Comparative transcriptome analysis and identification of candidate effectors in two related rust species (Gymnosporangium yamadae and Gymnosporangium asiaticum).
Identifieur interne : 000071 ( Main/Exploration ); précédent : 000070; suivant : 000072Comparative transcriptome analysis and identification of candidate effectors in two related rust species (Gymnosporangium yamadae and Gymnosporangium asiaticum).
Auteurs : Si-Qi Tao [République populaire de Chine] ; Bin Cao [République populaire de Chine] ; Cheng-Ming Tian [République populaire de Chine] ; Ying-Mei Liang [République populaire de Chine]Source :
- BMC genomics [ 1471-2164 ] ; 2017.
Descripteurs français
- KwdFr :
- Adaptation physiologique (génétique), Analyse de profil d'expression de gènes (MeSH), Annotation de séquence moléculaire (MeSH), Basidiomycota (génétique), Basidiomycota (métabolisme), Basidiomycota (physiologie), Gènes fongiques (génétique), Similitude de séquences d'acides nucléiques (MeSH), Variation génétique (MeSH), Évolution moléculaire (MeSH).
- MESH :
- génétique : Adaptation physiologique, Basidiomycota, Gènes fongiques.
- métabolisme : Basidiomycota.
- physiologie : Basidiomycota.
- Analyse de profil d'expression de gènes, Annotation de séquence moléculaire, Similitude de séquences d'acides nucléiques, Variation génétique, Évolution moléculaire.
English descriptors
- KwdEn :
- Adaptation, Physiological (genetics), Basidiomycota (genetics), Basidiomycota (metabolism), Basidiomycota (physiology), Evolution, Molecular (MeSH), Gene Expression Profiling (MeSH), Genes, Fungal (genetics), Genetic Variation (MeSH), Molecular Sequence Annotation (MeSH), Sequence Homology, Nucleic Acid (MeSH).
- MESH :
- genetics : Adaptation, Physiological, Basidiomycota, Genes, Fungal.
- metabolism : Basidiomycota.
- physiology : Basidiomycota.
- Evolution, Molecular, Gene Expression Profiling, Genetic Variation, Molecular Sequence Annotation, Sequence Homology, Nucleic Acid.
Abstract
BACKGROUND
Rust fungi constitute the largest group of plant fungal pathogens. However, a paucity of data, including genomic sequences, transcriptome sequences, and associated molecular markers, hinders the development of inhibitory compounds and prevents their analysis from an evolutionary perspective. Gymnosporangium yamadae and G. asiaticum are two closely related rust fungal species, which are ecologically and economically important pathogens that cause apple rust and pear rust, respectively, proved to be devastating to orchards. In this study, we investigated the transcriptomes of these two Gymnosporangium species during the telial stage of their lifecycles. The aim of this study was to understand the evolutionary patterns of these two related fungi and to identify genes that developed by selection.
RESULTS
The transcriptomes of G. yamadae and G. asiaticum were generated from a mixture of RNA from three biological replicates of each species. We obtained 49,318 and 54,742 transcripts, with N50 values of 1957 and 1664, for G. yamadae and G. asiaticum, respectively. We also identified a repertoire of candidate effectors and other gene families associated with pathogenicity. A total of 4947 pairs of putative orthologues between the two species were identified. Estimation of the non-synonymous/synonymous substitution rate ratios for these orthologues identified 116 pairs with Ka/Ks values greater than1 that are under positive selection and 170 pairs with Ka/Ks values of 1 that are under neutral selection, whereas the remaining 4661 genes are subjected to purifying selection. We estimate that the divergence time between the two species is approximately 5.2 Mya.
CONCLUSION
This study constitutes a de novo assembly and comparative analysis between the transcriptomes of the two rust species G. yamadae and G. asiaticum. The results identified several orthologous genes, and many expressed genes were identified by annotation. Our analysis of Ka/Ks ratios identified orthologous genes subjected to positive or purifying selection. An evolutionary analysis of these two species provided a relatively precise divergence time. Overall, the information obtained in this study increases the genetic resources available for research on the genetic diversity of the Gymnosporangium genus.
