Chromosome-level genome assembly of Lilford’s wall lizard, Podarcis lilfordi (Günther, 1874) from the Balearic Islands (Spain)

J. Gómez-Garrido, F. Cruz, T. Alioto, Nathalie Feiner, T. Uller, M. Gut, Ignacio Sanchez Escudero, G. Tavecchia, A. Rotger, Katherin Eliana Otalora Acevedo, L. Baldo
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引用次数: 1

Abstract

The Mediterranean lizard Podarcis lilfordi is an emblematic species of the Balearic Islands. The extensive phenotypic diversity among extant isolated populations makes the species a great insular model system for eco-evolutionary studies, as well as a challenging target for conservation management plans. Here we report the first high quality chromosome-level assembly and annotation of the P. lilfordi genome, along with its mitogenome, based on a mixed sequencing strategy (10X Genomics linked reads, Oxford Nanopore Technologies long reads and Hi-C scaffolding) coupled with extensive transcriptomic data (Illumina and PacBio). The genome assembly (1.5 Gb) is highly contiguous (N50 = 90 Mb) and complete, with 99% of the sequence assigned to candidate chromosomal sequences and >97% gene completeness. We annotated a total of 25,663 protein-coding genes, assigning 72% to known functions. Comparison to the genome of the related species Podarcis muralis revealed substantial similarity in genome size, annotation metrics, repeat content, and strong collinearity, despite their evolutionary distance (~18-20 MYA). This genome expands the repertoire of available reptilian genomes and will facilitate the exploration of the molecular and evolutionary processes underlying the extraordinary phenotypic diversity of this insular species, while providing a critical resource for conservation genomics.
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西班牙巴利阿里群岛利尔福德壁虎Podarcis lilfordi (g nther, 1874)的染色体水平基因组组装
地中海蜥蜴Podarcis lilfordi是巴利阿里群岛的标志性物种。在现存的孤立种群中广泛的表型多样性使该物种成为生态进化研究的一个重要的孤立模型系统,同时也是保护管理计划的一个具有挑战性的目标。在这里,我们报告了P. lilfordi基因组及其有丝分裂基因组的第一个高质量染色体水平组装和注释,基于混合测序策略(10X Genomics链接读取,Oxford Nanopore Technologies长读取和Hi-C脚手架)加上广泛的转录组数据(Illumina和PacBio)。基因组组装(1.5 Gb)是高度连续的(N50 = 90 Mb)和完整的,其中99%的序列分配给候选染色体序列,>97%的基因完整性。我们总共注释了25,663个蛋白质编码基因,其中72%为已知功能。与近缘种泥鳅(Podarcis muralis)的基因组比较发现,尽管它们的进化距离(~18-20 MYA)较远,但在基因组大小、注释指标、重复序列含量和强共线性方面存在显著的相似性。该基因组扩展了现有的爬行动物基因组库,将有助于探索这种岛屿物种非凡表型多样性背后的分子和进化过程,同时为保护基因组学提供重要资源。
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