A ddRAD-based genetic map and its integration with the genome assembly of Japanese eel (Anguilla japonica) provides insights into genome evolution after the teleost-specific genome duplication

Wang, Kai; Nomura, Kazuharu; Fujiwara, Atushi; Nakamura, Yoji; Yasuike, Motoshige; Ojima, Nobuhiko; Masaoka, Tetsuji; Ozaki, Akiyuki; Kazeto, Yukinori; Kobashi, Gén; Nagao, Jiro; Tanaka, Hideki; Kobayashi, Takanori; Ototake, Mitsuru

doi:10.1186/1471-2164-15-233

Cited by 67 publications

(69 citation statements)

References 51 publications

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“…Chromosome preparations, spreads, staining, capture and amplification were generated with the same methods described for axolotl (Keinath et al, 2015) with a few modifications: newts were dechorionated shortly after late neurula stage of development, embryos were dechorionated in 40% Holtfreter’s solution to account for the higher internal pressure of chorionic fluid, and chromosome spreading was performed in a high-humidity chamber held at 60°C (Keinath et al, 2015). We collected 24 individual chromosomes using laser capture microdissection as previously done in salamander (Keinath et al, 2015). Library preparation was performed using a Rubicon whole genome amplification (WGA) PicoPLEX™ DNA-seq (R300381), a bioanalyzer was used to check for presence of DNA, and resulting amplicons were sequenced on a HiSeq 2000 platform at Hudson Alpha Institute for Biotechnology.…”

Section: Methodsmentioning

confidence: 99%

“…Estimates of salamander genome sizes range from 10 – 120 gigabases (Gregory, 2015; Smith et al, 2009), with the smallest salamander genome exceeding the size of the largest anuran genome. Because all salamanders have large to extremely large genomes, it seems likely that genome size increased in the basal lineage that gave rise to all extant salamanders, between ~300 and 180 MYA (Hedges et al, 2015; Keinath et al, 2015; Zhang and Wake, 2009). This increase in size is thought to reflect an ancient expansion of repetitive DNA sequences (Keinath et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

“…Because all salamanders have large to extremely large genomes, it seems likely that genome size increased in the basal lineage that gave rise to all extant salamanders, between ~300 and 180 MYA (Hedges et al, 2015; Keinath et al, 2015; Zhang and Wake, 2009). This increase in size is thought to reflect an ancient expansion of repetitive DNA sequences (Keinath et al, 2015). This expansion appears to have affected salamander genome structure in a global sense because introns, intergenic regions and linkage map size are dramatically expanded in the axolotl (Smith et al, 2005; Smith et al, 2009; Voss et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

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A linkage map for the Newt Notophthalmus viridescens: Insights in vertebrate genome and chromosome evolution

Keinath

Voss

Tsonis

et al. 2017

Developmental Biology

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Genetic linkage maps are fundamental resources that enable diverse genetic and genomic approaches, including quantitative trait locus (QTL) analyses and comparative studies of genome evolution. It is straightforward to build linkage maps for species that are amenable to laboratory culture and genetic crossing designs, and that have relatively small genomes and few chromosomes. It is more difficult to generate linkage maps for species that do not meet these criteria. Here, we introduce a method to rapidly build linkage maps for salamanders, which are known for their enormous genome sizes. As proof of principle, we developed a linkage map with thousands of molecular markers (N=2349) for the Eastern newt (Notophthalmus viridescens). The map contains 12 linkage groups (152.3–934.7cM), only one more than the number of chromosome pairs. Importantly, this map was generated using RNA isolated from a single wild caught female and her 28 offspring. We used the map to reveal chromosome-scale conservation of synteny among N. viridescens, A. mexicanum (Urodela), and chicken (Amniota), and to identify large conserved segments between N. viridescens and Xenopus tropicalis (Anura). We also show that met1, a major effect QTL that regulates the expression of alternate metamorphic and paedomorphic modes of development in Ambystoma, associates with a chromosomal fusion that is not found in the N. viridescens map. Our results shed new light on the ancestral amphibian karyotype and reveal specific fusion and translocation events that shaped the genomes of three amphibian model taxa. The ability to rapidly build linkage maps for large salamander genomes will enable genetic and genomic analyses within this important vertebrate group, and more generally, empower comparative studies of vertebrate biology and evolution.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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A linkage map for the Newt Notophthalmus viridescens: Insights in vertebrate genome and chromosome evolution

Keinath

Voss

Tsonis

et al. 2017

Developmental Biology

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“…Physical and linkage maps for yellowtail (Seriola quinqueradiata), an important species in fish aquaculture in Japan was constructed using SNP obtained from NGS results and synteny with four model fish species was analyzed (Aoki et al, 2015). A double digest RAD (ddRAD)-based genetic linkage map was generated for the Japanese eel Anguilla japonica (Kai et al, 2014). The map for female spanned 1748.8 cM, whereas the map span for males was 1294.5 cM.…”

Section: Linkage Mapsmentioning

confidence: 99%

Single nucleotide polymorphism markers with applications in aquaculture and assessment of its impact on natural populations

Wenne

2017

Aquat. Living Resour.

