Exploring the utility of cross-laboratory RAD-sequencing datasets for phylogenetic analysis.
Exploring the utility of cross-laboratory RAD-sequencing datasets for phylogenetic analysis.
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DOI：
10.1186/s13104-015-1261-2
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发表时间：
2015-07-08
影响因子：
1.8
通讯作者：
Houston RD
中科院分区：
文献类型：
--
作者：
Gonen S;Bishop SC;Houston RD
限制性内切酶相关DNA测序(RAD-Seq)被广泛应用于产生全基因组序列和遗传标记数据集。Rad-Seq在种群水平和跨物种上都得到了广泛的利用，例如在构建系统发育树中。然而，不同实验室产生的RAD-Seq数据的一致性，以及跨物种直源RAD基因座在估计遗传关系中的潜在用途，尚未得到广泛研究。这项研究描述了使用SbfI RAD-SEQ数据来估计十个硬骨鱼物种之间的进化关系，并以先前建立的系统发育图为基准。随着物种间进化距离的增加，所识别的SbfI RAD基因座的数量减少，数千个座位在5个鲑科物种中保守(分歧~50My)，数百个座位在较远亲缘关系的硬骨鱼物种中保守(分歧~100-360My)。在亲缘关系较远的物种之间识别的大多数(>；70%)基因座起源于基因，这表明SbfI对基因区域的偏向有助于识别远距离的直系同源基因。鉴定了每个同源RAD基因座的种间单核苷酸变异。使用种间变异的串联序列估计的进化关系与之前发表的系统发育图是一致的，即使是远亲(分歧高达~360我)的物种也是如此。总体而言，这项研究表明，SbfI RAD基因座可以在近亲和远亲物种中识别。这对SbfI RAD-Seq的可重复性及其解决超出原始研究范围的研究问题的潜力具有积极意义。此外，这项研究中估计的树拓扑和关系与已发表的硬骨鱼系统发育的一致性表明，类似的元数据集可以用于利用现成的RAD-Seq数据集预测种群和物种之间的进化关系，但其关系仍未确定。本文的在线版本(doi：10.1186/s13104.0151261-2)包含补充材料，授权用户可以使用。
Restriction site-Associated DNA sequencing (RAD-Seq) is widely applied to generate genome-wide sequence and genetic marker datasets. RAD-Seq has been extensively utilised, both at the population level and across species, for example in the construction of phylogenetic trees. However, the consistency of RAD-Seq data generated in different laboratories, and the potential use of cross-species orthologous RAD loci in the estimation of genetic relationships, have not been widely investigated. This study describes the use of SbfI RAD-Seq data for the estimation of evolutionary relationships amongst ten teleost fish species, using previously established phylogeny as a benchmark. The number of orthologous SbfI RAD loci identified decreased with increasing evolutionary distance between the species, with several thousand loci conserved across five salmonid species (divergence ~50 MY), and several hundred conserved across the more distantly related teleost species (divergence ~100–360 MY). The majority (>70%) of loci identified between the more distantly related species were genic in origin, suggesting that the bias of SbfI towards genic regions is useful for identifying distant orthologs. Interspecific single nucleotide variants at each orthologous RAD locus were identified. Evolutionary relationships estimated using concatenated sequences of interspecific variants were congruent with previously published phylogenies, even for distantly (divergence up to ~360 MY) related species. Overall, this study has demonstrated that orthologous SbfI RAD loci can be identified across closely and distantly related species. This has positive implications for the repeatability of SbfI RAD-Seq and its potential to address research questions beyond the scope of the original studies. Furthermore, the concordance in tree topologies and relationships estimated in this study with published teleost phylogenies suggests that similar meta-datasets could be utilised in the prediction of evolutionary relationships across populations and species with readily available RAD-Seq datasets, but for which relationships remain uncharacterised. The online version of this article (doi:10.1186/s13104-015-1261-2) contains supplementary material, which is available to authorized users.