A genomic overview of short genetic variations in a basal chordate, Ciona intestinalis

BMC Genomics

Volumn 13, Issue 1, 2012, Pages

  Satou, Yutaka ^a   Shin i, Tadasu ^b   Kohara, Yuji ^b   Satoh, Nori ^c   Chiba, Shota ^a  

^a KYOTO UNIVERSITY   (Japan)

^b NATIONAL INSTITUTE OF GENETICS   (Japan)

^c OKINAWA INSTITUTE OF SCIENCE AND TECHNOLOGY GRADUATE UNIVERSITY   (Japan)

Author keywords

Ascidian; Ciona intestinalis; Short genetic variations; Single nucleotide polymorphisms (SNPs)

Indexed keywords

NUCLEOTIDE; PROTEIN;

ALLELE; ANIMAL GENOME; ARTICLE; CHORDATA; CIONA INTESTINALIS; EUCHROMATIN; GENETIC VARIABILITY; GENOME; GENOMICS; MOLECULAR EVOLUTION; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION;

AMINO ACID SUBSTITUTION; ANIMALS; BASE SEQUENCE; CHROMOSOMES; CIONA INTESTINALIS; DATABASES, GENETIC; GENE DELETION; GENETIC VARIATION; GENOME; INDEL MUTATION; MUTAGENESIS, INSERTIONAL; POLYMORPHISM, SINGLE NUCLEOTIDE; REFERENCE STANDARDS; REPRODUCIBILITY OF RESULTS;

ANIMALIA; ASCIDIA; CIONA INTESTINALIS;

EID: 84861555062     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-208     Document Type: Article

References (21)

1. Dehal P, Satou Y, Campbell RK, Chapman J, Degnan B, De Tomaso A, Davidson B, Di Gregorio A, Gelpke M, Goodstein DM, et al. The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. Science 2002, 298(5601):2157-2167. 10.1126/science.1080049, 12481130.
2. Wang J, Wang W, Li R, Li Y, Tian G, Goodman L, Fan W, Zhang J, Li J, Guo Y, et al. The diploid genome sequence of an Asian individual. Nature 2008, 456(7218):60-65. 10.1038/nature07484, 2716080, 18987735.
3. Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, Walenz BP, Axelrod N, Huang J, Kirkness EF, Denisov G, et al. The diploid genome sequence of an individual human. PLoS Biol 2007, 5(10):e254. 10.1371/journal.pbio.0050254, 1964779, 17803354.
4. Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, McGuire A, He W, Chen YJ, Makhijani V, Roth GT, et al. The complete genome of an individual by massively parallel DNA sequencing. Nature 2008, 452(7189):872-876. 10.1038/nature06884, 18421352.
5. Aparicio S, Chapman J, Stupka E, Putnam N, Chia JM, Dehal P, Christoffels A, Rash S, Hoon S, Smit A, et al. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 2002, 297(5585):1301-1310. 10.1126/science.1072104, 12142439.
6. Guryev V, Koudijs MJ, Berezikov E, Johnson SL, Plasterk RH, van Eeden FJ, Cuppen E. Genetic variation in the zebrafish. Genome Res 2006, 16(4):491-497. 10.1101/gr.4791006, 1457036, 16533913.
7. Sodergren E, Weinstock GM, Davidson EH, Cameron RA, Gibbs RA, Angerer RC, Angerer LM, Arnone MI, Burgess DR, Burke RD, et al. The genome of the sea urchin Strongylocentrotus purpuratus. Science 2006, 314(5801):941-952. 3159423, 17095691.
8. Putnam NH, Butts T, Ferrier DE, Furlong RF, Hellsten U, Kawashima T, Robinson-Rechavi M, Shoguchi E, Terry A, Yu JK, et al. The amphioxus genome and the evolution of the chordate karyotype. Nature 2008, 453(7198):1064-1071. 10.1038/nature06967, 18563158.
9. Silva N, Smith WC. Inverse correlation of population similarity and introduction date for invasive ascidians. PLoS ONE 2008, 3(6):e2552. 10.1371/journal.pone.0002552, 2430530, 18575620.
10. Denoeud F, Henriet S, Mungpakdee S, Aury JM, Da Silva C, Brinkmann H, Mikhaleva J, Olsen LC, Jubin C, Canestro C, et al. Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate. Science 2010, 330(6009):1381-1385. 10.1126/science.1194167, 21097902.
11. Vinson JP, Jaffe DB, O'Neill K, Karlsson EK, Stange-Thomann N, Anderson S, Mesirov JP, Satoh N, Satou Y, Nusbaum C, et al. Assembly of polymorphic genomes: algorithms and application to Ciona savignyi. Genome Res 2005, 15(8):1127-1135. 10.1101/gr.3722605, 1182225, 16077012.
12. Small KS, Brudno M, Hill MM, Sidow A. A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome. Genome Biol 2007, 8(3):R41. 10.1186/gb-2007-8-3-r41, 1868934, 17374142.
13. Small KS, Brudno M, Hill MM, Sidow A. Extreme genomic variation in a natural population. Proc Natl Acad Sci U S A 2007, 104(13):5698-5703. 10.1073/pnas.0700890104, 1838466, 17372217.
14. Boffelli D, Weer CV, Weng L, Lewis KD, Shoukry MI, Pachter L, Keys DN, Rubin EM. Intraspecies sequence comparisons for annotating genomes. Genome Res 2004, 14(12):2406-2411. 10.1101/gr.3199704, 534664, 15545499.
15. Sanger F, Coulson AR. A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J Mol Biol 1975, 94(3):441-448. 10.1016/0022-2836(75)90213-2, 1100841.
16. Satou Y, Mineta K, Ogasawara M, Sasakura Y, Shoguchi E, Ueno K, Yamada L, Matsumoto J, Wasserscheid J, Dewar K, et al. Improved genome assembly and evidence-based global gene model set for the chordate Ciona intestinalis: new insight into intron and operon populations. Genome Biol 2008, 9(10):R152. 10.1186/gb-2008-9-10-r152, 2760879, 18854010.
17. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990, 215(3):403-410.
18. Satou Y, Kawashima T, Shoguchi E, Nakayama A, Satoh N. An integrated database of the ascidian, Ciona intestinalis: towards functional genomics. Zoolog Sci 2005, 22(8):837-843. 10.2108/zsj.22.837, 16141696.
19. Ning Z, Cox AJ, Mullikin JC. SSAHA: a fast search method for large DNA databases. Genome Res 2001, 11(10):1725-1729. 10.1101/gr.194201, 311141, 11591649.
20. Yang Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Computer applications in the biosciences : CABIOS 1997, 13(5):555-556.
21. UniProtConsortium Ongoing and future developments at the Universal Protein Resource. Nucleic Acids Res 2011, 39(Database issue):D214-219. UniProtConsortium.