Diversity, distribution, and significance of transposable elements in the genome of the only selfing hermaphroditic vertebrate Kryptolebias marmoratus

Abstract

The Kryptolebias marmoratus is unique because it is the only self-fertilizing hermaphroditic vertebrate, known to date. It primarily reproduces by internal self-fertilization in a mixed ovary/testis gonad. Here, we report on a high-quality genome assembly for the K. marmoratus South Korea (SK) strain highlighting the diversity and distribution of transposable elements (TEs). We find that K. marmoratus genome maintains number and composition of TEs. This can be an important genomic attribute promoting genome recombination in this selfing fish, while, in addition to a mixed mating strategy, it may also represent a mechanism contributing to the evolutionary adaptation to ecological pressure of the species. Future work should help clarify this point further once genomic information is gathered for other taxa of the family Rivulidae that do not self-fertilize. We provide a valuable genome resource that highlights the potential impact of TEs on the genome evolution of a fish species with an uncommon life cycle.

The genome of the marine medaka Oryzias melastigma

“…The most abundant repeat type was class II DNA transposons (19.89%), and a total of 32.4% repeat sequences were interspersed in the marine medaka genome. In comparison with the genomes of Japanese medaka (25.4%) and mangrove killifish Kryptolebias marmoratus (27%) (Rhee et al., ), the O. melastigma genome contained more repeat sequences. This could be one of the reasons why we kept obtaining low‐quality sequence reads.…”

Additive and non-additive epigenetic signatures of hybridisation between fish species with different mating systems

“…Using the annotated K. marmoratus reference genome (Rhee et al (2017), we identified the genomic context of the DMCs common to the two comparisons between hybrids and parental species, i.e. within gene body, promoter or intergenic region (Supplementary material).…”

Transposable elements in vertebrates: species evolution and environmental adaptation

“…The relationship between TEs and environmental conditions and the comprehension of involved mechanisms are representing an attractive challenge for the scientific community. Recently, besides to mixed mating strategy, a putative correlation between TE diversity and ecological pressure has been suggested to explain the high genetic diversity of Kryptolebias marmoratus (mangrove killifish) genome compared to other killifish species (Rhee et al 2017).…”