German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, 04103, Germany.
Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstrasse 16-18, Leipzig, 04107, Germany.
Gigascience. 2019 Feb 1;8(2). doi: 10.1093/gigascience/giy160.
Lacerta viridis and Lacerta bilineata are sister species of European green lizards (eastern and western clades, respectively) that, until recently, were grouped together as the L. viridis complex. Genetic incompatibilities were observed between lacertid populations through crossing experiments, which led to the delineation of two separate species within the L. viridis complex. The population history of these sister species and processes driving divergence are unknown. We constructed the first high-quality de novo genome assemblies for both L. viridis and L. bilineata through Illumina and PacBio sequencing, with annotation support provided from transcriptome sequencing of several tissues. To estimate gene flow between the two species and identify factors involved in reproductive isolation, we studied their evolutionary history, identified genomic rearrangements, detected signatures of selection on non-coding RNA, and on protein-coding genes.
Here we show that gene flow was primarily unidirectional from L. bilineata to L. viridis after their split at least 1.15 million years ago. We detected positive selection of the non-coding repertoire; mutations in transcription factors; accumulation of divergence through inversions; selection on genes involved in neural development, reproduction, and behavior, as well as in ultraviolet-response, possibly driven by sexual selection, whose contribution to reproductive isolation between these lacertid species needs to be further evaluated.
The combination of short and long sequence reads resulted in one of the most complete lizard genome assemblies. The characterization of a diverse array of genomic features provided valuable insights into the demographic history of divergence among European green lizards, as well as key species differences, some of which are candidates that could have played a role in speciation. In addition, our study generated valuable genomic resources that can be used to address conservation-related issues in lacertids.
绿蜥蜴和双领蜥蜴是欧洲绿蜥蜴的姐妹种（分别为东部和西部进化枝），直到最近，它们还被归为绿蜥蜴复合体。通过杂交实验观察到蜥蜴种群之间存在遗传不相容性，这导致在绿蜥蜴复合体中划分出两个独立的物种。这两个姐妹种的种群历史和导致分化的过程尚不清楚。我们通过 Illumina 和 PacBio 测序构建了这两个物种的第一个高质量从头基因组组装，并通过对几种组织的转录组测序提供了注释支持。为了估计两个物种之间的基因流动并识别参与生殖隔离的因素，我们研究了它们的进化历史，鉴定了基因组重排，检测了非编码 RNA 和蛋白质编码基因的选择信号。
在这里，我们表明，自至少 115 万年前这两个物种分裂以来，基因流动主要是从双领蜥蜴单向流向绿蜥蜴。我们检测到非编码序列的正选择；转录因子的突变；通过倒位积累的分歧；涉及神经发育、生殖和行为的基因以及紫外线反应的选择，这些选择可能受到性选择的驱动，需要进一步评估其对这些蜥蜴种间生殖隔离的贡献。
短读长和长读长的组合产生了最完整的蜥蜴基因组组装之一。多样化的基因组特征的特征描述为欧洲绿蜥蜴的分化提供了有价值的见解，包括关键的物种差异，其中一些可能是在物种形成中发挥作用的候选者。此外，我们的研究产生了有价值的基因组资源，可用于解决蜥蜴类的保护相关问题。
