Maximum haplotype assembly of Rotaria macrura. Maximum haplotype assemblies were generated with a focus on maximising the separate assembly of heterozygous regions (ie, minimum assembly collapse).. Maximum haplotype assembly of Rotaria macrura

Bdelloid rotifers are microscopic invertebrates that have existed for millions of years apparently without sex or meiosis. They inhabit a variety of temporary and permanent freshwater habitats globally, and many species are remarkably tolerant of desiccation. Bdelloids offer an opportunity to better understand the evolution of sex and recombination, but previous work has emphasized desiccation as the cause of several unusual genomic features in this group. Here, we evaluate the relative effects of asexuality and desiccation tolerance on genome evolution by comparing whole genome sequences for three bdelloid species: Adineta ricciae (desiccation tolerant), Rotaria macrura and Rotaria magnacalcarata (both desiccation intolerant) to the only published bdelloid genome to date, that of Adineta vaga (also desiccation tolerant). We find that tetraploidy is conserved among all four bdelloid species, but homologous divergence in obligately aquatic Rotaria genomes is low, well within the range observed between alleles in obligately sexual, diploid animals. In addition, we find that homologous regions in A. ricciae are largely collinear and do not form palindromic repeats as observed in the published A. vaga assembly. These findings are contrary to current understanding of the role of desiccation in shaping the bdelloid genome, and indicate that various features interpreted as genomic evidence for long-term ameiotic evolution are not general to all bdelloid species, even within the same genus. Finally, we substantiate previous findings of high levels of horizontally transferred non-metazoan genes encoded in both desiccating and non-desiccating bdelloid species, and show that this is a unique feature of bdelloids among related animal phyla. Comparisons within bdelloids and to other desiccation-tolerant animals, however, again call into question the purported role of desiccation in horizontal transfer.

蛭形轮虫（bdelloid rotifers）是一类已存续数百万年的微观无脊椎动物，其生存过程中似乎从未经历有性生殖或减数分裂（meiosis）。该类群广泛栖息于全球各类暂时性及永久性淡水生境中，多数物种对脱水（desiccation）具备极强的耐受能力。蛭形轮虫为深入解析有性生殖与重组的演化机制提供了重要研究契机，但此前的相关研究多将该类群的多项异常基因组特征归因于脱水耐受效应。
本研究通过比对3种蛭形轮虫的全基因组序列——即耐脱水的*Adineta ricciae*、以及不耐脱水的*Rotaria macrura*与*Rotaria magnacalcarata*——并与迄今唯一已发表的蛭形轮虫基因组（*Adineta vaga*，同样耐脱水）进行对比，评估了无性生殖与脱水耐受各自对基因组演化的相对影响。
研究结果显示，四倍体性（tetraploidy）在全部4种蛭形轮虫中均保守存在，但专性水生的*Rotaria*属轮虫基因组的同源序列分化程度较低，完全处于专性有性生殖二倍体动物的等位基因分化区间内。此外，*A. ricciae*的同源区域整体呈现共线性，并未如已发表的*A. vaga*基因组组装结果那样形成回文重复序列（palindromic repeats）。
上述发现与当前学界关于脱水耐受在塑造蛭形轮虫基因组过程中所起作用的认知相悖，表明此前被解读为长期无减数分裂进化（ameiotic evolution）基因组证据的多项特征，并非所有蛭形轮虫类群所共有——即便在同一属内亦是如此。最后，本研究验证了此前的发现：无论是耐脱水还是不耐脱水的蛭形轮虫，其基因组中均编码大量水平转移的非后生动物基因（horizontally transferred non-metazoan genes）；且相较于其他相关动物门类（animal phyla），这一特征为蛭形轮虫所独有。不过，通过对蛭形轮虫内部以及与其他耐脱水动物的比较分析，我们再次对脱水耐受在水平基因转移过程中的假定作用提出了质疑。