对从两个在田间毒力上存在差异的分离样本的全基因组序列开发的基因组草图组装进行比较分析。

Comparative analysis of draft genome assemblies developed from whole genome sequences of two isolate samples differing in field virulence on .

作者信息

You Ming Pei, Akhatar Javed, Mittal Meenakshi, Barbetti Martin J, Maina Solomon, Banga Surinder S

机构信息

School of Agriculture and Environment and the UWA Institute of Agriculture, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.

Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004 Punjab, India.

出版信息

Biotechnol Rep (Amst). 2021 Jun 22;31:e00653. doi: 10.1016/j.btre.2021.e00653. eCollection 2021 Sep.

DOI:10.1016/j.btre.2021.e00653

PMID:34258242

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC8254085/

Abstract

causes downy mildew, a major disease of Brassicaceae species. We sequenced the genomes of two isolates of high (Sample B) and low (Sample C) virulence. Sequencing reads were first assembled with software's SOAPdenovo2, ABySS V2.1 and Velvet V1.1 and later combined to create meta-assemblies with genome sizes of 72.762 and 76.950Mb and predicted gene densities of 1628 and 1644 /Mb, respectively. We could annotate 12.255 and 13,030 genes with high proportions (91-92%) of complete BUSCOs for Sample B and C, respectively. Comparative analysis revealed conserved and varied molecular machinery underlying the physiological specialisation and infection capabilities. BLAST analysis against PHI gene database suggested a relatively higher loss of genes for virulence and pathogenicity in Sample C compared to Sample B, reflecting pathogen evolution through differential rates of mutation and selection. These studies will enable identification and monitoring of virulence factors prevailing in-field.

摘要

引发霜霉病，这是十字花科植物的一种主要病害。我们对两株高毒力（样本B）和低毒力（样本C）分离株的基因组进行了测序。测序读数首先使用SOAPdenovo2、ABySS V2.1和Velvet V1.1软件进行组装，随后合并以创建基因组大小分别为72.762和76.950Mb、预测基因密度分别为1628和1644个/Mb的元组装。对于样本B和C，我们分别能够注释12255和13030个基因，其中完整BUSCO的比例很高（91 - 92%）。比较分析揭示了生理特化和感染能力背后保守和多样的分子机制。针对PHI基因数据库的BLAST分析表明，与样本B相比，样本C中与毒力和致病性相关的基因损失相对较高，这反映了病原体通过不同的突变和选择速率进化。这些研究将有助于识别和监测田间流行的毒力因子。