Alamancos GP, Pagès A, Trincado JL, Bellora N, Eyras E. Leveraging transcript quantification for fast computation of alternative splicing profiles. RNA. 2015;21:1521–31.
Article
CAS
PubMed
PubMed Central
Google Scholar
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–10.
Article
CAS
PubMed
Google Scholar
Ashoub A, Müller N, Jiménez-Gómez JM, Brüggemann W. Prominent alterations of wild barley leaf transcriptome in response to individual and combined drought acclimation and heat shock conditions. Physiol Plant. 2018;163:18–29.
Article
CAS
PubMed
Google Scholar
Bazin J, Romero N, Rigo R, Charon C, Blein T, Ariel F, Crespi M. Nuclear speckle RNA binding proteins remodel alternative splicing and the non-coding Arabidopsis Transcriptome to regulate a cross-talk between Auxin and immune responses. Front Plant Sci. 2018;9:1209.
Article
PubMed
PubMed Central
Google Scholar
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bray NL, Pimentel H, Melsted P, Pachter L. Near-optimal probabilistic RNA-seq quantification. Nat Biotechnol. 2016;34:525–7.
Article
CAS
PubMed
Google Scholar
Brown JWS, Calixto CP, Zhang R. High-quality reference transcript datasets hold the key to transcript-specific RNA-sequencing analysis in plants. New Phytol. 2017;213:525–30.
Article
CAS
PubMed
Google Scholar
Busch A, Hertel KJ. Extensive regulation of NAGNAG alternative splicing: new tricks for the spliceosome? Genome Biol. 2012;13:143.
Article
PubMed
PubMed Central
Google Scholar
Calixto CPG, Tzioutziou NA, James AB, Hornyik C, Guo W, Zhang R, Nimmo HG, Brown JWS. Cold-dependent expression and alternative splicing of Arabidopsis long non-coding RNAs. Front Plant Sci. 2019;10:235.
Article
PubMed
PubMed Central
Google Scholar
Calixto CPG, Guo W, James AB, Tzioutziou NA, Entizne JC, Panter PE, Knight H, Nimmo HG, Zhang R, Brown JWS. Rapid and dynamic alternative splicing impacts the Arabidopsis cold response Transcriptome. Plant Cell. 2018;30:1424–44.
Article
CAS
PubMed
PubMed Central
Google Scholar
Calixto CPG, Simpson CG, Waugh R, Brown JWS. Alternative splicing of barley clock genes in response to low temperature. PLoS One. 2016;11:e0168028.
Article
PubMed
PubMed Central
CAS
Google Scholar
Capovilla G, Pajoro A, Immink RG, Schmid M. Role of alternative pre-mRNA splicing in temperature signaling. Curr Opin Plant Biol. 2015;27:97–103.
Article
CAS
PubMed
Google Scholar
Carvalho RF, Feijão CV, Duque P. On the physiological significance of alternative splicing events in higher plants. Protoplasma. 2013;250:639–50.
Article
CAS
PubMed
Google Scholar
Chamala S, Feng G, Chavarro C, Barbazuk WB. Genome-wide identification of evolutionarily conserved alternative splicing events in flowering plants. Front Bioeng Biotechnol. 2015;3:33.
Article
PubMed
PubMed Central
Google Scholar
Dahleen LS, Vander Wal LJ, Franckowiak JD. Characterization and molecular mapping of genes determining semidwarfism in barley. J Hered. 2005;96:654–62.
Article
CAS
PubMed
Google Scholar
Dawson IK, Russell J, Powell W, Steffenson B, Thomas WT, Waugh R. Barley: a translational model for adaptation to climate change. New Phytol. 2015;206:913–31.
Article
PubMed
Google Scholar
Dobin A, Gingeras TR. Optimizing RNA-Seq mapping with STAR. Methods Mol Biol. 2016;1415:245–62.
Article
CAS
PubMed
Google Scholar
Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29:15–21.
