Transcriptome analysis indicates considerable divergence in alternative splicing between duplicated genes in arabidopsis thaliana

Genetics

Volumn 198, Issue 4, 2014, Pages 1473-1481

  Tack, David C ^a   Pitchers, William R ^b   Adams, Keith L ^a  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^b MICHIGAN STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME; ARABIDOPSIS PROTEIN; CCA1 PROTEIN, ARABIDOPSIS; DNA BINDING PROTEIN; LHY PROTEIN, ARABIDOPSIS; TRANSCRIPTION FACTOR;

ALTERNATIVE RNA SPLICING; ARABIDOPSIS THALIANA; ARTICLE; BRACHYPODIUM; CCA1 GENE; DOWN REGULATION; DUPLICATE GENE; EXON; GENE DUPLICATION; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENE FREQUENCY; GENE LOSS; GENETIC CONSERVATION; GENETIC VARIABILITY; INTRON; INTRON RETENTION; LEAF TISSUE; LHY GENE; NONHUMAN; NONSENSE MEDIATED MRNA DECAY; PARALOGY; PLANT GENE; PLANT GENETICS; PLANT GENOME; POPULUS TRICHOCARPA; QUALITATIVE ANALYSIS; QUANTITATIVE GENETICS; RNA SEQUENCE; ARABIDOPSIS; GENE EXPRESSION PROFILING; GENETICS; MOLECULAR EVOLUTION;

ARABIDOPSIS THALIANA;

ALTERNATIVE SPLICING; ARABIDOPSIS; ARABIDOPSIS PROTEINS; DNA-BINDING PROTEINS; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENES, DUPLICATE; NONSENSE MEDIATED MRNA DECAY; TRANSCRIPTION FACTORS; TRANSCRIPTOME;

EID: 84915750474     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.114.169466     Document Type: Article

References (50)

