Ecological speciation promoted by divergent regulation of functional genes within African cichlid fishes
Ecological speciation promoted by divergent regulation of functional genes within African cichlid fishes
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非洲慈鲷功能基因的不同调控促进了生态物种形成
DOI：
10.1101/2022.01.07.475335
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发表时间：
2022
期刊：
影响因子：
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通讯作者：
Carruthers M
中科院分区：
文献类型：
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作者：
Carruthers M
沿深度梯度的快速生态物种形成在淡水鱼中反复发生，但促进这种多样性的分子机制通常尚不清楚。在非洲火山口湖Masoko湖，在过去的1000年里，CichlidAstatotilapia calliptera已经分化为浅海和深底栖生态形态，具有截然不同的颌骨结构。利用全基因组转录组数据，我们探索了两种主要的转录调控机制，表达和剪接-QTL变体，并检查了它们对支持功能表型的差异基因表达的贡献。我们发现了7550个差异表达基因，其中5.4%受顺式调控表达QTL调控，9.2%受顺式调控剪接QTL调控。我们还在与颅面发育相关的差异表达基因上发现了差异选择的强烈信号。这些结果表明，大规模的转录组修饰在物种形成的早期阶段发挥了重要作用。我们得出结论，在适应性多样化过程中，调控变异体是选择的重要目标，推动了与生态相关的基因表达的差异。
Rapid ecological speciation along depth gradients has taken place repeatedly in freshwater fishes, yet molecular mechanisms facilitating such diversification are typically unclear. In Lake Masoko, an African crater lake, the cichlidAstatotilapia callipterahas diverged into shallow-littoral and deep-benthic ecomorphs with strikingly different jaw structures within the last 1,000 years. Using genome-wide transcriptome data, we explore two major regulatory transcriptional mechanisms, expression and splicing-QTL variants, and examine their contributions to differential gene expression underpinning functional phenotypes. We identified 7,550 genes with significant differential expression between ecomorphs, of which 5.4% were regulated bycis-regulatory expression QTLs, and 9.2% were regulated bycis-regulatory splicing QTLs. We also found strong signals of divergent selection on differentially expressed genes associated with craniofacial development. These results suggest that large-scale transcriptome modification plays an important role during early-stage speciation. We conclude that regulatory variants are important targets of selection driving ecologically relevant divergence in gene expression during adaptive diversification.