Comparative analysis of genome sequences of the conifer tree pathogen, Heterobasidion annosum s.s.
Identifieur interne : 000600 ( Main/Exploration ); précédent : 000599; suivant : 000601Comparative analysis of genome sequences of the conifer tree pathogen, Heterobasidion annosum s.s.
Auteurs : Jaeyoung Choi [Finlande] ; Gir-Won Lee [Corée du Sud] ; Ki-Tae Kim [Corée du Sud] ; Jongbum Jeon [Corée du Sud] ; Nicolas Détry [Finlande] ; Hsiao-Che Kuo [Finlande] ; Hui Sun [Finlande] ; Fred O. Asiegbu [Finlande] ; Yong-Hwan Lee [Finlande, Corée du Sud]Source :
- Genomics data [ 2213-5960 ] ; 2017.
Abstract
The causal agent of root and butt rot of conifer trees, Heterobasidion annosum, is widespread in boreal forests and economically responsible for annual loss of approximately 50 million euros to forest industries in Finland alone and much more at European level. In order to further understand the pathobiology of this fungus at the genome level, a Finnish isolate of H. annosum sensu stricto (isolate 03012) was sequenced and analyzed with the genome sequences of 23 white-rot and 13 brown-rot fungi. The draft genome assembly of H. annosum has a size of 31.01 Mb, containing 11,453 predicted genes. Whole genome alignment showed that 84.38% of H. annosum genome sequences were aligned with those of previously sequenced H. irregulare TC 32-1 counterparts. The result is further supported by the protein sequence clustering analysis which revealed that the two genomes share 6719 out of 8647 clusters. When sequencing reads of H. annosum were aligned against the genome sequences of H. irregulare, six single nucleotide polymorphisms were found in every 1 kb, on average. In addition, 98.68% of SNPs were found to be homo-variants, suggesting that the two species have long evolved from different niches. Gene family analysis revealed that most of the white-rot fungi investigated had more gene families involved in lignin degradation or modification, including laccases and peroxidase. Comparative analysis of the two Heterobasidion spp. as well as white-/brown-rot fungi would provide new insights for understanding the pathobiology of the conifer tree pathogen.
DOI: 10.1016/j.gdata.2017.10.003
PubMed: 29085779
PubMed Central: PMC5654758
Affiliations:
- Corée du Sud, Finlande
- Région capitale de Séoul, Uusimaa
- Helsinki, Séoul
- Université d'Helsinki, Université nationale de Séoul
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last="Lee">Gir-Won Lee</name><affiliation wicri:level="4"><nlm:affiliation>National Instrumentation Center for Environmental Management, Seoul National University, Seoul 08826, Republic of Korea.</nlm:affiliation><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>National Instrumentation Center for Environmental Management, Seoul National University, Seoul 08826</wicri:regionArea><placeName><settlement type="city">Séoul</settlement><region type="capital">Région capitale de Séoul</region></placeName><orgName type="university">Université nationale de Séoul</orgName><placeName><settlement type="city">Séoul</settlement></placeName></affiliation></author><author><name sortKey="Kim, Ki Tae" sort="Kim, Ki Tae" uniqKey="Kim K" first="Ki-Tae" last="Kim">Ki-Tae Kim</name><affiliation wicri:level="4"><nlm:affiliation>Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea.</nlm:affiliation><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>Department of Agricultural Biotechnology, Seoul National University, Seoul 08826</wicri:regionArea><placeName><settlement type="city">Séoul</settlement><region type="capital">Région capitale de Séoul</region></placeName><orgName type="university">Université nationale de Séoul</orgName><placeName><settlement type="city">Séoul</settlement></placeName></affiliation></author><author><name sortKey="Jeon, Jongbum" sort="Jeon, Jongbum" uniqKey="Jeon J" first="Jongbum" last="Jeon">Jongbum Jeon</name><affiliation wicri:level="4"><nlm:affiliation>Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea.</nlm:affiliation><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>Department of Agricultural Biotechnology, Seoul National University, Seoul 08826</wicri:regionArea><placeName><settlement type="city">Séoul</settlement><region type="capital">Région capitale de Séoul</region></placeName><orgName type="university">Université nationale de Séoul</orgName><placeName><settlement type="city">Séoul</settlement></placeName></affiliation></author><author><name sortKey="Detry, Nicolas" sort="Detry, Nicolas" uniqKey="Detry N" first="Nicolas" last="Détry">Nicolas Détry</name><affiliation wicri:level="4"><nlm:affiliation>Department of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland.