PTGBase: An integrated database to study tandem duplicated genes in plants

Database

Volumn 2015, Issue , 2015, Pages

  Yu, Jingyin ^a   Ke, Tao ^b   Tehrim, Sadia ^a   Sun, Fengming ^a   Liao, Boshou ^a   Hua, Wei ^a  

^a INSTITUTE OF PLANT PROTECTION   (China)

^b NANYANG NORMAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

GENE DUPLICATION; GENETICS; MULTIGENE FAMILY; NUCLEIC ACID DATABASE; PLANT; PLANT GENE;

DATABASES, NUCLEIC ACID; GENE DUPLICATION; GENES, PLANT; MULTIGENE FAMILY; PLANTS;

EID: 84943327537     PISSN: 17580463     EISSN: None     Source Type: Journal    
DOI: 10.1093/database/bav017     Document Type: Article

References (43)

1. Davies, T.J., Barraclough, T.G., Chase, M.W. et al. (2004) Darwin's abominable mystery: Insights from a supertree of the angiosperms. Proc. Natl Acad. Sci. USA, 101, 1904-1909.
2. Waterston, R.H., Lindblad-Toh, K., Birney, E. et al. (2002) Initial sequencing and comparative analysis of the mouse genome. Nature, 420, 520-562.
3. Smith, S.F., Snell, P., Gruetzner, F. et al. (2002) Analyses of the extent of shared synteny and conserved gene orders between the genome of Fugu rubripes and human 20q. Genome Res., 12, 776-784.
4. Lockton, S. and Gaut, B.S. (2005) Plant conserved non-coding sequences and paralogue evolution. Trends Genet., 21, 60-65.
5. Wang, Y., Wang, X. and Paterson, A.H. (2012) Genome and gene duplications and gene expression divergence: a view from plants. Ann. N YAcad. Sci., 1256, 1-14.
6. Kane, J., Freeling, M. and Lyons, E. (2010) The evolution of a high copy gene array in Arabidopsis. J. Mol. Evol., 70, 531-544.
7. Clark, R.M., Schweikert, G. and Toomajian, C. et al. (2007) Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana. Science, 317, 338-342.
8. Rizzon, C., Ponger, L. and Gaut, B.S. (2006) Striking similarities in the genomic distribution of tandemly arrayed genes in Arabidopsis and rice. PLoS Comput. Biol., 2, e115.
9. Parniske, M., Wulff, B.B. and Bonnema, G. et al. (1999) Homologues of the Cf-9 disease resistance gene (Hcr9s) are present at multiple loci on the short arm of tomato chromosome 1. Mol. Plant Microb. Interact., 12, 93-102.
10. Leister, D. (2004) Tandem and segmental gene duplication and recombination in the evolution of plant disease resistance gene. Trends Genet, 20, 116-122.
11. Bellieny-Rabelo, D., Oliveira, A.E. and Venancio, T.M. (2013) Impact of whole-genome and tandem duplications in the expansion and functional diversification of the F-box family in legumes (Fabaceae). PLoS One, 8, e55127.
12. Hofberger, J.A., Lyons, E., Edger, P.P. et al. (2013) Whole genome and tandem duplicate retention facilitated glucosinolate pathway diversification in the mustard family. Genome Biol. Evol., 5, 2155-2173.
13. Liu, S., Liu, Y., Yang, X. et al. (2014) The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes. Nat Commun, 5, 3930.
14. Yu, J., Tehrim, S., Zhang, F. et al. (2014) Genome-wide comparative analysis of NBS-encoding genes between Brassica species and Arabidopsis thaliana. BMC Genomics, 15, 3.
15. Force, A., Lynch, M., Pickett, F.B. et al. (1999) Preservation of duplicate genes by complementary, degenerative mutations. Genetics, 151, 1531-1545.
16. Li, W.-H., Gojobori, T. and Nei, M. (1981) Pseudogenes as a paradigm of neutral evolution. Nature, 292, 237-239.
17. Soukup, S. W. (1974), Evolution by gene duplication. S. Ohno. Springer-Verlag, New York. 1970. 160 pp. Teratology, 9: 250-251. doi: 10.1002/tera.1420090224.
18. Blanc, G. and Wolfe, K.H. (2004) Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell, 16, 1667-1678.
19. Chang, C.H., Chang, Y.C., Underwood, A. et al. (2007) VNTRDB: a bacterial variable number tandem repeat locus database. Nucleic Acids Res., 35, D416-D421.
