Genome-wide analysis of positively selected genes in seasonal and non-seasonal breeding species

PLoS One. 2015 May 22;10(5):e0126736. doi: 10.1371/journal.pone.0126736. eCollection 2015.

Abstract

Some mammals breed throughout the year, while others breed only at certain times of year. These differences in reproductive behavior can be explained by evolution. We identified positively-selected genes in two sets of species with different degrees of relatedness including seasonal and non-seasonal breeding species, using branch-site models. After stringent filtering by sum of pairs scoring, we revealed that more genes underwent positive selection in seasonal compared with non-seasonal breeding species. Positively-selected genes were verified by cDNA mapping of the positive sites with the corresponding cDNA sequences. The design of the evolutionary analysis can effectively lower the false-positive rate and thus identify valid positive genes. Validated, positively-selected genes, including CGA, DNAH1, INVS, and CD151, were related to reproductive behaviors such as spermatogenesis and cell proliferation in non-seasonal breeding species. Genes in seasonal breeding species, including THRAP3, TH1L, and CMTM6, may be related to the evolution of sperm and the circadian rhythm system. Identification of these positively-selected genes might help to identify the molecular mechanisms underlying seasonal and non-seasonal reproductive behaviors.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Circadian Rhythm / genetics
  • Evolution, Molecular
  • Female
  • Gene Expression Regulation*
  • Genome*
  • Haplorhini
  • Humans
  • Male
  • Mice
  • Rats
  • Reproduction / genetics*
  • Seasons*
  • Selection, Genetic*
  • Spermatogenesis / genetics

Grants and funding

This study was funded by the National Science and Technology Support Program (2014BAI03B01, 2015BAI07B01), the Science and Technology Planning Project of Guangzhou (1561000294), the Science and Technology Planning Project of Guangdong Province(2013B060300025), and BGI-SCUT Innovation Fund Project (SW20130802). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.