Comparative analysis of complete chloroplast genome sequences of two tropical trees Machilus yunnanensis and Machilus balansae in the family Lauraceae
Identifieur interne : 000080 ( Pmc/Corpus ); précédent : 000079; suivant : 000081Comparative analysis of complete chloroplast genome sequences of two tropical trees Machilus yunnanensis and Machilus balansae in the family Lauraceae
Auteurs : Yu Song ; Wenpan Dong ; Bing Liu ; Chao Xu ; Xin Yao ; Jie Gao ; Richard T. CorlettSource :
- Frontiers in Plant Science [ 1664-462X ] ; 2015.
Abstract
Url:
DOI: 10.3389/fpls.2015.00662
PubMed: 26379689
PubMed Central: 4548089
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Comparative analysis of complete chloroplast genome sequences of two tropical trees <italic>Machilus yunnanensis</italic> and <italic>Machilus balansae</italic> in the family Lauraceae</title><author><name sortKey="Song, Yu" sort="Song, Yu" uniqKey="Song Y" first="Yu" last="Song">Yu Song</name><affiliation><nlm:aff id="aff1"><institution>Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences</institution><country>Mengla, China</country></nlm:aff></affiliation><affiliation><nlm:aff id="aff2"><institution>Graduate School of the Chinese Academy of Sciences</institution><country>Beijing, China</country></nlm:aff></affiliation></author><author><name sortKey="Dong, Wenpan" sort="Dong, Wenpan" uniqKey="Dong W" first="Wenpan" last="Dong">Wenpan Dong</name><affiliation><nlm:aff id="aff3"><institution>Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University</institution><country>Beijing, China</country></nlm:aff></affiliation><affiliation><nlm:aff id="aff4"><institution>State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences</institution><country>Beijing, China</country></nlm:aff></affiliation></author><author><name sortKey="Liu, Bing" sort="Liu, Bing" uniqKey="Liu B" first="Bing" last="Liu">Bing Liu</name><affiliation><nlm:aff id="aff4"><institution>State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences</institution><country>Beijing, China</country></nlm:aff></affiliation></author><author><name sortKey="Xu, Chao" sort="Xu, Chao" uniqKey="Xu C" first="Chao" last="Xu">Chao Xu</name><affiliation><nlm:aff id="aff4"><institution>State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences</institution><country>Beijing, China</country></nlm:aff></affiliation></author><author><name sortKey="Yao, Xin" sort="Yao, Xin" uniqKey="Yao X" first="Xin" last="Yao">Xin Yao</name><affiliation><nlm:aff id="aff1"><institution>Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences</institution><country>Mengla, China</country></nlm:aff></affiliation><affiliation><nlm:aff id="aff2"><institution>Graduate School of the Chinese Academy of Sciences</institution><country>Beijing, China</country></nlm:aff></affiliation></author><author><name sortKey="Gao, Jie" sort="Gao, Jie" uniqKey="Gao J" first="Jie" last="Gao">Jie Gao</name><affiliation><nlm:aff id="aff5"><institution>Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences</institution><country>Mengla, China</country></nlm:aff></affiliation></author><author><name sortKey="Corlett, Richard T" sort="Corlett, Richard T" uniqKey="Corlett R" first="Richard T." last="Corlett">Richard T. Corlett</name><affiliation><nlm:aff id="aff1"><institution>Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences</institution><country>Mengla, China</country></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">26379689</idno><idno type="pmc">4548089</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4548089</idno><idno type="RBID">PMC:4548089</idno><idno type="doi">10.3389/fpls.2015.00662</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000080</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Comparative analysis of complete chloroplast genome sequences of two tropical trees <italic>Machilus yunnanensis</italic> and <italic>Machilus balansae</italic> in the family Lauraceae</title><author><name sortKey="Song, Yu" sort="Song, Yu" uniqKey="Song Y" first="Yu" last="Song">Yu Song</name><affiliation><nlm:aff id="aff1"><institution>Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences</institution><country>Mengla, China</country></nlm:aff></affiliation><affiliation><nlm:aff id="aff2"><institution>Graduate School of the Chinese Academy of Sciences</institution><country>Beijing, China</country></nlm:aff></affiliation></author><author><name sortKey="Dong, Wenpan" sort="Dong, Wenpan" uniqKey="Dong W" first="Wenpan" last="Dong">Wenpan Dong</name><affiliation><nlm:aff id="aff3"><institution>Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University</institution><country>Beijing, China</country></nlm:aff></affiliation><affiliation><nlm:aff id="aff4"><institution>State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences</institution><country>Beijing, China</country></nlm:aff></affiliation></author><author><name sortKey="Liu, Bing" sort="Liu, Bing" uniqKey="Liu B" first="Bing" last="Liu">Bing Liu</name><affiliation><nlm:aff id="aff4"><institution>State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences</institution><country>Beijing, China</country></nlm:aff></affiliation></author><author><name sortKey="Xu, Chao" sort="Xu, Chao" uniqKey="Xu C" first="Chao" last="Xu">Chao Xu</name><affiliation><nlm:aff id="aff4"><institution>State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences</institution><country>Beijing, China</country></nlm:aff></affiliation></author><author><name sortKey="Yao, Xin" sort="Yao, Xin" uniqKey="Yao X" first="Xin" last="Yao">Xin Yao</name><affiliation><nlm:aff id="aff1"><institution>Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences</institution><country>Mengla, China</country></nlm:aff></affiliation><affiliation><nlm:aff id="aff2"><institution>Graduate School of the Chinese Academy of Sciences</institution><country>Beijing, China</country></nlm:aff></affiliation></author><author><name sortKey="Gao, Jie" sort="Gao, Jie" uniqKey="Gao J" first="Jie" last="Gao">Jie Gao</name><affiliation><nlm:aff id="aff5"><institution>Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences</institution><country>Mengla, China</country></nlm:aff></affiliation></author><author><name sortKey="Corlett, Richard T" sort="Corlett, Richard T" uniqKey="Corlett R" first="Richard T." last="Corlett">Richard T. Corlett</name><affiliation><nlm:aff id="aff1"><institution>Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences</institution><country>Mengla, China</country></nlm:aff></affiliation></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><italic>Machilus</italic> is a large (c. 100 sp.) genus of trees in the family Lauraceae, distributed in tropical and subtropical East Asia. Both molecular species identification and phylogenetic studies of this morphologically uniform genus have been constrained by insufficient variable sites among frequently used biomarkers. To better understand the mutation patterns in the chloroplast genome of <italic>Machilus</italic>, the complete plastomes of two species were sequenced. The plastomes of <italic>Machilus yunnanensis</italic> and <italic>M. balansae</italic> were 152, 622 and 152, 721 bp, respectively. Seven highly variable regions between the two <italic>Machilus</italic> species were identified and 297 mutation events, including one micro-inversion in the <italic>ccsA-ndhD</italic> region, 65 indels, and 231 substitutions, were accurately located. Thirty-six microsatellite sites were found for use in species identification and 95 single-nucleotide changes were identified in gene coding regions.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Aiyar, A" uniqKey="Aiyar A">A. Aiyar</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chang, C C" uniqKey="Chang C">C. C. 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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">26379689</article-id><article-id pub-id-type="pmc">4548089</article-id><article-id pub-id-type="doi">10.3389/fpls.2015.00662</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 analysis of complete chloroplast genome sequences of two tropical trees <italic>Machilus yunnanensis</italic> and <italic>Machilus balansae</italic> in the family Lauraceae</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Song</surname><given-names>Yu</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="aff" rid="aff2"><sup>2</sup></xref><xref ref-type="author-notes" rid="fn002"><sup>†</sup></xref><uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/248722"></uri></contrib><contrib contrib-type="author"><name><surname>Dong</surname><given-names>Wenpan</given-names></name><xref ref-type="aff" rid="aff3"><sup>3</sup></xref><xref ref-type="aff" rid="aff4"><sup>4</sup></xref><xref ref-type="author-notes" rid="fn002"><sup>†</sup></xref><uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/265793"></uri></contrib><contrib contrib-type="author"><name><surname>Liu</surname><given-names>Bing</given-names></name><xref ref-type="aff" rid="aff4"><sup>4</sup></xref><uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/265788"></uri></contrib><contrib contrib-type="author"><name><surname>Xu</surname><given-names>Chao</given-names></name><xref ref-type="aff" rid="aff4"><sup>4</sup></xref><uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/266002"></uri></contrib><contrib contrib-type="author"><name><surname>Yao</surname><given-names>Xin</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="aff" rid="aff2"><sup>2</sup></xref><uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/266224"></uri></contrib><contrib contrib-type="author"><name><surname>Gao</surname><given-names>Jie</given-names></name><xref ref-type="aff" rid="aff5"><sup>5</sup></xref><uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/258035"></uri></contrib><contrib contrib-type="author"><name><surname>Corlett</surname><given-names>Richard T.