A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns
A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns
复制标题
DOI：
10.1038/nature09632
复制
发表时间：
2010-12-09
期刊：
影响因子：
64.8
通讯作者：
Tautz, Diethard
中科院分区：
文献类型：
--
作者：
Domazet-Loso, Tomislav;Tautz, Diethard
系统发育和个体发育之间的相似之处已经讨论了近两个世纪，已经提出了许多理论来解释这种模式(1)。尤其难以捉摸的是系统型阶段，这是一个门中物种彼此特别相似的发展阶段(2-6)。尽管这以前被解释为对系统发育的概括(1)，但现在它被认为反映了个体发育进展阶段(2)，在这个阶段存在着对发育调节和基因相互作用的强烈限制(2，3)。几项研究表明，在这一阶段表达的基因进化速度较慢，但到目前为止还不可能得出与这一阶段相关的明确的分子特征(7-15)。在这里，我们使用系统地层学和特定阶段的基因表达数据的组合来生成一个累积指数，该指数反映了转录组在给定个体发育阶段的进化年龄。以斑马鱼个体发育和成体发育为模型，我们发现，系统发育阶段确实表达了最古老的转录组，而年轻的转录组在发育的早期和后期表达，从而忠实地反映了形态分化的沙漏模型(2，3)。繁殖活跃的动物表现出最年轻的转录组，雄性和雌性之间存在重大差异。值得注意的是，衰老的动物表现出越来越老的基因。与苍蝇和线虫的类似数据集的比较表明，这种模式发生在整个门。我们的结果表明，旧的转录组标志着系统发育阶段，而其他个体发育阶段的系统发育差异与新进化基因的表达有关。
Parallels between phylogeny and ontogeny have been discussed for almost two centuries, and a number of theories have been proposed to explain such patterns(1). Especially elusive is the phylotypic stage, a phase during development where species within a phylum are particularly similar to each other(2-6). Although this has formerly been interpreted as a recapitulation of phylogeny(1), it is now thought to reflect an ontogenetic progression phase(2), where strong constraints on developmental regulation and gene interactions exist(2,3). Several studies have shown that genes expressed during this stage evolve at a slower rate, but it has so far not been possible to derive an unequivocal molecular signature associated with this stage(7-15). Here we use a combination of phylostratigraphy(16) and stage-specific gene expression data to generate a cumulative index that reflects the evolutionary age of the transcriptome at given ontogenetic stages. Using zebrafish ontogeny and adult development as a model, we find that the phylotypic stage does indeed express the oldest transcriptome set and that younger sets are expressed during early and late development, thus faithfully mirroring the hourglass model of morphological divergence(2,3). Reproductively active animals show the youngest transcriptome, with major differences between males and females. Notably, ageing animals express increasingly older genes. Comparisons with similar data sets from flies and nematodes show that this pattern occurs across phyla. Our results indicate that an old transcriptome marks the phylotypic phase and that phylogenetic differences at other ontogenetic stages correlate with the expression of newly evolved genes.