Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA.
Department of Environmental Science, Policy and Management, University of California Berkeley, Berkeley, CA, USA.
Mol Ecol Resour. 2017 Nov;17(6):e160-e173. doi: 10.1111/1755-0998.12705. Epub 2017 Sep 5.
Molecular markers are powerful tools for studying patterns of relatedness and parentage within populations and for making inferences about social evolution. However, the development of molecular markers for simultaneous study of multiple species presents challenges, particularly when species exhibit genome duplication or polyploidy. We developed microsatellite markers for Synalpheus shrimp, a genus in which species exhibit not only great variation in social organization, but also interspecific variation in genome size and partial genome duplication. From the four primary clades within Synalpheus, we identified microsatellites in the genomes of four species and in the consensus transcriptome of two species. Ultimately, we designed and tested primers for 143 microsatellite markers across 25 species. Although the majority of markers were disomic, many markers were polysomic for certain species. Surprisingly, we found no relationship between genome size and the number of polysomic markers. As expected, markers developed for a given species amplified better for closely related species than for more distant relatives. Finally, the markers developed from the transcriptome were more likely to work successfully and to be disomic than those developed from the genome, suggesting that consensus transcriptomes are likely to be conserved across species. Our findings suggest that the transcriptome, particularly consensus sequences from multiple species, can be a valuable source of molecular markers for taxa with complex, duplicated genomes.
分子标记是研究群体内亲缘关系和亲子关系以及推断社会进化的有力工具。然而，开发用于同时研究多个物种的分子标记存在挑战，特别是当物种表现出基因组加倍或多倍体时。我们为 Synalpheus 虾属开发了微卫星标记，该属的物种不仅在社会组织方面存在巨大差异，而且在基因组大小和部分基因组加倍方面也存在种间差异。从 Synalpheus 的四个主要分支中，我们在四个物种的基因组和两个物种的共识转录组中鉴定了微卫星。最终，我们设计并测试了 25 个物种 143 个微卫星标记的引物。尽管大多数标记是二倍体，但某些物种的许多标记是多倍体。令人惊讶的是，我们没有发现基因组大小与多倍体标记数量之间的关系。正如预期的那样，为特定物种开发的标记在亲缘关系较近的物种中扩增效果更好，而在亲缘关系较远的物种中则较差。最后，来自转录组的标记比来自基因组的标记更有可能成功扩增且为二倍体，这表明共识转录组在物种间可能是保守的。我们的研究结果表明，转录组，特别是来自多个物种的共识序列，可以成为具有复杂、重复基因组的分类群的分子标记的宝贵来源。
