| [1] |
Ng SY, Lin L, Soh BS, Stanton LW. 2013. Long noncoding RNAs in development and disease of the central nervous system. Trends in Genetics 29:461−68 doi: 10.1016/j.tig.2013.03.002 |
| [2] |
van Werven FJ, Neuert G, Hendrick N, Lardenois A, Buratowski S, et al. 2012. Transcription of two long noncoding RNAs mediates mating-type control of gametogenesis in budding yeast. Cell 150:1170−81 doi: 10.1016/j.cell.2012.06.049 |
| [3] |
Flynn RA, Chang HY. 2014. Long noncoding RNAs in cell-fate programming and reprogramming. Cell Stem Cell 14:752−61 doi: 10.1016/j.stem.2014.05.014 |
| [4] |
Iyer MK, Niknafs YS, Malik R, Singhal U, Sahu A, et al. 2015. The landscape of long noncoding RNAs in the human transcriptome. Nature Genetics 47:199−208 doi: 10.1038/ng.3192 |
| [5] |
Shafiq S, Li J, Sun Q. 2016. Functions of plants long non-coding RNAs. Biochimica et Biophysica Acta - Gene Regulatory Mechanisms 1859:155−62 doi: 10.1016/j.bbagrm.2015.06.009 |
| [6] |
Marquardt S, Raitskin O, Wu Z, Liu F, Sun Q, et al. 2014. Functional consequences of splicing of the antisense transcript COOLAIR on FLC transcription. Molecular Cell 54:156−65 doi: 10.1016/j.molcel.2014.03.026 |
| [7] |
Zhang YC, Liao JY, Li ZY, Yu Y, Zhang JP, et al. 2014. Genome-wide screening and functional analysis identify a large number of long noncoding RNAs involved in the sexual reproduction of rice. Genome Biology 15:512 doi: 10.1186/s13059-014-0512-1 |
| [8] |
Wang Y, Fan X, Lin F, He G, Terzaghi W, et al. 2014. Arabidopsis noncoding RNA mediates control of photomorphogenesis by red light. PNAS 111:10359−64 doi: 10.1073/pnas.1409457111 |
| [9] |
Wang Y, Deng X, Zhu D. 2022. From molecular basics to agronomic benefits: Insights into noncoding RNA-mediated gene regulation in plants. Journal of Integrative Plant Biology 64:2290−308 doi: 10.1111/jipb.13420 |
| [10] |
Hong Y, Zhang Y, Cui J, Meng J, Chen Y, et al. 2022. The lncRNA39896-miR166b-HDZs module affects tomato resistance to Phytophthora infestans. Journal of Integrative Plant Biology 64:1979−93 doi: 10.1111/jipb.13339 |
| [11] |
Di C, Yuan J, Wu Y, Li J, Lin H, et al. 2014. Characterization of stress-responsive lncRNAs in Arabidopsis thaliana by integrating expression, epigenetic and structural features. The Plant Journal 80:848−61 doi: 10.1111/tpj.12679 |
| [12] |
Li L, Eichten SR, Shimizu R, Petsch K, Yeh CT, et al. 2014. Genome-wide discovery and characterization of maize long non-coding RNAs. Genome Biology 15:R40 doi: 10.1186/gb-2014-15-2-r40 |
| [13] |
Chialva C, Blein T, Crespi M, Lijavetzky D. 2021. Insights into long non-coding RNA regulation of anthocyanin carrot root pigmentation. Scientific Reports 11:4093 doi: 10.1038/s41598-021-83514-4 |
| [14] |
Golicz AA, Singh MB, Bhalla PL. 2018. The long intergenic noncoding RNA (LincRNA) landscape of the soybean genome. Plant Physiology 176:2133−47 doi: 10.1104/pp.17.01657 |
| [15] |
Zhang Y, Fan F, Zhang Q, Luo Y, Liu Q, et al. 2022. Identification and functional analysis of long non-coding RNA (lncRNA) in response to seed aging in rice. Plants 11:3223 doi: 10.3390/plants11233223 |
| [16] |
