for providing race T3 of the bacterial spot pathogen. The work was partly supported by the National Natural Science Foundation of China (31372073) and Beijing Modern Agro-industry Technology Research System (GCTDZJ2014033001).</p></ack><sec sec-type="supplementary-material" id="s7"><title>Supplementary material</title><p>The Supplementary Material for this article can be found online at: <ext-link ext-link-type="uri" xlink:href="http://journal.frontiersin.org/article/10.3389/fpls.2015.01173">http://journal.frontiersin.org/article/10.3389/fpls.2015.01173</ext-link></p><supplementary-material content-type="local-data" id="SM1"><label>Table S1</label><caption><p><bold>Genes and oligonucleotide sets used in quantitative and semi-quantitative RT-PCR experiments</bold>.</p></caption><media xlink:href="Table1.DOCX"><caption><p>Click here for additional data file.</p></caption></media></supplementary-material><supplementary-material content-type="local-data" id="SM2"><label>Table S2</label><caption><p><bold>Statistics of total tomato reference genes in different expression level intervals</bold>.</p></caption><media xlink:href="Table2.DOCX"><caption><p>Click here for additional data file.</p></caption></media></supplementary-material><supplementary-material content-type="local-data" id="SM3"><label>Table S3</label><caption><p><bold>Common down-regulated genes associated with “response to stimulus” according to Gene Ontology classification in tomato lines PI 114490 and OH 88119 at 6 h post-inoculation (HPI)</bold>.</p></caption><media xlink:href="Table3.DOCX"><caption><p>Click here for additional data file.</p></caption></media></supplementary-material><supplementary-material content-type="local-data" id="SM4"><label>Table S4</label><caption><p><bold>Gene ontology (GO) analysis of up-regulated genes for biological process in tomato lines PI 114490 and OH 88119 at 6 d post-inoculation</bold>.</p></caption><media xlink:href="Table4.DOCX"><caption><p>Click here for additional data file.</p></caption></media></supplementary-material><supplementary-material content-type="local-data" id="SM5"><label>Table S5</label><caption><p><bold>Sets of common differentially expressed genes in RNA-seq analysis with previous cDNA-AFLP results</bold>.</p></caption><media xlink:href="Table5.DOCX"><caption><p>Click here for additional data file.</p></caption></media></supplementary-material><supplementary-material content-type="local-data" id="SM6"><label>Image S1</label><caption><p><bold>Venn diagram showing the overlaps and specific expressed genes between mock samples and samples spray-inoculated with <italic>Xanthomonas perforans</italic> race T3 in tomato lines PI 114490 and OH 88119</bold>. PM and OM: PI 114490 and OH 88119 respective mock-treatment with the sterile solution containing 10 mM MgSO<sub>4</sub>.7H<sub>2</sub>O and 0.025%(v/v) Silwet L77. PT and OT: inoculation with bacterial spot race T3 in PI 114490 and OH 88119, respectively.</p></caption><media xlink:href="Image1.TIF"><caption><p>Click here for additional data file.</p></caption></media></supplementary-material><supplementary-material content-type="local-data" id="SM7"><label>Image S2</label><caption><p><bold>Distribution of the differentially expressed genes (DEGs) within Go secondary categories of molecular function, cellular component and biological process. (A)</bold> Go classification for DEGs identified from OT6h vs. OM. <bold>(B)</bold> Go classification for DEGs identified from OT6d vs. OM. <bold>(C)</bold> Go classification for DEGs identified from PT6h vs. PM. <bold>(D)</bold> Go classification for DEGs identified from PT6d vs. PM. PM and OM: PI 114490 and OH 88119 respective mock-treatment with the sterile solution containing 10 mM MgSO<sub>4</sub>.7H<sub>2</sub>O and 0.025%(v/v) Silwet L77. PT and OT: inoculation with bacterial spot race T3 in PI 114490 and OH 88119, respectively.</p></caption><media xlink:href="Image2.TIF"><caption><p>Click here for additional data file.</p></caption></media></supplementary-material></sec><ref-list><title>References</title><ref id="B1"><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Asai</surname><given-names>T.</given-names></name><name><surname>Tena</surname><given-names>G.</given-names></name><name><surname>Plotnikova</surname><given-names>J.</given-names></name><name><surname>Willmann</surname><given-names>M. R.</given-names></name><name><surname>Chiu</surname><given-names>W. L.</given-names></name><name><surname>Gomez-Gomez</surname><given-names>L.</given-names></name><etal></etal></person-group>. 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