Whole-genome sequencing reveals the extent of heterozygosity in a preferentially self-fertilizing hermaphroditic vertebrate.
Luana S. F. Lins,Shawn Trojahn,Alexandra Sockell,Muh-Ching Yee,Andrey Tatarenkov,Carlos Bustamante,Ryan L. Earley,Joanna L. Kelley +7 more
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TLDR
This study 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, and sequenced whole genomes from 15 lineages that were completely homozygous at microsatellite loci.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.read more
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Emersion behaviour underlies variation in gill morphology and aquatic respiratory function in the amphibious fish Kryptolebias marmoratus .
Andy J. Turko,Andrey Tatarenkov,Suzie Currie,Ryan L. Earley,Alexis Platek,D. S. Taylor,Patricia A. Wright +6 more
TL;DR: It is demonstrated that amphibious fishes that inhabit hypoxic aquatic habitats can use a fundamentally different strategy from that used by fully aquatic water-breathing fishes, relying on escape behaviour rather than metabolic depression or increased O2 extraction ability.
Journal ArticleDOI
Contrasting DNA methylation responses of inbred fish lines to different rearing environments
Waldir M. Berbel-Filho,Deiene Rodriguez-Barreto,Nikita Berry,Carlos Garcia de Leaniz,Sofia Consuegra +4 more
TL;DR: It is suggested that, at least in part, DNA methylation could depend on the dynamic interaction between the genotype and the environment, which could explain the plasticity of epigenetically mediated phenotypes.
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Early-life exposure to the endocrine disruptor 17-α-ethinylestradiol induces delayed effects in adult brain, liver and ovotestis proteomes of a self-fertilizing fish
TL;DR: The results suggest that estrogen-responsive pathways, such as lipid metabolism, inflammation, and the innate immune system were affected months after the exposure, and encourages future studies to investigate the role of DNA methylation in mediating the long-term effects of early-life exposures.
Journal ArticleDOI
The Role of Stochasticity in the Origin of Epigenetic Variation in Animal Populations.
TL;DR: Comparisons between the mutation and the epimutation rates showed a high level of the latter, suggesting a significant role of spontaneous epimutations in adaptation, and potential sources of such stochastic epigenetic variability in animals are explored, with a focus on DNA methylation.
Journal ArticleDOI
Genomic and physiological mechanisms underlying skin plasticity during water to air transition in an amphibious fish.
Yunwei Dong,Tessa S. Blanchard,Angela Noll,Picasso Vasquez,Juergen Schmitz,Scott P. Kelly,Patricia A. Wright,Andrew Whitehead +7 more
TL;DR: It is concluded that rapid plasticity of barrier, respiratory and ionoregulatory functions in skin evolved to support the amphibious lifestyle of K. marmoratus; similar processes may have facilitated the terrestrial radiation of other contemporary and ancient fishes.
References
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