Department of Plant Pathology, University of California Davis, Davis, USA.
Present address: Department of Plant Pathology, National Chung Hsing University, Taichung, Taiwan, ROC.
Microb Genom. 2022 Apr;8(4). doi: 10.1099/mgen.0.000819.
is a fungal pathogen that causes leaf mould of tomato. The reference genome of this pathogen was released in 2012 but its high repetitive DNA content prevented a contiguous assembly and further prohibited the analysis of its genome architecture. In this study, we combined third generation sequencing technology with the Hi-C chromatin conformation capture technique, to produce a high-quality and near complete genome assembly and gene annotation of a Race 5 isolate of . The resulting genome assembly contained 67.17 Mb organized into 14 chromosomes (Chr1-to-Chr14), all of which were assembled telomere-to-telomere. The smallest of the chromosomes, Chr14, is only 460 kb in size and contains 25 genes that all encode hypothetical proteins. Notably, PCR assays revealed that Chr14 was absent in 19 out of 24 isolates of a world-wide collection of , indicating that Chr14 is dispensable. Thus, is currently the second species of Capnodiales shown to harbour dispensable chromosomes. The genome of Race 5 is 49.7 % repetitive and contains 14 690 predicted genes with an estimated completeness of 98.9%, currently one of the highest among the Capnodiales. Genome structure analysis revealed a compartmentalized architecture composed of gene-dense and repeat-poor regions interspersed with gene-sparse and repeat-rich regions. Nearly 39.2 % of the Race 5 genome is affected by Repeat-Induced Point (RIP) mutations and evidence of RIP leakage toward non-repetitive regions was observed in all chromosomes, indicating the RIP plays an important role in the evolution of this pathogen. Finally, 345 genes encoding candidate effectors were identified in Race 5, with a significant enrichment of their location in gene-sparse regions, in accordance with the 'two-speed genome' model of evolution. Overall, the new reference genome of presents several notable features and is a valuable resource for studies in plant pathogens.
是一种真菌病原体，可导致番茄叶霉病。该病原体的参考基因组于 2012 年发布，但由于其高度重复的 DNA 含量，阻碍了连续组装，进一步阻止了其基因组结构的分析。在这项研究中，我们结合第三代测序技术和 Hi-C 染色质构象捕获技术，生成了一个高质量且近乎完整的 Race 5 分离株的基因组组装和基因注释。产生的基因组组装包含 67.17 Mb，组织成 14 条染色体（Chr1 到 Chr14），所有染色体均端到端组装。最小的染色体 Chr14 仅 460 kb 大小，包含 25 个基因，均编码假设蛋白。值得注意的是，PCR 检测表明，在来自全球的 24 个分离株中，有 19 个分离株缺失 Chr14，表明 Chr14 是可缺失的。因此，是目前第二个被证明含有可缺失染色体的 Capnodiales 物种。Race 5 的基因组重复率为 49.7%，包含 14690 个预测基因，估计完整性为 98.9%，是 Capnodiales 中最高的之一。基因组结构分析显示，它具有分隔的结构，由基因密集区和重复贫区与基因稀疏区和重复丰富区交错组成。Race 5 基因组的近 39.2%受到重复诱导点（RIP）突变的影响，并且在所有染色体上都观察到 RIP 向非重复区泄漏的证据，表明 RIP 在该病原体的进化中发挥了重要作用。最后，在 Race 5 中鉴定出 345 个编码候选效应子的基因，它们在基因稀疏区的位置显著富集，符合“双速基因组”进化模型。总体而言，新的 Race 5 参考基因组具有几个显著特征，是植物病原体研究的宝贵资源。
