{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,4,19]],"date-time":"2025-04-19T10:10:51Z","timestamp":1745057451790,"version":"3.37.3"},"reference-count":90,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2019,1,24]],"date-time":"2019-01-24T00:00:00Z","timestamp":1548288000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31570674","31800566"],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key R&D Program of China","doi-asserted-by":"crossref","award":["2018YFD0600101","2016YFD0600106"],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"crossref"}]},{"name":"International Science and Technology Cooperation and Exchange Fund"},{"DOI":"10.13039\/501100008766","name":"Fujian Agriculture and Forestry University","doi-asserted-by":"publisher","award":["KXGH17016"],"id":[{"id":"10.13039\/501100008766","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Natural Science Foundation of Fujian Province of China","award":["2018J01608"]},{"name":"Program for scientific and technological innovation team in university of Fujian province","award":["118\/KLA18069A"]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,9,1]]},"abstract":"Abstract<\/jats:title>\n \n Motivation<\/jats:title>\n MicroRNA (miRNA) and alternative splicing (AS)-mediated post-transcriptional regulation has been extensively studied in most eukaryotes. However, the interplay between AS and miRNAs has not been explored in plants. To our knowledge, the overall profile of miRNA target sites in circular RNAs (circRNA) generated by alternative back splicing has never been reported previously. To address the challenge, we identified miRNA target sites located in alternatively spliced regions of the linear and circular splice isoforms using the up-to-date single-molecule real-time (SMRT) isoform sequencing (Iso-Seq) and Illumina sequencing data in eleven plant species.<\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n In total, we identified 399\u2009401 and 114\u2009574 AS events from linear and circular RNAs, respectively. Among them, there were 64\u2009781 and 41\u2009146 miRNA target sites located in linear and circular AS region, respectively. In addition, we found 38\u2009913 circRNAs to be overlapping with 45\u2009648 AS events of its own parent isoforms, suggesting circRNA regulation of AS of linear RNAs by forming R-loop with the genomic locus. Here, we present a comprehensive database of miRNA targets in alternatively spliced linear and circRNAs (ASmiR) and a web server for deposition and identification of miRNA target sites located in the alternatively spliced region of linear and circular RNAs. This database is accompanied by an easy-to-use web query interface for meaningful downstream analysis. Plant research community can submit user-defined datasets to the web service to search AS regions harboring small RNA target sites. In conclusion, this study provides an unprecedented resource to understand regulatory relationships between miRNAs and AS in both gymnosperms and angiosperms.<\/jats:p>\n <\/jats:sec>\n \n Availability and implementation<\/jats:title>\n The readily accessible database and web-based tools are available at http:\/\/forestry.fafu.edu.cn\/bioinfor\/db\/ASmiR.<\/jats:p>\n <\/jats:sec>\n \n Supplementary information<\/jats:title>\n Supplementary data are available at Bioinformatics online.<\/jats:p>\n <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz038","type":"journal-article","created":{"date-parts":[[2019,1,21]],"date-time":"2019-01-21T20:21:36Z","timestamp":1548102096000},"page":"3119-3126","source":"Crossref","is-referenced-by-count":23,"title":["The interplay between microRNA and alternative splicing of linear and circular RNAs in eleven plant species"],"prefix":"10.1093","volume":"35","author":[{"given":"Huiyuan","family":"Wang","sequence":"first","affiliation":[{"name":"Basic Forestry and Proteomics Research Center, College of Forestry , Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology"}]},{"given":"Huihui","family":"Wang","sequence":"additional","affiliation":[{"name":"Basic Forestry and Proteomics Research Center, College of Forestry , Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology"}]},{"given":"Hangxiao","family":"Zhang","sequence":"additional","affiliation":[{"name":"Basic Forestry and Proteomics Research Center, College of Forestry , Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology"}]},{"given":"Sheng","family":"Liu","sequence":"additional","affiliation":[{"name":"College of Life Science, Fujian Agriculture and Forestry University , Fuzhou, China"}]},{"given":"Yongsheng","family":"Wang","sequence":"additional","affiliation":[{"name":"Basic