Adaptation and Conservation throughout the Drosophila melanogaster Life-Cycle
Adaptation and Conservation throughout the Drosophila melanogaster Life-Cycle
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DOI：
10.1093/gbe/evz086
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发表时间：
2019-05-01
影响因子：
3.3
通讯作者：
Salazar-Ciudad, Isaac
中科院分区：
文献类型：
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作者：
Coronado-Zamora, Marta;Salvador-Martinez, Irepan;Salazar-Ciudad, Isaac
以前对果蝇不同生活史阶段表达基因进化的研究还不能在使用非同义位点时将适应性替换与非适应性替换分开。在这里，我们通过结合来自黑腹果蝇的全基因组多态数据和黑腹果蝇和雅库巴果蝇之间的差异数据来克服这一限制。对于在modENCODE中报道的在黑腹果蝇不同生活史阶段表达的一组基因，我们估计了非同义和同义位点之间相对于多态的替换比率(α)，然后将阿尔法分解为适应性(omega(A))和非适应性(omega(Na))替换与同义替换的比率。我们发现，在胚胎发育中期和晚期表达的基因最保守，而在发育早期和胚胎后阶段表达的基因最不保守。重要的是，我们发现在早期发育中的低保守性是由于高比例的非适应性替换(高omega(NA))，而在胚胎后期，这是由于高比例的适应性替换(高omega(A))。通过对不同基因组特征(密码子偏向、平均内含子长度、外显子数目、重组率等)的估计，我们还发现在胚胎发育中后期表达的基因表现出最复杂的结构：它们更大，具有更多的外显子，更多的转录本，更长的内含子。此外，这些基因在所有阶段都有广泛的表达。我们认为，所有这些基因组特征都与胚胎中期和晚期发育的保护有关。在全球范围内，我们的研究支持生命周期中的保护和适应的沙漏模式。
Previous studies of the evolution of genes expressed at different life-cycle stages of Drosophila melanogaster have not been able to disentangle adaptive from nonadaptive substitutions when using nonsynonymous sites. Here, we overcome this limitation by combining whole-genome polymorphism data from D. melanogaster and divergence data between D. melanogaster and Drosophila yakuba. For the set of genes expressed at different life-cycle stages of D. melanogaster, as reported in modENCODE, we estimate the ratio of substitutions relative to polymorphism between nonsynonymous and synonymous sites (alpha) and then alpha is discomposed into the ratio of adaptive (omega(a)) and nonadaptive (omega(na)) substitutions to synonymous substitutions. We find that the genes expressed in mid- and late-embryonic development are the most conserved, whereas those expressed in early development and postembryonic stages are the least conserved. Importantly, we found that low conservation in early development is due to high rates of nonadaptive substitutions (high omega(na)), whereas in postembryonic stages it is due, instead, to high rates of adaptive substitutions (high omega(a)). By using estimates of different genomic features (codon bias, average intron length, exon number, recombination rate, among others), we also find that genes expressed in mid- and late-embryonic development show the most complex architecture: they are larger, have more exons, more transcripts, and longer introns. In addition, these genes are broadly expressed among all stages. We suggest that all these genomic features are related to the conservation of mid- and late-embryonic development. Globally, our study supports the hourglass pattern of conservation and adaptation over the life-cycle.