A chromosome-level genome assembly for the eastern fence lizard (Sceloporus undulatus), a reptile model for physiological and evolutionary ecology.
A chromosome-level genome assembly for the eastern fence lizard (Sceloporus undulatus), a reptile model for physiological and evolutionary ecology.
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DOI：
10.1093/gigascience/giab066
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发表时间：
2021-10-01
期刊：
影响因子：
9.2
通讯作者：
Schwartz TS
中科院分区：
文献类型：
--
作者：
Westfall AK;Telemeco RS;Grizante MB;Waits DS;Clark AD;Simpson DY;Klabacka RL;Sullivan AP;Perry GH;Sears MW;Cox CL;Cox RM;Gifford ME;John-Alder HB;Langkilde T;Angilletta MJ;Leaché AD;Tollis M;Kusumi K;Schwartz TS
高质量的基因组资源有助于对行为生态学、形态和生理适应以及基因组结构进化的研究。 Sceloporus属蜥蜴作为重要的生态、进化和生理模型有着悠久的历史，使其成为基因组资源开发的有价值的目标。我们提供了高质量的染色体水平参考基因组组装、SceUnd1.0（使用 10X Genomics Chromium、HiC 和 Pacific Biosciences 数据）以及东部栅栏蜥蜴 Sceloporus undulatus 的组织/发育阶段转录组。我们与其他蛇和蜥蜴组装体进行了同线性分析，以确定染色体进化的广泛模式，包括微染色体和大染色体的融合。我们还使用这个新组件为另外 34 个 Sceloporus 物种提供改进的基于参考的基因组组件。最后，我们使用 RNAseq 和全基因组重测序数据来比较 3 个组件，每个组件都代表了成本和工作量的增加：Supernova Assembly 使用来自 10X Genomics Chromium 的数据，HiRise Assembly 添加了来自 HiC 的数据，PBJelly Assembly 添加了来自 Pacific Biosciences 测序的数据。我们发现 Supernova Assembly 包含完整的基因组，是 RNAseq 和单核苷酸多态性调用的合适参考，但通过添加 HiC 数据提供的染色体水平支架允许同线性和全基因组关联作图分析。随后添加的 PacBio 数据使重叠群 N50 增加了一倍，但支架长度的增加可以忽略不计。这些新的基因组资源为生物体的高级分子分析提供了宝贵的工具，该生物体已成为生理学和进化生态学的模型。
High-quality genomic resources facilitate investigations into behavioral ecology, morphological and physiological adaptations, and the evolution of genomic architecture. Lizards in the genus Sceloporus have a long history as important ecological, evolutionary, and physiological models, making them a valuable target for the development of genomic resources. We present a high-quality chromosome-level reference genome assembly, SceUnd1.0 (using 10X Genomics Chromium, HiC, and Pacific Biosciences data), and tissue/developmental stage transcriptomes for the eastern fence lizard, Sceloporus undulatus. We performed synteny analysis with other snake and lizard assemblies to identify broad patterns of chromosome evolution including the fusion of micro- and macrochromosomes. We also used this new assembly to provide improved reference-based genome assemblies for 34 additional Sceloporus species. Finally, we used RNAseq and whole-genome resequencing data to compare 3 assemblies, each representing an increased level of cost and effort: Supernova Assembly with data from 10X Genomics Chromium, HiRise Assembly that added data from HiC, and PBJelly Assembly that added data from Pacific Biosciences sequencing. We found that the Supernova Assembly contained the full genome and was a suitable reference for RNAseq and single-nucleotide polymorphism calling, but the chromosome-level scaffolds provided by the addition of HiC data allowed synteny and whole-genome association mapping analyses. The subsequent addition of PacBio data doubled the contig N50 but provided negligible gains in scaffold length. These new genomic resources provide valuable tools for advanced molecular analysis of an organism that has become a model in physiology and evolutionary ecology.