Genomic Variants Among Threatened Acropora Corals
Genomic Variants Among Threatened Acropora Corals
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DOI：
10.1534/g3.119.400125
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发表时间：
2019-05-01
影响因子：
2.6
通讯作者：
Baums, Iliana B.
中科院分区：
文献类型：
--
作者：
Kitchen, Sheila. A.;Ratan, Aakrosh;Baums, Iliana B.
非模式生物的基因组序列数据越来越多，需要开发高效和可重复的工作流程。在这里，我们开发了第一个基因组资源和可重复的工作流程，为两个受威胁的造礁珊瑚属鹿角珊瑚。我们从加勒比海A的多个样品中产生了基因组序列数据。cervicornis（鹿角珊瑚）和A. palmata（埃尔克霍恩珊瑚），并预测了这两个物种和太平洋A.指状体使用限制性长度多态性分析验证了预测的核苷酸变体的子集，并证明其在区分两种加勒比acroporids和它们形成的杂交中是有用的（“A. prolifera”）。核苷酸变体可以从Galaxy服务器（usegalaxy.org）免费获得，并且可以在那里使用计算工具和存储的工作流程进行分析，这些工作流程只需要互联网浏览器。我们描述了这些数据和一些分析工具，集中在固定差异之间的A。cervicornis和A.掌形的特别是，我们发现，这两个物种之间的固定氨基酸的差异，丰富的蛋白质与发展，细胞应激反应，和主机的相互作用与相关的微生物，例如在ABC转运蛋白和超氧化物歧化酶。已确定的候选基因可能是这些受威胁物种如何应对不断变化的环境的功能差异的基础。用户可以通过添加来自其他物种的基因组数据来轻松扩展所呈现的分析。
Genomic sequence data for non-model organisms are increasingly available requiring the development of efficient and reproducible workflows. Here, we develop the first genomic resources and reproducible workflows for two threatened members of the reef-building coral genus Acropora. We generated genomic sequence data from multiple samples of the Caribbean A. cervicornis (staghorn coral) and A. palmata (elkhorn coral), and predicted millions of nucleotide variants among these two species and the Pacific A. digitifera. A subset of predicted nucleotide variants were verified using restriction length polymorphism assays and proved useful in distinguishing the two Caribbean acroporids and the hybrid they form ("A. prolifera"). Nucleotide variants are freely available from the Galaxy server (usegalaxy.org), and can be analyzed there with computational tools and stored workflows that require only an internet browser. We describe these data and some of the analysis tools, concentrating on fixed differences between A. cervicornis and A. palmata. In particular, we found that fixed amino acid differences between these two species were enriched in proteins associated with development, cellular stress response, and the host's interactions with associated microbes, for instance in the ABC transporters and superoxide dismutase. Identified candidate genes may underlie functional differences in how these threatened species respond to changing environments. Users can expand the presented analyses easily by adding genomic data from additional species, as they become available.