20. Hanada, K., Zou, C., Lehti-Shiu, M.D. et al. (2008) Importance of lineage-specific expansion of plant tandem duplicates in the adaptive response to environmental stimuli. Plant Physiol., 148, 993-1003.
21. Jiang, W.K., Liu, Y.L., Xia, E.H. et al. (2013) Prevalent role of gene features in determining evolutionary fates of whole-genome duplication duplicated genes in flowering plants. Plant Physiol., 161, 1844-1861.
22. Pal, C., Papp, B. and Hurst, L.D. (2001) Highly expressed genes in yeast evolve slowly. Genetics, 158, 927-931.
23. Chapman, B.A., Bowers, J.E., Feltus, F.A.et al. (2006) Buffering of crucial functions by paleologous duplicated genes may contribute cyclicality to angiosperm genome duplication. Proc. Natl Acad. Sci. USA, 103, 2730-2735.
24. Schnable, J.C., Springer, N.M. and Freeling, M. (2011) Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss. Proc. Natl Acad. Sci. USA, 108, 4069-4074.
25. Thomas, B.C., Pedersen, B. and Freeling, M. (2006) Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dosesensitive genes. Genome Res., 16, 934-946.
26. Moghe, G.D., Hufnagel, D.E., Tang, H. et al. (2014) Consequences of whole-genome triplication as revealed by comparative genomic analyses of the Wild Radish Raphanus raphanistrum and three other Brassicaceae species. The Plant Cell Online, 26, 1925-1937.
27. Ruitberg, C.M., Reeder, D.J. and Butler, J.M. (2001) STRBase: a short tandem repeat DNA database for the human identity testing community. Nucleic Acids Res., 29, 320-322.
28. Boby, T., Patch, A.M. and Aves, S.J. (2005) TRbase: a database relating tandem repeats to disease genes for the human genome. Bioinformatics, 21, 811-816.
29. Gelfand, Y., Rodriguez, A. and Benson, G. (2007) TRDB-the Tandem Repeats Database. Nucleic Acids Res., 35, D80-D87.
30. Hiller, M., Nikolajewa, S., Huse, K. et al. (2007) TassDB: a database of alternative tandem splice sites. Nucleic Acids Res., 35, D188-D192.
31. Le Fleche, P., Hauck, Y., Onteniente, L. et al. (2001) A tandem repeats database for bacterial genomes: application to the genotyping of Yersinia pestis and Bacillus anthracis. BMC Microbiol, 1, 2.
32. Hietaniemi, J. (2008) Comprehensive perl archive network. Helsinki, Finland: CPAN, pp. 6.
33. Altschul, S.F., Madden, T.L., Schaffer, A.A. et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
34. Huala, E., Dickerman, A.W., Garcia-Hernandez, M. et al. (2001) The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant. Nucleic Acids Res., 29, 102-105.
35. Yu, J., Zhao, M., Wang, X. et al. (2013) Bolbase: a comprehensive genomics database for Brassica oleracea. BMC Genomics, 14, 664.
36. Goodstein, D.M., Shu, S., Howson, R. et al. (2012) Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res., 40, D1178-D1186.
37. Li, L., Stoeckert, C.J., Jr. and Roos, D.S. (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res., 13, 2178-2189.
38. Conesa, A., Gotz, S., Garcia-Gomez, J.M. et al. (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics, 21, 3674-3676.
39. Quevillon, E., Silventoinen, V., Pillai, S. et al. (2005) InterProScan: protein domains identifier. Nucleic Acids Res., 33, W116-W120.
40. Tatusov, R.L., Galperin, M.Y., Natale, D.A. et al. (2000) The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res., 28, 33-36.
41. Lynch, M. and Conery, J.S. (2000) The evolutionary fate and consequences of duplicate genes. Science, 290, 1151-1155.
42. Papp, B., Pal, C. and Hurst, L.D. (2003) Dosage sensitivity and the evolution of gene families in yeast. Nature, 424, 194-197.
43. Argout, X., Salse, J., Aury, J.M. et al. (2011) The genome of Theobroma cacao. Nat. Genet., 43, 101-108.