基因家族扩增促进淡水蚌科双壳类Megalonaias nervosa的适应
Gene family amplification facilitates adaptation in freshwater Unionid bivalve Megalonaias nervosa
摘要：
由于生物体面临着激烈的快速变化的选择压力，需要新的遗传物质来促进适应。在遗传新颖性的来源中，基因复制和转座因子（TE）提供了新的基因或新的调控模式，可以促进进化变化。随着基因组测序技术的进步，当种群受到威胁时，可以更广泛地了解非模式物种中基因家族的增殖和TE含量的演变。淡水双壳类（蚌科）目前面临着严重的人为挑战。在美国，超过70%的物种受到威胁，濒危或灭绝，由于污染，水道筑坝和过度捕捞。我们已经为M创建了参考基因组。nervosa来确定基因组内容在面对这些广泛的环境挑战时是如何演变的。我们观察到最近的转座因子增殖的爆发，导致382 Mb的基因组内容的扩展。基因家族扩展很常见，每代每个基因的重复率为1.16 x 10 ^-8。细胞色素P450、ABC转运蛋白、Hsp70基因、von Willebrand蛋白、几丁质代谢基因、线粒体吞噬蛋白和视蛋白基因家族经历了显著更大的扩增并显示出选择的特征。我们使用进化理论来评估SNP和重复在进化变化中的相对贡献。估计表明，基因家族进化可能提供了一个特殊的基板的遗传变异在M。nervosa，Psgv = 0.185，而单个核苷酸变化的Psgv = 0.067。因此，我们认为基因家族进化是基因组中促进适应的“希望怪物”的来源。
英文摘要：
As organisms are faced with intense rapidly changing selective pressures, new genetic material is required to facilitate adaptation. Among sources of genetic novelty, gene duplications and transposable elements (TEs) offer new genes or new regulatory patterns that can facilitate evolutionary change. With advances in genome sequencing it is possible to gain a broader view of how gene family proliferation and TE content evolve in non-model species when populations become threatened. Freshwater bivalves (Unionidae) currently face severe anthropogenic challenges. Over 70% of species in the United States are threatened, endangered or extinct due to pollution, damming of waterways, and overfishing. We have created a reference genome for M. nervosa to determine how genome content has evolved in the face of these widespread environmental challenges. We observe a burst of recent transposable element proliferation causing a 382 Mb expansion in genome content. Gene family expansion is common, with a duplication rate of 1.16 x 10^-8 per gene per generation. Cytochrome P450, ABC transporters, Hsp70 genes, von Willebrand proteins, chitin metabolism genes, mitochondria eating proteins, and opsin gene families have experienced significantly greater amplification and show signatures of selection. We use evolutionary theory to assess the relative contribution of SNPs and duplications in evolutionary change. Estimates suggest that gene family evolution may offer an exceptional substrate of genetic variation in M. nervosa, with Psgv=0.185 compared with Psgv=0.067 for single nucleotide changes. Hence, we suggest that gene family evolution is a source of "hopeful monsters" within the genome that facilitate adaptation.
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