第勒尼安树蛙(Hyla sarda)的染色体水平基因组组装

Chromosome-level genome assembly of the Tyrrhenian tree frog (Hyla sarda).

作者信息

Paris Josephine R, Bisconti Roberta, Chiocchio Andrea, Abueg Linelle, Absolon Dominic E, Tilley Tatiana, Jain Nivesh, Balacco Jennifer, O'Toole Brian, Jarvis Erich D, Formenti Giulio, Salvi Daniele, Canestrelli Daniele

机构信息

Department of Health, Life and Environmental Sciences, University of L'Aquila, Coppito, Italy.

Department of Life and Environmental Sciences, Marche Polytechnic University, Ancona, Italy.

出版信息

Sci Data. 2025 Sep 2;12(1):1539. doi: 10.1038/s41597-025-05760-9.

Abstract

The Tyrrhenian tree frog (Hyla sarda) is a small cryptically coloured amphibian found in Corsica, Sardinia, and the Tuscan Archipelago. Investigation into the species' evolutionary history has revealed phenotypic changes triggered by glaciation-induced range expansion, but understanding the genetic basis of this trait variation has been hampered by the lack of a reference genome. To address this, we assembled a chromosome-level genome of Hyla sarda using PacBio HiFi long reads, Bionano optical maps, and Hi-C data. The assembly comprises 13 assembled chromosomes, spanning a total length of 4.15 Gb with a scaffold N50 of 385 Mb, a BUSCO completeness of 94.60%, and a k-mer completeness of 98.30%. Approximately 75% of the genome consists of repetitive elements. We annotated 22,847 protein-coding genes with a BUSCO completeness of 94.60% and an OMArk completeness of 93.74%. This high-quality assembly provides a valuable resource for studying phenotypic evolution and its genomic basis during range expansion, and will assist future investigations into the population and conservation genomics of Hyla sarda.

摘要

第勒尼安树蛙(Hyla sarda)是一种小型的、具有保护色的两栖动物,分布于科西嘉岛、撒丁岛和托斯卡纳群岛。对该物种进化历史的研究揭示了冰川作用导致的分布范围扩张所引发的表型变化,但由于缺乏参考基因组,对这种性状变异的遗传基础的理解受到了阻碍。为了解决这个问题,我们利用PacBio HiFi长读长、Bionano光学图谱和Hi-C数据组装了第勒尼安树蛙的染色体水平基因组。该组装包含13条组装好的染色体,总长度为4.15 Gb,支架N50为385 Mb,BUSCO完整性为94.60%,k-mer完整性为98.30%。大约75%的基因组由重复元件组成。我们注释了22847个蛋白质编码基因,BUSCO完整性为94.60%,OMArk完整性为93.74%。这个高质量的组装为研究分布范围扩张过程中的表型进化及其基因组基础提供了宝贵的资源,并将有助于未来对第勒尼安树蛙的种群和保护基因组学的研究。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/88cf/12405506/21332ff29692/41597_2025_5760_Fig1_HTML.jpg

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