Whole-genome sequencing reveals the extent of heterozygosity in a preferentially self-fertilizing hermaphroditic vertebrate

Abstract

The mangrove rivulus, Kryptolebias marmoratus, is one of only two self-fertilizing hermaphroditic fish species and inhabits mangrove forests. While selfing can be advantageous, it reduces heterozygosity and decreases genetic diversity. Studies using microsatellites found that there are variable levels of selfing among populations of K. marmoratus, but overall, there is a low rate of outcrossing and, therefore, low heterozygosity. In this study, we used whole-genome data to assess the levels of heterozygosity in different lineages of the mangrove rivulus and infer the phylogenetic relationships among those lineages. We sequenced whole genomes from 15 lineages that were completely homozygous at microsatellite loci and used single nucleotide polymorphisms (SNPs) to determine heterozygosity levels. More variation was uncovered than in studies using microsatellite data because of the resolution of full genome sequencing data. Moreover, missense polymorphisms were found most often in genes associated with immune function and reproduction. Inferred phylogenetic relationships suggest that lineages largely group by their geographic distribution. The use of whole-genome data provided further insight into genetic diversity in this unique species. Although this study was limited by the number of lineages that were available, these data suggest that there is previously undescribed variation within lineages of K. marmoratus that could have functional consequences and (or) inform us about the limits to selfing (e.g., genetic load, accumulation of deleterious mutations) and selection that might favor the maintenance of heterozygosity. These results highlight the need to sequence additional individuals within and among lineages.

Comparative genomic analysis of inbred rat strains reveals the existence of ancestral polymorphisms

“…These findings are concordant with some previous reports for other inbred species (Lilue et al 2018;Wang et al 2019), providing valuable insights for understanding the genetic characteristics and diversity in highly polymorphic loci in the process of inbreeding. Indeed, in the process of naturally occurring inbreeding, such loci are thought to be under balancing selection and are shown to be heterozygous (Sato et al 2002;Aguilar et al 2004;Lins et al 2018). Our results, together with the findings in other previously reported species (Lilue et al 2018;Wang et al 2019), suggest that balancing selection may also act on such loci in the process of artificial inbreeding.…”

Contrasting DNA methylation responses of inbred fish lines to different rearing environments

“…We used hermaphrodite fish from two highly inbred strains (R and DAN) of Kryptolebias marmoratus originally collected from Belize [49,50] and kept under laboratory conditions (25-27°C, 16-18‰ ppm salinity under a 12 h light:12 h dark photoperiod), for at least 20 selfing generations [51]. The R (also called 50.91) strain was collected in Belize (Twin Cayes) in the early 1990s while the DAN (Dan06) strain was also collected from Belize in the early 2000s [49].…”

Outbreeding depression as a selective force on mixed mating in the mangrove rivulus fish,Kryptolebias marmoratus

“…Hoffman et al (2014) compared the incidence of lungworm infection in seals with heterozygosity measured with microsatellites and single nucleotide polymorphisms (SNPs), and found a highly significant correlation between lung infection and heterozygosity with SNP data, but only a marginally significant trend with microsatellite genotyping. In rivulus, Lins et al (2018) reported a range of 0.0305% - 0.0554% SNP heterozygosity in individuals that were completely homozygous at 32 microsatellites, which is very small compared to outcrossing species but not zero.…”