PDF(Pubmed)
Abstract：
BACKGROUND: Obtaining de novo chromosome-level genome assemblies greatly enhances conservation and evolutionary biology studies. For many research teams, long-read sequencing technologies (that produce highly contiguous assemblies) remain unaffordable or unpractical. For the groups that display high synteny conservation, these limitations can be overcome by a reference-guided assembly using a close relative genome. Among chelonians, tortoises (Testudinidae) are considered one of the most endangered taxa, which calls for more genomic resources. Here we make the most of high synteny conservation in chelonians to produce the first chromosome-level genome assembly of the genus Testudo with one of the most iconic tortoise species in the Mediterranean basin: Testudo graeca.
RESULTS: We used high-quality, paired-end Illumina sequences to build a reference-guided assembly with the chromosome-level reference of Gopherus evgoodei. We reconstructed a 2.29 Gb haploid genome with a scaffold N50 of 107.598 Mb and 5.37% gaps. We sequenced 25,998 protein-coding genes, and identified 41.2% of the assembly as repeats. Demographic history reconstruction based on the genome revealed two events (population decline and recovery) that were consistent with previously suggested phylogeographic patterns for the species. This outlines the value of such reference-guided assemblies for phylogeographic studies.
CONCLUSIONS: Our results highlight the value of using close relatives to produce de novo draft assemblies in species where such resources are unavailable. Our annotated genome of T. graeca paves the way to delve deeper into the species\' evolutionary history and provides a valuable resource to enhance direct conservation efforts on their threatened populations.
RESULTS: We used high-quality, paired-end Illumina sequences to build a reference-guided assembly with the chromosome-level reference of Gopherus evgoodei. We reconstructed a 2.29 Gb haploid genome with a scaffold N50 of 107.598 Mb and 5.37% gaps. We sequenced 25,998 protein-coding genes, and identified 41.2% of the assembly as repeats. Demographic history reconstruction based on the genome revealed two events (population decline and recovery) that were consistent with previously suggested phylogeographic patterns for the species. This outlines the value of such reference-guided assemblies for phylogeographic studies.
CONCLUSIONS: Our results highlight the value of using close relatives to produce de novo draft assemblies in species where such resources are unavailable. Our annotated genome of T. graeca paves the way to delve deeper into the species\' evolutionary history and provides a valuable resource to enhance direct conservation efforts on their threatened populations.
摘要：
背景：从头获得染色体水平的基因组组装大大增强了保守性和进化生物学研究。对于许多研究团队来说，长读数测序技术(产生高度连续的组件)仍然无法承受或不切实际。对于表现出高同质性保守性的群体，这些限制可以通过使用紧密相关基因组的参考指导组装来克服.在chelonians中，乌龟（Testudinidae）被认为是最濒危的类群之一，这需要更多的基因组资源。在这里，我们充分利用了chelonians中的高度同理保守性，以产生Testudo属的第一个染色体水平基因组组装，这是地中海盆地中最具标志性的乌龟物种之一：Testudograeca。
结果：我们使用了高质量，配对末端Illumina序列，以Gopherusevgoodei的染色体水平参考建立参考指导的装配。我们重建了一个2.29Gb的单倍体基因组，其支架N50为107.598Mb，缺口为5.37％。我们测序了25,998个蛋白质编码基因，并确定41.2％的组装为重复。基于基因组的人口历史重建揭示了两个事件（种群减少和恢复），这与先前建议的物种系统地理模式一致。这概述了此类参考指导程序集对系统地理学研究的价值。
结论：我们的结果强调了在无法获得此类资源的物种中使用近亲产生从头草稿组件的价值。我们注释的T.graeca基因组为深入研究物种进化史铺平了道路，并提供了宝贵的资源来加强对其受威胁种群的直接保护工作。
结果：我们使用了高质量，配对末端Illumina序列，以Gopherusevgoodei的染色体水平参考建立参考指导的装配。我们重建了一个2.29Gb的单倍体基因组，其支架N50为107.598Mb，缺口为5.37％。我们测序了25,998个蛋白质编码基因，并确定41.2％的组装为重复。基于基因组的人口历史重建揭示了两个事件（种群减少和恢复），这与先前建议的物种系统地理模式一致。这概述了此类参考指导程序集对系统地理学研究的价值。
结论：我们的结果强调了在无法获得此类资源的物种中使用近亲产生从头草稿组件的价值。我们注释的T.graeca基因组为深入研究物种进化史铺平了道路，并提供了宝贵的资源来加强对其受威胁种群的直接保护工作。