Zhao L, Wang J, Li Y, Song T, Wu Y, et al. 2021. NONCODEV6: an updated database dedicated to long non-coding RNA annotation in both animals and plants. Nucleic Acids Research 49:D165−d71 doi: 10.1093/nar/gkaa1046 |
| [17] |
Di Marsico M, Paytuvi Gallart A, Sanseverino W, Aiese Cigliano R. 2022. GreeNC 2.0: a comprehensive database of plant long non-coding RNAs. Nucleic Acids Research 50:D1442−D1447 doi: 10.1093/nar/gkab1014 |
| [18] |
Jin J, Lu P, Xu Y, Li Z, Yu S, et al. 2021. PLncDB V2.0: a comprehensive encyclopedia of plant long noncoding RNAs. Nucleic Acids Research 49:D1489−d1495 doi: 10.1093/nar/gkaa910 |
| [19] |
Singh A, Vivek AT, Kumar S. 2021. AlnC: An extensive database of long non-coding RNAs in angiosperms. PLoS One 16:e0247215 doi: 10.1371/journal.pone.0247215 |
| [20] |
Lou D, Li F, Ge J, Fan W, Liu Z, et al. 2022. LncPheDB: a genome-wide lncRNAs regulated phenotypes database in plants. aBIOTECH 3:169−77 doi: 10.1007/s42994-022-00084-3 |
| [21] |
Zhang Z, Xu Y, Yang F, Xiao B, Li G. 2021. RiceLncPedia: a comprehensive database of rice long non-coding RNAs. Plant Biotechnology Journal 19:1492−94 doi: 10.1111/pbi.13639 |
| [22] |
Zhu M, Zhang M, Xing L, Li W, Jiang H, et al. 2017. Transcriptomic analysis of long non-coding RNAs and coding genes uncovers a complex regulatory network that is involved in maize seed development. Genes 8:274 doi: 10.3390/genes8100274 |
| [23] |
Li Y, Tan Z, Zeng C, Xiao M, Lin S, et al. 2023. Regulation of seed oil accumulation by lncRNAs in Brassica napus. Biotechnology for Biofuels and Bioproducts 16:22 doi: 10.1186/s13068-022-02256-1 |
| [24] |
Zhou YF, Zhang YC, Sun YM, Yu Y, Lei MQ, et al. 2021. The parent-of-origin lncRNA MISSEN regulates rice endosperm development. Nature Communications 12:6525 doi: 10.1038/s41467-021-26795-7 |
| [25] |
Guo G, Liu X, Sun F, Cao J, Huo N, et al. 2018. Wheat miR9678 affects seed germination by generating phased siRNAs and modulating abscisic acid/gibberellin signaling. The Plant Cell 30:796−814 doi: 10.1105/tpc.17.00842 |
| [26] |
Madhawan A, Sharma A, Bhandawat A, Rahim MS, Kumar P, et al. 2020. Identification and characterization of long non-coding RNAs regulating resistant starch biosynthesis in bread wheat (Triticum aestivum L.). Genomics 112:3065−74 doi: 10.1016/j.ygeno.2020.05.014 |
| [27] |
Cao P, Fan W, Li P, Hu Y. 2021. Genome-wide profiling of long noncoding RNAs involved in wheat spike development. BMC Genomics 22:493 doi: 10.1186/s12864-021-07851-4 |
| [28] |
Ma K, Shi W, Xu M, Liu J, Zhang F. 2018. Genome-wide identification and characterization of long non-coding RNA in wheat roots in response to Ca2+ channel blocker. Frontiers in Plant Science 9:244 doi: 10.3389/fpls.2018.00244 |
| [29] |
Shumayla, Sharma S, Taneja M, Tyagi S, Singh K, Upadhyay SK. 2017. Survey of High Throughput RNA-Seq Data Reveals Potential Roles for lncRNAs during Development and Stress Response in Bread Wheat. Frontiers in Plant Science 8:1019 doi: 10.3389/fpls.2017.01019 |
| [30] |