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="author-notes" rid="fn001"><sup>*</sup></xref><uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/266840"></uri></contrib></contrib-group><aff id="aff1"><sup>1</sup><institution>Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences</institution><country>Mengla, China</country></aff><aff id="aff2"><sup>2</sup><institution>Graduate School of the Chinese Academy of Sciences</institution><country>Beijing, China</country></aff><aff id="aff3"><sup>3</sup><institution>Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University</institution><country>Beijing, China</country></aff><aff id="aff4"><sup>4</sup><institution>State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences</institution><country>Beijing, China</country></aff><aff id="aff5"><sup>5</sup><institution>Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences</institution><country>Mengla, China</country></aff><author-notes><fn fn-type="edited-by"><p>Edited by: <italic>Maureen Hanson, Cornell University, USA</italic></p></fn><fn fn-type="edited-by"><p>Reviewed by: <italic>Tao Sun, Stanford University, USA; Kenneth Wolfe, University College Dublin, Ireland</italic></p></fn><corresp id="fn001">*Correspondence: <italic>Richard T. Corlett, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, China, <email xlink:type="simple">corlett@xtbg.org.cn</email></italic></corresp><fn fn-type="other" id="fn002"><p><sup>†</sup><italic>These authors have contributed equally to this work.</italic></p></fn><fn fn-type="other" id="fn003"><p>This article was submitted to Plant Genetics and Genomics, a section of the journal Frontiers in Plant Science</p></fn></author-notes><pub-date pub-type="epub"><day>25</day><month>8</month><year>2015</year></pub-date><pub-date pub-type="collection"><year>2015</year></pub-date><volume>6</volume><elocation-id>662</elocation-id><history><date date-type="received"><day>24</day><month>6</month><year>2015</year></date><date date-type="accepted"><day>11</day><month>8</month><year>2015</year></date></history><permissions><copyright-statement>Copyright © 2015 Song, Dong, Liu, Xu, Yao, Gao and Corlett.</copyright-statement><copyright-year>2015</copyright-year><copyright-holder>Song, Dong, Liu, Xu, Yao, Gao and Corlett</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><italic>Machilus</italic> is a large (c. 100 sp.) genus of trees in the family Lauraceae, distributed in tropical and subtropical East Asia. Both molecular species identification and phylogenetic studies of this morphologically uniform genus have been constrained by insufficient variable sites among frequently used biomarkers. To better understand the mutation patterns in the chloroplast genome of <italic>Machilus</italic>, the complete plastomes of two species were sequenced. The plastomes of <italic>Machilus yunnanensis</italic> and <italic>M. balansae</italic> were 152, 622 and 152, 721 bp, respectively. Seven highly variable regions between the two <italic>Machilus</italic> species were identified and 297 mutation events, including one micro-inversion in the <italic>ccsA-ndhD</italic> region, 65 indels, and 231 substitutions, were accurately located. Thirty-six microsatellite sites were found for use in species identification and 95 single-nucleotide changes were identified in gene coding regions.</p></abstract><kwd-group><kwd>mutation</kwd><kwd>genome</kwd><kwd>chloroplast</kwd><kwd><italic>Machilus</italic></kwd><kwd>Lauraceae</kwd></kwd-group><counts><fig-count count="3"></fig-count><table-count count="4"></table-count><equation-count count="0"></equation-count><ref-count count="43"></ref-count><page-count count="8"></page-count><word-count count="0"></word-count></counts></article-meta></front><body><sec><title>Introduction</title><p>The genus <italic>Machilus</italic> in the family Lauraceae includes nearly 100 tree species distributed in tropical and subtropical East and South Asia, with most species in China (<xref rid="B35" ref-type="bibr">Tang et al., 2010</xref>). <italic>Machilus</italic> species are known for their high-quality wood. Although the relationships among the genera traditionally recognized within the monophyletic ‘<italic>Persea</italic> group’ are still unclear, <italic>Machilus</italic> (with two misplaced species of <italic>Phoebe</italic>) forms a distinct, monophyletic, Asian clade (<xref rid="B3" ref-type="bibr">Chen et al., 2009</xref>; <xref rid="B27" ref-type="bibr">Rohwer et al., 2009</xref>; <xref rid="B21" ref-type="bibr">Li et al., 2011</xref>). At the species level, however, the reported nuclear <italic>ITS</italic> and <italic>LEAFY</italic> intron II sequences failed to resolve the phylogenetic and species identification problems in this genus. <xref rid="B27" ref-type="bibr">Rohwer et al. (2009)</xref> suggest that the extremely low genetic variation among species of <italic>Machilus</italic> could be explained by recent species differentiation and/or a greatly decreased substitution rate within the genus. Besides nuclear sequences, 14 chloroplast genomic markers (<italic>matK, trnK, accD, ndhJ, psbC-trnS, rpoB, rpoC1, trnD-trnT2, trnH-trnK, psbA-trnH, psbB-psbH, trnS-trnG, rpoB-trnC</italic>, and <italic>trnS-trnfM</italic>) also failed to resolve either the phylogenetic problems within the <italic>Persea</italic> group or species delineation within <italic>Machilus</italic> (<xref rid="B26" ref-type="bibr">Rohwer, 2000</xref>; <xref rid="B28" ref-type="bibr">Rohwer and Rudolph, 2005</xref>; <xref rid="B27" ref-type="bibr">Rohwer et al., 2009</xref>; <xref rid="B21" ref-type="bibr">Li et al., 2011</xref>). All of these results showed very little variation in those chloroplast genomic markers. This raises the question, are there any useful sequences for the phylogenetic classification of <italic>Machilus</italic> species in the chloroplast genome?</p><p>The chloroplast genome is more conserved than the nuclear genome in plants, but many mutation events in the chloroplast DNA sequence have been identified, including indels, substitutions, and inversions (<xref rid="B15" ref-type="bibr">Ingvarsson et al., 2003</xref>). At a high taxonomic level, a 22 kb DNA inversion event was used to confirm that the Barnadesioideae is the most basal lineage in the Asteraceae (<xref rid="B16" ref-type="bibr">Jansen and Palmer, 1987</xref>), and three DNA inversion events composed a nested set of phylogenetic characters to clarify the close relationship between the Poaceae and Joinvilleaceae (<xref rid="B10" ref-type="bibr">Doyle et al., 1992</xref>). At a low taxonomic level in ginseng, the DNA polymorphism rates of indels and SNPs between <italic>Panax ginseng</italic> and <italic>P. notoginseng</italic> were 0.40% (<xref rid="B6" ref-type="bibr">Dong et al., 2014</xref>), and 0.20% among four chloroplast genomes of different Chinese ginseng strains (<xref rid="B43" ref-type="bibr">Zhao et al., 2015</xref>). In rice, the DNA polymorphism rate of indels and SNPs between <italic>Oryza sativa</italic> and <italic>O. nivara</italic> were 0.02% (<xref rid="B23" ref-type="bibr">Masood et al., 2004</xref>), and 0.07% between <italic>O. sativa indica</italic> and <italic>O. sativa japonica</italic> (<xref rid="B34" ref-type="bibr">Tang et al., 2004</xref>). All of these results show that variable characters exist among the chloroplast genomes at the species level.</p><p>Here, two species of <italic>Machilus</italic> (Lauraceae) were selected to determine the entire chloroplast genome sequences. <italic>Machilus yunnanensis</italic> Lecomte is distributed at high altitudes in Yunnan, Sichuan, and Tibet of SW China (<xref rid="B38" ref-type="bibr">Wei and Werff, 2008</xref>), while <italic>M. balansae</italic> (Airy Shaw) F. N. Wei and S. C. Tang occurs mainly at low elevations in North Vietnam (<xref rid="B35" ref-type="bibr">Tang et al., 2010</xref>). By comparing these two complete chloroplast genomes we will try to answer the following questions: (1) What is the size range of chloroplast genomes in <italic>Machilus</italic>? (2) Which types of mutation events occurred in chloroplast genomes of <italic>Machilus</italic>? (3) Is there any highly variable region in the chloroplast genomes of <italic>Machilus</italic>? Comparisons were also made with the recently published chloroplast genome of <italic>Cinnamomum kanehirae</italic> (<xref rid="B40" ref-type="bibr">Wu et al., 2015</xref>).