A large set of microsatellites for the highly invasive earthworm Amynthas corticis predicted from low coverage genomes
A large set of microsatellites for the highly invasive earthworm Amynthas corticis predicted from low coverage genomes
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DOI：
10.1016/j.apsoil.2017.05.029
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发表时间：
2017-10-01
影响因子：
4.8
通讯作者：
Novo, M.
中科院分区：
文献类型：
--
作者：
Cunha, L.;Thornber, A.;Novo, M.
入侵物种会严重影响当地的生物多样性，给保护工作带来重大挑战。它们通常具有出色的可塑性，能够适应新的环境。了解它们的遗传背景是更好地理解入侵动态和制定适当的管理计划以及推断种群和进化模式的基础。在这里，我们提出了一套合理的工具，用于研究一种高度侵入性的寄生虫，megascolecid Amynthas corticis。我们在计算机上设计了一套针对微卫星区域（ca. 9400）从这里呈现的两个低覆盖度基因组。本研究提供了154个高质量的引物对，针对两个皮质远环蚓线粒体谱系中保守的多态性重复序列。根据该数据集，通过聚合酶链反应验证了一组引物对（15），扩增一致性为86%，证实了计算机模拟预测的准确性。其中9对引物用于种群遗传学研究，并在所研究的种群中呈现多态性，从而为这种全球入侵物种的未来研究显示了很大的潜力。本研究中使用的核标记物似乎概括和补充了先前研究中发现的线粒体关系。有趣的是，所有基因分型的个体在测试的基因座中显示出至少一个三倍体基因座谱，这可能是与其生活史相关的多倍性的证据，特别是通过孤雌生殖进行的无性生殖。
Invasive species can significantly affect local biodiversity and create important challenges for conservation. They usually present an outstanding plasticity that permits the adaptation to the new environments. Understanding their genetic background is fundamental to better comprehend invasion dynamics and elaborate proper management plans as well to infer population and evolutionary patterns. Here, we present a reasonable set of tools for the study of a highly invasive earthworm, the megascolecid Amynthas corticis. We designed in silico a large set of primers targeting microsatellite regions (ca. 9400) from two low coverage genomes presented here. This study provides 154 high quality primer pairs targeting polymorphic repeats conserved in two Amynthas corticis mitochondrial lineages. From this dataset, a set of primer pairs (15) was validated by polymerase chain reaction with 86% consistent amplification, confirming the accuracy of the in silico prediction. Nine of the primer pairs tested were selected for population genetics and presented polymorphism in the studied populations, thus showing promising potential for future studies of this global invasive species. The nuclear markers used in this study appear to recapitulate and complement the mitochondrial relationships found in a previous study. Interestingly, all genotyped individuals showed at least one triploid locus profile among the tested loci, which may be evidence of polyploidy associated to their life history, in particular to asexual reproduction by parthenogenesis.