Gapless genome assembly of Colletotrichum higginsianum reveals chromosome structure and association of transposable elements with secondary metabolite gene clusters
Autor(a) principal: | |
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Data de Publicação: | 2017 |
Outros Autores: | , , , , , , , , , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | LOCUS Repositório Institucional da UFV |
Texto Completo: | https://www.ncbi.nlm.nih.gov/pubmed/28851275 http://www.locus.ufv.br/handle/123456789/13887 |
Resumo: | The ascomycete fungus Colletotrichum higginsianum causes anthracnose disease of brassica crops and the model plant Arabidopsis thaliana. Previous versions of the genome sequence were highly fragmented, causing errors in the prediction of protein-coding genes and preventing the analysis of repetitive sequences and genome architecture. Here, we re-sequenced the genome using single-molecule real-time (SMRT) sequencing technology and, in combination with optical map data, this provided a gapless assembly of all twelve chromosomes except for the ribosomal DNA repeat cluster on chromosome 7. The more accurate gene annotation made possible by this new assembly revealed a large repertoire of secondary metabolism (SM) key genes (89) and putative biosynthetic pathways (77 SM gene clusters). The two mini-chromosomes differed from the ten core chromosomes in being repeat- and AT-rich and gene-poor but were significantly enriched with genes encoding putative secreted effector proteins. Transposable elements (TEs) were found to occupy 7% of the genome by length. Certain TE families showed a statistically significant association with effector genes and SM cluster genes and were transcriptionally active at particular stages of fungal development. All 24 subtelomeres were found to contain one of three highly- conserved repeat elements which, by providing sites for homologous recombination, were probably instrumental in four segmental duplications. The gapless genome of C. higginsianum provides access to repeat-rich regions that were previously poorly assembled, notably the mini-chromosomes and subtelomeres, and allowed prediction of the complete SM gene repertoire. It also provides insights into the potential role of TEs in gene and genome evolution and host adaptation in this asexual pathogen. |
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Dallery, Jean-FélixLapalu, NicolasZampounis, AntoniosPigné, SandrineLuyten, IsabelleAmselem, JoëlleWittenberg, Alexander H. J.Zhou, ShiguoQueiroz, Marisa V. deRobin, Guillaume P.Auger, AnnieHainaut, MatthieuHenrissat, BernardKim, Ki-TaeLee, Yong-HwanLespinet, OlivierSchwartz, David C.Thon, Michael R.Richard J. O’Connell2017-11-28T13:31:38Z2017-11-28T13:31:38Z2017-08-2914712164https://www.ncbi.nlm.nih.gov/pubmed/28851275http://www.locus.ufv.br/handle/123456789/13887The ascomycete fungus Colletotrichum higginsianum causes anthracnose disease of brassica crops and the model plant Arabidopsis thaliana. Previous versions of the genome sequence were highly fragmented, causing errors in the prediction of protein-coding genes and preventing the analysis of repetitive sequences and genome architecture. Here, we re-sequenced the genome using single-molecule real-time (SMRT) sequencing technology and, in combination with optical map data, this provided a gapless assembly of all twelve chromosomes except for the ribosomal DNA repeat cluster on chromosome 7. The more accurate gene annotation made possible by this new assembly revealed a large repertoire of secondary metabolism (SM) key genes (89) and putative biosynthetic pathways (77 SM gene clusters). The two mini-chromosomes differed from the ten core chromosomes in being repeat- and AT-rich and gene-poor but were significantly enriched with genes encoding putative secreted effector proteins. Transposable elements (TEs) were found to occupy 7% of the genome by length. Certain TE families showed a statistically significant association with effector genes and SM cluster genes and were transcriptionally active at particular stages of fungal development. All 24 subtelomeres