</p></sec><sec sec-type="materials|methods" id="s1"><title>Materials and Methods</title><sec><title>DNA Extraction and Sequencing</title><p>We collected young leaves of <italic>M. yunnanensis</italic> and <italic>M. balansae</italic> from single seedlings growing in the nursery of the Xishuangbanna Tropical Botanical Garden (XTBG) on May 20, 2014. We also collected fruiting branches of both mother trees (Supplementary Figure <xref ref-type="supplementary-material" rid="SM3">S1</xref>) and compared them with the types to confirm their identifications (Supplementary Figure <xref ref-type="supplementary-material" rid="SM3">S2</xref>). Genomic DNA was extracted from 1 g fresh leaves using the mCTAB method (<xref rid="B20" ref-type="bibr">Li et al., 2013</xref>). Both genomes were sequenced following <xref rid="B8" ref-type="bibr">Dong et al. (2013)</xref>, and their 138 pair specific primers were used to bridge gaps in the plastomes.</p></sec><sec><title>Chloroplast Genome Assembling and Annotation</title><p>Sanger sequence reads were proofread and assembled with Sequencher 4.10 (<ext-link ext-link-type="uri" xlink:href="http://www.genecodes.com">http://www.genecodes.com</ext-link>). All of the genes encoding proteins, transfer RNAs (tRNAs), and ribosomal RNAs (rRNAs) were annotated on <italic>Machilus</italic> plastomes using the Dual Organellar Genome Annotator (DOGMA) software (<xref rid="B41" ref-type="bibr">Wyman et al., 2004</xref>). To further verify the identified tRNA genes, the tRNAscan-SE 1.21 program was used to predict their corresponding structures (<xref rid="B30" ref-type="bibr">Schattner et al., 2005</xref>). The genome map of <italic>M. yunnanensis</italic> and <italic>M. balansae</italic> was drawn by GenomeVx (<xref rid="B5" ref-type="bibr">Conant and Wolfe, 2008</xref>).</p></sec><sec><title>Sliding Window Analysis of the Plastomes</title><p>After alignment using Clustal X 1.83 (<xref rid="B1" ref-type="bibr">Aiyar, 2000</xref>), the sequences were manually adjusted with Bioedit software (<ext-link ext-link-type="uri" xlink:href="http://www.mbio.ncsu.edu/bioedit/bioedit.html">http://www.mbio.ncsu.edu/bioedit/bioedit.html</ext-link>). Further, we conducted a sliding window analysis to evaluate the variability (Pi) all over the plastomes in DnaSP version 5 software (<xref rid="B22" ref-type="bibr">Librado and Rozas, 2009</xref>). The window length was set to 600 base pairs and the step size was set as 200 base pairs.</p></sec><sec><title>Mutation Events Analysis</title><p>To identify the microstructural mutations between <italic>M. yunnanensis</italic> and <italic>M. balansae</italic>, the two aligned sequences were further analyzed using DnaSP version 5 (<xref rid="B22" ref-type="bibr">Librado and Rozas, 2009</xref>) and MEGA version 5 (<xref rid="B33" ref-type="bibr">Tamura et al., 2011</xref>). Indel and SNP events were counted and positioned in the plastome using an R program. For the SSRs search, the minimum repeat unit was limited to eight for mononucleotides and four for dinucleotides. For non-SSR indel and SNP detection, the plastome of <italic>M. yunnanensis</italic> was used as a reference to determine the insertion or deletion events and transition (Ts) or transversion (Tv) events. In addition, the SNPs in the exon of the plastome were further classified into synonymous (S) and non-synonymous (N) substitutions. The gene classification was according to <xref rid="B2" ref-type="bibr">Chang et al. (2006)</xref>.</p></sec></sec><sec><title>Results</title><sec><title>Size, Gene Content, and Organization of <italic>M. yunnanensis</italic> and <italic>M. balansae</italic> Plastomes</title><p>The chloroplast genome of <italic>M. yunnanensis</italic> (deposited in GenBank: KT348516), with a length of 152, 622 bp, was 99 bp smaller than that of <italic>M. balansae</italic> (deposited in GenBank: KT348517) (<bold>Figure <xref ref-type="fig" rid="F1">1</xref></bold>), and 78 bp smaller than that of <italic>Cinnamomum kanehirae</italic> (152,700 bp, GenBank accession No. KR014245) (<xref rid="B40" ref-type="bibr">Wu et al., 2015</xref>). All three are smaller than the genome of <italic>Calycanthus fertilis</italic> (153, 337 bp, GenBank accession No. NC_004993) in the Calycanthaceae, which is in the same order as the Lauraceae (<xref rid="B12" ref-type="bibr">Goremykin et al., 2003</xref>). A+T content is 61% in all four species. The <italic>Machilus</italic> chloroplast genomes include a pair of inverted repeats (IRs) of 20, 074 bp in <italic>M. yunnanensis</italic> and <italic>M. balansae</italic>, separated by a large single copy (LSC) region of 93, 675 bp in <italic>M. yunnanensis</italic> and 93, 676 bp in <italic>M. balansae</italic> and a small single copy (SSC) region of 18, 799 bp in <italic>M. yunnanensis</italic> and 18, 897 bp in <italic>M. balansae</italic> (<bold>Table <xref ref-type="table" rid="T1">1</xref></bold>). Both contain 113 different functional genes, including 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes (Supplementary Table <xref ref-type="supplementary-material" rid="SM1">S1</xref>). The gene map is shown in <bold>Figure <xref ref-type="fig" rid="F1">1</xref></bold>. Among the functional genes, twelve protein-coding genes and six tRNA genes contain introns in both species (Supplementary Table <xref ref-type="supplementary-material" rid="SM1">S1</xref>).</p><fig id="F1" position="float"><label>FIGURE 1</label><caption><p><bold>Gene map of <italic>Machilus yunnanensis</italic> and <italic>M. balansae</italic> plastomes.</bold> The annotation of the genome was performed using DOGMA. The genes that are drawn outside of the circle are transcribed clockwise, while those inside are counterclockwise. Small single copy (SSC), large single copy (LSC), and inverted repeats (IRa, IRb) are indicated.</p></caption><graphic xlink:href="fpls-06-00662-g001"></graphic></fig><table-wrap id="T1" position="float"><label>Table 1</label><caption><p>Summary of two complete plastomes of <italic>Machilus</italic>.</p></caption><table frame="hsides" rules="groups" cellspacing="5" cellpadding="5"><thead><tr><th valign="top" align="left" rowspan="1" colspan="1"></th><th valign="top" align="left" rowspan="1" colspan="1"><italic>Machilus yunnanensis</italic></th><th valign="top" align="left" rowspan="1" colspan="1"><italic>Machilus balansae</italic></th></tr></thead><tbody><tr><td valign="top" align="left" rowspan="1" colspan="1">Total cpDNA size</td><td valign="top" align="left" rowspan="1" colspan="1">152,622</td><td valign="top" align="left" rowspan="1" colspan="1">152,721</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"> Length of large single copy (LSC) region</td><td valign="top" align="left" rowspan="1" colspan="1">93,675</td><td valign="top" align="left" rowspan="1" colspan="1">93,676</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"> Length of inverted repeat (IR) region</td><td valign="top" align="left" rowspan="1" colspan="1">20,074</td><td valign="top" align="left" rowspan="1" colspan="1">20,074</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"> Length of small single copy (SSC) region</td><td valign="top" align="left" rowspan="1" colspan="1">18,799</td><td valign="top" align="left" rowspan="1" colspan="1">18,897</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Total GC content (%)</td><td valign="top" align="left" rowspan="1" colspan="1">39.16</td><td valign="top" align="left" rowspan="1" colspan="1">39.15</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"> LSC</td><td valign="top" align="left" rowspan="1" colspan="1">37.93</td><td valign="top" align="left" rowspan="1" colspan="1">37.95</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"> IR</td><td valign="top" align="left" rowspan="1" colspan="1">44.44</td><td valign="top" align="left" rowspan="1" colspan="1">44.44</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"> SSC</td><td valign="top" align="left" rowspan="1" colspan="1">34.04</td><td valign="top" align="left" rowspan="1" colspan="1">33.90</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Total number of genes</td><td valign="top" align="left" rowspan="1" colspan="1">113</td><td valign="top" align="left" rowspan="1" colspan="1">113</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"> Protein encoding</td><td valign="top" align="left" rowspan="1" colspan="1">79</td><td valign="top" align="left" rowspan="1" colspan="1">79</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"> tRNA</td><td valign="top" align="left" rowspan="1" colspan="1">30</td><td valign="top" align="left" rowspan="1" colspan="1">30</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"> rRNA</td><td valign="top" align="left" rowspan="1" colspan="1">4</td><td valign="top" align="left" rowspan="1" colspan="1">4</td></tr></tbody></table></table-wrap></sec><sec><title>Divergence Hotspots of <italic>M. yunnanensis, M. balansae</italic>, and <italic>Cinnamomum kanehirae</italic> Plastomes</title><p>To elucidate the level of sequence divergence, the nucleotide variability (Pi) values within 600 bp in both chloroplast genomes of <italic>M. yunnanensis, M. balansae</italic>, and <italic>Cinnamomum kanehirae</italic> were calculated with DnaSP 5.0 software. Between two <italic>Machilus</italic> species these values varied from 0 to 0.01333 with a mean of 0.00154, indicating that the differences between the genomes were small. However, seven highly variable loci including the second intron of <italic>clpP, ndhF-rpl32, trnQ-psbI, rps8-rpl14, ycf2, rpl32-trnL</italic>, and <italic>ycf1</italic> were precisely located (<bold>Figure <xref ref-type="fig" rid="F2">2A</xref></bold>). All of these regions had much higher values than other regions (Pi > 0.008). Three of these loci lie in the LSC region, three in the SSC region, and one in the IR region. Among them, the introns of <italic>clpP, rpl32-trnL</italic>, and <italic>ycf1</italic> loci have been reported before as highly variable regions in seed plants (<xref rid="B7" ref-type="bibr">Dong et al., 2012</xref>), while <italic>ndhF-rpl32, trnQ-psbI, rps8-rpl14</italic>, and <italic>ycf2</italic> loci seem to be especially variable in <italic>Machilus</italic>. Among <italic>Cinnamomum kanehirae</italic> and the two <italic>Machilus</italic> species the Pi values varied from 0 to 0.02444, indicating that the differences between the two genera were larger than those between congeneric species. Three of the seven loci, including <italic>ndhF-rpl32, rpl32-trnL</italic>, and <italic>ycf1</italic>, were particularly highly variable between <italic>Cinnamomum</italic> and <italic>Machilus</italic> species (Pi > 0.015; <bold>Figure <xref ref-type="fig" rid="F2">2B</xref></bold>).