Reference-free population genomics from next-generation transcriptome data and the vertebrate-invertebrate gap.
Reference-free population genomics from next-generation transcriptome data and the vertebrate-invertebrate gap.
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DOI：
10.1371/journal.pgen.1003457
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发表时间：
2013-04
期刊：
影响因子：
4.5
通讯作者：
Galtier N
中科院分区：
文献类型：
--
作者：
Gayral P;Melo-Ferreira J;Glémin S;Bierne N;Carneiro M;Nabholz B;Lourenco JM;Alves PC;Ballenghien M;Faivre N;Belkhir K;Cahais V;Loire E;Bernard A;Galtier N
在动物中，种群基因组文献主要由两个分类群主导，即哺乳动物和果蝇，在这两个分类群中，完全测序和良好注释的基因组已经可用多年。来自其他后生动物门的数据很少，可能是因为绝大多数现存物种仍然缺乏密切相关的参考基因组。在这里，我们基于下一代测序转录组数据，从五种非模式动物物种的野生样本中实现了从头开始，无参考群体基因组分析。我们介绍了cDNA组装，读取映射，SNP/基因型调用和数据清洗的流水线，并特别关注隐藏的相似性检测问题。在两个可获得参考基因组的物种中，无论是否使用参考基因组，都获得了相似的结果，证明了我们的从头推断的稳健性。野兔、海龟、牡蛎、被囊动物和白蚁的种群基因组图谱被发现介于人类和果蝇之间，表明这两个物种之间不一致的基因组多样性模式并没有反映出脊椎动物与无脊椎动物之间的普遍差距。无脊椎动物的基因组平均多样性普遍高于脊椎动物（白蚁除外），这与种群规模倾向于前者大于后者的观点一致。然而，非同义与同义比率在脊椎动物和无脊椎动物之间没有显著差异，尽管它与两组内的遗传多样性呈负相关。本研究为非模式生物的全基因组种群分析以及种群大小对非同义与同义多样性的影响开辟了有希望的前景。到目前为止，对特定物种个体之间的基因组变异的分析仅限于少数模式生物，如人类和果蝇，这些模式生物有一个完整的测序和良好注释的参考基因组。本研究表明，由于下一代高通量测序技术和适当的基因型调用方法，在没有参考基因组的情况下，重新进行群体基因组分析是可能的。我们描述了5种非模式动物，2种脊椎动物和3种无脊椎动物的中性和选择性多态性的基因组水平，特别关注多拷贝基因的处理。分析表明种群大小对动物遗传多样性的影响，在我们的样本中，两种脊椎动物（野兔、海龟）和群居昆虫（白蚁）的多态性低于两种海洋无脊椎动物（牡蛎、被囊动物）。有趣的是，自然选择效率的基因组指标，无论是纯化的还是适应性的，在不同的生物体中并没有以一种简单、可预测的方式变化。这些结果证明，在了解基因组进化动力学的决定因素时，物种多样化采样的价值。
In animals, the population genomic literature is dominated by two taxa, namely mammals and drosophilids, in which fully sequenced, well-annotated genomes have been available for years. Data from other metazoan phyla are scarce, probably because the vast majority of living species still lack a closely related reference genome. Here we achieve de novo, reference-free population genomic analysis from wild samples in five non-model animal species, based on next-generation sequencing transcriptome data. We introduce a pipe-line for cDNA assembly, read mapping, SNP/genotype calling, and data cleaning, with specific focus on the issue of hidden paralogy detection. In two species for which a reference genome is available, similar results were obtained whether the reference was used or not, demonstrating the robustness of our de novo inferences. The population genomic profile of a hare, a turtle, an oyster, a tunicate, and a termite were found to be intermediate between those of human and Drosophila, indicating that the discordant genomic diversity patterns that have been reported between these two species do not reflect a generalized vertebrate versus invertebrate gap. The genomic average diversity was generally higher in invertebrates than in vertebrates (with the notable exception of termite), in agreement with the notion that population size tends to be larger in the former than in the latter. The non-synonymous to synonymous ratio, however, did not differ significantly between vertebrates and invertebrates, even though it was negatively correlated with genetic diversity within each of the two groups. This study opens promising perspective regarding genome-wide population analyses of non-model organisms and the influence of population size on non-synonymous versus synonymous diversity. The analysis of genomic variation between individuals of a given species has so far been restricted to a small number of model organisms, such as human and fruitfly, for which a fully sequenced, well-annotated reference genome was available. Here we show that, thanks to next-generation high-throughput sequencing technologies and appropriate genotype-calling methods, de novo population genomic analysis is possible in absence of a reference genome. We characterize the genomic level of neutral and selected polymorphism in five non-model animal species, two vertebrates and three invertebrates, paying particular attention to the treatment of multi-copy genes. The analyses demonstrate the influence of population size on genetic diversity in animals, the two vertebrates (hare, turtle) and the social insect (termite) being less polymorphic than the two marine invertebrates (oyster, tunicate) in our sample. Interestingly, genomic indicators of the efficiency of natural selection, both purifying and adaptive, did not vary in a simple, predictable way across organisms. These results prove the value of a diversified sampling of species when it comes to understand the determinants of genome evolutionary dynamics.
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