Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA.
Department of Biology, University of South Alabama, Mobile, AL 36688, USA.
Genome Biol Evol. 2022 Jul 2;14(7). doi: 10.1093/gbe/evac082.
Despite the medical significance to humans and important ecological roles filled by vipers, few high-quality genomic resources exist for these snakes outside of a few genera of pitvipers. Here we sequence, assemble, and annotate the genome of Fea's Viper (Azemiops feae). This taxon is distributed in East Asia and belongs to a monotypic subfamily, sister to the pitvipers. The newly sequenced genome resulted in a 1.56 Gb assembly, a contig N50 of 1.59 Mb, with 97.6% of the genome assembly in contigs >50 Kb, and a BUSCO completeness of 92.4%. We found that A. feae venom is primarily composed of phospholipase A2 (PLA2) proteins expressed by genes that likely arose from lineage-specific PLA2 gene duplications. Additionally, we show that renin, an enzyme associated with blood pressure regulation in mammals and known from the venoms of two viper species including A. feae, is expressed in the venom gland at comparative levels to known toxins and is present in the venom proteome. The cooption of this gene as a toxin may be more widespread in viperids than currently known. To investigate the historical population demographics of A. feae, we performed coalescent-based analyses and determined that the effective population size has remained stable over the last 100 kyr. This suggests Quaternary glacial cycles likely had minimal influence on the demographic history of A. feae. This newly assembled genome will be an important resource for studying the genomic basis of phenotypic evolution and understanding the diversification of venom toxin gene families.
尽管蝮蛇对人类具有重要的医学意义，并且在生态中发挥着重要作用，但除了少数几种烙铁头蛇属（pitvipers）之外，关于这些蛇类的高质量基因组资源却很少。在这里，我们对费氏竹叶青（Azemiops feae）的基因组进行了测序、组装和注释。该分类单元分布于东亚，属于单型亚科，与烙铁头蛇属为姐妹群。新测序的基因组得到了 1.56Gb 的组装结果，其 contig N50 为 1.59Mb，有 97.6%的基因组组装在长度大于 50Kb 的 contig 中，BUSCO 完整性为 92.4%。我们发现，A. feae 毒液主要由磷脂酶 A2 (PLA2) 蛋白组成，这些蛋白由基因表达，而这些基因可能是由谱系特异性 PLA2 基因复制而来的。此外，我们还表明，肾素是一种与哺乳动物血压调节相关的酶，已知存在于包括 A. feae 在内的两种蝮蛇毒液中，在毒液腺中的表达水平与已知毒素相当，并且存在于毒液蛋白质组中。该基因作为毒素的共选择可能比目前已知的更为广泛存在于蝮蛇科中。为了研究 A. feae 的历史种群动态，我们进行了基于合并的分析，并确定其有效种群大小在过去 100 千年中保持稳定。这表明第四纪冰川周期对 A. feae 的种群历史可能影响很小。这个新组装的基因组将成为研究表型进化的基因组基础和理解毒液毒素基因家族多样化的重要资源。
