Shared Patterns of Gene Expression and Protein Evolution Associated with Adaptation to Desert Environments in Rodents.
Shared Patterns of Gene Expression and Protein Evolution Associated with Adaptation to Desert Environments in Rodents.
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DOI：
10.1093/gbe/evac155
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发表时间：
2022-11-04
影响因子：
3.3
通讯作者：
Nachman, Michael W.
中科院分区：
文献类型：
--
作者：
Bittner, Noelle K. J.;Mack, Katya L.;Nachman, Michael W.
沙漠专业化在啮齿动物中多次出现，通常与一系列趋同表型有关，包括肾脏的修饰以减轻水分流失。然而，沙漠啮齿动物的表型趋同在分子水平上的反映程度尚不清楚。在这里，我们对肾脏mRNA进行测序，并组装了三对啮齿动物物种的转录组，以寻找与适应沙漠相关的基因表达和氨基酸序列的共同差异。我们在代表7000万年进化的三个家族中的沙漠专家和非沙漠亲属之间进行了遗传学独立的比较。总体而言，基因表达模式忠实地概括了这六个类群的进化提供了一个强有力的进化信号的mRNA丰度水平。我们还发现，8.6%的基因表现出沙漠和非沙漠类群之间的表达分歧的共享模式，其中大部分可能反映了趋同进化，并表示在独立的基因进化模型下的机会超过预期。除了这些共同的变化，我们还观察到许多物种对特定的基因表达变化，表明适应沙漠的情况包括独特和共同的变化。蛋白质进化的模式揭示了少数基因显示出正选择的证据，其中大多数没有显示出基因表达的共同变化。总的来说，我们的研究结果表明，基因调控的趋同变化在啮齿动物沙漠适应的复杂性状中起着重要作用。
Desert specialization has arisen multiple times across rodents and is often associated with a suite of convergent phenotypes, including modification of the kidneys to mitigate water loss. However, the extent to which phenotypic convergence in desert rodents is mirrored at the molecular level is unknown. Here, we sequenced kidney mRNA and assembled transcriptomes for three pairs of rodent species to search for shared differences in gene expression and amino acid sequence associated with adaptation to deserts. We conducted phylogenetically independent comparisons between a desert specialist and a non-desert relative in three families representing ∼70 million years of evolution. Overall, patterns of gene expression faithfully recapitulated the phylogeny of these six taxa providing a strong evolutionary signal in levels of mRNA abundance. We also found that 8.6% of all genes showed shared patterns of expression divergence between desert and non-desert taxa, much of which likely reflects convergent evolution, and representing more than expected by chance under a model of independent gene evolution. In addition to these shared changes, we observed many species-pair-specific changes in gene expression indicating that instances of adaptation to deserts include a combination of unique and shared changes. Patterns of protein evolution revealed a small number of genes showing evidence of positive selection, the majority of which did not show shared changes in gene expression. Overall, our results suggest that convergent changes in gene regulation play an important role in the complex trait of desert adaptation in rodents.
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影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
5.3
作者：
Alders, Marielle;Al-Gazali, Lihadh;Hennekam, Raoul C.
通讯作者：
Hennekam, Raoul C.
DOI：
10.1111/j.2517-6161.1995.tb02031.x
发表时间：
1995-01-01
影响因子：
5.8
作者：
BENJAMINI, Y;HOCHBERG, Y
通讯作者：
HOCHBERG, Y
影响因子：
14.9
作者：
Finn RD;Mistry J;Tate J;Coggill P;Heger A;Pollington JE;Gavin OL;Gunasekaran P;Ceric G;Forslund K;Holm L;Sonnhammer EL;Eddy SR;Bateman A
通讯作者：
Bateman A
影响因子：
14.9
作者：
Bairoch, A;Apweiler, R
通讯作者：
Apweiler, R