Phytopathology-Applied Microbiology, Earth and Life Institute, UCLouvain, Louvain-la-Neuve, Belgium.
State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, 315211 Ningbo, China.
Genomics. 2022 Jan;114(1):9-22. doi: 10.1016/j.ygeno.2021.11.018. Epub 2021 Nov 16.
Genomic knowledge of the tree of life is biased to specific groups of organisms. For example, only six full genomes are currently available in the rhizaria clade. Here, we have applied metagenomic techniques enabling the assembly of the genome of Polymyxa betae (Rhizaria, Plasmodiophorida) RES F41 isolate from unpurified zoospore holobiont and comparison with the A26-41 isolate. Furthermore, the first P. betae mitochondrial genome was assembled. The two P. betae nuclear genomes were highly similar, each with just ~10.2 k predicted protein coding genes, ~3% of which were unique to each isolate. Extending genomic comparisons revealed a greater overlap with Spongospora subterranea than with Plasmodiophora brassicae, including orthologs of the mammalian cation channel sperm-associated proteins, raising some intriguing questions about zoospore physiology. This work validates our metagenomics pipeline for eukaryote genome assembly from unpurified samples and enriches plasmodiophorid genomics; providing the first full annotation of the P. betae genome.
生物进化树的基因组知识偏向于特定的生物群体。例如，根肿菌门中目前仅有 6 个完整基因组。在这里，我们应用宏基因组技术，成功组装了来自未纯化游动孢子共生体的野油菜根肿菌 F41 分离株 Polymyxa betae（根肿菌门、根肿菌纲）的基因组，并与 A26-41 分离株进行了比较。此外，我们还组装了第一个野油菜根肿菌的线粒体基因组。两个野油菜根肿菌的核基因组高度相似，每个基因组都有约 10.2 k 个预测的蛋白质编码基因，其中约 3%是每个分离株特有的。扩展基因组比较发现，与 Plasmodiophora brassicae 相比，野油菜根肿菌与 Spongospora subterranea 的重叠更多，包括哺乳动物阳离子通道精子相关蛋白的同源物，这引发了一些关于游动孢子生理学的有趣问题。这项工作验证了我们用于从未纯化样本组装真核生物基因组的宏基因组学管道，并丰富了根肿菌门的基因组学；提供了野油菜根肿菌基因组的第一个完整注释。
