Graduate School of Life Sciences, Tohoku University, Sendai, Japan.
National Museum of Natural History of Cuba, Havana, Cuba.
BMC Ecol Evol. 2022 Nov 4;22(1):129. doi: 10.1186/s12862-022-02086-7.
Detecting genomic variants and their accumulation processes during species diversification and adaptive radiation is important for understanding the molecular and genetic basis of evolution. Anolis lizards in the West Indies are good models for studying evolutionary mechanisms because of the repeated evolution of their morphology and the ecology. We performed de novo genome assembly of six Cuban Anolis lizards with different ecomorphs and thermal habitats (Anolis isolepis, Anolis allisoni, Anolis porcatus, Anolis allogus, Anolis homolechis, and Anolis sagrei). We carried out a comparative analysis of these genome assemblies to investigate the genetic changes that occurred during their diversification.
We reconstructed novel draft genomes with relatively long scaffolds and high gene completeness, with the scaffold N50 ranging from 5.56 to 39.79 Mb and vertebrate Benchmarking Universal Single-Copy Orthologs completeness ranging from 77.5% to 86.9%. Comparing the repeat element compositions and landscapes revealed differences in the accumulation process between Cuban trunk-crown and trunk-ground species and separate expansions of several families of LINE in each Cuban trunk-ground species. Duplicated gene analysis suggested that the proportional differences in duplicated gene numbers among Cuban Anolis lizards may be associated with differences in their habitat ranges. Additionally, Pairwise Sequentially Markovian Coalescent analysis suggested that the effective population sizes of each species may have been affected by Cuba's geohistory.
We provide draft genomes of six Cuban Anolis lizards and detected species and lineage-specific transposon accumulation and gene copy number changes that may be involved in adaptive evolution. The change processes in the past effective population size was also estimated, and the factors involved were inferred. These results provide new insights into the genetic basis of Anolis lizard diversification and are expected to serve as a stepping stone for the further elucidation of their diversification mechanisms.
在物种多样化和适应性辐射过程中检测基因组变异及其积累过程对于理解进化的分子和遗传基础非常重要。西印度群岛的鬣蜥是研究进化机制的良好模型，因为它们的形态和生态多次进化。我们对六种具有不同生态型和热生境的古巴鬣蜥（Anolis isolepis、Anolis allisoni、Anolis porcatus、Anolis allogus、Anolis homolechis 和 Anolis sagrei）进行了从头基因组组装。我们对这些基因组组装进行了比较分析，以研究它们在多样化过程中发生的遗传变化。
我们重建了具有相对较长支架和较高基因完整性的新型草图基因组，支架 N50 范围从 5.56 到 39.79 Mb，脊椎动物基准通用单拷贝直系同源物完整性范围从 77.5%到 86.9%。比较重复元件组成和景观揭示了古巴干冠和干地物种之间积累过程的差异，以及每个古巴干地物种中几个 LINE 家族的单独扩张。重复基因分析表明，古巴鬣蜥中重复基因数量的比例差异可能与其栖息地范围的差异有关。此外，成对顺序马尔可夫合并分析表明，每个物种的有效种群大小可能受到古巴地质历史的影响。
我们提供了六种古巴鬣蜥的草图基因组，并检测到物种和谱系特异性转座子积累和基因拷贝数变化，这些变化可能参与了适应性进化。还估计了过去有效种群大小的变化过程，并推断了涉及的因素。这些结果为鬣蜥多样化的遗传基础提供了新的见解，并有望成为进一步阐明其多样化机制的垫脚石。
