Genomewide gene-associated microsatellite markers for the model invasive ascidian, Ciona intestinalis species complex
Genomewide gene-associated microsatellite markers for the model invasive ascidian, Ciona intestinalis species complex
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模型入侵海鞘、海鞘复合体的全基因组基因相关微卫星标记
DOI：
10.1111/1755-0998.12481
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发表时间：
2016-05-01
影响因子：
7.7
通讯作者：
Zhan, Aibin
中科院分区：
文献类型：
--
作者：
Lin, Yaping;Chen, Yiyong;Zhan, Aibin
花瓶调皮，塞奥纳肠道物种复合物已成为生态和进化研究的良好模型，尤其是那些专注于与迅速变化的环境相关的微观进化的模型。但是，遍布全基因组的遗传标记仍然缺乏。在这里，我们表征了一大批全基因组基因相关的微卫星标记，用于c.intestinalis spa（= c.robusta）。生物信息学分析从表达的序列标签（ESTS）中鉴定出4654个微卫星，其中2126个成功分配给染色体的2126个以进行进一步分析。基于染色体上的分布均匀度，功能注释和引物设计的适用性，我们选择了545个候选微卫星来进一步表征。在放大验证和变异评估后，至少有来自西班牙Arenys de Mar（n = 24-48）和南非开普敦的两个人群中的至少有218个基因座是多态的（n = 24-33） 。观察到的杂合性和预期的杂合性的数量分别为2至11、1，0至0.833和0.021至0.818，以及西班牙和非洲人群的2至10、0至0.879和0.879和0.031至0.845。当对所有微卫星的跨物种实用程序进行测试时，只有60个基因座（25.8％）可以成功放大，并且在C.intestinalis spb中，所有基因座都是多态的。高水平的全基因组多态性可能导致低传递性。预计此处表征的大量微卫星标志物将为使用C.intestinalis作为模型提供有用的全基因组资源，用于生态和进化研究。
The vase tunicate, Ciona intestinalis species complex, has become a good model for ecological and evolutionary studies, especially those focusing on microevolution associated with rapidly changing environments. However, genomewide genetic markers are still lacking. Here, we characterized a large set of genomewide gene-associated microsatellite markers for C.intestinalis spA (=C.robusta). Bioinformatic analysis identified 4654 microsatellites from expressed sequence tags (ESTs), 2126 of which successfully assigned to chromosomes were selected for further analysis. Based on the distribution evenness on chromosomes, function annotation and suitability for primer design, we chose 545 candidate microsatellites for further characterization. After amplification validation and variation assessment, 218 loci were polymorphic in at least one of the two populations collected from the coast of Arenys de Mar, Spain (N=24-48), and Cape Town, South Africa (N=24-33). The number of alleles, observed heterozygosity and expected heterozygosity ranged from 2 to 11, 0 to 0.833 and 0.021 to 0.818, and from 2 to 10, 0 to 0.879 and 0.031 to 0.845 for the Spanish and African populations, respectively. When all microsatellites were tested for cross-species utility, only 60 loci (25.8%) could be successfully amplified and all loci were polymorphic in C.intestinalis spB. A high level of genomewide polymorphism is likely responsible for the low transferability. The large set of microsatellite markers characterized here is expected to provide a useful genomewide resource for ecological and evolutionary studies using C.intestinalis as a model.