Forestry and Proteomics Research Center, College of Forestry , Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology"},{"name":"College of Life Science, Fujian Agriculture and Forestry University , Fuzhou, China"}]},{"given":"Yubang","family":"Gao","sequence":"additional","affiliation":[{"name":"Basic Forestry and Proteomics Research Center, College of Forestry , Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology"},{"name":"College of Life Science, Fujian Agriculture and Forestry University , Fuzhou, China"}]},{"given":"Feihu","family":"Xi","sequence":"additional","affiliation":[{"name":"Basic Forestry and Proteomics Research Center, College of Forestry , Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology"},{"name":"College of Life Science, Fujian Agriculture and Forestry University , Fuzhou, China"}]},{"given":"Liangzhen","family":"Zhao","sequence":"additional","affiliation":[{"name":"Basic Forestry and Proteomics Research Center, College of Forestry , Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology"}]},{"given":"Bo","family":"Liu","sequence":"additional","affiliation":[{"name":"College of Forestry, Fujian Agriculture and Forestry University , Fuzhou, China"}]},{"given":"Anireddy S N","family":"Reddy","sequence":"additional","affiliation":[{"name":"Colorado State University Department of Biology, Program in Molecular Plant Biology, Program in Cell and Molecular Biology, , Fort Collins, CO, USA"}]},{"given":"Chentao","family":"Lin","sequence":"additional","affiliation":[{"name":"Basic Forestry and Proteomics Research Center, College of Forestry , Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology"},{"name":"University of California Department of Molecular Cell & Developmental Biology, , Los Angeles, CA, USA"}]},{"given":"Lianfeng","family":"Gu","sequence":"additional","affiliation":[{"name":"Basic Forestry and Proteomics Research Center, College of Forestry , Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology"}]}],"member":"286","published-online":{"date-parts":[[2019,1,24]]},"reference":[{"key":"2023062711304711600_btz038-B1","doi-asserted-by":"crossref","first-page":"11706","DOI":"10.1038\/ncomms11706","article-title":"A survey of the sorghum transcriptome using single-molecule long reads","volume":"7","author":"Abdel-Ghany","year":"2016","journal-title":"Nat. Commun"},{"key":"2023062711304711600_btz038-B2","doi-asserted-by":"crossref","first-page":"e46679","DOI":"10.1371\/journal.pone.0046679","article-title":"Improving PacBio long read accuracy by short read alignment","volume":"7","author":"Au","year":"2012","journal-title":"PLoS One"},{"key":"2023062711304711600_btz038-B3","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1007\/s11103-008-9334-4","article-title":"Characterization and comparison of intron structure and alternative splicing between Medicago truncatula, Populus trichocarpa, Arabidopsis and rice","volume":"67","author":"Baek","year":"2008","journal-title":"Plant Mol. Biol"},{"key":"2023062711304711600_btz038-B4","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2164-14-359","article-title":"The developing xylem transcriptome and genome-wide analysis of alternative splicing in Populus trichocarpa (black cottonwood) populations","volume":"14","author":"Bao","year":"2013","journal-title":"BMC Genomics"},{"key":"2023062711304711600_btz038-B5","doi-asserted-by":"crossref","first-page":"1185","DOI":"10.1126\/science.1159151","article-title":"Widespread translational inhibition by plant miRNAs and siRNAs","volume":"320","author":"Brodersen","year":"2008","journal-title":"Science"},{"key":"2023062711304711600_btz038-B92","doi-asserted-by":"crossref","first-page":"3722","DOI":"10.1038\/ncomms4722","article-title":"Sample sequencing of vascular plants demonstrates widespread conservation and divergence of microRNAs","volume":"5","author":"Chavez Montes","year":"2014","journal-title":"Nat. Commun"},{"key":"2023062711304711600_btz038-B6","doi-asserted-by":"crossref","first-page":"3528","DOI":"10.1093\/bioinformatics\/btw496","article-title":"PcircRNA_finder: a software for circRNA prediction in plants","volume":"32","author":"Chen","year":"2016","journal-title":"Bioinformatics"},{"key":"2023062711304711600_btz038-B7","doi-asserted-by":"crossref","first-page":"1292","DOI":"10.1111\/nph.14901","article-title":"Circular RNAs mediated by transposons are associated with transcriptomic and phenotypic variation in maize","volume":"217","author":"Chen","year":"2018","journal-title":"New