were found to contain one of three highly- conserved repeat elements which, by providing sites for homologous recombination, were probably instrumental in four segmental duplications. The gapless genome of C. higginsianum provides access to repeat-rich regions that were previously poorly assembled, notably the mini-chromosomes and subtelomeres, and allowed prediction of the complete SM gene repertoire. It also provides insights into the potential role of TEs in gene and genome evolution and host adaptation in this asexual pathogen.engBMC Genomics18(1):667, Aug 2017Fungal genomeSMRT sequencingOptical mapTransposable elementsSecondary metabolism genesSubtelomeresSegmental duplicationAccessory chromosomesColletotrichum higginsianumGapless genome assembly of Colletotrichum higginsianum reveals chromosome structure and association of transposable elements with secondary metabolite gene clustersinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfinfo:eu-repo/semantics/openAccessreponame:LOCUS Repositório Institucional da UFVinstname:Universidade Federal de Viçosa (UFV)instacron:UFVORIGINALdocument.pdfdocument.pdfTexto completoapplication/pdf4384630https://locus.ufv.br//bitstream/123456789/13887/1/document.pdf95bf2fcc90526da243970c19b6298c1aMD51LICENSElicense.txtlicense.txttext/plain; charset=utf-81748https://locus.ufv.br//bitstream/123456789/13887/2/license.txt8a4605be74aa9ea9d79846c1fba20a33MD52THUMBNAILdocument.pdf.jpgdocument.pdf.jpgIM Thumbnailimage/jpeg5046https://locus.ufv.br//bitstream/123456789/13887/3/document.pdf.jpg042b02d30ce1f4b02565a25ce84afc0aMD53123456789/138872017-11-28 22:00:38.915oai:locus.ufv.br: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Repositório InstitucionalPUBhttps://www.locus.ufv.br/oai/requestfabiojreis@ufv.bropendoar:21452017-11-29T01:00:38LOCUS Repositório Institucional da UFV - Universidade Federal de Viçosa (UFV)false |
dc.title.en.fl_str_mv |
Gapless genome assembly of Colletotrichum higginsianum reveals chromosome structure and association of transposable elements with secondary metabolite gene clusters |
title |
Gapless genome assembly of Colletotrichum higginsianum reveals chromosome structure and association of transposable elements with secondary metabolite gene clusters |
spellingShingle |
Gapless genome assembly of Colletotrichum higginsianum reveals chromosome structure and association of transposable elements with secondary metabolite gene clusters Dallery, Jean-Félix Fungal genome SMRT sequencing Optical map Transposable elements Secondary metabolism genes Subtelomeres Segmental duplication Accessory chromosomes Colletotrichum higginsianum |
title_short |
Gapless genome assembly of Colletotrichum higginsianum reveals chromosome structure and association of transposable elements with secondary metabolite gene clusters |
title_full |
Gapless genome assembly of Colletotrichum higginsianum reveals chromosome structure and association of transposable elements with secondary metabolite gene clusters |
title_fullStr |
Gapless genome assembly of Colletotrichum higginsianum reveals chromosome structure and association of transposable elements with secondary metabolite gene clusters |
title_full_unstemmed |
Gapless genome assembly of Colletotrichum higginsianum reveals chromosome structure and association of transposable elements with secondary metabolite gene clusters |
title_sort |
Gapless genome assembly of Colletotrichum higginsianum reveals chromosome structure and association of transposable elements with secondary metabolite gene clusters |
author |
Dallery, Jean-Félix |
author_facet |
Dallery, Jean-Félix Lapalu, Nicolas Zampounis, Antonios Pigné, Sandrine Luyten, Isabelle Amselem, Joëlle Wittenberg, Alexander H. J. Zhou, Shiguo Queiroz, Marisa V. de Robin, Guillaume P. Auger, Annie Hainaut, Matthieu Henrissat, Bernard Kim, Ki-Tae Lee, Yong-Hwan Lespinet, Olivier Schwartz, David C. Thon, Michael R. Richard J. O’Connell |
author_role |
author |
author2 |
