Analysis of expressed sequence tags and alternative splicing genes in sacred lotus (Nelumbo nucifera Gaertn.)

Plant OMICS

Volumn 6, Issue 4, 2013, Pages 311-317

  VanBuren, Robert ^a   Walters, Braden ^b   Ming, Ray ^a   Min, Xiang Jia ^b  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b YOUNGSTOWN STATE UNIVERSITY   (United States)

Author keywords

Alternative splicing; Exon, intron, sacred lotus; Expressed sequence tags

Indexed keywords

EID: 84884325264     PISSN: 18360661     EISSN: 18363644     Source Type: Journal    
DOI: None     Document Type: Article

References (22)

1. Baek JM, Han P, Iandolino A, Cook DR (2008) Characterization and comparison of intron structure and alternative splicing between Medicago truncatula, Populus trichocarpa, Arabidopsis and rice. Plant Mol Biol. 674:99-510
2. Filichkin SA, Priest HD, Givan SA, Shen R, Bryant DW, Fox SE, Wong WK, Mockler TC (2010) Genome-wide mapping of alternative splicing in Arabidopsis thaliana. Genome Res. 20:45-58
3. Florea L, Hartzell G, Zhang Z, Rubin GM, Miller W (1998) A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res. 8:967-974
4. Foissac S, Sammeth M (2007) ASTALAVISTA: dynamic and flexible analysis of alternative splicing events in custom gene datasets. Nucleic Acids Res 35:W297-99.
5. Lambert JD, Chan XY, Spiecker B, Sweet HC (2010) Characterizing the embryonic transcriptome of the snail ilyanassa. Integr Comp Biol. 50:768-777
6. Lareau LF, Brooks AN, Soergel DAW, Meng Q, Brenner SE (2007) The coupling of alternative splicing and nonsense mediated mRNA decay. In: Blencowe BJ and Graveley BR (ed) Alternative splicing in the postgenomic era. Landes Biosciences, Austin, TX, p 191-212
7. Mastrangelo AM, Marone D, Laidò G, De Leonardis AM, De Vita P (2012) Alternative splicing: enhancing ability to cope with stress via transcriptome plasticity. Plant Sci. 185-186: 40-49.
8. McCarthy FM, Wang N, Magee GB, Williams WP, Luthe DS, Burgess SC (2006) AgBase: a functional genomics resource for agriculture. BMC Genomics. 7:229
9. McGuire AM, Pearson MD, Neafsey DE, Galagan JE (2005) Cross-kingdom patterns of alternative splicing and splice recognition. Genome Biol. 9:R50
10. Min XJ (2013) ASFinder: a tool for genome-wide identification of alternatively spliced transcripts from EST-derived sequences. Int J Bioinform Res Appl. 9:221-226
11. Min, XJ, Butler G, Storms R, Tsang A (2005) OrfPredictor: predicting protein-coding regions in EST-derived sequences. Nucleic Acids Res 33:W677-W680
12. Ming R, Vanburen R, Liu Y, Yang M, Han Y, Li LT, Zhang Q, Kim MJ, Schatz MC,Campbell M, Li J, Bowers JE, Tang H, Lyons E, Ferguson AA, Narzisi G, Nelson DR, Blaby-Haas CE, Gschwend AR, Jiao Y, Der JP, Zeng F, Han J, Min XJ, Hudson KA,Singh R, Grennan AK, Karpowicz SJ, Watling JR, Ito K, Robinson SA, Hudson ME, Yu Q, Mockler TC, Carroll A, Zheng Y, Sunkar R, Jia R, Chen N, Arro J, Wai CM, Wafula E, Spence A, Han Y, Xu L, Zhang J, Peery R, Haus MJ, Xiong W, Walsh JA, Wu J, Wang ML, Zhu YJ, Paull RE, Britt AB, Du C, Downie SR, Schuler MA, Michael TP, Long SP, Ort DR, Schopf JW, Gang DR, Jiang N, Yandell M, Depamphilis CW, Merchant SS, Paterson AH, Buchanan BB, Li S, Shen-Miller J. (2013) Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.). Genome Biol. 14: R41
13. Ner-Gaon H, Leviatan N, Rubin E, Fluhr R (2007) Comparative cross-species alternative splicing in plants. Plant Physiol. 144:1632-1641
14. Reddy AS (2007) Alternative splicing of pre-messenger RNAs in plants in the genomic era. Annu Rev Plant Biol. 58:267-294
15. Reddy ASN, Rogers MF, Richardson DN, Hamilton M and Ben-Hur A (2012) Deciphering the plant splicing code: experimental and computational approaches for predicting alternative splicing and splicing regulatory elements. Front Plant Sci. 3:18.
16. Roberts GC, Smith CW (2002) Alternative splicing: combinatorial output from the genome. Curr Opin Chem Biol. 6:375-383
17. Sablok G, Gupta PK, Baek JM, Vazquez F, Min XJ (2011) Genome-wide survey of alternative splicing in the grass Brachypodium distachyon: an emerging model biosystem for plant functional genomics. Biotechnol Lett. 33:629-636
18. Stamm S, Ben-Ari S, Rafalska I, Tang Y, Zhang Z, Toiber D, Thanaraj TA, Soreq H (2005) Function of alternative splicing. Gene 344:1-20
19. Walters B, Lum G, Sablok G, Min XJ (2013) Genome-wide landscape of alternative splicing events in Brachypodium distachyon. DNA Res. 20:163-171
20. Wang B, Brendel V (2006) Genome wide comparative analysis of alternative splicing in plants. Proc Natl Acad Sci USA 103:7175-7180
21. Wang BB, O'Toole M, Brendel V, Young ND. (2008) Cross-species EST alignments reveal novel and conserved alternative splicing events in legumes. BMC Plant Biol. 8:17
22. Yu Q, Moore PH, Albert HH, Roader AH, Ming R (2005) Cloning and characterization of a FLORICAULA/LEAFY ortholog, PFL, in polygamous papaya. Cell Res. 15:576-584