A draft genome sequence of the rose black spot fungus Diplocarpon rosae reveals a high degree of genome duplication.

Black spot is one of the most severe and damaging diseases of garden roses. We present the draft genome sequence of its causative agent Diplocarpon rosae as a working tool to generate molecular markers and to analyze functional and structural characteristics of this fungus.The isolate DortE4 was seq...

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Main Authors: Enzo Neu, Jonathan Featherston, Jasper Rees, Thomas Debener
Format: Article
Language:English
Published: Public Library of Science (PLoS) 2017-01-01
Series:PLoS ONE
Online Access:http://europepmc.org/articles/PMC5628827?pdf=render
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spelling doaj-57ec9982646a4bdb8c076c0d19611a752020-11-25T01:46:53ZengPublic Library of Science (PLoS)PLoS ONE1932-62032017-01-011210e018531010.1371/journal.pone.0185310A draft genome sequence of the rose black spot fungus Diplocarpon rosae reveals a high degree of genome duplication.Enzo NeuJonathan FeatherstonJasper ReesThomas DebenerBlack spot is one of the most severe and damaging diseases of garden roses. We present the draft genome sequence of its causative agent Diplocarpon rosae as a working tool to generate molecular markers and to analyze functional and structural characteristics of this fungus.The isolate DortE4 was sequenced with 191x coverage of different read types which were assembled into 2457 scaffolds. By evidence supported genome annotation with the MAKER pipeline 14,004 gene models were predicted and transcriptomic data indicated that 88.5% of them are expressed during the early stages of infection. Analyses of k-mer distributions resulted in unexpectedly large genome size estimations between 72.5 and 91.4 Mb, which cannot be attributed to its repeat structure and content of transposable elements alone, factors explaining such differences in other fungal genomes. In contrast, different lines of evidences demonstrate that a huge proportion (approximately 80%) of genes are duplicated, which might indicate a whole genome duplication event. By PCR-RFLP analysis of six paralogous gene pairs of BUSCO orthologs, which are expected to be single copy genes, we could show experimentally that the duplication is not due to technical error and that not all isolates tested possess all of the paralogs.The presented genome sequence is still a fragmented draft but contains almost the complete gene space. Therefore, it provides a useful working tool to study the interaction of D. rosae with the host and the influence of a genome duplication outside of the model yeast in the background of a phytopathogen.http://europepmc.org/articles/PMC5628827?pdf=render
collection DOAJ
language English
format Article
sources DOAJ
author Enzo Neu
Jonathan Featherston
Jasper Rees
Thomas Debener
spellingShingle Enzo Neu
Jonathan Featherston
Jasper Rees
Thomas Debener
A draft genome sequence of the rose black spot fungus Diplocarpon rosae reveals a high degree of genome duplication.
PLoS ONE
author_facet Enzo Neu
Jonathan Featherston
Jasper Rees
Thomas Debener
author_sort Enzo Neu
title A draft genome sequence of the rose black spot fungus Diplocarpon rosae reveals a high degree of genome duplication.
title_short A draft genome sequence of the rose black spot fungus Diplocarpon rosae reveals a high degree of genome duplication.
title_full A draft genome sequence of the rose black spot fungus Diplocarpon rosae reveals a high degree of genome duplication.
title_fullStr A draft genome sequence of the rose black spot fungus Diplocarpon rosae reveals a high degree of genome duplication.
title_full_unstemmed A draft genome sequence of the rose black spot fungus Diplocarpon rosae reveals a high degree of genome duplication.
title_sort draft genome sequence of the rose black spot fungus diplocarpon rosae reveals a high degree of genome duplication.
publisher Public Library of Science (PLoS)
series PLoS ONE
issn 1932-6203
publishDate 2017-01-01
description Black spot is one of the most severe and damaging diseases of garden roses. We present the draft genome sequence of its causative agent Diplocarpon rosae as a working tool to generate molecular markers and to analyze functional and structural characteristics of this fungus.The isolate DortE4 was sequenced with 191x coverage of different read types which were assembled into 2457 scaffolds. By evidence supported genome annotation with the MAKER pipeline 14,004 gene models were predicted and transcriptomic data indicated that 88.5% of them are expressed during the early stages of infection. Analyses of k-mer distributions resulted in unexpectedly large genome size estimations between 72.5 and 91.4 Mb, which cannot be attributed to its repeat structure and content of transposable elements alone, factors explaining such differences in other fungal genomes. In contrast, different lines of evidences demonstrate that a huge proportion (approximately 80%) of genes are duplicated, which might indicate a whole genome duplication event. By PCR-RFLP analysis of six paralogous gene pairs of BUSCO orthologs, which are expected to be single copy genes, we could show experimentally that the duplication is not due to technical error and that not all isolates tested possess all of the paralogs.The presented genome sequence is still a fragmented draft but contains almost the complete gene space. Therefore, it provides a useful working tool to study the interaction of D. rosae with the host and the influence of a genome duplication outside of the model yeast in the background of a phytopathogen.
url http://europepmc.org/articles/PMC5628827?pdf=render
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