Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA.
School of Biological Sciences, University of Oklahoma, Norman, OK 73019, USA.
G3 (Bethesda). 2024 Aug 7;14(8). doi: 10.1093/g3journal/jkae110.
Body size is a fundamental trait that drives multiple evolutionary and ecological patterns. Caenorhabditis inopinata is a fig-associated nematode that is exceptionally large relative to other members of the genus, including Caenorhabditis elegans. We previously showed that C. inopinata is large primarily due to postembryonic cell size expansion that occurs during the larval-to-adult transition. Here, we describe gene expression patterns in C. elegans and C. inopinata throughout this developmental period to understand the transcriptional basis of body size change. We performed RNA-seq in both species across the L3, L4, and adult stages. Most genes are differentially expressed across all developmental stages, consistent with C. inopinata's divergent ecology and morphology. We also used a model comparison approach to identify orthologues with divergent dynamics across this developmental period between the 2 species. This included genes connected to neurons, behavior, stress response, developmental timing, and small RNA/chromatin regulation. Multiple hypodermal collagens were also observed to harbor divergent developmental dynamics across this period, and genes important for molting and body morphology were also detected. Genes associated with transforming growth factor β signaling revealed idiosyncratic and unexpected transcriptional patterns given their role in body size regulation in C. elegans. This widespread transcriptional divergence between these species is unexpected and maybe a signature of the ecological and morphological divergence of C. inopinata. Alternatively, transcriptional turnover may be the rule in the Caenorhabditis genus, indicative of widespread developmental system drift among species. This work lays the foundation for future functional genetic studies interrogating the bases of body size evolution in this group.
体型是驱动多种进化和生态模式的基本特征。不期而遇的食蚜虫线虫是一种与榕果共生的线虫，与该属的其他成员（包括秀丽隐杆线虫）相比，它的体型异常大。我们之前曾表明，不期而遇的食蚜虫线虫体型较大主要是由于胚胎后细胞大小的扩张，这种扩张发生在幼虫到成虫的过渡阶段。在这里，我们描述了秀丽隐杆线虫和不期而遇的食蚜虫线虫在整个发育期间的基因表达模式，以了解体型变化的转录基础。我们在这两个物种的 L3、L4 和成虫阶段进行了 RNA-seq。大多数基因在所有发育阶段都有差异表达，这与不期而遇的食蚜虫线虫的独特生态和形态一致。我们还使用模型比较方法来识别在这两个物种之间跨越这一发育时期具有不同动态的直系同源物。这包括与神经元、行为、应激反应、发育时间和小 RNA/染色质调控相关的基因。在这一时期，还观察到多个真皮胶原具有不同的发育动态，检测到蜕皮和体型的重要基因。与转化生长因子 β信号相关的基因显示出与其在秀丽隐杆线虫中调节体型的作用不同的特有的和意外的转录模式。这些物种之间广泛的转录差异是出乎意料的，可能是不期而遇的食蚜虫线虫的生态和形态差异的特征。或者，转录周转率可能是 Caenorhabditis 属的规则，表明物种之间存在广泛的发育系统漂移。这项工作为未来的功能遗传研究奠定了基础，这些研究将探讨该类群中体型进化的基础。