</nlm:affiliation><country xml:lang="fr">Finlande</country><wicri:regionArea>Department of Forest Sciences, University of Helsinki, 00014 Helsinki</wicri:regionArea><orgName type="university">Université d'Helsinki</orgName><placeName><settlement type="city">Helsinki</settlement><region type="région" nuts="2">Uusimaa</region></placeName></affiliation></author><author><name sortKey="Kuo, Hsiao Che" sort="Kuo, Hsiao Che" uniqKey="Kuo H" first="Hsiao-Che" last="Kuo">Hsiao-Che Kuo</name><affiliation wicri:level="4"><nlm:affiliation>Department of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland.</nlm:affiliation><country xml:lang="fr">Finlande</country><wicri:regionArea>Department of Forest Sciences, University of Helsinki, 00014 Helsinki</wicri:regionArea><orgName type="university">Université d'Helsinki</orgName><placeName><settlement type="city">Helsinki</settlement><region type="région" nuts="2">Uusimaa</region></placeName></affiliation></author><author><name sortKey="Sun, Hui" sort="Sun, Hui" uniqKey="Sun H" first="Hui" last="Sun">Hui Sun</name><affiliation wicri:level="4"><nlm:affiliation>Department of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland.</nlm:affiliation><country xml:lang="fr">Finlande</country><wicri:regionArea>Department of Forest Sciences, University of Helsinki, 00014 Helsinki</wicri:regionArea><orgName type="university">Université d'Helsinki</orgName><placeName><settlement type="city">Helsinki</settlement><region type="région" nuts="2">Uusimaa</region></placeName></affiliation></author><author><name sortKey="Asiegbu, Fred O" sort="Asiegbu, Fred O" uniqKey="Asiegbu F" first="Fred O" last="Asiegbu">Fred O. Asiegbu</name><affiliation wicri:level="4"><nlm:affiliation>Department of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland.</nlm:affiliation><country xml:lang="fr">Finlande</country><wicri:regionArea>Department of Forest Sciences, University of Helsinki, 00014 Helsinki</wicri:regionArea><orgName type="university">Université d'Helsinki</orgName><placeName><settlement type="city">Helsinki</settlement><region type="région" nuts="2">Uusimaa</region></placeName></affiliation></author><author><name sortKey="Lee, Yong Hwan" sort="Lee, Yong Hwan" uniqKey="Lee Y" first="Yong-Hwan" last="Lee">Yong-Hwan Lee</name><affiliation wicri:level="4"><nlm:affiliation>Department of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland.</nlm:affiliation><country xml:lang="fr">Finlande</country><wicri:regionArea>Department of Forest Sciences, University of Helsinki, 00014 Helsinki</wicri:regionArea><orgName type="university">Université d'Helsinki</orgName><placeName><settlement type="city">Helsinki</settlement><region type="région" nuts="2">Uusimaa</region></placeName></affiliation><affiliation wicri:level="4"><nlm:affiliation>Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea.</nlm:affiliation><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>Department of Agricultural Biotechnology, Seoul National University, Seoul 08826</wicri:regionArea><placeName><settlement type="city">Séoul</settlement><region type="capital">Région capitale de Séoul</region></placeName><orgName type="university">Université nationale de Séoul</orgName><placeName><settlement type="city">Séoul</settlement></placeName></affiliation><affiliation wicri:level="4"><nlm:affiliation>Center for Fungal Genetic Resources, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea.</nlm:affiliation><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>Center for Fungal Genetic Resources, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826</wicri:regionArea><placeName><settlement type="city">Séoul</settlement><region type="capital">Région capitale de Séoul</region></placeName><orgName type="university">Université nationale de Séoul</orgName><placeName><settlement type="city">Séoul</settlement></placeName></affiliation></author></analytic><series><title level="j">Genomics data</title><idno type="ISSN">2213-5960</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The causal agent of root and butt rot of conifer trees, <i>Heterobasidion annosum</i>, is widespread in boreal forests and economically responsible for annual loss of approximately 50 million euros to forest industries in Finland alone and much more at European level. In order to further understand the pathobiology of this fungus at the genome level, a Finnish isolate of <i>H. annosum sensu stricto</i> (isolate 03012) was sequenced and analyzed with the genome sequences of 23 white-rot and 13 brown-rot fungi. The draft genome assembly of <i>H. annosum</i> has a size of 31.01 Mb, containing 11,453 predicted genes. Whole genome alignment showed that 84.38% of <i>H. annosum</i> genome sequences were aligned with those of previously sequenced <i>H. irregulare</i> TC 32-1 counterparts. The result is further supported by the protein sequence clustering analysis which revealed that the two genomes share 6719 out of 8647 clusters. When sequencing reads of <i>H. annosum</i> were aligned against the genome sequences of <i>H. irregulare</i>, six single nucleotide polymorphisms were found in every 1 kb, on average. In addition, 98.68% of SNPs were found to be homo-variants, suggesting that the two species have long evolved from different niches. Gene family analysis revealed that most of the white-rot fungi investigated had more gene families involved in lignin degradation or modification, including laccases and peroxidase. Comparative analysis of the two <i>Heterobasidion</i> spp. as well as white-/brown-rot fungi would provide new insights for understanding the pathobiology of the conifer tree pathogen.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">29085779</PMID><DateRevised><Year>2020</Year><Month>09</Month><Day>30</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">2213-5960</ISSN><JournalIssue CitedMedium="Print"><Volume>14</Volume><PubDate><Year>2017</Year><Month>Dec</Month></PubDate></JournalIssue><Title>Genomics data</Title><ISOAbbreviation>Genom Data</ISOAbbreviation></Journal><ArticleTitle>Comparative analysis of genome sequences of the conifer tree pathogen, <i>Heterobasidion annosum s.s</i>.</ArticleTitle><Pagination><MedlinePgn>106-113</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.gdata.2017.10.003</ELocationID><Abstract><AbstractText>The causal agent of root and butt rot of conifer trees, <i>Heterobasidion annosum</i>, is widespread in boreal forests and economically responsible for annual loss of approximately 50 million euros to forest industries in Finland alone and much more at European level. In order to further understand the pathobiology of this fungus at the genome level, a Finnish isolate of <i>H. annosum sensu stricto</i> (isolate 03012) was sequenced and analyzed with the genome sequences of 23 white-rot and 13 brown-rot fungi. The draft genome assembly of <i>H. annosum</i> has a size of 31.01 Mb, containing 11,453 predicted genes. Whole genome alignment showed that 84.38% of <i>H. annosum</i> genome sequences were aligned with those of previously sequenced <i>H. irregulare</i> TC 32-1 counterparts. The result is further supported by the protein sequence clustering analysis which revealed that the two genomes share 6719 out of 8647 clusters. When sequencing reads of <i>H. annosum</i> were aligned against the genome sequences of <i>H. irregulare</i>, six single nucleotide polymorphisms were found in every 1 kb, on average. In addition, 98.68% of SNPs were found to be homo-variants, suggesting that the two species have long evolved from different niches. Gene family analysis revealed that most of the white-rot fungi investigated had more gene families involved in lignin degradation or modification, including laccases and peroxidase. Comparative analysis of the two <i>Heterobasidion</i> spp. as well as white-/brown-rot fungi would provide new insights for understanding the pathobiology of the conifer tree pathogen.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Choi</LastName><ForeName>Jaeyoung</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Department of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lee</LastName><ForeName>Gir-Won</ForeName><Initials>GW</Initials><AffiliationInfo><Affiliation>National Instrumentation Center for Environmental Management, Seoul National University, Seoul 08826, Republic of Korea.