DOI: 10.1186/s12864-017-4059-x
PubMed: 28830353
PubMed Central: PMC5567642
Affiliations:
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China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, 100083</wicri:regionArea><wicri:noRegion>100083</wicri:noRegion></affiliation></author><author><name sortKey="Liang, Ying Mei" sort="Liang, Ying Mei" uniqKey="Liang Y" first="Ying-Mei" last="Liang">Ying-Mei Liang</name><affiliation wicri:level="1"><nlm:affiliation>Museum of Beijing Forestry University, Beijing, 100083, China. liangym@bjfu.edu.cn.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Museum of Beijing Forestry University, Beijing, 100083</wicri:regionArea><wicri:noRegion>100083</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2017" 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(MeSH)</term><term>Variation génétique (MeSH)</term><term>Évolution moléculaire (MeSH)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Adaptation, Physiological</term><term>Basidiomycota</term><term>Genes, Fungal</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Adaptation physiologique</term><term>Basidiomycota</term><term>Gènes fongiques</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Basidiomycota</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Basidiomycota</term></keywords><keywords scheme="MESH" qualifier="physiologie" xml:lang="fr"><term>Basidiomycota</term></keywords><keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Basidiomycota</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Evolution, Molecular</term><term>Gene Expression Profiling</term><term>Genetic Variation</term><term>Molecular Sequence 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However, a paucity of data, including genomic sequences, transcriptome sequences, and associated molecular markers, hinders the development of inhibitory compounds and prevents their analysis from an evolutionary perspective. Gymnosporangium yamadae and G. asiaticum are two closely related rust fungal species, which are ecologically and economically important pathogens that cause apple rust and pear rust, respectively, proved to be devastating to orchards. In this study, we investigated the transcriptomes of these two Gymnosporangium species during the telial stage of their lifecycles. The aim of this study was to understand the evolutionary patterns of these two related fungi and to identify genes that developed by selection.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>The transcriptomes of G. yamadae and G. asiaticum were generated from a mixture of RNA from three biological replicates of each species. We obtained 49,318 and 54,742 transcripts, with N50 values of 1957 and 1664, for G. yamadae and G. asiaticum, respectively. We also identified a repertoire of candidate effectors and other gene families associated with pathogenicity. A total of 4947 pairs of putative orthologues between the two species were identified. Estimation of the non-synonymous/synonymous substitution rate ratios for these orthologues identified 116 pairs with Ka/Ks values greater than1 that are under positive selection and 170 pairs with Ka/Ks values of 1 that are under neutral selection, whereas the remaining 4661 genes are subjected to purifying selection. We estimate that the divergence time between the two species is approximately 5.2 Mya.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSION</b></p><p>This study constitutes a de novo assembly and comparative analysis between the transcriptomes of the two rust species G. yamadae and G. asiaticum. The results identified several orthologous genes, and many expressed genes were identified by annotation. Our analysis of Ka/Ks ratios identified orthologous genes subjected to positive or purifying selection. An evolutionary analysis of these two species provided a relatively precise divergence time. Overall, the information obtained in this study increases the genetic resources available for research on the genetic diversity of the Gymnosporangium genus.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">28830353</PMID><DateCompleted><Year>2018</Year><Month>04</Month><Day>02</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2164</ISSN><JournalIssue CitedMedium="Internet"><Volume>18</Volume><Issue>1</Issue><PubDate><Year>2017</Year><Month>Aug</Month><Day>23</Day></PubDate></JournalIssue><Title>BMC genomics</Title><ISOAbbreviation>BMC Genomics</ISOAbbreviation></Journal><ArticleTitle>Comparative transcriptome analysis and identification of candidate effectors in two related rust species (Gymnosporangium yamadae and Gymnosporangium asiaticum).