Department of Herpetology, American Museum of Natural History, New York, NY 10024, USA.
INBRE Data Science Core, University of Wyoming, Laramie, WY 82071, USA.
G3 (Bethesda). 2023 Aug 9;13(8). doi: 10.1093/g3journal/jkad113.
The number of reference genomes of snakes lags behind several other vertebrate groups (e.g. birds and mammals). However, in the last two years, a concerted effort by researchers from around the world has produced new genomes of snakes representing members from several new families. Here, we present a high-quality, annotated genome of the central ratsnake (Pantherophis alleghaniensis), a member of the most diverse snake lineage, Colubroidea. Pantherophis alleghaniensis is found in the central part of the Nearctic, east of the Mississippi River. This genome was sequenced using 10X Chromium synthetic long reads and polished using Illumina short reads. The final genome assembly had an N50 of 21.82 Mb and an L50 of 22 scaffolds with a maximum scaffold length of 82.078 Mb. The genome is composed of 49.24% repeat elements dominated by long interspersed elements. We annotated this genome using transcriptome assemblies from 14 tissue types and recovered 28,368 predicted proteins. Finally, we estimated admixture proportions between two species of ratsnakes and discovered that this specimen is an admixed individual containing genomes from the western (Pantherophis obsoletus) and central ratsnakes (P. alleghaniensis). We discuss the importance of considering interspecific admixture in downstream approaches for inferring demography and phylogeny.
蛇类的参考基因组数量落后于其他几个脊椎动物群体（例如鸟类和哺乳动物）。然而，在过去的两年中，来自世界各地的研究人员共同努力，产生了新的蛇类基因组，代表了几个新家族的成员。在这里，我们展示了一种高质量的、注释过的中央鼠蛇（ Pantherophis alleghaniensis ）基因组，中央鼠蛇是多样性最高的蛇类谱系 Colubroidea 的成员。 Pantherophis alleghaniensis 分布在北美中部，密西西比河以东。该基因组是使用 10X Chromium 合成长读长测序的，并使用 Illumina 短读长进行了优化。最终基因组组装的 N50 为 21.82Mb，L50 为 22 个支架，最大支架长度为 82.078Mb。基因组由 49.24%的重复元件组成，主要是长散布元件。我们使用来自 14 种组织类型的转录组组装来注释这个基因组，共预测到 28368 个蛋白质。最后，我们估计了两种鼠蛇之间的混合物比例，并发现这个标本是一个混合个体，包含了西部（ Pantherophis obsoletus ）和中央鼠蛇（ P. alleghaniensis ）的基因组。我们讨论了在推断种群历史和系统发育的下游方法中考虑种间混合的重要性。
