Journal of Heredity

Powell, Daniel; Jackson, Nicola; Kaur, Parwinder; Dudchenko, Olga; Aiden, Erez Lieberman; Georges, Arthur; Frère, Céline Henria

doi: 10.1093/jhered/esae054pmid: 39364696

Squamate reptiles are a highly diverse and intriguing group of tetrapods, offering valuable insights into the evolution of amniotes. The Australian water dragon (Intellagama lesueurii) is a member of the Agamidae and sister to the core mesic Australian endemic radiation (Amphibolurinae). The species is renowned for its urban adaptability and complex social systems. We report a 1.8 Gb chromosome-length genome assembly together with the annotation of 23,675 protein-coding genes. Comparative analysis with other squamate genomes highlights gene family expansions associated with immune function, energetic homeostasis, and wound healing. This reference genome will serve as a valuable resource for studies of evolution and environmental resilience in lizards.

Andjel, Lucija; Kratochvíl, Lukáš; Rovatsos, Michail

doi: 10.1093/jhered/esae070pmid: 39575506

The faster-X/Z effect hypothesis states that genes linked to X/Z chromosomes should accumulate mutations faster than autosomal genes. Although faster evolution of X/Z-linked genes has been reported in several plant and animal lineages, conflicting results have been reported in others. We examined the faster-Z effect in chameleons of the genus Furcifer, a lineage with differentiated ZZ/ZW chromosomes for at least 20 million yr. We sequenced the genomes of four species of Furcifer chameleons in the Illumina platform and compared the substitution rates of synonymous and non-synonymous mutations and their ratios among autosomal, Z-specific, and pseudoautosomal protein-coding genes. The inclusion of two chameleon outgroups lacking the differentiated ZZ/ZW sex chromosomes allowed us to control for gene-specific evolutionary rates that might confound the testing of the faster-X/Z effect. Significant differences in evolutionary rates were found between autosomal, Z-specific, and pseudoautosomal genes of Furcifer chameleons. However, the inclusion of the outgroups with different sex chromosomes suggests that these genes had different evolutionary rates prior to their incorporation into the differentiated ZZ/ZW sex chromosomes of the Furcifer genus. The results highlight the need to control for differences in the evolutionary rates of individual genes when testing for the faster-X/Z effect.

Roseman, Marissa A; Mason, Andrew J; Bode, Emily R; Bolton, Peri E; Nachtigall, Pedro G; Peterman, William E; Gibbs, H Lisle

doi: 10.1093/jhered/esae075pmid: 39704347

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.