Nematodes are a widespread and diverse group comprising free-living and parasitic species, some of which have major detrimental effects on crops, animals, and human health. Genomic comparisons of nematodes may help reveal the genetic bases for the evolution of parasitic lifestyles. Fatty acid and retinol-binding proteins (FARs) are thought to be unique to nematodes and play essential roles in their development, reproduction, infection, and possibly parasitism through promoting the uptake, transport, and distribution of lipid and retinol. However, the evolution of FAR family proteins across the phylum Nematoda remains elusive. We report here the evolutionary relationship of the FAR gene family across nematodes. No FAR was found in Trichocephalida species and Romanomermis culicivorax from Clade I, and FAR could be found in species from Clades III, IV, and V. FAR proteins are conserved in Clade III species and separated into three clusters. Tandem duplications and high divergence events lead to variable richness and low homology of FARs in Steinernema of Clade IVa, Strongyloides of Clade IVb, and intestinal parasitic nematodes from Clades Vc and Ve. Moreover, different richness and sequence variations of FARs in pine wood, root-knot, stem, and cyst nematodes might be determined by reproduction mode or parasitism. However, murine lungworm Angiostrongylus and bovine lungworm Dictyocaulus viviparus from Clade Vd have only 3–4 orthologs of FAR. RNA-seq data showed that far genes, especially far-1 and far-2, were highly expressed in most nematodes. Angiostrongylus cantonensis FAR-1 and FAR-3 have low sequence homology and distinct ligand-binding properties, leading to differences in the cavity volume of proteins. These data indicate that FAR proteins diverged early and experienced low selective pressure to form genus-level diversity. The far genes are present in endophyte or root-colonized bacteria of Streptomyces, Kitasatospora sp., Bacillus subtilis, and Lysobacter, suggesting that bacterial far genes might be derived from plant-parasitic nematodes by horizontal gene transfer. Data from these comparative analyses have provided insights into genus-level diversity of FAR proteins in the phylum Nematoda. FAR diversification provides a glimpse into the complicated evolution history across free-living and parasitic nematodes.

中文翻译：

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FAR蛋白的属级进化关系反映了自由生活和寄生线虫生活方式的多样性

线虫是一个广泛而多样的群体，包括自由生活和寄生物种，其中一些对作物、动物和人类健康具有重大不利影响。线虫的基因组比较可能有助于揭示寄生生活方式进化的遗传基础。脂肪酸和视黄醇结合蛋白 (FAR) 被认为是线虫独有的，通过促进脂质和视黄醇的摄取、运输和分布，在其发育、繁殖、感染和可能的寄生中发挥重要作用。然而，FAR 家族蛋白在线虫门中的进化仍然难以捉摸。我们在这里报告 FAR 基因家族在线虫中的进化关系。在进化枝 I 的 Trichocephalida 物种和 Romanomermis culicivorax 中没有发现 FAR，而在进化枝 III 的物种中可以发现 FAR，IV 和 V. FAR 蛋白在进化枝 III 物种中是保守的，并分成三个簇。串联重复和高分化事件导致 FAR 在进化枝 IVa 的 Steinerema、进化枝 IVb 的类圆线虫和进化枝 Vc 和 Ve 的肠道寄生线虫中的可变丰富度和低同源性。此外，松材线虫、根结线虫、茎线虫和胞囊线虫中FARs的不同丰富度和序列变异可能由繁殖方式或寄生方式决定。然而，来自 Clade Vd 的鼠肺虫 Angiostrongylus 和牛肺虫 Dictyocaulus viviparus 只有 3-4 个 FAR 直系同源物。RNA-seq 数据显示 far 基因，尤其是 far-1 和 far-2，在大多数线虫中高度表达。广州管圆线虫 FAR-1 和 FAR-3 具有低序列同源性和独特的配体结合特性，导致蛋白质空腔体积的差异。这些数据表明，FAR 蛋白早期分化并经历了低选择压力以形成属水平的多样性。far 基因存在于链霉菌属、北孢子菌属、枯草芽孢杆菌和溶菌属的内生菌或根定殖细菌中，这表明细菌 far 基因可能通过水平基因转移从植物寄生线虫中获得。来自这些比较分析的数据提供了对线虫门中 FAR 蛋白属级多样性的见解。FAR 多样化提供了对自由生活和寄生线虫复杂进化历史的一瞥。far 基因存在于链霉菌属、北孢子菌属、枯草芽孢杆菌和溶菌属的内生菌或根定殖细菌中，这表明细菌 far 基因可能通过水平基因转移从植物寄生线虫中获得。来自这些比较分析的数据提供了对线虫门中 FAR 蛋白属级多样性的见解。FAR 多样化提供了对自由生活和寄生线虫复杂进化历史的一瞥。far 基因存在于链霉菌属、北孢子菌属、枯草芽孢杆菌和溶菌属的内生菌或根定殖细菌中，这表明细菌 far 基因可能通过水平基因转移从植物寄生线虫中获得。来自这些比较分析的数据提供了对线虫门中 FAR 蛋白属级多样性的见解。FAR 多样化提供了对自由生活和寄生线虫复杂进化历史的一瞥。