Phytol"},{"key":"2023062711304711600_btz038-B8","doi-asserted-by":"crossref","first-page":"8283","DOI":"10.1093\/nar\/gkv751","article-title":"The RNA-binding protein HOS5 and serine\/arginine-rich proteins RS40 and RS41 participate in miRNA biogenesis in Arabidopsis","volume":"43","author":"Chen","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023062711304711600_btz038-B9","first-page":"1","article-title":"A lariat-derived circular RNA is required for plant development in Arabidopsis","author":"Cheng","year":"2017","journal-title":"Sci. China Life Sci"},{"key":"2023062711304711600_btz038-B10","doi-asserted-by":"crossref","first-page":"1126","DOI":"10.1016\/j.molp.2017.03.003","article-title":"PlantcircBase: a database for plant circular RNAs","volume":"10","author":"Chu","year":"2017","journal-title":"Mol. Plant"},{"key":"2023062711304711600_btz038-B11","doi-asserted-by":"crossref","first-page":"3674","DOI":"10.1093\/bioinformatics\/bti610","article-title":"Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research","volume":"21","author":"Conesa","year":"2005","journal-title":"Bioinformatics"},{"key":"2023062711304711600_btz038-B12","doi-asserted-by":"crossref","first-page":"17053","DOI":"10.1038\/nplants.2017.53","article-title":"A circRNA from SEPALLATA3 regulates splicing of its cognate mRNA through R-loop formation","volume":"3","author":"Conn","year":"2017","journal-title":"Nat. Plants"},{"key":"2023062711304711600_btz038-B13","doi-asserted-by":"crossref","first-page":"635.","DOI":"10.1038\/nature11119","article-title":"The tomato genome sequence provides insights into fleshy fruit evolution","volume":"485","author":"Consortium","year":"2012","journal-title":"Nature"},{"key":"2023062711304711600_btz038-B14","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"2023062711304711600_btz038-B15","doi-asserted-by":"crossref","first-page":"5.","DOI":"10.3389\/fpls.2018.00005","article-title":"Abiotic stresses modulate landscape of poplar transcriptome via alternative splicing, differential intron retention, and isoform ratio switching","volume":"9","author":"Filichkin","year":"2018","journal-title":"Front. Plant Sci"},{"key":"2023062711304711600_btz038-B16","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1101\/gr.093302.109","article-title":"Genome-wide mapping of alternative splicing in Arabidopsis thaliana","volume":"20","author":"Filichkin","year":"2010","journal-title":"Genome Res"},{"key":"2023062711304711600_btz038-B17","first-page":"3","article-title":"PRAPI: post-transcriptional regulation analysis pipeline for Iso-Seq","volume":"1","author":"Gao","year":"2017","journal-title":"Bioinformatics"},{"key":"2023062711304711600_btz038-B18","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1111\/j.1755-0998.2010.02960.x","article-title":"SNP discovery in black cottonwood (Populus trichocarpa) by population transcriptome resequencing","volume":"11","author":"Geraldes","year":"2011","journal-title":"Mol. Ecol. Resources"},{"key":"2023062711304711600_btz038-B19","doi-asserted-by":"crossref","first-page":"D154","DOI":"10.1093\/nar\/gkm952","article-title":"miRBase: tools for microRNA genomics","volume":"36","author":"Griffiths-Jones","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"2023062711304711600_btz038-B20","doi-asserted-by":"crossref","first-page":"881","DOI":"10.1038\/nbt0808-881","article-title":"Sequencing sliced ends reveals microRNA targets","volume":"26","author":"Henderson","year":"2008","journal-title":"Nat. Biotechnol"},{"key":"2023062711304711600_btz038-B21","doi-asserted-by":"crossref","first-page":"192","DOI":"10.1186\/s12864-015-1399-2","article-title":"Genome wide comparative analysis of the effects of PRMT5 and PRMT4\/CARM1 arginine methyltransferases on the Arabidopsis thaliana transcriptome","volume":"16","author":"Hernando","year":"2015","journal-title":"BMC Genomics"},{"key":"2023062711304711600_btz038-B22","doi-asserted-by":"crossref","first-page":"R34","DOI":"10.1186\/gb-2014-15-2-r34","article-title":"A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection","volume":"15","author":"Hoffmann","year":"2014","journal-title":"Genome Biol"},{"key":"2023062711304711600_btz038-B23","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1038\/280339a0","article-title":"Electron microscopic evidence for the circular form of RNA in the cytoplasm of eukaryotic cells","volume":"280","author":"Hsu","year":"1979","journal-title":"Nature"},{"key":"2023062711304711600_btz038-B24","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1261\/rna.035667.112","article-title":"Circular RNAs are abundant, conserved, and associated with ALU