A Genetic Map for the Only Self-Fertilizing Vertebrate

et al. 2017

Sci Rep

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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.

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

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

Rhee

Choi

et al. 2017

Sci Rep

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“…A high-resolution genetic map is very useful in diverse genomic research and has been applied to many fish species (Amores et al 2011; Li et al 2015; Shao et al 2015; Xiao et al 2015; Wang et al 2015; Kanamori et al 2016). In this study, a high-density genetic map of O. melastigma was constructed using RAD sequencing and was used for verifying the previously published marine medaka reference genome and for aligning the scaffolds at the chromosomal level.…”

Section: Discussionmentioning

confidence: 99%

“…A genetic linkage map is a very useful tool to understand genetic architecture such as chromosome structure, segregation distortion regions, recombination rate, and recombination hotspots (Myers et al 2005; Zhu et al 2014; Guo et al 2013; Shifman et al 2006). Furthermore, it provides a framework for mapping the chromosomal location of single-gene traits and quantitative traits of interest, and helps to facilitate candidate gene cloning, and comparative genomic analysis with some genome information together (Lee et al 2005; Amores et al 2011; Feng et al 2015; Zhu et al 2013; Li et al 2015; Shao et al 2015; Wang et al 2015; Xiao et al 2015; Kanamori et al 2016). A high-density genetic map also plays an important role in assembling whole genome sequences by examining the accuracy of de novo genome assembly (Dukic et al 2016; Rhee et al 2017; Wang et al 2017).…”

mentioning

confidence: 99%

Construction of High-Resolution RAD-Seq Based Linkage Map, Anchoring Reference Genome, and QTL Mapping of the Sex Chromosome in the Marine Medaka Oryzias melastigma

Lee

Choi

et al. 2019

Preprint

Medaka (Oryzias spp.) is an important fish species in ecotoxicology and 31 considered as a model species due to its biological features including small body size and 32 short generation time. Since Japanese medaka Oryzias latipes is a freshwater species with 33 access to an excellent genome resources, the marine medaka Oryzias melastigma is also 34 applicable for marine ecotoxicology. In genome era, a high-density genetic linkage map is a 35 very useful resource in genomic research, providing a means for comparative genomic 36 analysis and verification of de novo genome assembly. In this study, we developed a high-37 density genetic linkage map for O. melastigma using restriction-site associated DNA 38 sequencing (RAD-seq). The genetic map consisted of 24 linkage groups with 2,481 RAD-tag 39 markers. The total map length was 1,784 cM with an average marker space of 0.72 cM. The 40 genetic map was integrated with the reference-assisted chromosome assembly (RACA) of O. 41 melastigma, which anchored 90.7% of the assembled sequence onto the linkage map. The 42 values of complete Benchmarking Universal Single-Copy Orthologs (BUSCO) were similar 43 to RACA assembly but N50 (23.74 Mb; total genome length 779.4 Mb; gap 5.29%) increased 44 to 29.99 Mb (total genome length 778.7 Mb; gap 5.2%). Using MapQTL analysis with a 45 single nucleotide polymorphism markers, we identified a major quantitative trait locus for sex 46 traits on the Om10. The integration of the genetic map with the reference genome of marine 47 medaka will serve as a good resource for studies in molecular toxicology, genomics, 48 CRISPR/Cas9, and epigenetics. 49 50 KEYWORDS Marine medaka, Oryzias melastigma, linkage map, reference genome, sex, 51 quantitative trait locus 52 3 Many fish species are useful for ecotoxicological research, as they indicate an early 53 warning of environmental contamination caused by various aquatic pollutants (Arellano-54 Aguilar et al. 2009). Recently, an increase in the contamination levels in estuaries and coastal 55 water due to anthropogenic pollutants emphasizes the needs for marine sentinel model fish 56 species. Medaka (Oryzias spp.) is an important fish species in ecotoxicology and considered a 57 model species, as its biological features include certain advantages such as small body size 58 and short generation time (Kim et al. 2016). Japanese medaka Oryzias latipes is important 59 and widely used model species for the studies of genetics, evolution, and ecotoxicological 60 study, with abundant genomic resources. Since O. latipes is a freshwater species, their 61 responses to environmental toxicants can be different in those of marine fish (Shi et al. 2008; 62

“…As a valuable model for experimental research, the genetic compositions of laboratory stocks were analyzed in the self-fertilizing fish K. marmoratus (Tatarenkov et al 2010). After these analyses, the PAN-RS strain of K. marmoratus was renamed as K. hermaphroditus, which is also self-fertilizing (Kanamori et al 2016). Intraspecific nucleotide variation of the complete mitogenome was 0.23% between two strains of K. marmoratus (Tatarenkov et al 2015).…”

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confidence: 99%

Complete mitochondrial genome of the mangrove killifish Kryptolebias hermaphroditus (Cyprinodontiformes, Rivulidae)

Mitochondrial DNA Part B

Hwang

Hagiwara

et al. 2016

Self Cite

The complete mitochondrial genome was sequenced from the mangrove killifish ( Kryptolebias hermaphroditus ). The genome sequence was 17,487 bp in size, and the gene order and contents were identical with those of the congeneric species ( K. marmoratus ) in the genus Kryptolebias with emphasis on the second control region (795 bp). Of 13 protein-coding genes (PGCs), 5 genes ( ND2 , CO2 , CO3 , ND3 , and Cytb ) had incomplete stop codons as shown in K. marmoratus . Furthermore, the stop codon of ND6 gene was AGG, while the start codon of CO1 gene was GTG. The base composition of K. hermaphroditus mitogenome showed an anti-G bias (13.45% and 8.19%) on the second and third position of the protein-coding genes (PCGs), respectively.