Sequencing multiple species that share the same ecological niche may be a new frontier for genomic studies. While such studies should shed light on molecular convergence, genomic-level analyses have been unsuccessful, due mainly to the absence of empirical controls. Woody plant species that colonized the global tropical coasts, collectively referred to as mangroves, are ideal for convergence studies. Here, we sequenced the genomes/transcriptomes of 16 species belonging in three major mangrove clades. To detect convergence in a large phylogeny, a CCS+ model is implemented, extending the more limited CCS method (convergence at conservative sites). Using the empirical control for reference, the CCS+ model reduces the noises drastically, thus permitting the identification of 73 convergent genes with P_true (probability of true convergence) > 0.9. Products of the convergent genes tend to be on the plasma membrane associated with salinity tolerance. Importantly, convergence is more often manifested at a higher level than at amino-acid (AA) sites. Relative to >50 plant species, mangroves strongly prefer 4 AAs and avoid 5 others across the genome. AA substitutions between mangrove species strongly reflect these tendencies. In conclusion, the selection of taxa, the number of species and, in particular, the empirical control are all crucial for detecting genome-wide convergence. We believe this large study of mangroves is the first successful attempt at detecting genome-wide site convergence.

中文翻译：

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海陆交界处木本植物基因组的趋同适应

对共享相同生态位的多个物种进行测序可能是基因组研究的新前沿。虽然这些研究应该阐明分子收敛，但基因组水平的分析一直没有成功，主要是由于缺乏经验控制。殖民全球热带海岸的木本植物物种，统称为红树林，是收敛研究的理想选择。在这里，我们对属于三个主要红树林进化枝的 16 个物种的基因组/转录组进行了测序。为了检测大型系统发育中的收敛，实施了 CCS+ 模型，扩展了更有限的 CCS 方法（保守站点的收敛）。使用经验控制作为参考，CCS+ 模型大大降低了噪音，从而允许识别 73 个具有P _{true 的}收敛基因（真正收敛的概率）> 0.9。收敛基因的产物往往位于​​与耐盐性相关的质膜上。重要的是，与氨基酸 (AA) 位点相比，收敛更常表现在更高的水平上。相对于 50 种以上的植物物种，红树林强烈偏爱 4 种 AA，并避免整个基因组中的 5 种。红树林物种之间的 AA 替代强烈反映了这些趋势。总之，分类群的选择、物种数量，尤其是经验控制对于检测全基因组收敛都至关重要。我们相信这项对红树林的大型研究是检测全基因组位点收敛的第一次成功尝试。