Comparative Transcriptomics across Nematode Life Cycles Reveal Gene Expression Conservation and Correlated Evolution in Adjacent Developmental Stages
Comparative Transcriptomics across Nematode Life Cycles Reveal Gene Expression Conservation and Correlated Evolution in Adjacent Developmental Stages
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DOI：
10.1093/gbe/evaa110
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发表时间：
2020-07-01
影响因子：
3.3
通讯作者：
Tsai, Isheng Jason
中科院分区：
文献类型：
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作者：
Lu, Min R.;Lai, Cheng-Kuo;Tsai, Isheng Jason
线虫是一种数量丰富的动物，其栖息地和生活方式多种多样。有些是自由生活的，而另一些则寄生于动物或植物中，后者的感染能力在发育阶段发生变化，以感染宿主并完成生命周期。为了确定转录组进化与线虫形态差异之间的关系，我们比较了8种线虫不同发育阶段的48个转录组。转录组广泛聚集在胚胎期、幼虫期和成虫期，发育可塑性期与普通幼虫期在幼虫分支内分开。这表明，在转录组进化过程中，发育是生活方式改变（如寄生）后的主要决定因素。这种模式的部分原因是组织特异性基因——比如卵母细胞和皮下组织中的基因——以不同的比例表达。虽然线虫通常有3-5个幼虫期，但这些幼虫期的转录组在每个物种内都是高度相关的，这表明不同物种之间的幼虫期高度相似。对于秀丽隐杆线虫-桥状隐杆线虫和甾类圆线虫-委内瑞拉圆线虫的比较，我们发现接近50%的基因在多个阶段表达，而它们的一半同源基因也在多个但不同的阶段表达。这种频繁的表达变化导致了在相邻阶段协调一致的转录组进化，从而在线虫进化过程中产生物种特异性转录组。我们的研究为线虫转录组在胚胎发育之后的进化提供了第一个见解。
Nematodes are highly abundant animals with diverse habitats and lifestyles. Some are free living whereas others parasitize animals or plants, and among the latter, infection abilities change across developmental stages to infect hosts and complete life cycles. To determine the relationship between transcriptome evolution and morphological divergences among nematodes, we compared 48 transcriptomes of different developmental stages across eight nematode species. The transcriptomes were clustered broadly into embryo, larva, and adult stages, with the developmental plastic stages were separated from common larval stages within the larval branch. This suggests that development was the major determining factor after lifestyle changes, such as parasitism, during transcriptome evolution. Such patterns were partly accounted for by tissue-specific genes-such as those in oocytes and the hypodermis-being expressed at different proportions. Although nematodes typically have 3-5 larval stages, the transcriptomes for these stages were found to be highly correlated within each species, suggesting high similarity among larval stages across species. For the Caenorhabditis elegans-Caenorhabditis briggsae and Strongyloides stercoralis-Strongyloides venezuelensis comparisons, we found that similar to 50% of genes were expressed at multiple stages, whereas half of their orthologs were also expressed in multiple but different stages. Such frequent changes in expression have resulted in concerted transcriptome evolution across adjacent stages, thus generating species-specific transcriptomes over the course of nematode evolution. Our study provides a first insight into the evolution of nematode transcriptomes beyond embryonic development.