Xu S, Dong Q, Deng M, Lin D, Xiao J, et al. 2021. The vernalization-induced long non-coding RNA VAS functions with the transcription factor TaRF2b to promote TaVRN1 expression for flowering in hexaploid wheat. Molecular Plant 14:1525−38 doi: 10.1016/j.molp.2021.05.026 |
| [31] |
Clavijo BJ, Venturini L, Schudoma C, Accinelli GG, Kaithakottil G, et al. 2017. An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations. Genome Research 27:885−96 doi: 10.1101/gr.217117.116 |
| [32] |
Wang X, Chen S, Shi X, Liu D, Zhao P, et al. 2019. Hybrid sequencing reveals insight into heat sensing and signaling of bread wheat. The Plant Journal 98:1015−32 doi: 10.1111/tpj.14299 |
| [33] |
Wei J, Cao H, Liu J, Zuo J, Fang Y, et al. 2019. Insights into transcriptional characteristics and homoeolog expression bias of embryo and de-embryonated kernels in developing grain through RNA-Seq and Iso-Seq. Functional & Integrative Genomics 19:919−32 doi: 10.1007/s10142-019-00693-0 |
| [34] |
Chen S, Zhou Y, Chen Y, Gu J. 2018. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34:i884−i890 doi: 10.1093/bioinformatics/bty560 |
| [35] |
Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, et al. 2013. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29:15−21 doi: 10.1093/bioinformatics/bts635 |
| [36] |
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25:2078−79 doi: 10.1093/bioinformatics/btp352 |
| [37] |
Wu TD, Watanabe CK. 2005. GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics 21:1859−75 doi: 10.1093/bioinformatics/bti310 |
| [38] |
Chen Y, Guo Y, Guan P, Wang Y, Wang X, et al. 2023. A wheat integrative regulatory network from large-scale complementary functional datasets enables trait-associated gene discovery for crop improvement. Molecular Plant 16:393−414 doi: 10.1016/j.molp.2022.12.019 |
| [39] |
Zhao X, Li J, Lian B, Gu H, Li Y, et al. 2018. Global identification of Arabidopsis lncRNAs reveals the regulation of MAF4 by a natural antisense RNA. Nature Communications 9:5056 doi: 10.1038/s41467-018-07500-7 |
| [40] |
Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, et al. 2015. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nature Biotechnology 33:290−95 doi: 10.1038/nbt.3122 |
| [41] |
Kang YJ, Yang D, Kong L, Hou M, Meng Y, et al. 2017. CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features. Nucleic Acids Research 45:W12−W16 doi: 10.1093/nar/gkx428 |
| [42] |
Sun L, Luo H, Bu D, Zhao G, Yu K, et al. 2013. Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts. Nucleic Acids Research 41:e166 doi: 10.1093/nar/gkt646 |
| [43] |
Pertea G, Pertea M. 2020. GFF Utilities: GffRead and GffCompare. F1000 Research 9:304 doi: 10.12688/f1000research.23297.2 |
| [44] |
Bray NL, Pimentel H, Melsted P, Pachter L. 2016. Near-optimal probabilistic RNA-seq quantification. Nature Biotechnology 34:525−27 doi: 10.1038/nbt.3519 |
| [45] |
Schmittgen TD, Livak KJ. 2008. Analyzing real-time PCR data by the comparative C(T) method. Nature Protocols 3:1101−8 doi: 10.1038/nprot.2008.73 |
| [46] |
Zhang P, Jondiko TO, Tilley M, Awika JM. 2014. Effect of high molecular weight glutenin subunit composition in common wheat on dough properties and steamed bread quality. Journal of the Science of Food and Agriculture 94:2801−6 doi: 10.1002/jsfa.6635 |
