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

Abstract

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.

Molecular physiology of copepods - from biomarkers to transcriptomes and back again

“…In addition, TRGs are strongly associated with adaptation to changing environments (Schlötterer, 2015). For example, TRGs are overrepresented in responses by C. elegans to extreme environments (Zhou et al, 2015) and Daphnia magna to a suite of environmental perturbations (Orsini et al, 2018). Weighted gene co-expression network analysis (WGCNA) methods can provide powerful insight into regulatory patterns of TRGs by identifying clusters or modules of genes with similar expression patterns.…”

Many but not all lineage-specific genes can be explained by homology detection failure

“…Also referred to as "taxonomicallyrestricted genes" [2,3], and as "orphan genes" when found only in a single species [4,5], they are ubiquitous in the genomes of sequenced organisms. For example, by previous reports, 23% of C. elegans genes are specific to the Caenorhabditis genus [6]; 6% of honey bee genes are specific to insects [7]; 25% of ash tree genes are specific to the species [8]; and 1% of human genes are specific to primates [9].…”

A genome scan of diversifying selection in Ophiocordyceps zombie‐ant fungi suggests a role for enterotoxins in co‐evolution and host specificity

“…Gene losses can also be adaptive (Juárez‐Vázquez et al., ), particularly in pathogens, as the absence of a molecule recognized by the host may enable the pathogen to colonize its host without triggering a response from the host immune system (Albalat & Cañestro, ; Ghanbarnia et al., ; Rouxel & Balesdent, ). Gene duplications and losses result in the presence of species‐specific genes, which are often overrepresented among the genes involved in adaptation (Gladieux et al., ; Lespinet, Wolf, Koonin, & Aravind, ; Zhou et al., ). Adaptation may also occur through positive selection, with rapid amino acid substitutions, typically detected as higher rates of nonsynonymous substitutions (d N ) than of synonymous substitutions (d S ) among orthologous genes of closely related species (Ina, ; Kimura, ).…”

“…often overrepresented among the genes involved in adaptation (Gladieux et al, 2014;Lespinet, Wolf, Koonin, & Aravind, 2002;Zhou et al, 2015). Adaptation may also occur through positive selection, with rapid amino acid substitutions, typically detected as higher rates of nonsynonymous substitutions (d N ) than of synonymous substitutions (d S ) among orthologous genes of closely related species (Ina, 1996;Kimura, 1983).…”