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Whole Genome Sequencing of Greater Amberjack (Seriola dumerili) for SNP Identification on Aligned Scaffolds and Genome Structural Variation Analysis Using Parallel Resequencing
Joint Authors
Araki, Kazuo
Aokic, Jun-ya
Kawase, Junya
Hamada, Kazuhisa
Ozaki, Akiyuki
Fujimoto, Hiroshi
Yamamoto, Ikki
Usuki, Hironori
Source
International Journal of Genomics
Issue
Vol. 2018, Issue 2018 (31 Dec. 2018), pp.1-12, 12 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2018-03-28
Country of Publication
Egypt
No. of Pages
12
Main Subjects
Abstract EN
Greater amberjack (Seriola dumerili) is distributed in tropical and temperate waters worldwide and is an important aquaculture fish.
We carried out de novo sequencing of the greater amberjack genome to construct a reference genome sequence to identify single nucleotide polymorphisms (SNPs) for breeding amberjack by marker-assisted or gene-assisted selection as well as to identify functional genes for biological traits.
We obtained 200 times coverage and constructed a high-quality genome assembly using next generation sequencing technology.
The assembled sequences were aligned onto a yellowtail (Seriola quinqueradiata) radiation hybrid (RH) physical map by sequence homology.
A total of 215 of the longest amberjack sequences, with a total length of 622.8 Mbp (92% of the total length of the genome scaffolds), were lined up on the yellowtail RH map.
We resequenced the whole genomes of 20 greater amberjacks and mapped the resulting sequences onto the reference genome sequence.
About 186,000 nonredundant SNPs were successfully ordered on the reference genome.
Further, we found differences in the genome structural variations between two greater amberjack populations using BreakDancer.
We also analyzed the greater amberjack transcriptome and mapped the annotated sequences onto the reference genome sequence.
American Psychological Association (APA)
Araki, Kazuo& Aokic, Jun-ya& Kawase, Junya& Hamada, Kazuhisa& Ozaki, Akiyuki& Fujimoto, Hiroshi…[et al.]. 2018. Whole Genome Sequencing of Greater Amberjack (Seriola dumerili) for SNP Identification on Aligned Scaffolds and Genome Structural Variation Analysis Using Parallel Resequencing. International Journal of Genomics،Vol. 2018, no. 2018, pp.1-12.
https://search.emarefa.net/detail/BIM-1172859
Modern Language Association (MLA)
Araki, Kazuo…[et al.]. Whole Genome Sequencing of Greater Amberjack (Seriola dumerili) for SNP Identification on Aligned Scaffolds and Genome Structural Variation Analysis Using Parallel Resequencing. International Journal of Genomics No. 2018 (2018), pp.1-12.
https://search.emarefa.net/detail/BIM-1172859
American Medical Association (AMA)
Araki, Kazuo& Aokic, Jun-ya& Kawase, Junya& Hamada, Kazuhisa& Ozaki, Akiyuki& Fujimoto, Hiroshi…[et al.]. Whole Genome Sequencing of Greater Amberjack (Seriola dumerili) for SNP Identification on Aligned Scaffolds and Genome Structural Variation Analysis Using Parallel Resequencing. International Journal of Genomics. 2018. Vol. 2018, no. 2018, pp.1-12.
https://search.emarefa.net/detail/BIM-1172859
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1172859