| [47] |
Xing L, Xi Y, Qiao X, Huang C, Wu Q, et al. 2021. The landscape of lncRNAs in Cydia pomonella provides insights into their signatures and potential roles in transcriptional regulation. BMC Genomics 22:4 doi: 10.1186/s12864-020-07313-3 |
| [48] |
IWGSC, Appels R, Eversole K, Stein N, Feuillet C, et al. 2018. Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science 361:eaar7191 doi: 10.1126/science.aar7191 |
| [49] |
Juery C, Concia L, De Oliveira R, Papon N, Ramírez-González R, et al. 2021. New insights into homoeologous copy number variations in the hexaploid wheat genome. Plant Genome 14:e20069 doi: 10.1002/tpg2.20069 |
| [50] |
Julca I, Ferrari C, Flores-Tornero M, Proost S, Lindner AC, et al. 2021. Comparative transcriptomic analysis reveals conserved programmes underpinning organogenesis and reproduction in land plants. Nature Plants 7:1143−59 doi: 10.1038/s41477-021-00958-2 |
| [51] |
Priyam A, Woodcroft BJ, Rai V, Moghul I, Munagala A, et al. 2019. Sequenceserver: A modern graphical user interface for custom BLAST databases. Molecular Biology and Evolution 36:2922−24 doi: 10.1093/molbev/msz185 |
| [52] |
Yang Z, Wang Z, Wang W, Xie X, Chai L, et al. 2022. ggComp enables dissection of germplasm resources and construction of a multiscale germplasm network in wheat. Plant Physiology 188:1950−65 doi: 10.1093/plphys/kiac029 |
| [53] |
Gao Y, An K, Guo W, Chen Y, Zhang R, et al. 2021. The endosperm-specific transcription factor TaNAC019 regulates glutenin and starch accumulation and its elite allele improves wheat grain quality. The Plant Cell 33:603−22 doi: 10.1093/plcell/koaa040 |
| [54] |
Guo D, Hou Q, Zhang R, Lou H, Li Y, et al. 2020. Over-expressing TaSPA-B reduces prolamin and starch accumulation in wheat (Triticum aestivum L.) grains. International Journal of Molecular Sciences 21:3257 doi: 10.3390/ijms21093257 |
| [55] |
Wang H, Li Y, Chern M, Zhu Y, Zhang L, et al. 2021. Suppression of rice miR168 improves yield, flowering time and immunity. Nature Plants 7:129−36 doi: 10.1038/s41477-021-00852-x |
| [56] |
Utsugi S, Ashikawa I, Nakamura S, Shibasaka M. 2020. TaABI5, a wheat homolog of Arabidopsis thaliana ABA insensitive 5, controls seed germination. Journal of Plant Research 133:245−56 doi: 10.1007/s10265-020-01166-3 |
| [57] |
Finkelstein RR, Lynch TJ. 2000. The Arabidopsis abscisic acid response gene ABI5 encodes a basic leucine zipper transcription factor. The Plant Cell 12:599−609 doi: 10.1105/tpc.12.4.599 |
| [58] |
Bardou F, Ariel F, Simpson CG, Romero-Barrios N, Laporte P, et al. 2014. Long noncoding RNA modulates alternative splicing regulators in Arabidopsis. Developmental Cell 30:166−76 doi: 10.1016/j.devcel.2014.06.017 |
| [59] |
Bulger M, Groudine M. 2011. Functional and mechanistic diversity of distal transcription enhancers. Cell 144:327−39 doi: 10.1016/j.cell.2011.01.024 |
| [60] |
Marques AC, Hughes J, Graham B, Kowalczyk MS, Higgs DR, et al. 2013. Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs. Genome Biology 14:R131 doi: 10.1186/gb-2013-14-11-r131 |