Bedoya Ana M, Leaché Adam D
Department of Biology, University of Washington, Seattle, WA 98105, USA.
Burke Museum of Natural History and Culture, Seattle, WA 98105, USA.
G3 (Bethesda). 2021 Feb 9;11(2). doi: 10.1093/g3journal/jkab036.
Spiny lizards in the genus Sceloporus are a model system among squamate reptiles for studies of chromosomal evolution. While most pleurodont iguanians retain an ancestral karyotype formula of 2n = 36 chromosomes, Sceloporus exhibits substantial karyotype variation ranging from 2n = 22 to 46 chromosomes. We present two annotated chromosome-scale genome assemblies for the Plateau Fence Lizard (Sceloporus tristichus) to facilitate research on the role of pericentric inversion polymorphisms on adaptation and speciation. Based on previous karyotype work using conventional staining, the S. tristichus genome is characterized as 2n = 22 with six pairs of macrochromosomes and five pairs of microchromosomes and a pericentric inversion polymorphism on chromosome 7 that is geographically variable. We provide annotated, chromosome-scale genomes for two lizards located at opposite ends of a dynamic hybrid zone that are each fixed for different inversion polymorphisms. The assembled genomes are 1.84-1.87 Gb (1.72 Gb for scaffolds mapping to chromosomes) with a scaffold N50 of 267.5 Mb. Functional annotation of the genomes resulted in ∼15K predicted gene models. Our assemblies confirmed the presence of a 4.62-Mb pericentric inversion on chromosome 7, which contains 62 annotated coding genes with known functions. In addition, we collected population genomics data using double digest RAD-sequencing for 44 S. tristichus to estimate population structure and phylogeny across the Colorado Plateau. These new genomic resources provide opportunities to perform genomic scans and investigate the formation and spread of pericentric inversions in a naturally occurring hybrid zone.
强棱蜥属（Sceloporus）的多刺蜥蜴是有鳞目爬行动物中用于染色体进化研究的一个模式系统。虽然大多数侧生齿鬣蜥保留了2n = 36条染色体的祖先核型公式，但强棱蜥表现出显著的核型变异，范围从2n = 22条到46条染色体。我们展示了高原围栏蜥（Sceloporus tristichus）的两个注释后的染色体水平基因组组装，以促进对臂间倒位多态性在适应和物种形成中作用的研究。基于之前使用传统染色的核型研究工作，高原围栏蜥的基因组特征为2n = 22，有六对大染色体和五对小染色体，以及7号染色体上一个在地理上可变的臂间倒位多态性。我们为位于一个动态杂交带两端的两只蜥蜴提供了注释后的染色体水平基因组，它们各自固定为不同的倒位多态性。组装后的基因组大小为1.84 - 1.87Gb（映射到染色体的支架为1.72Gb），支架N50为267.5Mb。基因组的功能注释产生了约15000个预测基因模型。我们的组装证实了7号染色体上存在一个4.62Mb的臂间倒位，其中包含62个具有已知功能的注释编码基因。此外，我们使用双酶切RAD测序收集了44只高原围栏蜥的群体基因组数据，以估计科罗拉多高原的群体结构和系统发育。这些新的基因组资源为进行基因组扫描以及研究自然杂交带中臂间倒位的形成和传播提供了机会。
