ArticleBMC genomics2014
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.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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38 citing papers in PubMed, 71 citations in OpenAlex.
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- High-Density Genetic Map Construction and Quantitative Trait Locus Analysis of Fruit- and Oil-Related Traits inInternational journal of molecular sciences · 2024Article
- A chromosome-level reference genome assembly of the Reeve's moray eel (Gymnothorax reevesii).Scientific data · 2023Article
- A Chromosome-level assembly of the Japanese eel genome, insights into gene duplication and chromosomal reorganization.GigaScience · 2022Article
- Tempo and mode in karyotype evolution revealed by a probabilistic model incorporating both chromosome number and morphology.PLoS genetics · 2021Article
- Genotyping Strategies Using ddRAD Sequencing in Farmed Arctic Charr (Animals : an open access journal from MDPI · 2021Article
- A high-density SNP-based genetic map and several economic traits-related loci in Pelteobagrus vachelli.BMC genomics · 2020Article
- Mapping a double flower phenotype-associated gene DcAP2L in Dianthus chinensis.Journal of experimental botany · 2020Article
- Construction of a High-Density Genetic Linkage Map and QTL Mapping for Growth-Related Traits in Takifugu bimaculatus.Marine biotechnology (New York, N.Y.) · 2020Article
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- Genome-Wide Variant Identification and High-Density Genetic Map Construction Using RADseq forG3 (Bethesda, Md.) · 2019Article
- Constructing High-Density Genetic Maps and Developing Sexing Markers in Northern Snakehead (Channa argus).Marine biotechnology (New York, N.Y.) · 2019Article
- The yellowtail (Seriola quinqueradiata) genome and transcriptome atlas of the digestive tract.DNA research : an international journal for rapid publication of reports on genes and genomes · 2018Article
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- Applications of genotyping by sequencing in aquaculture breeding and genetics.Reviews in aquaculture · 2018Review
- Exploring the phylogeography of a hexaploid freshwater fish by RAD sequencing.Ecology and evolution · 2018Article
- SLAF-based high-density genetic map construction and QTL mapping for major economic traits in sea urchin Strongylocentrotus intermedius.Scientific reports · 2018Article
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- Rhodopsin gene evolution in early teleost fishes.PloS one · 2018Article
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Authors and funding
14 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundRecent advancements in next-generation sequencing technology have enabled cost-effective sequencing of whole or partial genomes, permitting the discovery and characterization of molecular polymorphisms. Double-digest restriction-site associated DNA sequencing (ddRAD-seq) is a powerful and inexpensive approach to developing numerous single nucleotide polymorphism (SNP) markers and constructing a high-density genetic map. To enrich genomic resources for Japanese eel (Anguilla japonica), we constructed a ddRAD-based genetic map using an Ion Torrent Personal Genome Machine and anchored scaffolds of the current genome assembly to 19 linkage groups of the Japanese eel. Furthermore, we compared the Japanese eel genome with genomes of model fishes to infer the history of genome evolution after the teleost-specific genome duplication.
resultsWe generated the ddRAD-based linkage map of the Japanese eel, where the maps for female and male spanned 1748.8 cM and 1294.5 cM, respectively, and were arranged into 19 linkage groups. A total of 2,672 SNP markers and 115 Simple Sequence Repeat markers provide anchor points to 1,252 scaffolds covering 151 Mb (13%) of the current genome assembly of the Japanese eel. Comparisons among the Japanese eel, medaka, zebrafish and spotted gar genomes showed highly conserved synteny among teleosts and revealed part of the eight major chromosomal rearrangement events that occurred soon after the teleost-specific genome duplication.
conclusionsThe ddRAD-seq approach combined with the Ion Torrent Personal Genome Machine sequencing allowed us to conduct efficient and flexible SNP genotyping. The integration of the genetic map and the assembled sequence provides a valuable resource for fine mapping and positional cloning of quantitative trait loci associated with economically important traits and for investigating comparative genomics of the Japanese eel.
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