Department of Biotechnology, Rama Devi Women's University, Vidya Vihar, Bhubaneswar, Odisha, 751022, India.
School of Applied Sciences, Centurion University of Technology and Management, Bhubaneswar, Odisha, India.
BMC Genom Data. 2024 Nov 5;25(1):95. doi: 10.1186/s12863-024-01276-0.
Purple blotch, caused by the necrotrophic pathogen Alternaria porri, is one of the most economically significant diseases of onion and allied crops. While the virulent nature of many Alternaria spp. has been identified, the pathogenic repertoire of A. porri is still unknown. The objective of this work was to sequence the genome of A. porri using the PacBio SMRT sequencing strategy and analyse the repertoire of CAZymes, secondary metabolites, secretome and effectors in A. porri. Our research group is working to identify onion germplasm with purple blotch resistance and to understand the genetics of the pathogen. The reported de-novo assembly will contribute to the analysis of potential variants and the gene repertoire contributing to the virulence and pathogenicity of the purple blotch pathogen.
Long-read sequencing on a PacBio Sequel II system resulted in a 32.98 Mb (20 contigs) assembly with an N50 of 2, 657, 264 bp, the longest contig length of 5.05 Mb, and a GC content of 51.06%. The Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis resulted in 99.7% genome completeness at the Dothideomycetes lineage, representing a high-quality genome assembly. AUGUSTUS ab initio analysis resulted in 9875 protein-coding genes. Of the 6776 pathogenicity-related genes, 537 genes with effector functions were identified. Likewise, the glycoside hydrolases (434) were the most dominant group of the total 837 predicted CAZymes. The assembled genome of A. porri showed distinctive similarities to the genomes of A. alternata and A. brassicicola, the causal agents of leaf blight of onion and leaf spot of Brassica crops, respectively.
由腐霉病菌（Alternaria porri）引起的紫斑病是洋葱和相关作物中最具经济意义的病害之一。虽然许多链格孢菌的毒力特性已被确定，但腐霉病菌的致病谱仍不清楚。本研究的目的是使用 PacBio SMRT 测序策略对 A. porri 基因组进行测序，并分析 A. porri 中的 CAZymes、次生代谢物、分泌组和效应子。我们的研究小组正在努力鉴定具有抗紫斑病的洋葱种质资源，并了解病原体的遗传学。报告的从头组装将有助于分析潜在的变体和基因谱，这些变体和基因谱有助于紫斑病病原体的毒力和致病性。
在 PacBio Sequel II 系统上进行长读测序，得到了一个 32.98 Mb（20 个 contigs）的组装体，N50 为 2,657,264 bp，最长 contig 长度为 5.05 Mb，GC 含量为 51.06%。基准通用单拷贝直系同源物（BUSCO）分析结果显示，在 Dothideomycetes 谱系中基因组完整性达到 99.7%，这代表了一个高质量的基因组组装。AUGUSTUS 从头分析得到了 9875 个编码蛋白的基因。在 6776 个与致病性相关的基因中，鉴定出了 537 个具有效应子功能的基因。同样，糖苷水解酶（434 个）是 837 个预测的 CAZymes 中最主要的一组。腐霉病菌的组装基因组与洋葱叶枯病和十字花科作物叶斑病的病原菌链格孢菌（A. alternata）和 A. brassicicola 的基因组有明显的相似性。