Article
CAS
PubMed
Google Scholar
Filichkin S, Priest HD, Megraw M, Mockler TC. Alternative splicing in plants: directing traffic at the crossroads of adaptation and environmental stress. Curr Opin Plant Biol. 2015;24:125–35.
Article
CAS
PubMed
Google Scholar
Engström PG, Steijger T, Sipos B, Grant GR, Kahles A, Rätsch G, Goldman N, Hubbard TJ, Harrow J, Guigó R, Bertone P, RGASP Consortium. Systematic evaluation of spliced alignment programs for RNA-seq data. Nat Methods. 2013;10:1185–91.
Article
PubMed
PubMed Central
CAS
Google Scholar
Gan X, Stegle O, Behr J, Steffen JG, Drewe P, Hildebrand KL, Lyngsoe R, Schultheiss SJ, Osborne EJ, Sreedharan VT, et al. Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature. 2011;477:419–23.
Article
CAS
PubMed
PubMed Central
Google Scholar
Guo G, Dondup D, Yuan X, Gu F, Wang D, Jia F, Lin Z, Baum M, Zhang J. Rare allele of HvLox-1 associated with lipoxygenase activity in barley (Hordeum vulgare L.). Theor Appl Genet. 2014;127:2095–103.
Article
CAS
PubMed
PubMed Central
Google Scholar
Guo W, Tzioutziou N, Stephen G, Milne I, Calixto C, Waugh R, Brown JWS, Zhang R. 3D RNA-seq - a powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists. bioRxiv. 2019; https://doi.org/10.1101/656686.
Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, MacManes MD, et al. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc. 2013;8:1494–512.
Article
CAS
PubMed
Google Scholar
Hayer KE, Pizarro A, Lahens NF, Hogenesch JB, Grant GR. Benchmark analysis of algorithms for determining and quantifying full-length mRNA splice forms from RNA-seq data. Bioinformatics. 2015;31:3938–45.
CAS
PubMed
PubMed Central
Google Scholar
International Barley Sequencing Consortium. A physical, genetic and functional sequence assembly of the barley genome. Nature. 2012;491:711–6.
Article
CAS
Google Scholar
Janiak A, Kwasniewski M, Sowa M, Gajek K, Żmuda K, Kościelniak J, Szarejko I. No time to waste: Transcriptome study reveals that drought tolerance in barley may be attributed to stressed-like expression patterns that exist before the occurrence of stress. Front Plant Sci. 2018;8:2212.
Article
PubMed
PubMed Central
Google Scholar
Kalyna M, Simpson CG, Syed NH, Lewandowska D, Marquez Y, Kusenda B, Marshall J, Fuller J, Cardle L, McNicol J, Dinh HQ, Barta A, Brown JWS. Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis. Nucleic Acids Res. 2012;40:2454–69.
Article
CAS
PubMed
Google Scholar
Kim SH, Koroleva OA, Lewandowska D, Pendle AF, Clark GP, Simpson CG, Shaw PJ, Brown JWS. Aberrant mRNA transcripts and the nonsense-mediated decay proteins UPF2 and UPF3 are enriched in the Arabidopsis nucleolus. Plant Cell. 2009;21:2045–57.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kintlová M, Blavet N, Cegan R, Hobza R. Transcriptome of barley under three different heavy metal stress reaction. Genom Data. 2017;13:15–7.
Article
PubMed
PubMed Central
Google Scholar
Laloum T, Martin G, Duque P. Alternative splicing control of abiotic stress responses. Trends Plant Sci. 2018;23:140–50.
Article
CAS
PubMed
Google Scholar
Lee Y, Rio DC. Mechanisms and regulation of alternative pre-mRNA splicing. Annu Rev Biochem. 2015;84:291–323.
