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

IF 3 2区 生物学 Q2 EVOLUTIONARY BIOLOGY Journal of Heredity Pub Date : 2024-12-20 DOI:10.1093/jhered/esae075
Marissa A Roseman, Andrew J Mason, Emily R Bode, Peri E Bolton, Pedro G Nachtigall, William E Peterman, H Lisle Gibbs
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Abstract

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. 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 suggests 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.

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来源期刊
Journal of Heredity
Journal of Heredity 生物-遗传学
CiteScore
5.20
自引率
6.50%
发文量
63
审稿时长
6-12 weeks
期刊介绍: Over the last 100 years, the Journal of Heredity has established and maintained a tradition of scholarly excellence in the publication of genetics research. Virtually every major figure in the field has contributed to the journal. Established in 1903, Journal of Heredity covers organismal genetics across a wide range of disciplines and taxa. Articles include such rapidly advancing fields as conservation genetics of endangered species, population structure and phylogeography, molecular evolution and speciation, molecular genetics of disease resistance in plants and animals, genetic biodiversity and relevant computer programs.
期刊最新文献
Insights from the timber rattlesnake (Crotalus horridus) genome for MHC gene architecture and evolution in threatened rattlesnakes. A chromosome-level genome of the giant vinegaroon Mastigoproctus giganteus exhibits the signature of pre-Silurian whole genome duplication. Chromosome-level genome assembly of the king horseshoe bat (Rhinolophus rex) provides insights into its conservation status and chromosomal evolution of Rhinolophus. Development of a panel of SNP loci in the emblematic southern damselfly (Coenagrion mercuriale) using a hybrid method: pitfalls and recommendations for large-scale SNP genotyping in a non-model endangered species. "Genome Assembly Of The Winter Ant, Prenolepis Imparis".
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