Phylogenomic analysis of Pristionchus nematodes with the focus on orphan genes

Abstract

Proteins perform the bulk of the activity inside each living cell. Thus, it is important that a gene coding for a given protein remains conserved to maintain the proper folding of the primary amino acid sequence. Sequence homology between genes from different species allows us to trace the shared ancestry of the individual genes and species. However, the field of comparative genomics, which deals with sequence comparison, is filled with protein-coding genes that lack detectable sequence homology outside a species or a group of closely related species, such genes are classified as ‘Orphan genes’. During my doctoral research, I have tried to answer the following questions: Are Pristionchus pacificus orphan genes real or not? If yes, how old are these genes and how do they originate? I verified the protein-coding nature of orphan genes by estimating the selection pressure on their primary amino acid sequence. These findings indicate that the majority of orphan genes are under strong selection against non-synonymous amino acid changes and hence are real protein-coding genes. Further, by sequencing the genomes of six Pristionchus and two non-Pristionchus Diplogastrid species, I have generated a phylogenomic dataset with an underlying ladder-like structure around P. pacificus. This has allowed me to uncover the dynamics that shape the evolution of young and old gene families. Further, by demonstrating the diverse gene origin mechanisms, I have also determined that both sequence divergence and de novo gene creation contribute to the emergence of novel genes in Pristionchus nematodes. My results indicate that the genes without homology are biologically important and must not be ignored.