</p><fig id="F2" position="float"><label>FIGURE 2</label><caption><p><bold>Sliding window analysis of the whole plastomes of <italic>M. yunnanensis</italic> and <italic>M. balansae</italic><bold>(A)</bold> and those of <italic>Cinnamomum kanehirae</italic> and the two <italic>Machilus</italic> species <bold>(B)</bold>.</bold> (window length: 600 bp, step size: 200 bp). X-axis: position of the midpoint of a window, Y-axis: nucleotide diversity of each window.</p></caption><graphic xlink:href="fpls-06-00662-g002"></graphic></fig></sec><sec><title>Number and Forms of Microstructural Mutations</title><p>Indel markers display no ambiguity in complex mutation patterns with the advantages of low cost and high precision. To detect more variable sites in <italic>Machilus</italic>, indel mutations between the chloroplast genomes of <italic>M. yunnanensis</italic> and <italic>M. balansae</italic> were compared. There are 52 indels in gene spacer regions, 12 indels in introns, and one in the exon of <italic>ndhF</italic>. Further, these indels were classified into 36 simple sequences repeat (SSR) indels (<bold>Table <xref ref-type="table" rid="T2">2</xref></bold>) and 29 non-SSR indels (<bold>Table <xref ref-type="table" rid="T3">3</xref></bold>). For the SSR indels, there are 34 single nucleotide repeats A/T ranged from 8 to 19 bp, one 9 bp single nucleotide repeat C in the <italic>petA-psbJ</italic> gene spacer region, and one double nucleotide repeat AT with 5 and 7 bp in the <italic>petN-psbM</italic> region (<bold>Table <xref ref-type="table" rid="T2">2</xref></bold>). The sizes of most non-SSR indels ranged from 1 to 7 bp, while that within the <italic>ndhF-rpl32, trnH-psbA</italic>, and <italic>psbM-trnD</italic> gene spacer sequences were 94 bp, 22 bp, and 21 bp, respectively (<bold>Table <xref ref-type="table" rid="T3">3</xref></bold>). Of all of these indel events, 83.08% of sites were in the LSC region while 3.07% of sites were in the IR regions. In addition, one micro-inversion event with five bases was detected in the <italic>ccsA-ndhD</italic> gene spacer region (Supplementary Figure <xref ref-type="supplementary-material" rid="SM3">S3</xref>).</p><table-wrap id="T2" position="float"><label>Table 2</label><caption><p>Location of simple sequence repeats in the <italic>Machilus</italic> plastomes.</p></caption><table frame="hsides" rules="groups" cellspacing="5" cellpadding="5"><thead><tr><th valign="top" align="left" rowspan="1" colspan="1">No.</th><th valign="top" align="left" rowspan="1" colspan="1">Location</th><th valign="top" align="left" rowspan="1" colspan="1">Region</th><th valign="top" align="left" rowspan="1" colspan="1">Motif</th><th valign="top" align="center" colspan="2" rowspan="1">No. of Repeats<hr></hr></th></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"></td><th valign="top" align="left" rowspan="1" colspan="1"><italic>M. yunnanensis</italic></th><th valign="top" align="left" rowspan="1" colspan="1"><italic>M. balansae</italic></th></tr></thead><tbody><tr><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>trnK-rps16</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">T</td><td valign="top" align="left" rowspan="1" colspan="1">12</td><td valign="top" align="left" rowspan="1" colspan="1">14</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">2</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>trnK-rps16</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">T</td><td valign="top" align="left" rowspan="1" colspan="1">9</td><td valign="top" align="left" rowspan="1" colspan="1">10</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">3</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>rps16</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intron</td><td valign="top" align="left" rowspan="1" colspan="1">T</td><td valign="top" align="left" rowspan="1" colspan="1">9</td><td valign="top" align="left" rowspan="1" colspan="1">10</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">4</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>rps16</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intron</td><td valign="top" align="left" rowspan="1" colspan="1">A</td><td valign="top" align="left" rowspan="1" colspan="1">14</td><td valign="top" align="left" rowspan="1" colspan="1">10</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">5</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>rps16-trnQ</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">T</td><td valign="top" align="left" rowspan="1" colspan="1">11</td><td valign="top" align="left" rowspan="1" colspan="1">18</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">6</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>trnS-trnG</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">T</td><td valign="top" align="left" rowspan="1" colspan="1">8</td><td valign="top" align="left" rowspan="1" colspan="1">9</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">7</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>trnG-trnG</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">T</td><td valign="top" align="left" rowspan="1" colspan="1">10</td><td valign="top" align="left" rowspan="1" colspan="1">11</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">8</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>rps2-rpoC2</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">T</td><td valign="top" align="left" rowspan="1" colspan="1">12</td><td valign="top" align="left" rowspan="1" colspan="1">10</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">9</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>petN-psbM</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">AT</td><td valign="top" align="left" rowspan="1" colspan="1">5</td><td valign="top" align="left" rowspan="1" colspan="1">7</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">10</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>trnD-trnY</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">A</td><td valign="top" align="left" rowspan="1" colspan="1">10</td><td valign="top" align="left" rowspan="1" colspan="1">11</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">11</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>trnT-psbD</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">T</td><td valign="top" align="left" rowspan="1" colspan="1">8</td><td valign="top" align="left" rowspan="1" colspan="1">7</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">12</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>trnG-trnfM</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">A</td><td valign="top" align="left" rowspan="1" colspan="1">18</td><td valign="top" align="left" rowspan="1" colspan="1">19</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">13</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>psaA-ycf3</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">T</td><td valign="top" align="left" rowspan="1" colspan="1">13</td><td valign="top" align="left" rowspan="1" colspan="1">15</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">14</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>ycf3</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intron</td><td valign="top" align="left" rowspan="1" colspan="1">T</td><td valign="top" align="left" rowspan="1" colspan="1">11</td><td valign="top" align="left" rowspan="1" colspan="1">10</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">15</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>trnT-trnL</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">A</td><td valign="top" align="left" rowspan="1" colspan="1">12</td><td valign="top" align="left" rowspan="1" colspan="1">11</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">16</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>ndhC-trnV</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">T</td><td valign="top" align="left" rowspan="1" colspan="1">11</td><td valign="top" align="left" rowspan="1" colspan="1">12</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">17</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>trnM-atpE</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">T</td><td valign="top" align="left" rowspan="1" colspan="1">14</td><td