STAGdb: a 30K SNP genotyping array and Science Gateway for Acropora corals and their dinoflagellate symbionts
STAGdb: a 30K SNP genotyping array and Science Gateway for Acropora corals and their dinoflagellate symbionts
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DOI：
10.1038/s41598-020-69101-z
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发表时间：
2020-07-27
影响因子：
4.6
通讯作者：
Baums, I. B.
中科院分区：
文献类型：
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作者：
Kitchen, S. A.;Von Kuster, G.;Baums, I. B.
标准化的基因型鉴定对于无性繁殖并形成大型克隆种群的动物（如珊瑚）是必要的。我们开发了一个高分辨率的基于杂交的基因型阵列，再加上分析工作流程和数据库的最物种属的珊瑚，鹿角珊瑚，和他们的共生体。我们设计的阵列共同分析主机和共生体的基础上双等位基因单核苷酸多态性（SNP）标记的基因组数据的两个加勒比鹿角珊瑚物种，以及他们的优势甲藻共生体，共生藻'Fitti'。选择SNP来解析宿主（称为基因组）和共生体（称为菌株）的多位点基因型，区分宿主种群并确定加勒比顶孔珊瑚之间珊瑚杂种的祖先。也可以使用SNP基因座的子集对太平洋acroporids进行基因分型，并且额外的标记使得能够检测属于Breviolum、Cladocopioid和Durusdinium属的共生体。基于这些SNP标记产生宿主的多位点基因型的分析工具被组合在称为Acroporid基因分型标准工具（STAG）的工作流程中。STAG的工作流程和数据库包含在定制的银河环境（https：//coralsnp.science.psu.edu/galaxy/）中，该环境允许对宿主基因和共生体菌株进行一致的识别，并作为开发其他珊瑚属阵列的模板。STAG数据可用于跟踪恢复规划所需的采样基因组的时间和空间变化，并可应用于下游基因组分析。使用STAG，我们发现双向杂交和人口结构内加勒比acroporids和检测一个神秘的Acroporid物种在太平洋。
Standardized identification of genotypes is necessary in animals that reproduce asexually and form large clonal populations such as coral. We developed a high-resolution hybridization-based genotype array coupled with an analysis workflow and database for the most speciose genus of coral, Acropora, and their symbionts. We designed the array to co-analyze host and symbionts based on bi-allelic single nucleotide polymorphisms (SNP) markers identified from genomic data of the two Caribbean Acropora species as well as their dominant dinoflagellate symbiont, Symbiodinium 'fitti'. SNPs were selected to resolve multi-locus genotypes of host (called genets) and symbionts (called strains), distinguish host populations and determine ancestry of coral hybrids between Caribbean acroporids. Pacific acroporids can also be genotyped using a subset of the SNP loci and additional markers enable the detection of symbionts belonging to the genera Breviolum, Cladocopium, and Durusdinium. Analytic tools to produce multi-locus genotypes of hosts based on these SNP markers were combined in a workflow called the Standard Tools for Acroporid Genotyping (STAG). The STAG workflow and database are contained within a customized Galaxy environment (https://coralsnp.science.psu.edu/galaxy/), which allows for consistent identification of host genet and symbiont strains and serves as a template for the development of arrays for additional coral genera. STAG data can be used to track temporal and spatial changes of sampled genets necessary for restoration planning and can be applied to downstream genomic analyses. Using STAG, we uncover bi-directional hybridization between and population structure within Caribbean acroporids and detect a cryptic Acroporid species in the Pacific.