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kim</LastName><ForeName>Ki-Tae</ForeName><Initials>KT</Initials><AffiliationInfo><Affiliation>Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jeon</LastName><ForeName>Jongbum</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Détry</LastName><ForeName>Nicolas</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>Department of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kuo</LastName><ForeName>Hsiao-Che</ForeName><Initials>HC</Initials><AffiliationInfo><Affiliation>Department of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sun</LastName><ForeName>Hui</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Department of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Asiegbu</LastName><ForeName>Fred O</ForeName><Initials>FO</Initials><AffiliationInfo><Affiliation>Department of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lee</LastName><ForeName>Yong-Hwan</ForeName><Initials>YH</Initials><AffiliationInfo><Affiliation>Department of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Center for Fungal Genetic Resources, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2017</Year><Month>10</Month><Day>25</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Genom Data</MedlineTA><NlmUniqueID>101634120</NlmUniqueID><ISSNLinking>2213-5960</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Annosum root rot</Keyword><Keyword MajorTopicYN="N">Comparative genomics</Keyword><Keyword MajorTopicYN="N">Conifer tree pathogen</Keyword><Keyword MajorTopicYN="N">Heterobasidion annosum</Keyword><Keyword MajorTopicYN="N">Whole genome sequencing</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2017</Year><Month>06</Month><Day>21</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2017</Year><Month>09</Month><Day>21</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2017</Year><Month>10</Month><Day>15</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2017</Year><Month>11</Month><Day>1</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2017</Year><Month>11</Month><Day>1</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2017</Year><Month>11</Month><Day>1</Day><Hour>6</Hour><Minute>1</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">29085779</ArticleId><ArticleId IdType="doi">10.1016/j.gdata.2017.10.003</ArticleId><ArticleId IdType="pii">S2213-5960(17)30127-7</ArticleId><ArticleId IdType="pmc">PMC5654758</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>Mol Plant Pathol. 2005 Jul 1;6(4):395-409</Citation><ArticleIdList><ArticleId 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Sud</li><li>Finlande</li></country><region><li>Région capitale de Séoul</li><li>Uusimaa</li></region><settlement><li>Helsinki</li><li>Séoul</li></settlement><orgName><li>Université d'Helsinki</li><li>Université nationale de Séoul</li></orgName></list><tree><country name="Finlande"><region name="Uusimaa"><name sortKey="Choi, Jaeyoung" sort="Choi, Jaeyoung" uniqKey="Choi J" first="Jaeyoung" last="Choi">Jaeyoung Choi</name></region><name sortKey="Asiegbu, Fred O" sort="Asiegbu, Fred O" uniqKey="Asiegbu F" first="Fred O" last="Asiegbu">Fred O. Asiegbu</name><name sortKey="Detry, Nicolas" sort="Detry, Nicolas" uniqKey="Detry N" first="Nicolas" last="Détry">Nicolas Détry</name><name sortKey="Kuo, Hsiao Che" sort="Kuo, Hsiao Che" uniqKey="Kuo H" first="Hsiao-Che" last="Kuo">Hsiao-Che Kuo</name><name sortKey="Lee, Yong Hwan" sort="Lee, Yong Hwan" uniqKey="Lee Y" first="Yong-Hwan" last="Lee">Yong-Hwan Lee</name><name sortKey="Sun, Hui" sort="Sun, Hui" uniqKey="Sun H" first="Hui" last="Sun">Hui Sun</name></country><country name="Corée du Sud"><region name="Région capitale de Séoul"><name sortKey="Lee, Gir Won" sort="Lee, Gir Won" uniqKey="Lee G" first="Gir-Won" last="Lee">Gir-Won Lee</name></region><name sortKey="Jeon, Jongbum" sort="Jeon, Jongbum" uniqKey="Jeon J" first="Jongbum" last="Jeon">Jongbum Jeon</name><name sortKey="Kim, Ki Tae" sort="Kim, Ki Tae" uniqKey="Kim K" first="Ki-Tae" last="Kim">Ki-Tae Kim</name><name sortKey="Lee, Yong Hwan" sort="Lee, Yong Hwan" uniqKey="Lee Y" first="Yong-Hwan" last="Lee">Yong-Hwan Lee</name><name sortKey="Lee, Yong Hwan" sort="Lee, Yong Hwan" uniqKey="Lee Y" first="Yong-Hwan" last="Lee">Yong-Hwan Lee</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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