Yu Min, Zhang Dong, Zhao Xumao
State Key Laboratory of Grassland Agro-Ecosystems, and College of Ecology, Lanzhou University, Lanzhou 730000, China.
State Key Laboratory of Grassland Agro-Ecosystems, and College of Ecology, Lanzhou University, Lanzhou 730000, China.
Gene. 2022 Oct 5;840:146761. doi: 10.1016/j.gene.2022.146761. Epub 2022 Jul 26.
Gene order has been utilized as a phylogenetic signal for many taxa. However, its phylogenetic performance has not been evaluated in Nematoda. As there is only one nematode mitogenome available to date, in the Diplogasteridae family, we sequenced the mitogenome of Allodiplogaster sp. and constructed a phylogeny for Nematoda using this updated mitogenome dataset. We then compared this phylogeny to one constructed using gene order. The complete mitochondrial genome of Allodiplogaster sp. was 13,953 bp in size and included 22 tRNAs, two rRNAs, and 12 protein-coding genes. To assess how Allodiplogaster sp. is related to other nematode species, we used Bayesian inference and maximum likelihood algorithms to construct phylogenetic trees of the Nematoda. We found that: 1) The target species Allodiplogaster sp. is closely related to Allodiplogaster sudhausi. The topology of the mitogenome based phylogeny was nearly identical to previous phylogenies created using 18S rRNA data, except for the placement of the Strongyloididae family. 2) The maximum likelihood tree constructed using gene order was roughly consistent with the mitogenome-based tree at the family level, but not at the species level. 3) Protein-coding genes were ordered differently in Allodiplogaster sp. versus Allodiplogaster sudhausi; this represents the first report of such a reordering in the class Chromadorea in our study. Our study confirms that gene order represents useful phylogenetic information for the Nematoda: the maximum likelihood tree based on gene order provided additional support for the nematode phylogeny constructed using molecular data.
基因顺序已被用作许多分类单元的系统发育信号。然而，其在系统发育方面的表现尚未在线虫纲中得到评估。由于迄今为止在双胃线虫科中仅有一个线虫线粒体基因组可用，我们对异双胃线虫属物种的线粒体基因组进行了测序，并使用这个更新的线粒体基因组数据集构建了线虫纲的系统发育树。然后，我们将这个系统发育树与使用基因顺序构建的系统发育树进行了比较。异双胃线虫属物种的完整线粒体基因组大小为13,953 bp，包括22个tRNA、两个rRNA和12个蛋白质编码基因。为了评估异双胃线虫属物种与其他线虫物种的关系，我们使用贝叶斯推断和最大似然算法构建了线虫纲的系统发育树。我们发现：1）目标物种异双胃线虫属物种与苏氏异双胃线虫密切相关。基于线粒体基因组的系统发育树的拓扑结构与之前使用18S rRNA数据创建的系统发育树几乎相同，只是类圆线虫科的位置有所不同。2）使用基因顺序构建的最大似然树在科级水平上与基于线粒体基因组的树大致一致，但在种级水平上不一致。3）异双胃线虫属物种与苏氏异双胃线虫的蛋白质编码基因顺序不同；这是我们研究中关于色矛纲此类重排的首次报道。我们的研究证实，基因顺序代表了线虫纲有用的系统发育信息：基于基因顺序的最大似然树为使用分子数据构建的线虫系统发育树提供了额外支持。
