A whole genome duplication drives the genome evolution of Phytophthora betacei, a closely related species to Phytophthora infestans.
A whole genome duplication drives the genome evolution of Phytophthora betacei, a closely related species to Phytophthora infestans.
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DOI：
10.1186/s12864-021-08079-y
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发表时间：
2021-11-05
期刊：
影响因子：
4.4
通讯作者：
Restrepo S
中科院分区：
文献类型：
--
作者：
Ayala-Usma DA;Cárdenas M;Guyot R;Mares MC;Bernal A;Muñoz AR;Restrepo S
疫霉属病原体是几种高价值作物和林业物种（如马铃薯、番茄、可可和橡树等）中许多毁灭性疾病的病原体。甜菜疫霉是最近描述的几乎仅在树番茄中引起晚疫病的物种，并且它与在马铃薯作物和其他茄科中引起疾病的致病疫霉密切相关。本研究报告了使用长读SMRT测序技术组装和注释其第一个物种P. betacei P8084和来自EC-1谱系的哥伦比亚菌株P. infestans RC 1 -10的基因组。我们的研究结果表明，P. betacei具有迄今为止最大的疫霉属的测序基因组大小为270 Mb。与致病疫霉相比，中度转座因子入侵和全基因组复制可能解释了其基因组大小的扩展，而致病疫霉RC 1 -10在转座因子的活性下扩展了其基因组。致病疫霉RC 1 -10中分类和未分类的转座因子相对于甜菜疫霉的高多样性和丰度（就拷贝数而言）证明了长读技术发现生物体基因组中新的重复因子的能力。我们的数据还支持了贝氏疟原虫作为一个独立物种和作为致病疫霉的姐妹群的系统发育位置。最后，我们发现没有证据支持P. betacei P8084的基因组遵循与P. infestans和其他丝状植物病原体相同的基因密集/基因稀疏结构的想法。这项研究提供了第一个全基因组范围的P. betacei图片，并扩大了P. infestans的基因组资源。这是一个贡献的基因组生物学的理解和进化史的疫霉属物种属于亚支1c。在线版本包含补充材料，可在10.1186/s12864-021-08079-y获得。
Pathogens of the genus Phytophthora are the etiological agents of many devastating diseases in several high-value crops and forestry species such as potato, tomato, cocoa, and oak, among many others. Phytophthora betacei is a recently described species that causes late blight almost exclusively in tree tomatoes, and it is closely related to Phytophthora infestans that causes the disease in potato crops and other Solanaceae. This study reports the assembly and annotation of the genomes of P. betacei P8084, the first of its species, and P. infestans RC1-10, a Colombian strain from the EC-1 lineage, using long-read SMRT sequencing technology. Our results show that P. betacei has the largest sequenced genome size of the Phytophthora genus so far with 270 Mb. A moderate transposable element invasion and a whole genome duplication likely explain its genome size expansion when compared to P. infestans, whereas P. infestans RC1-10 has expanded its genome under the activity of transposable elements. The high diversity and abundance (in terms of copy number) of classified and unclassified transposable elements in P. infestans RC1-10 relative to P. betacei bears testimony of the power of long-read technologies to discover novel repetitive elements in the genomes of organisms. Our data also provides support for the phylogenetic placement of P. betacei as a standalone species and as a sister group of P. infestans. Finally, we found no evidence to support the idea that the genome of P. betacei P8084 follows the same gene-dense/gense-sparse architecture proposed for P. infestans and other filamentous plant pathogens. This study provides the first genome-wide picture of P. betacei and expands the genomic resources available for P. infestans. This is a contribution towards the understanding of the genome biology and evolutionary history of Phytophthora species belonging to the subclade 1c. The online version contains supplementary material available at 10.1186/s12864-021-08079-y.
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