1. Ast, G., 2004 How did alternative splicing evolve? Nat. Rev. Genet. 5: 773-782.
2. Barbosa-Morais, N. L., M. Irimia, Q. Pan, H. Y. Xiong, S. Gueroussov et al., 2012 The evolutionary landscape of alternative splicing in vertebrate species. Science 338: 1587-1593.
3. Blanc, G., and K. H. Wolfe, 2004a Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 16: 1667-1678.
4. Blanc, G., and K. H. Wolfe, 2004b Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. Plant Cell 16: 1679-1691.
5. Blanc, G., K. Hokamp, and K. H. Wolfe, 2003 A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome. Genome Res. 13: 137-144.
6. Boue, S., I. Letunic, and P. Bork, 2003 Alternative splicing and evolution. BioEssays 25: 1031-1034.
7. Bowers, J. E., B. A. Chapman, J. Rong, and A. H. Paterson, 2003 Unraveling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422: 433-438.
8. Casneuf, T., S. De Bodt, J. Raes, S. Maere, and Y. Van de Peer, 2006 Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana. Genome Biol. 7: R13.
9. Chen, M., and J. L. Manley, 2009 Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches. Nat. Rev. Mol. Cell Biol. 10: 741-754.
10. Cui, L., P. K. Wall, J. H. Leebens-Mack, B. G. Lindsay, D. E. Soltis et al., 2006 Widespread genome duplications throughout the history of flowering plants. Genome Res. 16: 738-749.
11. Conant, G. C., and K. H. Wolfe, 2008 Turning a hobby into a job; how duplicated genes find new functions. Nat. Rev. Genet. 9: 938-950.
12. Cusack, B. P., and K. H. Wolfe, 2007 When gene marriages don't work out: divorce by subfunctionalization. Trends Genet. 23: 270-272.
13. Darracq, A., and K. L. Adams, 2013 Features of evolutionarily conserved alternative splicing events between Brassica and Arabidopsis. New Phytol. 199: 252-263.
14. Dong, M. A., E. M. Farré, and M. F. Thomashow, 2011 Circadian clock-associated 1 and late elongated hypocotyl regulate expression of the C-repeat binding factor (CBF) pathway in Arabidopsis. Proc. Natl. Acad. Sci. USA 108: 7241-7246.
15. Drechsel, G., A. Kahles, A. K. Kesarwani, E. Stauffer, J. Behr et al., 2013 Nonsense-mediated decay of alternative precursor mRNA splicing variants is a major determinant of the Arabidopsis steady state transcriptome. Plant Cell 10: 3726-3742.
16. Duvick, J., A. Fu, U. Muppirala, M. Sabharwal, W. D. Wikerson et al., 2008 PlantGDB: a resource for comparative plant genomics. Nucleic Acids Res. 36: 959-965.
17. Eden, E., D. Lipson, S. Yogev, and Z. Yakhini, 2007 Discovering motifs in ranked lists of DNA sequences. PLoS Comput. Biol. 3: e39.
18. Eden, E., R. Navon, I. Stienfeld, D. Lipson, and Z. Yakhini, 2009 GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists. BMC Bioinformatics 10: 48.
19. Edgar, R., M. Domrachev, and A. E. Lach, 2002 Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 30: 207-210.
20. Filichkin, S. A., H. D. Priest, S. A. Givan, R. Shen, D. W. Bryant et al., 2010 Genome-wide mapping of alternative splicing in Arabidopsis thaliana. Genome Res. 20: 45-58.
21. Filichkin, S. A., and T. C. Mockler, 2012 Unproductive alternative splicing and nonsense mRNAs: a widespread phenomenon among plant circadian clock genes. Biol. Direct 7: 20.
22. Force, A., M. Lynch, F. B. Pickett, A. Amores, Y. L. Yan et al., 1999 Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151: 1531-1545.
23. Fujiwara, S., A. Oda, R. Yoshida, K. Niinuma, K. Miyata et al., 2008 Circadian clock proteins LHY and CCA1 regulate SVP protein accumulation to control flowering in Arabidopsis. Plant Cell 20: 2960-2971.
24. Han, M. V., J. P. Demuth, C. L. Mc, C. Grath, C. Casola et al., 2009 Adaptive evolution of young gene duplicates in mammals. Genome Res. 5: 859-867.
25. Huelga, S. C., A. Q. Vu, J. D. Arnold, T. Y. Liang, P. P. Liu et al., 2012 Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins. Cell Rep. 1: 167-178.
26. Jiao, Y., N. J. Wickett, S. Ayyampalayam, A. S. Chanderbali, L. Landherr et al., 2011 Ancestral polyploidy in seed plants and angiosperms. Nature 473: 97-100.
27. Kalyna, M., C. G. Simpson, N. H. Syed, D. Lewandowska, Y. Marquez et al., 2011 Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis. Nucleic Acids Res. 40: 2454-2469.
28. Kasahara, M., 2007 The 2R hypothesis: an update. Curr. Opin. Immunol. 19: 547-552.
29. Lister, J. A., J. Close, and D. W. Rabile, 2001 Duplicate mitf genes in zebrafish: complementary expression and conservation of melanogenic potential. Dev. Biol. 237: 333-344.
30. Liu, S., G. J. Baute, and K. L. Adams, 2011 Organ and cell typespecific complementary expression patterns and regulatory neofunctionalization between duplicated genes in Arabidopsis thaliana. Genome Biol. Evol. 3: 1419-1436.
31. Lu, T., G. Lu, D. Fan, C. Zhu, W. Li et al., 2010 Function annotation of rice transcriptome at single nucleotide resolution by RNA-seq. Genome Res. 20: 1238-1249.
32. Marquez, Y., J. W. Brown, C. Simpson, A. Barta, and M. Kalyna, 2012 Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis. Genome Res. 22: 1184-1195.
33. Marshall, A. N., M. C. Montealegre, C. Jimenez-Lopez, M. C. Lorenz, and A. van Hoof, 2013 Alternative splicing and subfunctionalization generates functional diversity in fungal proteomes. PLoS Genet. 9: e1003376.
34. McManus, J. C., J. D. Coolon, J. Eipper-Mains, P. J. Wittkopp, and B. R. Gravely, 2014 Evolution of splicing regulatory networks in Drosophila. Genome Res. 24: 786-796.
35. Nilsen, T. W., and B. R. Gravely, 2010 Expansion of the eukaryotic proteome by alternative splicing. Nature 463: 457-463.
36. Proost, S., M. Van Bel, L. Sterck, K. Billiau, T. Van Parys et al., 2009 PLAZA: a comparative genomics resource to study gene and genome evolution in plants. Plant Cell 21: 3718-3731.
37. Reddy, A. S. N., Y.Marquez, M.Kalyna, andA. Barta, 2013 Complexity of the alternative splicing landscape in plants. Plant Cell 25: 3657- 3683.
38. Renny-Byfield, S., J. P. Gallagher, C. E. Grover, E. Szadkowski, J. T. Page et al., 2014 Ancient gene duplicates in Gossypium (Cotton) exhibit near-complete expression divergence. Genome Biol. Evol. 6: 559-571.
39. Sanchez, S. E., E. Petrillo, E. J. Beckwith, X. Zhang, M. L. Rugnone et al., 2010 A methyl transferase links the circadian clock to the regulation of alternative splicing. Nature 468: 112- 116.
40. Schnable, J. C., N.M. Springer, andM. Freeling, 2011 Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss. Proc. Natl. Acad. Sci. USA 108: 4069-4074.
41. Schöning, J. C., C. Streitner, I. M. Meyer, Y. Gao, and D. Staiger, 2008 Reciprocal regulation of glycine-rich RNA-binding proteins via an interlocked feedback loop coupling alternative splicing to nonsense-mediated decay in Arabidopsis. Nucleic Acids Res. 36: 6977-6987.
42. Sémon, M., and K. H. Wolfe, 2007 Consequences of genome duplication. Curr. Opin. Genet. Dev. 17: 505-512.
43. Seo, P. J., M. Park, M. Lim, S. Kin, M. Lee et al., 2012 A selfregulatory circuit of CIRCADIAN CLOCK-ASSOCIATED1 underlies the circadian clock regulation of temperature responses in Arabidopsis. Plant Cell 24: 2427-2442.
44. Shen, Y., Z. Zhou, Z. Wang, W. Li, C. Fang et al., 2014 Global dissection of alternative splicing in paleopolyploid soybean. Plant Cell 26: 996-1008.
45. Sorek, R., R. Shamir, and G. Ast, 2004 How prevalent is functional alternative splicing in the human genome? Trends Genet. 20: 68-71.
46. Staiger, D., and J. W. S. Brown, 2013 Alternative splicing at the intersection of biological timing, development, and stress responses. Plant Cell 25: 3640-3656.
47. Stamatakis, A., 2006 RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688-2690.
48. Wang, B. B., and V. Brendel, 2006 Genomewide comparative analysis of alternative splicing in plants. Proc. Natl. Acad. Sci. USA 103: 7175-7180.
49. Wu, T. D., and C. K. Watanabe, 2005 Gmap: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics 21: 1859-1875.
50. Zhang, P. G., S. Z. Huang, A. Pin, and K. L. Adams, 2010 Extensive divergence in alternative splicing patterns after gene and genome duplication during the evolutionary history of Arabidopsis. Mol. Biol. Evol. 27: 1686-1697.