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Comparative genomics and association analysis identifies virulence genes of Cercospora sojina in soybean

BACKGROUND: Recently, a new strain of Cercospora sojina (Race15) has been identified, which has caused the breakdown of resistance in most soybean cultivars in China. Despite this serious yield reduction, little is known about why this strain is more virulent than others. Therefore, we sequenced the...

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Autores principales: Gu, Xin, Ding, Junjie, Liu, Wei, Yang, Xiaohe, Yao, Liangliang, Gao, Xuedong, Zhang, Maoming, Yang, Shuai, Wen, Jingzhi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7032006/
https://www.ncbi.nlm.nih.gov/pubmed/32075575
http://dx.doi.org/10.1186/s12864-020-6581-5
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author Gu, Xin
Ding, Junjie
Liu, Wei
Yang, Xiaohe
Yao, Liangliang
Gao, Xuedong
Zhang, Maoming
Yang, Shuai
Wen, Jingzhi
author_facet Gu, Xin
Ding, Junjie
Liu, Wei
Yang, Xiaohe
Yao, Liangliang
Gao, Xuedong
Zhang, Maoming
Yang, Shuai
Wen, Jingzhi
author_sort Gu, Xin
collection PubMed
description BACKGROUND: Recently, a new strain of Cercospora sojina (Race15) has been identified, which has caused the breakdown of resistance in most soybean cultivars in China. Despite this serious yield reduction, little is known about why this strain is more virulent than others. Therefore, we sequenced the Race15 genome and compared it to the Race1 genome sequence, as its virulence is significantly lower. We then re-sequenced 30 isolates of C. sojina from different regions to identifying differential virulence genes using genome-wide association analysis (GWAS). RESULTS: The 40.12-Mb Race15 genome encodes 12,607 predicated genes and contains large numbers of gene clusters that have annotations in 11 different common databases. Comparative genomics revealed that although these two genomes had a large number of homologous genes, their genome structures have evolved to introduce 245 specific genes. The most important 5 candidate virulence genes were located on Contig 3 and Contig 1 and were mainly related to the regulation of metabolic mechanisms and the biosynthesis of bioactive metabolites, thereby putatively affecting fungi self-toxicity and reducing host resistance. Our study provides insight into the genomic basis of C. sojina pathogenicity and its infection mechanism, enabling future studies of this disease. CONCLUSIONS: Via GWAS, we identified five candidate genes using three different methods, and these candidate genes are speculated to be related to metabolic mechanisms and the biosynthesis of bioactive metabolites. Meanwhile, Race15 specific genes may be linked with high virulence. The genes highly prevalent in virulent isolates should also be proposed as candidates, even though they were not found in our SNP analysis. Future work should focus on using a larger sample size to confirm and refine candidate gene identifications and should study the functional roles of these candidates, in order to investigate their potential roles in C. sojina pathogenicity.
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spelling pubmed-70320062020-02-25 Comparative genomics and association analysis identifies virulence genes of Cercospora sojina in soybean Gu, Xin Ding, Junjie Liu, Wei Yang, Xiaohe Yao, Liangliang Gao, Xuedong Zhang, Maoming Yang, Shuai Wen, Jingzhi BMC Genomics Research Article BACKGROUND: Recently, a new strain of Cercospora sojina (Race15) has been identified, which has caused the breakdown of resistance in most soybean cultivars in China. Despite this serious yield reduction, little is known about why this strain is more virulent than others. Therefore, we sequenced the Race15 genome and compared it to the Race1 genome sequence, as its virulence is significantly lower. We then re-sequenced 30 isolates of C. sojina from different regions to identifying differential virulence genes using genome-wide association analysis (GWAS). RESULTS: The 40.12-Mb Race15 genome encodes 12,607 predicated genes and contains large numbers of gene clusters that have annotations in 11 different common databases. Comparative genomics revealed that although these two genomes had a large number of homologous genes, their genome structures have evolved to introduce 245 specific genes. The most important 5 candidate virulence genes were located on Contig 3 and Contig 1 and were mainly related to the regulation of metabolic mechanisms and the biosynthesis of bioactive metabolites, thereby putatively affecting fungi self-toxicity and reducing host resistance. Our study provides insight into the genomic basis of C. sojina pathogenicity and its infection mechanism, enabling future studies of this disease. CONCLUSIONS: Via GWAS, we identified five candidate genes using three different methods, and these candidate genes are speculated to be related to metabolic mechanisms and the biosynthesis of bioactive metabolites. Meanwhile, Race15 specific genes may be linked with high virulence. The genes highly prevalent in virulent isolates should also be proposed as candidates, even though they were not found in our SNP analysis. Future work should focus on using a larger sample size to confirm and refine candidate gene identifications and should study the functional roles of these candidates, in order to investigate their potential roles in C. sojina pathogenicity. BioMed Central 2020-02-19 /pmc/articles/PMC7032006/ /pubmed/32075575 http://dx.doi.org/10.1186/s12864-020-6581-5 Text en © The Author(s). 2020 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Gu, Xin
Ding, Junjie
Liu, Wei
Yang, Xiaohe
Yao, Liangliang
Gao, Xuedong
Zhang, Maoming
Yang, Shuai
Wen, Jingzhi
Comparative genomics and association analysis identifies virulence genes of Cercospora sojina in soybean
title Comparative genomics and association analysis identifies virulence genes of Cercospora sojina in soybean
title_full Comparative genomics and association analysis identifies virulence genes of Cercospora sojina in soybean
title_fullStr Comparative genomics and association analysis identifies virulence genes of Cercospora sojina in soybean
title_full_unstemmed Comparative genomics and association analysis identifies virulence genes of Cercospora sojina in soybean
title_short Comparative genomics and association analysis identifies virulence genes of Cercospora sojina in soybean
title_sort comparative genomics and association analysis identifies virulence genes of cercospora sojina in soybean
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7032006/
https://www.ncbi.nlm.nih.gov/pubmed/32075575
http://dx.doi.org/10.1186/s12864-020-6581-5
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