Roseman Marissa A, Mason Andrew J, Bode Emily R, Bolton Peri E, Nachtigall Pedro G, Peterman William E, Gibbs H Lisle
School of Environment and Natural Resources, The Ohio State University, Columbus, OH, United States.
Ohio Biodiversity Conservation Partnership, The Ohio State University, Columbus, OH, United States.
J Hered. 2025 Aug 23;116(5):591-602. doi: 10.1093/jhered/esae075.
Conservation of threatened species can benefit from an evaluation of genes in the major histocompatibility complex (MHC), whose loci encode proteins that bind pathogens and are often under strong selection to maintain diversity in immune response to diseases. Despite this gene family's importance to disease resistance, little is known about these genes in reptiles including snakes. To address this issue, we assembled and annotated a highly contiguous genome assembly for the timber rattlesnake (Crotalus horridus), a pit viper which is threatened or endangered in parts of its range, and analyzed this new genome along with three other rattlesnake genomes to characterize snake MHC loci. We identified highly duplicated MHC Class I and Class IIβ genes in all species typified by a genomic architecture of discrete gene clusters localized on chromosome 2. The number of loci varied between species from 14 to 23 for MHC I and from 8 to 32 for MHC IIβ and was greater than previously identified in the few non-genome-based studies of reptile MHC to date. We present evidence of the gene family's complex evolutionary history, with extensive duplication and loss concurrent with speciation resulting in incomplete lineage sorting. The differences in gene number between species combined with a dynamic evolutionary history suggest that gene family expansion/contraction via rapid duplication/gene loss may represent an important mechanism for generating genetic diversity in rattlesnake MHC. Our work demonstrates the utility of whole-genome sequences for identifying functional genetic variation in the form of MHC genes relevant for conservation genomic studies in threatened snakes.
对濒危物种的保护可受益于对主要组织相容性复合体（MHC）中基因的评估，该复合体的基因座编码与病原体结合的蛋白质，并且通常受到强烈选择以维持对疾病免疫反应的多样性。尽管这个基因家族对疾病抗性很重要，但在包括蛇类在内的爬行动物中，人们对这些基因却知之甚少。为了解决这个问题，我们组装并注释了东部菱斑响尾蛇（Crotalus horridus）的高度连续的基因组序列，它是一种蝰蛇，在其分布范围的部分地区受到威胁或濒临灭绝。我们分析了这个新基因组以及其他三种响尾蛇基因组，以表征蛇类的MHC基因座。我们在所有物种中都鉴定出了高度重复的MHC I类和IIβ类基因，其典型特征是位于2号染色体上的离散基因簇的基因组结构。不同物种的基因座数量有所不同，MHC I为14至23个，MHC IIβ为8至32个，这一数量比之前在少数基于非基因组的爬行动物MHC研究中所确定的数量更多。我们提供了该基因家族复杂进化历史的证据，即广泛的复制和丢失与物种形成同时发生，导致不完全的谱系分选。物种间基因数量的差异以及动态的进化历史表明，通过快速复制/基因丢失实现的基因家族扩张/收缩可能是响尾蛇MHC中产生遗传多样性的重要机制。我们的工作证明了全基因组序列在识别与濒危蛇类保护基因组研究相关的MHC基因形式的功能遗传变异方面的实用性。
