Evolutionary analyses of non-family genes in plants

Plant Journal

Volumn 73, Issue 5, 2013, Pages 788-797

  Ye, Chu Yu ^a,b   Li, Ting ^a,c   Yin, Hengfu ^a   Weston, David J ^a   Tuskan, Gerald A ^a   Tschaplinski, Timothy J ^a   Yang, Xiaohan ^a  

^a OAK RIDGE NATIONAL LABORATORY   (United States)

^b BEIJING FORESTRY UNIVERSITY   (China)

^c PIONEER HI BRED INTERNATIONAL INC   (United States)

Author keywords

comparative genomics; evolution; functional genomics; non family genes; plant genome

Indexed keywords

ARABIDOPSIS; BIOLOGICAL PROCESS; COMPARATIVE GENOMICS; COMPARATIVE STUDIES; EVOLUTION; FUNCTIONAL GENOMICS; GENE DUPLICATIONS; GENE FAMILIES; GENE LOSS; HUB PROTEINS; PLANT GENOMES; PLANT LINEAGES; PLANT SPECIES; PROTEIN SEQUENCES; PROTEIN-PROTEIN INTERACTION NETWORKS; SEGMENTAL DUPLICATIONS; SPECIES SPECIFICS; STRESS RESPONSE; SYSTEMATIC ANALYSIS;

BIOLOGY; PROTEINS;

GENES;

ARABIDOPSIS; ARTICLE; GENE DUPLICATION; GENETICS; GENOMICS; MOLECULAR EVOLUTION; MOLECULAR GENETICS; PHYLOGENY; PLANT GENE; PLANT GENOME; SPECIES DIFFERENCE; VIRIDIPLANTAE;

ARABIDOPSIS; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENES, PLANT; GENOME, PLANT; GENOMICS; MOLECULAR SEQUENCE ANNOTATION; PHYLOGENY; SPECIES SPECIFICITY; VIRIDIPLANTAE;

ARABIDOPSIS; DICOTYLEDONEAE; MAGNOLIOPHYTA; VIRIDIPLANTAE;

EID: 84874484607     PISSN: 09607412     EISSN: 1365313X     Source Type: Journal    
DOI: 10.1111/tpj.12073     Document Type: Article

References (44)

