Study On Retrogenes Within Caenorhabditis Sp.5 And Lineage-specific Genes Within C. Elegans

The completed genome sequence of Caenorhabditis sp.5 presents an excellent opportunity to identify retrogenes within the C. sp.5. Serving as evolutionary seeds, retrogenes could be studied to explore the evolution of new genes and the molecular mechanisms underlying the formation of new phenotypes. We identified a total of 43 retrogenes and their corresponding chimeric genes. Among these,29 were found to be intact retrogenes and 14 to be retropseudogenes. Surprisingly, a high number of retrogenes appear to be functional and possibly involved in catalysis. The proportion of the retrogenes with chimeric genes is the highest among Caenorhabditis nematodes. In addition, the Ks distribution shows that C. sp.5 has more retrogenes with high Ks, which may explain the high functionality of them in Caenorhabditis species. Our results on the prevalence of these retrogenes will be helpful in the comprehensive understanding of this newly discovered species.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) within C. elegans. We identified two sets of LSGs using BLAST:one included C. elegans species-specific genes (1423, SSGs), and the other consisted of Caenorhabditis genus-specific genes (4539, GSGs). The two sets of genes were characterized and analyzed with ESTs and full-length cDNAs as well as the RNA-Seq method. To identify the potential functions of these genes, we searched WormBase to find their annotations and predicted functions using the online server ProtFun. Among all of the LSGs, functions such as sex determination, specific stress, immune response, and morphogenesis were prevalent in C. elegans, which may suggest that these specific genes are related to the Caenorhabditis nematodes’special ability to survive in severe and extreme environments and the issue of the genomic basis of the complex phenotype.Collectively, we systematically identified the retrogenes within C. sp.5 and the LSGs in C. elegans, and analyzed their characterization, expression, protein function, and etc. Our findings might motivate the developing of the molecular mechanism of evolution of these genes, as well as the formation of phenotypes. With our researches, the two sets of genes were further annotated and considered to be likely related with catalysis and adaptation.