Article
CAS
PubMed
PubMed Central
Google Scholar
Liu H, Liu H, Zhou L, Zhang Z, Zhang X, Wang M, Li H, Lin Z. Parallel domestication of the heading date 1 gene in cereals. Mol Biol Evol. 2015;32:2726–37.
Article
CAS
PubMed
Google Scholar
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.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mascher M, Gundlach H, Himmelbach A, Beier S, Twardziok SO, Wicker T, Radchuk V, Dockter C, Hedley PE, Russell J, et al. A chromosome conformation capture ordered sequence of the barley genome. Nature. 2017;544:427–33.
Article
CAS
PubMed
Google Scholar
Mastrangelo AM, Marone D, Laidò G, De Leonardis AM, De Vita P. Alternative splicing: enhancing ability to cope with stress via transcriptome plasticity. Plant Sci. 2012;185-186:40–9.
Article
CAS
PubMed
Google Scholar
Matsumoto T, Tanaka T, Sakai H, Amano N, Kanamori H, Kurita K, Kikuta A, Kamiya K, Yamamoto M, Ikawa H, et al. Comprehensive sequence analysis of 24,783 barley full-length cDNAs derived from 12 clone libraries. Plant Physiol. 2011;156:20–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mrízová K, Holasková E, Öz MT, Jiskrová E, Frébort I, Galuszka P. Transgenic barley: a prospective tool for biotechnology and agriculture. Biotechnol Adv. 2014;32:137–57.
Article
PubMed
CAS
Google Scholar
Nilsen TW, Graveley BR. Expansion of the eukaryotic proteome by alternative splicing. Nature. 2010;463:457–63.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ouyang S, Zhu W, Hamilton J, Lin H, Campbell M, Childs K, Thibaud-Nissen F, Malek RL, Lee Y, Zheng L, et al. 2007. The TIGR Rice Genome Annotation Resource: improvements and new features. Nucleic Acids Res. 35 (Database issue):D883-7.
Article
CAS
PubMed
Google Scholar
Panahi B, Mohammadi SA, Ebrahimi Khaksefidi R, Fallah Mehrabadi J, Ebrahimie E. Genome-wide analysis of alternative splicing events in Hordeum vulgare: highlighting retention of intron-based splicing and its possible function through network analysis. FEBS Lett. 2015;589:3564–75.
Article
CAS
PubMed
Google Scholar
Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C. Salmon provides fast and bias-aware quantification of transcript expression. Nat Methods. 2017;14:417–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol. 2015;33:290–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pham AT, Maurer A, Pillen K, Brien C, Dowling K, Berger B, Eglinton JK, March TJ. Genome-wide association of barley plant growth under drought stress using a nested association mapping population. BMC Plant Biol. 2019;19:134.
Article
PubMed
PubMed Central
Google Scholar
Reddy AS, Marquez Y, Kalyna M, Barta A. Complexity of the alternative splicing landscape in plants. Plant Cell. 2013;25:3657–83.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ren P, Meng Y, Li B, Ma X, Si E, Lai Y, Wang J, Yao L, Yang K, Shang X, Wang H. Molecular Mechanisms of Acclimatization to Phosphorus Starvation and Recovery Underlying Full-Length Transcriptome Profiling in Barley (Hordeum vulgare L.). Front Plant Sci. 2018;9:500.
Article
PubMed
PubMed Central
Google Scholar
Russell J, Mascher M, Dawson IK, Kyriakidis S, Calixto C, Freund F, Bayer M, Milne I, Marshall-Griffiths T, Heinen S, et al. Exome sequencing of geographically diverse barley landraces and wild relatives gives insights into environmental adaptation. Nat Genet. 2016;48:1024–30.
Article
CAS
PubMed
Google Scholar
Schindler S, Szafranski K, Hiller M, Ali GS, Palusa SG, Backofen R, Platzer M, Reddy AS. Alternative splicing at NAGNAG acceptors in Arabidopsis thaliana SR and SR-related protein-coding genes. BMC Genomics. 2008;9:159.