valign="top" align="left" rowspan="1" colspan="1">10</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">18</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>psaI-ycf4</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">A</td><td valign="top" align="left" rowspan="1" colspan="1">7</td><td valign="top" align="left" rowspan="1" colspan="1">6</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">19</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>petA-psbJ</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">C</td><td valign="top" align="left" rowspan="1" colspan="1">8</td><td valign="top" align="left" rowspan="1" colspan="1">9</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">20</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>psbE-petL</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">T</td><td valign="top" align="left" rowspan="1" colspan="1">8</td><td valign="top" align="left" rowspan="1" colspan="1">9</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">21</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>psbE-petL</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">T</td><td valign="top" align="left" rowspan="1" colspan="1">9</td><td valign="top" align="left" rowspan="1" colspan="1">8</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">22</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>rps18-rpl20</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">T</td><td valign="top" align="left" rowspan="1" colspan="1">12</td><td valign="top" align="left" rowspan="1" colspan="1">15</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">23</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>rpl20-rps12</italic></td><td valign="top" align="left" rowspan="1" colspan="1">intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">A</td><td valign="top" align="left" rowspan="1" colspan="1">14</td><td valign="top" align="left" rowspan="1" colspan="1">13</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">24</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>clpP</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intron</td><td valign="top" align="left" rowspan="1" colspan="1">T</td><td valign="top" align="left" rowspan="1" colspan="1">11</td><td valign="top" align="left" rowspan="1" colspan="1">9</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">25</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>clpP</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intron</td><td valign="top" align="left" rowspan="1" colspan="1">T</td><td valign="top" align="left" rowspan="1" colspan="1">12</td><td valign="top" align="left" rowspan="1" colspan="1">13</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">26</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>clpP</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intron</td><td valign="top" align="left" rowspan="1" colspan="1">A</td><td valign="top" align="left" rowspan="1" colspan="1">17</td><td valign="top" align="left" rowspan="1" colspan="1">12</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">27</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>clpP</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intron</td><td valign="top" align="left" rowspan="1" colspan="1">T</td><td valign="top" align="left" rowspan="1" colspan="1">14</td><td valign="top" align="left" rowspan="1" colspan="1">13</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">28</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>petB-petB</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">A</td><td valign="top" align="left" rowspan="1" colspan="1">9</td><td valign="top" align="left" rowspan="1" colspan="1">10</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">29</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>rps8-rpl14</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">T</td><td valign="top" align="left" rowspan="1" colspan="1">13</td><td valign="top" align="left" rowspan="1" colspan="1">11</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">30</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>rpl14-rpl16</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">T</td><td valign="top" align="left" rowspan="1" colspan="1">15</td><td valign="top" align="left" rowspan="1" colspan="1">16</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">31</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>rpl16-rps3</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">T</td><td valign="top" align="left" rowspan="1" colspan="1">10</td><td valign="top" align="left" rowspan="1" colspan="1">12</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">32</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>rps3-rps19</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">T</td><td valign="top" align="left" rowspan="1" colspan="1">9</td><td valign="top" align="left" rowspan="1" colspan="1">8</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">33</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>rps19-rpl2</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">T</td><td valign="top" align="left" rowspan="1" colspan="1">9</td><td valign="top" align="left" rowspan="1" colspan="1">10</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">34</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>rpl32-trnL</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">T</td><td valign="top" align="left" rowspan="1" colspan="1">11</td><td valign="top" align="left" rowspan="1" colspan="1">15</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">35</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>ccsA-ndhD</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">T</td><td valign="top" align="left" rowspan="1" colspan="1">10</td><td valign="top" align="left" rowspan="1" colspan="1">12</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">36</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>rps15-ycf1</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">T</td><td valign="top" align="left" rowspan="1" colspan="1">14</td><td valign="top" align="left" rowspan="1" colspan="1">13</td></tr></tbody></table></table-wrap><table-wrap id="T3" position="float"><label>Table 3</label><caption><p>Forms and numbers of indel mutation events in the plastome between the two <italic>Machilus</italic> species.</p></caption><table frame="hsides" rules="groups" cellspacing="5" cellpadding="5"><thead><tr><th valign="top" align="left" rowspan="1" colspan="1">No.</th><th valign="top" align="left" rowspan="1" colspan="1">Location</th><th valign="top" align="left" rowspan="1" colspan="1">region</th><th valign="top" align="left" rowspan="1" colspan="1">Motif</th><th valign="top" align="left" rowspan="1" colspan="1">Size</th><th valign="top" align="left" rowspan="1" colspan="1">Driection<sup>a</sup></th></tr></thead><tbody><tr><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>trnH-psbA</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">aaaacaaaatgttgtacataaa</td><td valign="top" align="left" rowspan="1" colspan="1">22</td><td valign="top" align="left" rowspan="1" colspan="1">Deletion</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">2</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>rps16-trnQ</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">cttgta</td><td valign="top" align="left" rowspan="1" colspan="1">6</td><td valign="top" align="left" rowspan="1" colspan="1">Deletion</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">3</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>trnG</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intron</td><td valign="top" align="left" rowspan="1" colspan="1">c</td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">Insertion</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">4</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>trnG</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intron</td><td valign="top" align="left" rowspan="1" colspan="1">tga</td><td valign="top" align="left" rowspan="1" colspan="1">3</td><td valign="top" align="left" rowspan="1" colspan="1">Deletion</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">5</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>atpF</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intron</td><td valign="top" align="left" rowspan="1" colspan="1">tg</td><td valign="top" align="left" rowspan="1" colspan="1">2</td><td valign="top" align="left" rowspan="1" colspan="1">Deletion</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">6</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>psbM-trnD</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">tacatggaccaggagcaatcg</td><td valign="top" align="left" rowspan="1" colspan="1">21</td><td valign="top" align="left" rowspan="1" colspan="1">Insertion</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">7</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>trnE-trnT</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">taatt</td><td valign="top" align="left" rowspan="1" colspan="1">5</td><td valign="top" align="left" rowspan="1" colspan="1">Insertion</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">8</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>ycf3-trnS</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">tgtat</td><td valign="top" align="left" rowspan="1" colspan="1">5</td><td