1. Brandao, M.M., Dantas, L.L., and, Silva-Filho, M.C., (2009) AtPIN: Arabidopsis thaliana protein interaction network. BMC Bioinformatics, 10, 454.
2. Briesemeister, S., Rahnenfuhrer, J., and, Kohlbacher, O., (2010) YLoc-an interpretable web server for predicting subcellular localization. Nucleic Acids Res. 38, W497-W502.
3. Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., and, Madden, T.L., (2009) BLAST+: architecture and applications. BMC Bioinformatics, 10, 421.
4. Cannon, S.B., Mitra, A., Baumgarten, A., Young, N.D., and, May, G., (2004) The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana. BMC Plant Biol. 4, 1-21.
5. Chauve, C., Doyon, J.P., and, El-Mabrouk, N., (2008) Gene family evolution by duplication, speciation, and loss. J. Comput. Biol. 15, 1043-1062.
6. Conesa, A., Gotz, S., Garcia-Gomez, J.M., Terol, J., Talon, M., and, Robles, M., (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics, 21, 3674-3676. (Pubitemid 41264107)
7. De Grassi, A., Lanave, C., and, Saccone, C., (2008) Genome duplication and gene-family evolution: the case of three OXPHOS gene families. Gene, 421, 1-6.
8. Demuth, J.P., and, Hahn, M.W., (2009) The life and death of gene families. BioEssays, 31, 29-39.
9. Du, Z., Zhou, X., Ling, Y., Zhang, Z., and, Su, Z., (2010) agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res. 38, W64-W70.
10. Duarte, J.M., Wall, P.K., Edger, P.P., Landherr, L.L., Ma, H., Pires, J.C., Leebens-Mack, J., and, dePamphilis, C.W., (2010) Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels. BMC Evol. Biol. 10, 61.
11. Enright, A.J., Van Dongen, S., and, Ouzounis, C.A., (2002) An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 30, 1575-1584. (Pubitemid 34679732)
12. Freeling, M., (2009) Bias in plant gene content following different sorts of duplication: tandem, whole-genome, segmental, or by transposition. Annu. Rev. Plant Biol. 60, 433-453.
13. Goodstein, D.M., Shu, S., Howson, R., et al. (2012) Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res. 40, D1178-D1186.
14. Guo, W.J., Li, P., Ling, J., and, Ye, S.P., (2007) Significant comparative characteristics between orphan and nonorphan genes in the rice (Oryza sativa L.) genome. Comp. Funct. Genomics, 21676, doi:10.1155/2007/21676. (Pubitemid 350226778)
15. He, X., and, Zhang, J., (2006) Why do hubs tend to be essential in protein networks? PLoS Genet. 2, e88.
16. Horton, P., Park, K.J., Obayashi, T., Fujita, N., Harada, H., Adams-Collier, C.J., and, Nakai, K., (2007) WoLF PSORT: protein localization predictor. Nucleic Acids Res. 35, W585-W587.
17. Hrabak, E.M., Chan, C.W., Gribskov, M., et al. (2003) The Arabidopsis CDPK-SnRK superfamily of protein kinases. Plant Physiol. 132, 666-680. (Pubitemid 36725704)
18. Hughes, A.L., (1994) The evolution of functionally novel proteins after gene duplication. Proc. Biol. Sci. 256, 119-124. (Pubitemid 24168165)
19. Kilian, J., Whitehead, D., Horak, J., Wanke, D., Weinl, S., Batistic, O., D'Angelo, C., Bornberg-Bauer, E., Kudla, J., and, Harter, K., (2007) The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses. Plant J. 50, 347-363. (Pubitemid 46624141)
20. Liao, B.Y., and, Zhang, J.Z., (2007) Mouse duplicate genes are as essential as singletons. Trends Genet. 23, 378-381.
21. Movahedi, S., Van de Peer, Y., and, Vandepoele, K., (2011) Comparative network analysis reveals that tissue specificity and gene function are important factors influencing the mode of expression evolution in Arabidopsis and rice. Plant Physiol. 156, 1316-1330.
22. Nakano, T., Suzuki, K., Fujimura, T., and, Shinshi, H., (2006) Genome-wide analysis of the ERF gene family in Arabidopsis and rice. Plant Physiol. 140, 411-432. (Pubitemid 43956266)
23. Nam, J., Kim, J., Lee, S., An, G.H., Ma, H., and, Nei, M.S., (2004) Type I MADS-box genes have experienced faster birth-and-death evolution than type II MADS-box genes in angiosperms. Proc. Natl Acad. Sci. USA, 101, 1910-1915. (Pubitemid 38228989)
