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Article; Agriculture and Environmental Biotechnology

Induced splice site mutation generates alternative intron splicing in starch synthase II (SSII) gene in rice

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Pages 1093-1099 | Received 30 Jan 2017, Accepted 21 Aug 2017, Published online: 31 Aug 2017

References

  • Ball SG, Morell MK. From bacterial glycogen to starch: understanding the biogenesis of the plant starch granule. Annu Rev Plant Biol. 2003;54:207–233.
  • James MG, Denyer K, Myers AM. Starch synthesis in the cereal endosperm. Curr Opin Plant Biol. 2003;6:215–222.
  • Pfister B, Zeeman SC. Formation of starch in plant cells. Cell Mol Life Sci. 2016;73:2781–2807.
  • Roy SW, Irimia M. Diversity and evolution of spliceosomal systems. Methods Mol Biol. 2014;1126:13–33.
  • Dacks JB, Doolittle WF. Reconstructing/deconstructing the earliest eukaryotes: how comparative genomics can help. Cell. 2001;107:419–425.
  • Boutz PL, Bhutkar A, Sharp PA. Detained introns are a novel, widespread class of post-transcriptionally spliced introns. Genes Dev. 2015;29:63–80.
  • Mercer TR, Clark MB, Andersen SB, et al. Genome-wide discovery of human splicing branchpoints. Genome Res. 2015;25:290–303.
  • Hsiao Y-HE, Bahn JH, Lin X, et al. Alternative splicing modulated by genetic variants demonstrates accelerated evolution regulated by highly conserved proteins. Genome Res. 2016;26:440–450.
  • Tran VDT, Souiai O, Romero-Barrios N, et al. Detection of generic differential RNA processing events from RNA-seq data. RNA Biol. 2016;13:59–67.
  • Fedorov A, Cao X, Saxonov S, et al. Intron distribution difference for 276 ancient and 131 modern genes suggests the existence of ancient introns. Proc Natl Acad Sci USA. 2001;98:13177–13182.
  • Bondarenko VS, Gelfand MS. Evolution of the exon-intron structure in ciliate genomes. PloS One. 2016 [cited 2017 Feb 25];11:e0161476. DOI:10.1371/journal.pone.0161476
  • Keane PA, Seoighe C. Intron length coevolution across mammalian genomes. Mol Biol Evol. 2016;33:2682–2691.
  • de Souza SJ, Long M, Klein RJ, et al. Toward a resolution of the introns early/late debate: only phase zero introns are correlated with the structure of ancient proteins. Proc Natl Acad Sci USA. 1998;95:5094–5099.
  • Roy SW, Nosaka M, de Souza SJ, et al. Centripetal modules and ancient introns. Gene. 1999;238:85–91.
  • Logsdon JM. The recent origins of spliceosomal introns revisited. Curr Opin Genet Dev. 1998;8:637–648.
  • Zhaxybayeva O, Gogarten JP. Spliceosomal introns: new insights into their evolution. Curr Biol. 2003;13:R764–766.
  • Yenerall P, Zhou L. Identifying the mechanisms of intron gain: progress and trends. Biol Direct. 2012 [cited 2017 Feb 25];7:29. DOI:10.1186/1745-6150-7-29
  • Srinivasan A, Jiménez-Gómez JM, Fornara F, et al. Alternative splicing enhances transcriptome complexity in desiccating seeds. J Integr Plant Biol. 2016;58:947–958.
  • Chong A, Zhang G, Bajic VB. Information for the coordinates of exons (ICE): a human splice sites database. Genomics. 2004;84:762–766.
  • Croft L, Schandorff S, Clark F, et al. ISIS, the intron information system, reveals the high frequency of alternative splicing in the human genome. Nat Genet. 2000;24:340–341.
  • Modrek B, Lee C. A genomic view of alternative splicing. Nat Genet. 2002;30:13–19.
  • Thanaraj TA, Clark F. Human GC-AG alternative intron isoforms with weak donor sites show enhanced consensus at acceptor exon positions. Nucleic Acids Res. 2001;29:2581–2593.
  • Swarup R, Crespi M, Bennett MJ. One gene, many proteins: mapping cell-specific alternative splicing in plants. Dev Cell. 2016;39:383–385.
  • Li S, Yamada M, Han X, et al. High-resolution expression map of the Arabidopsis root reveals alternative splicing and lincRNA regulation. Dev Cell. 2016;39:508–522.
  • Farrer T, Roller AB, Kent WJ, et al. Analysis of the role of Caenorhabditis elegans GC-AG introns in regulated splicing. Nucleic Acids Res. 2002;30:3360–3367.
  • Mornkham T, Wangsomnuk PP, Fu Y-B, et al. Extractions of high quality RNA from the seeds of Jerusalem artichoke and other plant species with high levels of starch and lipid. Plants Basel Switz. 2013;2:302–316.
  • Ma XB, Yang J. An optimized preparation method to obtain high-quality RNA from dry sunflower seeds. Genet Mol Res. 2011;10:160–168.
  • Hirose T, Terao T. A comprehensive expression analysis of the starch synthase gene family in rice (Oryza sativa L.). Planta. 2004;220:9–16.
  • Jiang H, Dian W, Liu F, et al. Molecular cloning and expression analysis of three genes encoding starch synthase II in rice. Planta. 2004;218:1062–1070.
  • Rice Chromosome 10 Sequencing Consortium. In-depth view of structure, activity, and evolution of rice chromosome 10. Science. 2003;300:1566–1569.
  • Thanaraj TA. A clean data set of EST-confirmed splice sites from Homo sapiens and standards for clean-up procedures. Nucleic Acids Res. 1999;27:2627–2637.
  • Rodríguez-Trelles F, Tarrío R, Ayala FJ. Origins and evolution of spliceosomal introns. Annu Rev Genet. 2006;40:47–76.
  • Farlow A, Meduri E, Schlötterer C. DNA double-strand break repair and the evolution of intron density. Trends Genet. 2011;27:1–6.
  • Roy SW, Gilbert W. The evolution of spliceosomal introns: patterns, puzzles and progress. Nat Rev Genet. 2006;7:211–221.
  • Ma M-Y, Che X-R, Porceddu A, et al. Evaluation of the mechanisms of intron loss and gain in the social amoebae Dictyostelium. BMC Evol Biol. 2015 [cited 2017 Feb 25];15:286. DOI:10.1186/s12862-015-0567-y