Insights from the timber rattlesnake (<em>Crotalus horridus</em>) genome for MHC gene architecture and evolution in threatened rattlesnakes

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/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. 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 ..., , , # Insights from the timber rattlesnake (Crotalus horridus) genome for MHC gene architecture and evolution in threatened rattlesnakes

[https://doi.org/10.5061/dryad.z612jm6nd](https://doi.org/10.5061/dryad.z612jm6nd)

## Description of the data and file structure

This dataset contains files produced and used for analyses in Roseman et al. to characterize major histocompatibility (MHC) genes in several rattlesnake species. While intermediate files can be generated from the code available at [https://github.com/marissaroseman/Rattlesnake_MHC](https://github.com/marissaroseman/Rattlesnake_MHC) using genome data published on NCBI (see Supplemental Table S3 for GenBank accession numbers). Major files for replicating the analysis or conducting similar studies are included here. These include:

* A database of MHC coding sequences annotated in other reptile species (**Reptile_MHC_Database.fasta**)

- Sequence alignments of MHC I and IIB genes for the four studied rattlesnake species (**MHCI_4...

受威胁物种的保护工作可借助对主要组织相容性复合体（Major Histocompatibility Complex, MHC）基因的评估得以推进——该复合体的基因座编码可结合病原体的蛋白质，且通常处于强烈的选择压力之下，以维持疾病免疫应答的多样性。尽管该基因家族对疾病抗性至关重要，但包括蛇类在内的爬行类中这类基因的相关研究仍较为匮乏。为解决这一问题，本研究对森林响尾蛇（Crotalus horridus）——一种在其分布部分区域处于受威胁或濒危状态的蝰科蝮亚科蛇类——进行了高连续性基因组组装与注释，并结合另外三种响尾蛇的基因组开展分析，以解析蛇类MHC基因座的特征。本研究在所有物种中均鉴定出大量重复的MHC I类和IIβ类基因，其基因组架构表现为定位于2号染色体上的离散基因簇。不同物种的MHC I类基因座数量介于14至23之间，MHC IIβ类基因座数量介于8至32之间，均多于此前少数已报道的结果……# 基于森林响尾蛇（Crotalus horridus）基因组解析受威胁响尾蛇的MHC基因结构与演化

[https://doi.org/10.5061/dryad.z612jm6nd](https://doi.org/10.5061/dryad.z612jm6nd)

## 数据集与文件结构说明

本数据集包含Roseman等人在多项研究中用于解析多种响尾蛇主要组织相容性复合体（MHC）基因的相关分析文件。中间文件可通过NCBI公开的基因组数据，结合[https://github.com/marissaroseman/Rattlesnake_MHC](https://github.com/marissaroseman/Rattlesnake_MHC)仓库中的代码生成（GenBank登录号详见补充表S3）。本数据集包含用于复现该分析或开展同类研究的核心文件，具体包括：
* 其他爬行类物种中注释得到的MHC编码序列数据库（**Reptile_MHC_Database.fasta**）
- 四种研究用响尾蛇的MHC I类与IIB类基因序列比对文件（**MHCI_4...**）