Genome-wide identification of lineage-specific genes within Caenorhabditis elegans

•We characterized the genetic features of LSGs and analyzed their expression profiles at different developmental stages.•The origin analysis of LSGs showed that gene duplication and exaptation from TEs mainly are the generating mechanisms.•Predicted functions of LSGs may indicate how Caenorhabditis nematodes exhibit strong adaptation to environments..

With the rapid growth of sequencing technology, a number of genomes and transcriptomes of various species have been sequenced, contributing to the study of lineage-specific genes (LSGs). We identified two sets of LSGs using BLAST: one included Caenorhabditis elegans species-specific genes (1423, SSGs), and the other consisted of Caenorhabditis genus-specific genes (4539, GSGs). The subsequent characterization and analysis of the SSGs and GSGs showed that they have significant differences in evolution and that most LSGs were generated by gene duplication and integration of transposable elements (TEs). We then performed temporal expression profiling and protein function prediction and observed that many SSGs and GSGs are expressed and that genes involved with sex determination, specific stress, immune response, and morphogenesis are over-represented, suggesting that these specific genes may be related to the Caenorhabditis nematodes' special ability to survive in severe and extreme environments.