valign="top" align="left" rowspan="1" colspan="1">Deletion</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">9</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>trnS-rps4</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">g</td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">Deletion</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">10</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>trnS-rps4</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">aagag</td><td valign="top" align="left" rowspan="1" colspan="1">5</td><td valign="top" align="left" rowspan="1" colspan="1">Insertion</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">11</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>ndhC-trnV</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">attaaat</td><td valign="top" align="left" rowspan="1" colspan="1">7</td><td valign="top" align="left" rowspan="1" colspan="1">Deletion</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">12</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>ndhC-trnV</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">a</td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">Deletion</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">13</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>trnV</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intron</td><td valign="top" align="left" rowspan="1" colspan="1">t</td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">Deletion</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">14</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>ycf4-cemA</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">ttctat</td><td valign="top" align="left" rowspan="1" colspan="1">6</td><td valign="top" align="left" rowspan="1" colspan="1">Insertion</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">15</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>rpl16</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intron</td><td valign="top" align="left" rowspan="1" colspan="1">ggat</td><td valign="top" align="left" rowspan="1" colspan="1">4</td><td valign="top" align="left" rowspan="1" colspan="1">Deletion</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">16</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>rpl2-rpl2</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">tc</td><td valign="top" align="left" rowspan="1" colspan="1">2</td><td valign="top" align="left" rowspan="1" colspan="1">Insertion</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">17</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>ycf1-ndhF</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">a</td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">Deletion</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">18</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>ndhF</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Exon</td><td valign="top" align="left" rowspan="1" colspan="1">ttcgaa</td><td valign="top" align="left" rowspan="1" colspan="1">6</td><td valign="top" align="left" rowspan="1" colspan="1">Insertion</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">19</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>ndhF-rpl32</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">aatcaagatatacaagatataaaagaact<break></break>caaatatgatttttcattcttaattattctgatt<break></break>ctttccaaactattgaaaaaaaaaaaaaaac</td><td valign="top" align="left" rowspan="1" colspan="1">94</td><td valign="top" align="left" rowspan="1" colspan="1">Deletion</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">20</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>ndhF-rpl32</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">t</td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">Deletion</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">21</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>rpl32-trnL</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">g</td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">Deletion</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">22</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>rps15-ycf1</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">a</td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">Deletion</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">23</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>rpl23-rpl2</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">ag</td><td valign="top" align="left" rowspan="1" colspan="1">2</td><td valign="top" align="left" rowspan="1" colspan="1">Insertion</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">24</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>atpF-atpH</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">c</td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">Insertion</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">25</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>ycf3-trnS</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">a</td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">Insertion</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">26</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>ndhC-trnV</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">a</td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">Insertion</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">27</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>rpl32-trnL</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">t</td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">Deletion</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">28</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>rbcL-accD</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">t</td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">Insertion</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">29</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>rbcL-accD</italic></td><td valign="top" align="left" rowspan="1" colspan="1">Intergenic</td><td valign="top" align="left" rowspan="1" colspan="1">t</td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">Insertion</td></tr></tbody></table><table-wrap-foot><attrib><italic><sup>a</sup>The plastome of <italic>M. yunnanensis</italic> was used as a reference.</italic></attrib></table-wrap-foot></table-wrap></sec><sec><title>Numbers and Pattern of SNP Mutations</title><p>SNP markers are the most abundant type of mutations, but have never been screened in <italic>Machilus</italic> species. We detected 95 SNPs, including 48 Ts and 47 Tv, in gene coding regions (<bold>Figure <xref ref-type="fig" rid="F3">3</xref></bold>) and 136 SNPs, including 58 Ts and 78 Tv, in non-coding regions (Supplementary Table <xref ref-type="supplementary-material" rid="SM2">S2</xref>). The Tv to Ts ratio was 1: 0.74. Among the Tv, 14 were Tv between T and A, 9 were Tv between C and G, and the other 101 were related to GC content changes. Among substitution events in the gene coding regions, non-synonymous and synonymous substitutions shared 48 and 47 of 95 sites in the entire plastomes, and 23 of 79 genes had non-synonymous substitution sites. However, two genes <italic>psaA</italic> and <italic>ycf1</italic> had more non-synonymous than synonymous substitutions sites, suggesting these two genes had a relatively high evolution rate (<bold>Table <xref ref-type="table" rid="T4">4</xref></bold>). In all of these substitution events, 74.03% of SNP sites were in the LSC region while 1.73% of SNP sites were in the IR regions.</p><fig id="F3" position="float"><label>FIGURE 3</label><caption><p><bold>The patterns of nucleotide substitutions among <italic>M. yunnanensis</italic> and <italic>M. balansae</italic> plastomes.</bold> The patterns were divided into six types as indicated by the six non-strand-specific base-substitution types (i.e., numbers of considered G to A and C to T sites for each respective set of associated mutation types). The plastome of <italic>M. yunnanensis</italic> was used as a reference.</p></caption><graphic xlink:href="fpls-06-00662-g003"></graphic></fig><table-wrap id="T4" position="float"><label>Table 4</label><caption><p>Comparisons of mutational changes, number of transitions (Ts) and transversions (Tv), synonymous (S), and non-synonymous (N) substitutions per gene of protein coding chloroplast genes between <italic>M. yunnanensis</italic> and <italic>M. balansae</italic>.