Dramatic evolutionary changes of conserved noncoding elements accompanied by extraordinary features of Caenorhabditis inopinata

Phenotypic evolution is caused by mutations in noncoding and protein-coding regions. Conserved noncoding elements (CNEs) have—at least partially—gene regulatory functions and contribute to the evolution of organisms by modifying their gene expression. While evolutionary changes of CNEs—such as loss and accelerated evolution—have been intensively studied in vertebrates, only a few studies have focused on invertebrates. The availability of detailed functional genomic information of the model nematode Caenorhabditis elegans and recent accumulation of genome sequences within the same genus facilitate the use of these nematodes in comparative genomics focusing on CNEs. The recently discovered species Caenorhabditis inopinata has several peculiar traits characterized by a larger body size than that of its close relatives and are regarded as an appropriate species that links phenotypic evolution with genomic changes. Herein, using comparative genomics and transcriptomics in C. inopinata , we analyzed the evolution of CNEs and their functions during phenotypic evolution. We detected substantial evolutionary changes in CNEs in C. inopinata compared to other relatives—changes frequently associated with body morphology and behavior corresponding to extraordinary body size and unique life cycles. Our study revealed an association between noncoding elements and substantial phenotypic evolution in invertebrates.