Comparative developmental transcriptomics reveals rewiring of a highly conserved gene regulatory network during a major life history switch in the sea urchin genus Heliocidaris

The ecologically significant shift in developmental strategy from planktotrophic (feeding) to lecithotrophic (nonfeeding) development in the sea urchin genus Heliocidaris is one of the most comprehensively studied life history transitions in any animal. Although the evolution of lecithotrophy involved substantial changes to larval development and morphology, it is not known to what extent changes in gene expression underlie the developmental differences between species, nor do we understand how these changes evolved within the context of the well-defined gene regulatory network (GRN) underlying sea urchin development. To address these questions, we used RNA-seq to measure expression dynamics across development in three species: the lecithotroph Heliocidaris erythrogramma, the closely related planktotroph H. tuberculata, and an outgroup planktotroph Lytechinus variegatus. Using well-established statistical methods, we developed a novel framework for identifying, quantifying, and polarizing evolutionary changes in gene expression profiles across the transcriptome and within the GRN. We found that major changes in gene expression profiles were more numerous during the evolution of lecithotrophy than during the persistence of planktotrophy, and that genes with derived expression profiles in the lecithotroph displayed specific characteristics as a group that are consistent with the dramatically altered developmental program in this species. Compared to the transcriptome, changes in gene expression profiles within the GRN were even more pronounced in the lecithotroph. We found evidence for conservation and likely divergence of particular GRN regulatory interactions in the lecithotroph, as well as significant changes in the expression of genes with known roles in larval skeletogenesis. We further use coexpression analysis to identify genes of unknown function that may contribute to both conserved and derived developmental traits between species. Collectively, our results indicate that distinct evolutionary processes operate on gene expression during periods of life history conservation and periods of life history divergence, and that this contrast is even more pronounced within the GRN than across the transcriptome as a whole.

海胆属（Heliocidaris）中发育策略从浮游营养型（摄食性）向卵黄营养型（非摄食性）的生态学意义重大转变，是所有动物类群中研究最为全面的生活史转变之一。尽管卵黄营养型的演化涉及幼虫发育与形态的显著改变，但目前尚不清楚基因表达变化在多大程度上构成物种间发育差异的分子基础，同时我们也未能明晰这些变化是如何在海胆发育的明确界定的基因调控网络（GRN）框架下演化的。为解答上述问题，我们借助RNA测序（RNA-seq）对三个物种的全发育阶段的基因表达动态进行了定量检测：卵黄营养型物种Heliocidaris erythrogramma、与其亲缘关系紧密的浮游营养型物种H. tuberculata，以及外类群浮游营养型物种Lytechinus variegatus。我们采用成熟的统计学分析方法，构建了一套全新的分析框架，用于鉴定、定量并极化转录组及基因调控网络内基因表达谱的演化变化。研究发现，卵黄营养型演化过程中基因表达谱的重大变化数量，远多于浮游营养型物种维持自身发育模式过程中的变化；且该卵黄营养型物种中具有衍生表达谱的基因作为一个整体，展现出与该物种显著改变的发育程序相符的特定特征。与整个转录组相比，该卵黄营养型物种的基因调控网络内基因表达谱变化更为显著。我们发现了该卵黄营养型物种中基因调控网络调控交互作用的保守性与潜在分化的证据，同时也发现了已知参与幼虫骨骼发生的基因的表达存在显著变化。我们进一步通过共表达分析，鉴定出一批功能未知的基因，这些基因可能参与物种间保守及衍生的发育性状的形成。综上，我们的研究结果表明，在生活史保守与生活史分化的不同时期，不同演化过程对基因表达的调控存在差异，且这种差异在基因调控网络内部比在整个转录组中更为显著。