</p></caption><table frame="hsides" rules="groups" cellspacing="5" cellpadding="5"><thead><tr><td valign="top" align="left" rowspan="1" colspan="1"></td><th valign="top" align="left" rowspan="1" colspan="1">Gene</th><th valign="top" align="left" rowspan="1" colspan="1">Ts</th><th valign="top" align="left" rowspan="1" colspan="1">Tv</th><th valign="top" align="left" rowspan="1" colspan="1">S</th><th valign="top" align="left" rowspan="1" colspan="1">N</th></tr></thead><tbody><tr><td valign="top" align="left" rowspan="1" colspan="1">Photosynthetic apparatus</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>psaA</italic></td><td valign="top" align="left" rowspan="1" colspan="1">2</td><td valign="top" align="left" rowspan="1" colspan="1">2</td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">3</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"><italic>psaB</italic></td><td valign="top" align="left" rowspan="1" colspan="1">0</td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">0</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"><italic>psaJ</italic></td><td valign="top" align="left" rowspan="1" colspan="1">2</td><td valign="top" align="left" rowspan="1" colspan="1">0</td><td valign="top" align="left" rowspan="1" colspan="1">2</td><td valign="top" align="left" rowspan="1" colspan="1">0</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"><italic>psbA</italic></td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">0</td><td valign="top" align="left" rowspan="1" colspan="1">0</td><td valign="top" align="left" rowspan="1" colspan="1">1</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"><italic>psbL</italic></td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">0</td><td valign="top" align="left" rowspan="1" colspan="1">0</td><td valign="top" align="left" rowspan="1" colspan="1">1</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"><italic>psbT</italic></td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">2</td><td valign="top" align="left" rowspan="1" colspan="1">0</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"><italic>petA</italic></td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">0</td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">0</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"><italic>ycf4</italic></td><td valign="top" align="left" rowspan="1" colspan="1">0</td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">0</td><td valign="top" align="left" rowspan="1" colspan="1">1</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" colspan="5" rowspan="1"><hr></hr></td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"><bold>Total</bold></td><td valign="top" align="left" rowspan="1" colspan="1"><bold>8</bold></td><td valign="top" align="left" rowspan="1" colspan="1"><bold>5</bold></td><td valign="top" align="left" rowspan="1" colspan="1"><bold>7</bold></td><td valign="top" align="left" rowspan="1" colspan="1"><bold>6</bold></td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Photosynthetic metabolism</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>atpA</italic></td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">0</td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">0</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"><italic>atpB</italic></td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">1</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"><italic>atpE</italic></td><td valign="top" align="left" rowspan="1" colspan="1">3</td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">4</td><td valign="top" align="left" rowspan="1" colspan="1">0</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"><italic>atpF</italic></td><td valign="top" align="left" rowspan="1" colspan="1">0</td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">0</td><td valign="top" align="left" rowspan="1" colspan="1">1</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"><italic>atpI</italic></td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">0</td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">0</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"><italic>ndhA</italic></td><td valign="top" align="left" rowspan="1" colspan="1">0</td><td valign="top" align="left" rowspan="1" colspan="1">2</td><td valign="top" align="left" rowspan="1" colspan="1">0</td><td valign="top" align="left" rowspan="1" colspan="1">2</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"><italic>ndhD</italic></td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">0</td><td valign="top" align="left" rowspan="1" colspan="1">0</td><td valign="top" align="left" rowspan="1" colspan="1">1</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"><italic>ndhE</italic></td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">1</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"><italic>ndhF</italic></td><td valign="top" align="left" rowspan="1" colspan="1">2</td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">3</td><td valign="top" align="left" rowspan="1" colspan="1">0</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"><italic>ndhG</italic></td><td valign="top" align="left" rowspan="1" colspan="1">3</td><td valign="top" align="left" rowspan="1" colspan="1">0</td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">2</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"><italic>ndhH</italic></td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">0</td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">0</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"><italic>ndhK</italic></td><td valign="top" align="left" rowspan="1" colspan="1">2</td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">2</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"><italic>rbcL</italic></td><td valign="top" align="left" rowspan="1" colspan="1">0</td><td valign="top" align="left" rowspan="1" colspan="1">2</td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">1</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" colspan="5" rowspan="1"><hr></hr></td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"><bold>Total</bold></td><td valign="top" align="left" rowspan="1" colspan="1"><bold>16</bold></td><td valign="top" align="left" rowspan="1" colspan="1"><bold>10</bold></td><td valign="top" align="left" rowspan="1" colspan="1"><bold>15</bold></td><td valign="top" align="left" rowspan="1" colspan="1"><bold>11</bold></td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Gene expression</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>rpl2</italic></td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">0</td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">0</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"><italic>rpl14</italic></td><td valign="top" align="left" rowspan="1" colspan="1">2</td><td valign="top" align="left" rowspan="1" colspan="1">2</td><td valign="top" align="left" rowspan="1" colspan="1">2</td><td valign="top" align="left" rowspan="1" colspan="1">2</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"><italic>rpoA</italic></td><td valign="top" align="left" rowspan="1" colspan="1">0</td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">0</td><td valign="top" align="left" rowspan="1" colspan="1">1</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"><italic>rpoB</italic></td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">0</td><td valign="top" align="left" rowspan="1" colspan="1">2</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"><italic>rpoC1</italic></td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">0</td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">0</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"><italic>rpoC2</italic></td><td valign="top" align="left" rowspan="1" colspan="1">4</td><td valign="top" align="left" rowspan="1" colspan="1">3</td><td valign="top" align="left" rowspan="1" colspan="1">5</td><td valign="top" align="left" rowspan="1" colspan="1">2</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"><italic>rps3</italic></td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">1</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"><italic>rps4</italic></td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">0</td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">0</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"><italic>rps14</italic></td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">0</td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">0</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"><italic>rps18</italic></td><td valign="top" align="left" rowspan="1" colspan="1">0</td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">0</td><td valign="top" align="left" rowspan="1" colspan="1">1</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" colspan="5" rowspan="1"><hr></hr></td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"><bold>Total</bold></td><td valign="top" align="left" rowspan="1" colspan="1"><bold>12</bold></td><td valign="top" align="left" rowspan="1" colspan="1"><bold>9</bold></td><td valign="top" align="left" rowspan="1" colspan="1"><bold>12</bold></td><td valign="top" align="left" rowspan="1" colspan="1"><bold>9</bold></td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1">Other Genes</td><td valign="top" align="left" rowspan="1" colspan="1"><italic>ycf1</italic></td><td valign="top" align="left" rowspan="1" colspan="1">6</td><td valign="top" align="left" rowspan="1" colspan="1">12</td><td valign="top" align="left" rowspan="1" colspan="1">6</td><td valign="top" align="left" rowspan="1" colspan="1">12</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"><italic>ycf2</italic></td><td valign="top" align="left" rowspan="1" colspan="1">3</td><td valign="top" align="left" rowspan="1" colspan="1">6</td><td valign="top" align="left" rowspan="1" colspan="1">4</td><td valign="top" align="left" rowspan="1" colspan="1">5</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"><italic>ccsA</italic></td><td valign="top" align="left" rowspan="1" colspan="1">0</td><td valign="top" align="left" rowspan="1" colspan="1">2</td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">1</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"><italic>cemA</italic></td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">1</td><td