24. Obayashi, T., Kinoshita, K., Nakai, K., Shibaoka, M., Hayashi, S., Saeki, M., Shibata, D., Saito, K., and, Ohta, H., (2007) ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis. Nucleic Acids Res. 35, D863-D869. (Pubitemid 46056323)
25. Ohno, S., (1970) Evolution by Gene Duplication. New York: Springer-Verlag.
26. Olex, A.L., and, Fetrow, J.S., (2011) SC(2)ATmd: a tool for integration of the figure of merit with cluster analysis for gene expression data. Bioinformatics, 27, 1330-1331.
27. Ooka, H., Satoh, K., Doi, K., et al. (2003) Comprehensive analysis of NAC family genes in Oryza sativa and Arabidopsis thaliana. DNA Res. 10, 239-247. (Pubitemid 38249931)
28. Parenicova, L., de Folter, S., Kieffer, M., et al. (2003) Molecular and phylogenetic analyses of the complete MADS-box transcription factor family in Arabidopsis: new openings to the MADS world. Plant Cell, 15, 1538-1551. (Pubitemid 36872595)
29. Proost, S., Pattyn, P., Gerats, T., and, Van de Peer, Y., (2011) Journey through the past: 150 million years of plant genome evolution. Plant J. 66, 58-65.
30. Schmid, M., Davison, T.S., Henz, S.R., Pape, U.J., Demar, M., Vingron, M., Scholkopf, B., Weigel, D., and, Lohmann, J.U., (2005) A gene expression map of Arabidopsis thaliana development. Nat. Genet. 37, 501-506. (Pubitemid 40617278)
31. Supek, F., Bosnjak, M., Skunca, N., and, Smuc, T., (2011) REVIGO summarizes and visualizes long lists of gene ontology terms. PLoS One, 6, e21800.
32. Usadel, B., Obayashi, T., Mutwil, M., Giorgi, F.M., Bassel, G.W., Tanimoto, M., Chow, A., Steinhauser, D., Persson, S., and, Provart, N.J., (2009) Co-expression tools for plant biology: opportunities for hypothesis generation and caveats. Plant Cell Environ. 32, 1633-1651.
33. Vallabhajosyula, R.R., Chakravarti, D., Lutfeali, S., Ray, A., and, Raval, A., (2009) Identifying hubs in protein interaction networks. PLoS One, 4, e5344.
34. Van de Peer, Y., Fawcett, J.A., Proost, S., Sterck, L., and, Vandepoele, K., (2009) The flowering world: a tale of duplications. Trends Plant Sci. 14, 680-688.
35. Verrier, P.J., Bird, D., Burla, B., et al. (2008) Plant ABC proteins-a unified nomenclature and updated inventory. Trends Plant Sci. 13, 151-159.
36. Wang, D., Zhang, Y., Zhang, Z., Zhu, J., and, Yu, J., (2010) KaKs-Calculator 2.0: A toolkit incorporating gamma-series methods and sliding window strategies. Genomics Proteomics Bioinformatics, 8, 77-80.
37. Yang, X., Tuskan, G.A., and, Cheng, M.Z., (2006) Divergence of the Dof gene families in poplar, Arabidopsis, and rice suggests multiple modes of gene evolution after duplication. Plant Physiol. 142, 820-830. (Pubitemid 44764611)
38. Yang, X., Kalluri, U.C., Jawdy, S., Gunter, L.E., Yin, T., Tschaplinski, T.J., Weston, D.J., Ranjan, P., and, Tuskan, G.A., (2008) The F-box gene family is expanded in herbaceous annual plants relative to woody perennial plants. Plant Physiol. 148, 1189-1200. (Pubitemid 352847485)
39. Yang, X., Ye, C.Y., Bisaria, A., Tuskan, G.A., and, Kalluri, U.C., (2011a) Identification of candidate genes in Arabidopsis and Populus cell wall biosynthesis using text-mining, co-expression network analysis and comparative genomics. Plant Sci. 181, 675-687.
40. Yang, X., Ye, C.Y., Cheng, Z.M., Tschaplinski, T.J., Wullschleger, S.D., Yin, W.L., Xia, X.L., and, Tuskan, G.A., (2011b) Genomic aspects of research involving polyploid plants. Plant Cell Tiss. Org. 104, 387-397.
41. Ye, C.Y., Li, T., Tuskan, G.A., Tschaplinski, T.J., and, Yang, X., (2011) Comparative analysis of GT14/GT14-like gene family in Arabidopsis, Oryza, Populus, Sorghum and Vitis. Plant Sci. 181, 688-695.
42. Yin, Y., Chen, H., Hahn, M.G., Mohnen, D., and, Xu, Y., (2010) Evolution and function of the plant cell wall synthesis-related glycosyltransferase family 8. Plant Physiol. 153, 1729-1746.
43. Yonekura-Sakakibara, K., and, Hanada, K., (2011) An evolutionary view of functional diversity in family 1 glycosyltransferases. Plant J. 66, 182-193.
44. Yu, C.S., Chen, Y.C., Lu, C.H., and, Hwang, J.K., (2006) Prediction of protein subcellular localization. Proteins, 64, 643-651.