A revised leopard gecko (Eublepharis macularius) reference genome. Eublepharis macularius

As genomic resources across squamate reptiles (lizards and snakes) have lagged behind other vertebrate systems, such as birds and mammals, high quality reference genomes across the group are scarce. Indeed, of the 23 chromosome-scale reference genomes across the order only 12 of the ~60 squamate families are represented. Within geckos (infraorder Gekkota), a species-rich clade of lizards, chromosome-level genomes are exceptionally sparse representing only two of the seven extant gecko families. Using the latest advances in genome sequencing and assembly methods, we add a gekkotan third family to this list by generating an updated reference genome for the leopard gecko, Eublepharis macularius (Eublepharidae). This updated reference genome, sequenced using PacBio HiFi, was assembled into only 132 contigs and was further scaffolded using HiC data into 75 total scaffolds, with all 19 chromosomes represented. We determined that 9 of the 19 chromosomes were assembled as single contigs, while the other 10 chromosomes were scaffolded together from two or more contigs.

由于有鳞目爬行动物（蜥蜴和蛇）的基因组学资源相较于鸟类、哺乳类等其他脊椎动物类群仍存在显著滞后，该类群的高质量参考基因组资源极为匮乏。事实上，在该目已发布的23个染色体级参考基因组中，仅覆盖了约60个有鳞目科中的12个。作为物种多样性丰富的蜥蜴演化支，壁虎（壁虎亚目Gekkota）的染色体级参考基因组同样极度稀缺，仅覆盖了现存7个壁虎科中的2个。本研究依托最新的基因组测序与组装技术进展，通过对豹纹守宫（Eublepharis macularius，睑虎科Eublepharidae）构建更新版参考基因组，为该类群新增1个壁虎科的参考基因组，使壁虎类的覆盖科数达到3个。该更新版参考基因组采用PacBio HiFi测序技术完成测序，初始组装仅得到132个重叠群（contigs），随后通过Hi-C数据将其进一步支架化为75个总支架，完整覆盖了豹纹守宫的全部19条染色体。经分析，19条染色体中有9条可通过单个重叠群直接组装完成，剩余10条则由2个或多个重叠群经支架化拼接得到。