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-An increase in aquatic animal production can be achieved by extending aquaculture areas geographically, utilizing new species for culture, and using new technologies. Among new technologies useful for the increase of aquaculture production is the application of genetics and genomics. New molecular tools that benefit aquaculture have been developed. There has been a large number of experimental and review papers published concerning molecular markers and the range of their applications, including aquaculture and food product analyses. Analysis of single nucleotide polymorphisms (SNPs) has emerged as genotyping technology with wide and significant applications in aquaculture. SNPs can be used for construction of genetic linkage maps, finding quantitative trait loci (QTL) for useful traits like growth, body weight, grilsing, thermal and low oxygen tolerance, resistance to stress and diseases, mapping sex determination loci and identification of progeny in selection and chromosome manipulation experiments, assessment of genomic selectionand marker assisted selection in aquaculture. Genome-wide association studies (GWAS) facilitate the finding associations between SNPs and a trait in related or unrelated specimens. However, many traits are complex and can be controlled by number of QTL. Genotyping by genome reduction complexity sequencing emerged as an efficient and applicable technology in genomic selection. Identification of genes, sequences and nucleotides (substitutions) directly influencing phenotypic variations opens the possibility of marker-assisted selection for desirable characters in culture. SNP and QTL associations can be enhanced using genome editing technology. Examples of successful applications of SNPs in aquaculture of fish, crustacean and mollusk species, representing most geographic areas, and ecological risks assessment are reviewed.

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“…This method is popular and has been used in many studies since its inception (Figure S1). RAD sequencing has been used, particularly in fish, to identify population divergence (Boehm, Waldman, Robinson, & Hickerson, 2015; Ferchaud & Hansen, 2016; Larson et al., 2014), for SNP identification in polyploid fish (Hohenlohe, Amish, Catchen, Allendorf, & Luikart, 2011; Ogden et al., 2013; Palti et al., 2014), in phylogeographic studies (Macher et al., 2015; Reitzel, Herrera, Layden, Martindale, & Shank, 2013), for QTL analysis (Gagnaire, Normandeau, Pavey, & Bernatchez, 2013; Houston et al., 2012; Yoshizawa et al., 2015), for linkage mapping (Brieuc, Waters, Seeb, & Naish, 2014; Henning, Lee, Franchini, & Meyer, 2014), in hybridization studies (Hand et al., 2015; Lamer et al., 2014; Pujolar et al., 2014), for exploration of genome architecture and evolution (Brawand et al., 2014; Kai et al., 2014; Waples, Seeb, & Seeb, 2016), and in phylogenetic analyses (Gonen, Bishop, & Houston, 2015; Wagner et al., 2013). This methodology should be particularly suited to phylogeographic studies as the inference power from large numbers of markers may identify patterns that are not easily visible in traditional analyses based on relatively few loci (Davey et al., 2011).…”

Section: Introductionmentioning

confidence: 99%

Exploring the phylogeography of a hexaploid freshwater fish by RAD sequencing

Stobie

Oosthuizen

Cunningham

et al. 2018

Ecology and Evolution

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The KwaZulu‐Natal yellowfish (Labeobarbus natalensis) is an abundant cyprinid, endemic to KwaZulu‐Natal Province, South Africa. In this study, we developed a single‐nucleotide polymorphism (SNP) dataset from double‐digest restriction site‐associated DNA (ddRAD) sequencing of samples across the distribution. We addressed several hidden challenges, primarily focusing on proper filtering of RAD data and selecting optimal parameters for data processing in polyploid lineages. We used the resulting high‐quality SNP dataset to investigate the population genetic structure of L. natalensis. A small number of mitochondrial markers present in these data had disproportionate influence on the recovered genetic structure. The presence of singleton SNPs also confounded genetic structure. We found a well‐supported division into northern and southern lineages, with further subdivision into five populations, one of which reflects north–south admixture. Approximate Bayesian Computation scenario testing supported a scenario where an ancestral population diverged into northern and southern lineages, which then diverged to yield the current five populations. All river systems showed similar levels of genetic diversity, which appears unrelated to drainage system size. Nucleotide diversity was highest in the smallest river system, the Mbokodweni, which, together with adjacent small coastal systems, should be considered as a key catchment for conservation.

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A ddRAD-based genetic map and its integration with the genome assembly of Japanese eel (Anguilla japonica) provides insights into genome evolution after the teleost-specific genome duplication

Cited by 67 publications

References 51 publications

A linkage map for the Newt Notophthalmus viridescens: Insights in vertebrate genome and chromosome evolution

A linkage map for the Newt Notophthalmus viridescens: Insights in vertebrate genome and chromosome evolution

Single nucleotide polymorphism markers with applications in aquaculture and assessment of its impact on natural populations

Exploring the phylogeography of a hexaploid freshwater fish by RAD sequencing

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