Lapalu, Nicolas Zampounis, Antonios Pigné, Sandrine Luyten, Isabelle Amselem, Joëlle Wittenberg, Alexander H. J. Zhou, Shiguo Queiroz, Marisa V. de Robin, Guillaume P. Auger, Annie Hainaut, Matthieu Henrissat, Bernard Kim, Ki-Tae Lee, Yong-Hwan Lespinet, Olivier Schwartz, David C. Thon, Michael R. Richard J. O’Connell |
author2_role |
author author author author author author author author author author author author author author author author author author |
dc.contributor.author.fl_str_mv |
Dallery, Jean-Félix Lapalu, Nicolas Zampounis, Antonios Pigné, Sandrine Luyten, Isabelle Amselem, Joëlle Wittenberg, Alexander H. J. Zhou, Shiguo Queiroz, Marisa V. de Robin, Guillaume P. Auger, Annie Hainaut, Matthieu Henrissat, Bernard Kim, Ki-Tae Lee, Yong-Hwan Lespinet, Olivier Schwartz, David C. Thon, Michael R. Richard J. O’Connell |
dc.subject.pt-BR.fl_str_mv |
Fungal genome SMRT sequencing Optical map Transposable elements Secondary metabolism genes Subtelomeres Segmental duplication Accessory chromosomes Colletotrichum higginsianum |
topic |
Fungal genome SMRT sequencing Optical map Transposable elements Secondary metabolism genes Subtelomeres Segmental duplication Accessory chromosomes Colletotrichum higginsianum |
description |
The ascomycete fungus Colletotrichum higginsianum causes anthracnose disease of brassica crops and the model plant Arabidopsis thaliana. Previous versions of the genome sequence were highly fragmented, causing errors in the prediction of protein-coding genes and preventing the analysis of repetitive sequences and genome architecture. Here, we re-sequenced the genome using single-molecule real-time (SMRT) sequencing technology and, in combination with optical map data, this provided a gapless assembly of all twelve chromosomes except for the ribosomal DNA repeat cluster on chromosome 7. The more accurate gene annotation made possible by this new assembly revealed a large repertoire of secondary metabolism (SM) key genes (89) and putative biosynthetic pathways (77 SM gene clusters). The two mini-chromosomes differed from the ten core chromosomes in being repeat- and AT-rich and gene-poor but were significantly enriched with genes encoding putative secreted effector proteins. Transposable elements (TEs) were found to occupy 7% of the genome by length. Certain TE families showed a statistically significant association with effector genes and SM cluster genes and were transcriptionally active at particular stages of fungal development. All 24 subtelomeres were found to contain one of three highly- conserved repeat elements which, by providing sites for homologous recombination, were probably instrumental in four segmental duplications. The gapless genome of C. higginsianum provides access to repeat-rich regions that were previously poorly assembled, notably the mini-chromosomes and subtelomeres, and allowed prediction of the complete SM gene repertoire. It also provides insights into the potential role of TEs in gene and genome evolution and host adaptation in this asexual pathogen. |
publishDate |
2017 |
dc.date.accessioned.fl_str_mv |
2017-11-28T13:31:38Z |
dc.date.available.fl_str_mv |
2017-11-28T13:31:38Z |
dc.date.issued.fl_str_mv |
2017-08-29 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
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info:eu-repo/semantics/article |
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dc.identifier.uri.fl_str_mv |
https://www.ncbi.nlm.nih.gov/pubmed/28851275 http://www.locus.ufv.br/handle/123456789/13887 |
dc.identifier.issn.none.fl_str_mv |
14712164 |
identifier_str_mv |
14712164 |
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https://www.ncbi.nlm.nih.gov/pubmed/28851275 http://www.locus.ufv.br/handle/123456789/13887 |
dc.language.iso.fl_str_mv |
eng |
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eng |
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18(1):667, Aug 2017 |
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openAccess |
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BMC Genomics |
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BMC Genomics |
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LOCUS Repositório Institucional da UFV |
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