Comparative genomics reveals molecular mechanisms underlying health and reproduction in cryptorchid mammals

Abstract

Background Mammals have wide variations in testicular position, with scrotal testes in some species and ascrotal testes in others. Although cryptorchidism is hazardous to human health, some mammalian taxa are natural cryptorchids. However, the evolution of testicular position and the molecular mechanisms underlying the maintenance of health, including reproductive health, in ascrotal mammals are not clear. Results In the present study, comparative genomics and evolutionary analyses revealed that genes associated with the extracellular matrix and muscle, contributing to the development of the gubernaculum, were involved in the evolution of testicular position in mammals. Moreover, genes related to testicular position were significantly associated with spermatogenesis and sperm fertility. These genes showed rapid evolution and the signature of positive selection, with specific substitutions in ascrotal mammals. Genes associated with testicular position were significantly enriched in functions and pathways related to cancer, DNA repair, DNA replication, and autophagy. Conclusions Our results revealed that alterations in gubernaculum development contributed to the evolution of testicular position in mammals and provided the first support for two hypotheses for variation in testicular position in mammals, the “cooling hypothesis”, which proposes that the scrotum provides a cool environment for acutely heat-sensitive sperm and the “training hypothesis”, which proposes that the scrotum develops the sperm by exposing them to an exterior environment. Further, we identified cancer resistance and DNA repair as potential protective mechanisms in natural cryptorchids. These findings provide general insights into cryptorchidism and have implications for health and infertility both in humans and domestic mammals.

GENOME REPORT: Chromosome-scale genome assembly of the African spiny mouse (Acomys cahirinus)

“…Thirty-one of the significant genes with Ka/Ks > 1.0 were enriched with PANTHER GO-Slim terms for biological processes, including spermatid development (GO:0007286, 34.2-fold enrichment, FDR = 0.0184) and germ cell development (GO:0007281, 46.9-fold enrichment, FDR = 8.59E-05). These results suggest that important differences at the amino acid level between Mus and Acomys contribute to postspeciation differences in reproductive development, which is a common result in comparative genomics analyses across mammalian species (Chai et al 2021) and may be indicative of the rapid generation times and reproductive output in murid rodents.…”

Genome Report: chromosome-scale genome assembly of the African spiny mouse (Acomys cahirinus)

“…These results suggest that important differences at the amino acid level between M. musculus and A. cahirinus contribute to post-speciation differences in reproductive development. This is a common result in comparative genomics analyses across mammalian species ( Chai et al 2021 ), and yet it may be indicative of A. cahirinus ’ adaptations underlying their novel menstrual cycle, longer gestational times, and precocial births vs M. musculus ’ more rapid estrous cycles and altricial birthing strategies ( Bellofiore et al 2017 ). Other A. cahirinus Ka/Ks > 1.0 genes with molecular function and biological process enriched terms of interest include catalytic activity (GO:0003824), metabolic processes (GO:0008152), and immune system processes (GO:0002376).…”

Unraveling genomic features and phylogenomics through the analysis of three Mexican endemic Myotis genomes

“…In the last decade, comparative genomic analyses have been used in different groups of mammals for the detection of genetic variation, gene rearrangements, evolution of gene families, functional genomics and phylogenomics, among others ( Gorbunova et al, 2014 ; Zoonomia Consortium, 2020 ; Chai et al., 2021 ; Yuan et al, 2021 ). To date, there are about 50 bat genome assemblies available in the NCBI GenBank database, which have been used to identify unique bat evolutionary traits ( e.g.…”