Article
PubMed
PubMed Central
CAS
Google Scholar
Shi Y, Sha G, Sun X. Genome-wide study of NAGNAG alternative splicing in Arabidopsis. Planta. 2014;239:127–38.
Article
CAS
PubMed
Google Scholar
Shirasu K, Lahaye T, Tan MW, Zhou F, Azevedo C, Schulze-Lefert P. A novel class of eukaryotic zinc-binding proteins is required for disease resistance signaling in barley and development in C. elegans. Cell. 1999;99:355–66.
Article
CAS
PubMed
Google Scholar
Simpson CG, Fuller J, Maronova M, Kalyna M, Davidson D, McNicol J, Barta A, Brown JWS. Monitoring changes in alternative precursor messenger RNA splicing in multiple gene transcripts. Plant J. 2008;53:1035–48.
Article
CAS
PubMed
Google Scholar
Sokal RR, Rohlf FJ. The principles and practice of statistics in biological research. 3rd ed. New York: W. H. Freeman; 1995.
Google Scholar
Soneson C, Love MI, Patro R, Hussain S, Malhotra D, Robinson MD. A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs. Life Sci Alliance. 2019;2:e201800175.
Article
PubMed
PubMed Central
Google Scholar
Staiger D, Brown JWS. Alternative splicing at the intersection of biological timing, development, and stress responses. Plant Cell. 2013;25:3640–56.
Article
CAS
PubMed
PubMed Central
Google Scholar
Szakonyi D, Duque P. Alternative splicing as a regulator of early plant development. Front Plant Sci. 2018;9:1174.
Article
PubMed
PubMed Central
Google Scholar
Thatcher SR, Zhou W, Leonard A, Wang BB, Beatty M, Zastrow-Hayes G, Zhao X, Baumgarten A, Li B. Genome-wide analysis of alternative splicing in Zea mays: landscape and genetic regulation. Plant Cell. 2014;26:3472–87.
Article
CAS
PubMed
PubMed Central
Google Scholar
Veeneman BA, Shukla S, Dhanasekaran SM, Chinnaiyan AM, Nesvizhskii AI. Two-pass alignment improves novel splice junction quantification. Bioinformatics. 2016;32:43–9.
CAS
PubMed
Google Scholar
Wu TD, Watanabe CK. GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics. 2005;21:1859–75.
Article
CAS
PubMed
Google Scholar
Zhang Q, Zhang X, Wang S, Tan C, Zhou G, Li C. Involvement of alternative splicing in barley seed germination. PLoS One. 2016a;11:e0152824.
Article
PubMed
PubMed Central
CAS
Google Scholar
Zhang Q, Zhang X, Pettolino F, Zhou G, Li C. Changes in cell wall polysaccharide composition, gene transcription and alternative splicing in germinating barley embryos. J Plant Physiol. 2016b;191:127–39.
Article
CAS
PubMed
Google Scholar
Zhang R, Calixto CPG, Marquez Y, Venhuizen P, Tzioutziou NA, Guo W, Spensley M, Entizne JC, Lewandowska D, Ten Have S, et al. A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing. Nucleic Acids Res. 2017a;45:5061–73.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang R, Calixto CP, Tzioutziou NA, James AB, Simpson CG, Guo W, Marquez Y, Kalyna M, Patro R, Eyras E, et al. AtRTD - a comprehensive reference transcript dataset resource for accurate quantification of transcript-specific expression in Arabidopsis thaliana. New Phytol. 2015;208:96–101.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang XN, Shi Y, Powers JJ, Gowda NB, Zhang C, Ibrahim HMM, Ball HB, Chen SL, Lu H, Mount SM. Transcriptome analyses reveal SR45 to be a neutral splicing regulator and a suppressor of innate immunity in Arabidopsis thaliana. BMC Genomics. 2017b;8:772.
Article
CAS
Google Scholar