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Article Addendum

Genomic architecture and functional relationships of intronless, constitutively- and alternatively-spliced genes in Brachypodium distachyon

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Article: e1042640 | Received 06 Apr 2015, Accepted 12 Apr 2015, Published online: 31 Aug 2015

References

  • Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB. Alternative isoform regulation in human tissue transcriptomes. Nature 2008; 456:470-6; PMID:18978772; http://dx.doi.org/10.1038/nature07509
  • Krawczak M, Thomas NST, Hundrieser B, Mort M, Wittig M, Hampe J, Cooper DN. Single base-pair substitutions in exon–intron junctions of human genes: nature, distribution, and consequences for mRNA splicing. Hum Mutat 2007; 28:150-8; PMID:17001642; http://dx.doi.org/10.1002/humu.20400
  • Marquez Y, Brown JWS, Simpson C, Barta A, Kalyna M. Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis. Genome Res 2012; 22:1184-95; PMID:22391557; http://dx.doi.org/10.1101/gr.134106.111
  • Zhang G, Guo G, Hu X, Zhang Y, Li Q, Li R, Zhuang R, Lu Z, He Z, Fang X, et al. Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome. Genome Res 2010; 20:646-54; PMID:20305017; http://dx.doi.org/10.1101/gr.100677.109
  • Filichkin SA, Priest HD, Givan SA, Shen R, Bryant DW, Fox SE, Wong WK, Mockler TC. Genome-wide mapping of alternative splicing in Arabidopsis thaliana. Genome Res 2010; 20:45-58; PMID:19858364; http://dx.doi.org/10.1101/gr.093302.109
  • Shen Y, Zhou Z, Wang Z, Li W, Fang C, Wu M, Ma Y, Liu T, Kong LA, Peng DL, et al. Global dissection of alternative splicing in paleopolyploid soybean. Plant Cell 2014; 26:996-1008; PMID:24681622; http://dx.doi.org/10.1105/tpc.114.122739
  • Reddy ASN, Marquez Y, Kalyna M, Barta A. Complexity of the alternative splicing landscape in plants. Plant Cell 2013; 25:3657-83; PMID:24179125; http://dx.doi.org/10.1105/tpc.113.117523
  • Staiger D, Brown JWS. Alternative splicing at the intersection of biological timing, development, and stress responses. Plant Cell 2013; 25:3640-56; PMID:24179132; http://dx.doi.org/10.1105/tpc.113.113803
  • Brkljacic J, Grotewold E, Scholl R, Mockler T, Garvin DF, Vain P, Brutnell T, Sibout R, Bevan M, Budak H, et al. Brachypodium as a model for the grasses: Today and the future. Plant Physiol 2011; 157:3-13; PMID:21771916; http://dx.doi.org/10.1104/pp.111.179531
  • Catalán P, Chalhoub B, Chochois V, Garvin DF, Hasterok R, Manzaneda AJ, Mur LA, Pecchioni N, Rasmussen SK, Vogel JP, et al. Update on the genomics and basic biology of Brachypodium. International Brachypodium Initiative (IBI). Trends Plant Sci 2014; 19:414-8; http://dx.doi.org/10.1016/j.tplants.2014.05.002
  • The International Brachypodium Initiative. Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 2010; 463:763-8; PMID:20148030; http://dx.doi.org/10.1038/nature08747.
  • Mandadi KK, Scholthof K-BG. Characterization of a viral synergism in the monocot Brachypodium distachyon reveals distinctly altered host molecular processes associated with disease. Plant Physiol 2012; 160:1432-52; PMID:22961132; http://dx.doi.org/10.1104/pp.112.204362
  • Mandadi KK, Pyle JD, Scholthof K-BG. Comparative analysis of antiviral responses in Brachypodium distachyon and Setaria viridis reveal conserved and unique outcomes among C3 and C4 plant defenses. Mol Plant Microbe Interact 2014; 27:1277-90; PMID:25296115; http://dx.doi.org/10.1094/MPMI-05-14-0152-R
  • Mandadi KK, Scholthof K-BG. Plant immune responses against viruses: How does a virus cause disease? Plant Cell 2013; 25:1489-505; PMID:23709626; http://dx.doi.org/10.1105/tpc.113.111658
  • Mandadi KK, Scholthof K-BG. Genome-wide analysis of alternative splicing landscapes modulated during plant-virus interactions in Brachypodium distachyon. Plant Cell 2015; 27:71-85; PMID:25634987; http://dx.doi.org/10.1105/tpc.114.133991
  • Reddy ASN. Alternative splicing of pre-messenger RNAs in plants in the genomic era. Annu Rev Plant Biol 2007; 58:267-94; PMID:17222076; http://dx.doi.org/10.1146/annurev.arplant.58.032806.103754
  • Du Z, Zhou X, Ling Y, Zhang Z, Su Z. agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res 2010; 38:W64-W70; PMID:20435677; http://dx.doi.org/10.1093/nar/gkq310
  • Supek F, Bošnjak M, Škunca N, Šmuc T. REVIGO summarizes and visualizes long lists of gene ontology terms. PLOS ONE 2011; 6:e21800; PMID:21789182; http://dx.doi.org/10.1371/journal.pone.0021800
  • Sagan L. On the origin of mitosing cells. J Theor Biol 1967; 14:225-74; http://dx.doi.org/10.1016/0022-5193(67)90079-3
  • Baum D. The origin of primary plastids: A pas de deux or a ménage à trois? Plant Cell 2013; 25:4-6; PMID:23371952; http://dx.doi.org/10.1105/tpc.113.109496

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