鸟类基因组及演化生物学研究

Z染色体演化

文章引用

Zong-ji Wang, Ji-lin Zhang, Wei Yang, Na An, Pei Zhang, Guo-jie Zhang, and Qi Zhou, 'Temporal Genomic Evolution of Bird Sex Chromosomes', BMC Evolutionary Biology (2014).

英文摘要

Sex chromosomes exhibit many unusual patterns in sequence and gene expression relative to autosomes. Birds have evolved a female heterogametic sex system (male ZZ, female ZW), through stepwise suppression of recombination between chrZ and chrW. To address the broad patterns and complex driving forces of Z chromosome evolution, we analyze here 45 newly available bird genomes and four species’ transcriptomes, over their course of recombination loss between the sex chromosomes. We show Z chromosomes in general have a significantly higher substitution rate in introns and synonymous protein-coding sites than autosomes, driven by the male-to-female mutation bias (‘male-driven evolution’ effect). Our genome-wide estimate reveals that the degree of such a bias ranges from 1.6 to 3.8 among different species. G+C content of third codon positions exhibits the same trend of gradual changes with that of introns, between chrZ and autosomes or regions with increasing ages of becoming Z-linked, therefore codon usage bias in birds is probably driven by the mutational bias. On the other hand, Z chromosomes also evolve significantly faster at nonsynonymous sites relative to autosomes (‘fast-Z’ evolution). And species with a lower level of intronic heterozygosities tend to evolve even faster on the Z chromosome. Further analysis of fast-evolving genes’ enriched functional categories and sex-biased expression patterns support that, fast-Z evolution in birds is mainly driven by genetic drift. Finally, we show in species except for chicken, gene expression becomes more male-biased within Z-linked regions that have became hemizygous in females for a longer time, suggesting a lack of global dosage compensation in birds, and the reported regional dosage compensation in chicken has only evolved very recently. In conclusion, we uncover that the sequence and expression patterns of Z chromosome genes covary with their ages of becoming Z-linked. In contrast to the mammalian X chromosomes, such patterns are mainly driven by mutational bias and genetic drift in birds, due to the opposite sex-biased inheritance of Z vs. X.

文章解读

鸟类Z染色体的演化“STYLE”

文/王宗吉

自然界中,多数生物的性别差异是由性染色体决定的,性染色体类型主要包括XY型(雄性异配型)和ZW型(雌性异配型)。XY型在哺乳动物包括人类中很常见,ZW型广泛存在于鱼类,爬行类和鸟类。目前我们对鸟类Z染色体演化的认知很大程度上来源于家鸡的相关研究,缺乏对其它鸟类,乃至更为普遍的Z染色体演化过程的了解。

最近,研究人员通过分析45种鸟类基因组以及其中4种鸟类的转录组,系统地阐述了Z染色体更为普遍的演化过程和内在的演化动力。

细胞在减数分裂过程中,每对常染色体之间的重组可以进行基因交换,可以使得两条常染色体保持相近的基因序列。然而在性染色体(XY或者ZW)由于要维持在两性之间的差异表达,在长久的演化过程中使得性染色体之间会逐渐发生重组抑制。由于重组抑制开始产生的时间不同,会导致在相应区域呈现不同的序列分歧,即重组抑制发生越早,随着突变的积累,基因序列在两条性染色体上的差异会越来越大,因此会在两条性染色体之间的序列比较上形成“分层”现象。例如,人类性染色体最古老的“分层”区域的形成可以追溯到两亿四千万年前。

研究人员结合已检测的鸟类性染色体“分层”数据,通过对常染色体和Z染色体同源序列的比较分析,发现Z染色体在内含子和同义突变位点具有更高的替换速率,并且“分层”越古老,其替换速率越高。

与此同时,研究人员发现鸟类Z染色体上的非同义突变位点比常染色体具有更快的演化速率(“Z染色体快速演化”效应),并且越年轻的“分层”,其非同义突变位点的演化速率越快。关于“Z染色体快速演化”的原因,一方面可能来源于对雌性有利的隐形突变基因的固定,另一方面可能来源于遗传漂变对轻微有害突变基因的固定。研究人员通过对快速演化基因的功能富集、性别特异表达以及内含子SNP密度等证据的分析,排除了前者的可能性,最终认为鸟类“Z染色体快速演化”主要是由于遗传漂变导致的。

剂量补偿效应是指雌雄个体的性染色体基因虽然存在拷贝数差异(如X或者Z上的基因),但在两种性别中都表达相等或近乎相等的有效剂量。研究人员通过比较四个具有代表性的鸟类转录组,发现鸟类缺乏全面的剂量补偿,而在家鸡中之前发现的区域性剂量补偿只是近期演化而来的。

本研究系统全面地揭示了鸟类Z染色体的序列及基因表达特征,发现这些特征主要是突变的特异性以及遗传漂变导致,加深了对鸟类Z染色体演化的认识。

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