</ArticleTitle><Pagination><MedlinePgn>651</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/s12864-017-4059-x</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Rust fungi constitute the largest group of plant fungal pathogens. However, a paucity of data, including genomic sequences, transcriptome sequences, and associated molecular markers, hinders the development of inhibitory compounds and prevents their analysis from an evolutionary perspective. Gymnosporangium yamadae and G. asiaticum are two closely related rust fungal species, which are ecologically and economically important pathogens that cause apple rust and pear rust, respectively, proved to be devastating to orchards. In this study, we investigated the transcriptomes of these two Gymnosporangium species during the telial stage of their lifecycles. The aim of this study was to understand the evolutionary patterns of these two related fungi and to identify genes that developed by selection.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">The transcriptomes of G. yamadae and G. asiaticum were generated from a mixture of RNA from three biological replicates of each species. We obtained 49,318 and 54,742 transcripts, with N50 values of 1957 and 1664, for G. yamadae and G. asiaticum, respectively. We also identified a repertoire of candidate effectors and other gene families associated with pathogenicity. A total of 4947 pairs of putative orthologues between the two species were identified. Estimation of the non-synonymous/synonymous substitution rate ratios for these orthologues identified 116 pairs with Ka/Ks values greater than1 that are under positive selection and 170 pairs with Ka/Ks values of 1 that are under neutral selection, whereas the remaining 4661 genes are subjected to purifying selection. We estimate that the divergence time between the two species is approximately 5.2 Mya.</AbstractText><AbstractText Label="CONCLUSION" NlmCategory="CONCLUSIONS">This study constitutes a de novo assembly and comparative analysis between the transcriptomes of the two rust species G. yamadae and G. asiaticum. The results identified several orthologous genes, and many expressed genes were identified by annotation. Our analysis of Ka/Ks ratios identified orthologous genes subjected to positive or purifying selection. An evolutionary analysis of these two species provided a relatively precise divergence time. Overall, the information obtained in this study increases the genetic resources available for research on the genetic diversity of the Gymnosporangium genus.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Tao</LastName><ForeName>Si-Qi</ForeName><Initials>SQ</Initials><AffiliationInfo><Affiliation>The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, 100083, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cao</LastName><ForeName>Bin</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, 100083, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tian</LastName><ForeName>Cheng-Ming</ForeName><Initials>CM</Initials><AffiliationInfo><Affiliation>The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, 100083, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Liang</LastName><ForeName>Ying-Mei</ForeName><Initials>YM</Initials><AffiliationInfo><Affiliation>Museum of Beijing Forestry University, Beijing, 100083, China. liangym@bjfu.edu.cn.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D003160">Comparative Study</PublicationType><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2017</Year><Month>08</Month><Day>23</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC Genomics</MedlineTA><NlmUniqueID>100965258</NlmUniqueID><ISSNLinking>1471-2164</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000222" MajorTopicYN="N">Adaptation, Physiological</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D001487" MajorTopicYN="N">Basidiomycota</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName><QualifierName UI="Q000502" MajorTopicYN="N">physiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D019143" MajorTopicYN="N">Evolution, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020869" MajorTopicYN="Y">Gene Expression Profiling</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005800" MajorTopicYN="N">Genes, Fungal</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014644" MajorTopicYN="N">Genetic Variation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D058977" MajorTopicYN="N">Molecular 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Acids Res. 1997 Sep 1;25(17):3389-402</Citation><ArticleIdList><ArticleId IdType="pubmed">9254694</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>République populaire de Chine</li></country></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Tao, Si Qi" sort="Tao, Si Qi" uniqKey="Tao S" first="Si-Qi" last="Tao">Si-Qi Tao</name></noRegion><name sortKey="Cao, Bin" sort="Cao, Bin" uniqKey="Cao B" first="Bin" last="Cao">Bin Cao</name><name sortKey="Liang, Ying Mei" sort="Liang, Ying Mei" uniqKey="Liang Y" first="Ying-Mei" last="Liang">Ying-Mei Liang</name><name sortKey="Tian, Cheng Ming" sort="Tian, Cheng Ming" uniqKey="Tian C" first="Cheng-Ming" last="Tian">Cheng-Ming Tian</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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