valign="top" align="left" rowspan="1" colspan="1">1</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"><italic>matK</italic></td><td valign="top" align="left" rowspan="1" colspan="1">2</td><td valign="top" align="left" rowspan="1" colspan="1">2</td><td valign="top" align="left" rowspan="1" colspan="1">2</td><td valign="top" align="left" rowspan="1" colspan="1">2</td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" colspan="5" rowspan="1"><hr></hr></td></tr><tr><td valign="top" align="left" rowspan="1" colspan="1"></td><td valign="top" align="left" rowspan="1" colspan="1"><bold>Total</bold></td><td valign="top" align="left" rowspan="1" colspan="1"><bold>48</bold></td><td valign="top" align="left" rowspan="1" colspan="1"><bold>47</bold></td><td valign="top" align="left" rowspan="1" colspan="1"><bold>48</bold></td><td valign="top" align="left" rowspan="1" colspan="1"><bold>47</bold></td></tr></tbody></table></table-wrap></sec></sec><sec><title>Discussion</title><p>This study produced two complete chloroplast genomes for species in the Lauraceae, which comprises nearly 3500 species in over 50 genera worldwide. For species identification and population structure analysis in this family, the rapidly developed molecular markers such as indels and SNPs have been proved to have significant potential. Global alignment of 13 <italic>Gossypium</italic> plastomes (Malvaceae) indicated that the total number of SNPs varied from 6 to 1000 and the number of indels ranged from 3 to 178, which supported that the plastome divergence was approximate 0.00159 to 0.00454 within allotetraploids of <italic>Gossypium</italic> (<xref rid="B42" ref-type="bibr">Xu et al., 2012</xref>). Plastome comparative analysis of five <italic>Camellia</italic> species identified 15 molecular markers with over 1.5% sequence divergences, which were used to promote the further phylogenetic analysis and species identification of <italic>Camellia</italic> species (<xref rid="B13" ref-type="bibr">Huang et al., 2014</xref>). The indel and SNP variable sites of plastomes of 12 Triticeae species were used to estimate that barley diverged from rye and wheat around 8.5 million years ago and rye diverged from <italic>Triticum aestivum</italic> around 3.5 million years ago (<xref rid="B24" ref-type="bibr">Middleton et al., 2014</xref>). These results show that molecular markers including indels and SNPs are useful tools in research.</p><p>Out of the 65 indel markers between <italic>M. yunnanensis</italic> and <italic>M. balansae</italic> plastomes, the largest indel is located within the intergenic sequence <italic>ndhF-rpl32</italic> (94 bp) in the SSC region. Another two large indels were found within <italic>trnH-psbA</italic> (22 bp) and <italic>psbM-trnD</italic> (21 bp) in the LSC region. Previous work in other plants has identified large indels in intergenic spacers, such as <italic>ndhF</italic>–<italic>rpl32, rpoB</italic>–<italic>trnC, trnE-trnT, rpl32-trnL, trnQ-rps16</italic>, and protein coding genes, such as <italic>accD, rpl20, ycf1</italic>, and <italic>ycf15</italic> (<xref rid="B31" ref-type="bibr">Shaw et al., 2007</xref>; <xref rid="B25" ref-type="bibr">Nashima et al., 2015</xref>). Most of these large indel events occurred in single copy regions but not IR regions. The 36 SSR loci identified in this study may be useful in population and evolutionary studies as well, as they were in <italic>Panax ginseng</italic> (<xref rid="B18" ref-type="bibr">Kim and Lee, 2004a</xref>), <italic>Cucumis sativus</italic> (<xref rid="B17" ref-type="bibr">Kim et al., 2006</xref>), <italic>Vigna radiata</italic> (<xref rid="B36" ref-type="bibr">Tangphatsornruang et al., 2010</xref>), and <italic>Pyrus pyrifolia</italic> (<xref rid="B37" ref-type="bibr">Terakami et al., 2012</xref>). In addition, one micro-inversion of five nucleotides was detected between <italic>M. yunnanensis</italic> and <italic>M. balansae</italic> plastomes, which indicate that differences in micro-inversion events could exist between <italic>Machilus</italic> species as previously report in <italic>Solanum</italic> species (<xref rid="B19" ref-type="bibr">Kim and Lee, 2004b</xref>; <xref rid="B11" ref-type="bibr">Gargano et al., 2012</xref>).</p><p>Besides the indel markers, 231 SNP markers were detected between <italic>M. yunnanensis</italic> and <italic>M. balansae</italic> plastomes, which indicated that the nucleotide substitution events in the chloroplast genome of <italic>Machilus</italic> species are more than that between species of rice and less than species of ginseng, potato, and orange. Comparative analysis of genomes found 159 SNP sites between two chloroplast genomes of <italic>O. sativa</italic> and <italic>O. nivara</italic> (<xref rid="B23" ref-type="bibr">Masood et al., 2004</xref>), 464 between plastomes of <italic>P. ginseng</italic> and <italic>P. notoginseng</italic> (<xref rid="B6" ref-type="bibr">Dong et al., 2014</xref>), 591 between plastomes of <italic>Solanum tuberosum</italic> and <italic>S. bulbocastanum</italic> (<xref rid="B4" ref-type="bibr">Chung et al., 2006</xref>), and 330 between plastomes of <italic>Citrus sinensis</italic> and <italic>C. aurantiifolia</italic> (<xref rid="B32" ref-type="bibr">Su et al., 2014</xref>). For the 95 SNP markers in gene coding regions, non-synonymous and synonymous substitutions shared similar numbers of 48 and 47 sites in the entire <italic>Machilus</italic> plastomes, implying that constraint mechanisms of substitution existed. Under the constraint background, photosynthetic metabolism genes <italic>atpE</italic> and <italic>ndhF</italic> and gene expression genes <italic>rpoC2</italic> and <italic>rpl2</italic> shared the extra synonymous substitution sites which are equal with the non-synonymous substitution sites of <italic>ycf1, ycf2</italic>, and photosynthetic apparatus gene <italic>psaA</italic>.</p><p>The Indel and SNP mutation events in the genome were not random but clustered as “hotspots” (<xref rid="B31" ref-type="bibr">Shaw et al., 2007</xref>; <xref rid="B39" ref-type="bibr">Worberg et al., 2007</xref>). Such mutational dynamics created the highly variable regions in the genome. In <italic>M. yunnanensis</italic> and <italic>M. balansae</italic> plastomes, we identified seven highly variable loci including the second intron of <italic>clpP, ndhF-rpl32, trnQ-psbI, rps8-rpl14, ycf2, rpl32-trnL</italic>, and <italic>ycf1</italic>. Three of the seven, including <italic>ndhF-rpl32, rpl32-trnL</italic>, and <italic>ycf1</italic>, were particularly highly variable between <italic>Machilus</italic> and <italic>Cinnamomum</italic> plastomes. The second intron of <italic>clpP, rpl32-trnL</italic>, and <italic>ycf1</italic> were the focus of previous analyses investigating sequence variation in seed plants (<xref rid="B7" ref-type="bibr">Dong et al., 2012</xref>, <xref rid="B9" ref-type="bibr">2015</xref>; <xref rid="B29" ref-type="bibr">Sarkinen and George, 2013</xref>). The <italic>ycf2</italic> and <italic>ndhF-rpl32</italic> loci have also been widely used for phylogenetic studies (<xref rid="B31" ref-type="bibr">Shaw et al., 2007</xref>; <xref rid="B14" ref-type="bibr">Huang et al., 2010</xref>). Here, two rarely reported highly variable loci <italic>rps8-rpl14</italic> and <italic>trnQ-psbI</italic> were present in <italic>Machilus</italic> plastomes. In contrast, none of the 14 regions in the chloroplast genome used previously for phylogenetic analysis were found to be variable (<xref rid="B27" ref-type="bibr">Rohwer et al., 2009</xref>; <xref rid="B21" ref-type="bibr">Li et al., 2011</xref>). All of these seven highly variable regions and the indel or SNP markers are better to use for phylogenetic studies at the species level in <italic>Machilus</italic>. We encourage researchers working on the Lauraceae family to use the seven highly variable regions identified in this study for phylogenetic analysis.</p></sec><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></body><back><ack><p>We would like to thank Prof. Shiliang Zhou from the Institute of Botany, Chinese Academy of Sciences, and two reviewers for useful suggestions. This work was supported by the 1000 Talents Program (WQ20110491035).</p></ack><sec sec-type="supplementary material"><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.2015.00662">http://journal.frontiersin.org/article/10.3389/fpls.2015.00662</ext-link></p><supplementary-material content-type="local-data" id="SM1"><media xlink:href="Table_1.XLSX"><caption><p>Click here for additional data file.</p></caption></media></supplementary-material><supplementary-material content-type="local-data" id="SM2"><media xlink:href="Table_2.XLSX"><caption><p>Click here for additional data file.</p></caption></media></supplementary-material><supplementary-material content-type="local-data" id="SM3"><media xlink:href="Image_1.PDF"><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>Aiyar</surname><given-names>A.</given-names></name></person-group> (<year>2000</year>). <article-title>The use of CLUSTAL W and CLUSTAL X for multiple sequence alignment.</article-title><source><italic>Methods Mol. 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