First Draft Genome for Red Sea Bream of Family Sparidae

Overview

Journal Front Genet

Date 2019 Jan 9

PMID 30619468

Citations 15

Authors

Ga-Hee Shin

Younhee Shin

Myunghee Jung

Ji-Man Hong

Sangmin Lee

Sathiyamoorthy Subramaniyam

Eun-Soo Noh

Eun-Ha Shin

Eun-Hee Park

Jung Youn Park

Young-Ok Kim

Kwnag-Min Choi

Bo-Hye Nam

Chan-Il Park

Affiliations

Soon will be listed here.

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References

De la Herran R, Rejon C, Rejon M, Garrido-Ramos M . The molecular phylogeny of the Sparidae (Pisces, Perciformes) based on two satellite DNA families. Heredity (Edinb). 2002; 87(Pt 6):691-7. DOI: 10.1046/j.1365-2540.2001.00967.x. View

Bao Z, Eddy S . Automated de novo identification of repeat sequence families in sequenced genomes. Genome Res. 2002; 12(8):1269-76. PMC: 186642. DOI: 10.1101/gr.88502. View

Haas B, Delcher A, Mount S, Wortman J, Smith Jr R, Hannick L . Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res. 2003; 31(19):5654-66. PMC: 206470. DOI: 10.1093/nar/gkg770. View

Slater G, Birney E . Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics. 2005; 6:31. PMC: 553969. DOI: 10.1186/1471-2105-6-31. View

Price A, Jones N, Pevzner P . De novo identification of repeat families in large genomes. Bioinformatics. 2005; 21 Suppl 1:i351-8. DOI: 10.1093/bioinformatics/bti1018. View

Stanke M, Schoffmann O, Morgenstern B, Waack S . Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. BMC Bioinformatics. 2006; 7:62. PMC: 1409804. DOI: 10.1186/1471-2105-7-62. View

Haas B, Salzberg S, Zhu W, Pertea M, Allen J, Orvis J . Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biol. 2008; 9(1):R7. PMC: 2395244. DOI: 10.1186/gb-2008-9-1-r7. View

Blanco E, Parra G, Guigo R . Using geneid to identify genes. Curr Protoc Bioinformatics. 2008; Chapter 4:Unit 4.3. DOI: 10.1002/0471250953.bi0403s18. View

Gotz S, Garcia-Gomez J, Terol J, Williams T, Nagaraj S, Nueda M . High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res. 2008; 36(10):3420-35. PMC: 2425479. DOI: 10.1093/nar/gkn176. View

10.

Li R, Fan W, Tian G, Zhu H, He L, Cai J . The sequence and de novo assembly of the giant panda genome. Nature. 2009; 463(7279):311-7. PMC: 3951497. DOI: 10.1038/nature08696. View

11.

Marcais G, Kingsford C . A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics. 2011; 27(6):764-70. PMC: 3051319. DOI: 10.1093/bioinformatics/btr011. View

12.

Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley D . Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc. 2012; 7(3):562-78. PMC: 3334321. DOI: 10.1038/nprot.2012.016. View

13.

Chin C, Alexander D, Marks P, Klammer A, Drake J, Heiner C . Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods. 2013; 10(6):563-9. DOI: 10.1038/nmeth.2474. View

14.

Bolger A, Lohse M, Usadel B . Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014; 30(15):2114-20. PMC: 4103590. DOI: 10.1093/bioinformatics/btu170. View

15.

Lopez M, Neira R, Yanez J . Applications in the search for genomic selection signatures in fish. Front Genet. 2015; 5:458. PMC: 4294200. DOI: 10.3389/fgene.2014.00458. View

16.

Blanco Gonzalez E, Aritaki M, Knutsen H, Taniguchi N . Effects of Large-Scale Releases on the Genetic Structure of Red Sea Bream (Pagrus major, Temminck et Schlegel) Populations in Japan. PLoS One. 2015; 10(5):e0125743. PMC: 4439072. DOI: 10.1371/journal.pone.0125743. View

17.

Bao W, Kojima K, Kohany O . Repbase Update, a database of repetitive elements in eukaryotic genomes. Mob DNA. 2015; 6:11. PMC: 4455052. DOI: 10.1186/s13100-015-0041-9. View

18.

Simao F, Waterhouse R, Ioannidis P, Kriventseva E, Zdobnov E . BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015; 31(19):3210-2. DOI: 10.1093/bioinformatics/btv351. View

19.

Nam B, Jung M, Subramaniyam S, Yoo S, Markkandan K, Moon J . Transcriptome Analysis Revealed Changes of Multiple Genes Involved in Haliotis discus hannai Innate Immunity during Vibrio parahemolyticus Infection. PLoS One. 2016; 11(4):e0153474. PMC: 4835058. DOI: 10.1371/journal.pone.0153474. View

20.

Goodwin S, McPherson J, McCombie W . Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet. 2016; 17(6):333-51. PMC: 10373632. DOI: 10.1038/nrg.2016.49. View