Host-associated microbes display remarkable convergence in genome repertoire resulting from selection to supplement missing host functions. Nutritional supplementation has been proposed in the verrucomicrobial endosymbiont Xiphinematobacter sp., which lives within a globally widespread group of plant-parasitic nematodes that vector damaging nepoviruses to plants. Only one genome sequence has been published from this symbiont, leaving unanswered questions about its diversity, host range, role, and selective pressures within its hosts. Because its hosts are exceptionally resistant to culturing, this symbiont is best studied through advanced genomic approaches. To analyze the role of Xiphinematobacter sp. in its host, sequencing was performed on nematode communities, and then genomes were extracted for comparative genomics, gene ontology enrichment tests, polymorphism analysis, de Bruijn-based genome-wide association studies, and tests of pathway- and site-specific selection on genes predicted play a role in the symbiosis. Results showed a closely clustered set of Xiphinematobacter isolates with reduced genomes of ∼917 kbp, for which a new species was proposed. Symbionts shared only 2.3% of genes with outgroup Verrucomicrobia, but comparative analyses showed high conservation of all 10 essential amino acid (EAA) biosynthesis pathways plus several vitamin pathways. These findings were supported by gene ontology enrichment tests and high polymorphisms in these pathways compared with background. Genome-wide association analysis confirmed high between-species fixation of alleles with significant functional enrichment for EAA and thiamine synthesis. Strong positive selection was detected on sites within these pathways, despite several being under increased purifying selection. Together, these results suggest that supplementation of EAAs missing in the host diet may drive this widespread symbiosis.

中文翻译：

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必需氨基酸富集和正选择突出了内共生体在全球病毒载体害虫中的作用


与宿主相关的微生物在基因组库中表现出显着的趋同性，这是由于选择补充宿主缺失的功能而产生的。已提出对疣状微生物内共生菌剑线杆菌进行营养补充，该线虫生活在全球广泛分布的植物寄生线虫群中，将破坏性线虫病毒传播给植物。该共生体仅公布了一个基因组序列，关于其多样性、宿主范围、作用和宿主内的选择压力等问题尚未得到解答。由于其宿主对培养具有极强的抵抗力，因此最好通过先进的基因组方法来研究这种共生体。分析剑线杆菌属的作用。在其宿主中，对线虫群落进行测序，然后提取基因组用于比较基因组学、基因本体富集测试、多态性分析、基于 de Bruijn 的全基因组关联研究以及基因路径和位点特异性选择测试预测在共生中发挥作用。结果显示，一组紧密聚集的剑线杆菌分离株的基因组减少了~917 kbp，为此提出了一个新物种。共生体与外群疣微菌仅有 2.3% 的基因相同，但比较分析显示，所有 10 种必需氨基酸 (EAA) 生物合成途径以及多种维生素途径均高度保守。这些发现得到了基因本体富集测试和这些途径与背景相比的高多态性的支持。全基因组关联分析证实了等位基因的高度物种间固定，并且 EAA 和硫胺素合成的功能显着富集。 在这些途径内的位点上检测到强阳性选择，尽管有一些位点处于增强的纯化选择之下。总之，这些结果表明补充宿主饮食中缺失的 EAA 可能会推动这种广泛的共生。