repeats","volume":"19","author":"Jeck","year":"2013","journal-title":"RNA"},{"key":"2023062711304711600_btz038-B25","doi-asserted-by":"crossref","first-page":"e139","DOI":"10.1093\/nar\/gku693","article-title":"sPARTA: a parallelized pipeline for integrated analysis of plant miRNA and cleaved mRNA data sets, including new miRNA target-identification software","volume":"42","author":"Kakrana","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2023062711304711600_btz038-B26","doi-asserted-by":"crossref","first-page":"R72.","DOI":"10.1186\/gb-2011-12-8-r72","article-title":"TopHat-Fusion: an algorithm for discovery of novel fusion transcripts","volume":"12","author":"Kim","year":"2011","journal-title":"Genome Biol"},{"key":"2023062711304711600_btz038-B27","doi-asserted-by":"crossref","first-page":"R25","DOI":"10.1186\/gb-2009-10-3-r25","article-title":"Ultrafast and memory-efficient alignment of short DNA sequences to the human genome","volume":"10","author":"Langmead","year":"2009","journal-title":"Genome Biol"},{"key":"2023062711304711600_btz038-B29","doi-asserted-by":"crossref","first-page":"D19","DOI":"10.1093\/nar\/gkq1019","article-title":"The sequence read archive","volume":"39","author":"Leinonen","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"2023062711304711600_btz038-B30","doi-asserted-by":"crossref","first-page":"1060","DOI":"10.1038\/ng.703","article-title":"The developmental dynamics of the maize leaf transcriptome","volume":"42","author":"Li","year":"2010","journal-title":"Nat. Genet"},{"key":"2023062711304711600_btz038-B31","doi-asserted-by":"crossref","first-page":"1695","DOI":"10.1007\/s00438-016-1212-1","article-title":"Genome-wide analysis of shoot growth-associated alternative splicing in moso bamboo","volume":"291","author":"Li","year":"2016","journal-title":"Mol. Genet. Genomics"},{"key":"2023062711304711600_btz038-B32","doi-asserted-by":"crossref","first-page":"508","DOI":"10.1016\/j.devcel.2016.10.012","article-title":"High-resolution expression map of the Arabidopsis root reveals alternative splicing and lincRNA regulation","volume":"39","author":"Li","year":"2016","journal-title":"Dev. Cell"},{"key":"2023062711304711600_btz038-B33","doi-asserted-by":"crossref","first-page":"e1006422","DOI":"10.1371\/journal.pgen.1006422","article-title":"Intron lariat RNA inhibits microRNA biogenesis by sequestering the dicing complex in Arabidopsis","volume":"12","author":"Li","year":"2016","journal-title":"PLoS Genet"},{"key":"2023062711304711600_btz038-B34","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1016\/j.plantsci.2014.03.004","article-title":"Comparative expression analysis of resistant and susceptible Populus clones inoculated with Septoria musiva","volume":"223","author":"Liang","year":"2014","journal-title":"Plant Sci"},{"key":"2023062711304711600_btz038-B35","doi-asserted-by":"crossref","first-page":"1278","DOI":"10.3389\/fpls.2017.01278","article-title":"Identifying and characterizing the circular RNAs during the lifespan of arabidopsis leaves","volume":"8","author":"Liu","year":"2017","journal-title":"Front. Plant Sci"},{"key":"2023062711304711600_btz038-B36","doi-asserted-by":"crossref","first-page":"2186","DOI":"10.1105\/tpc.105.033456","article-title":"Novel and mechanical stress\u2013responsive microRNAs in Populus trichocarpa that are absent from Arabidopsis","volume":"17","author":"Lu","year":"2005","journal-title":"Plant Cell"},{"key":"2023062711304711600_btz038-B37","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1111\/j.1365-313X.2008.03497.x","article-title":"Stress\u2014responsive microRNAs in populus","volume":"55","author":"Lu","year":"2008","journal-title":"Plant J"},{"key":"2023062711304711600_btz038-B38","doi-asserted-by":"crossref","first-page":"2076","DOI":"10.1261\/rna.052282.115","article-title":"Transcriptome-wide investigation of circular RNAs in rice","volume":"21","author":"Lu","year":"2015","journal-title":"RNA"},{"key":"2023062711304711600_btz038-B39","doi-asserted-by":"crossref","first-page":"1238","DOI":"10.1101\/gr.106120.110","article-title":"Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq","volume":"20","author":"Lu","year":"2010","journal-title":"Genome Res"},{"key":"2023062711304711600_btz038-B40","doi-asserted-by":"crossref","first-page":"348","DOI":"10.1016\/j.bbrc.2017.05.051","article-title":"Identification and characterization of novel lncRNAs in Arabidopsis thaliana","volume":"488","author":"Lu","year":"2017","journal-title":"Biochem. Biophys. Res. Commun"},{"key":"2023062711304711600_btz038-B41","doi-asserted-by":"crossref","first-page":"1574","DOI":"10.1093\/bioinformatics\/btx797","article-title":"TarHunter, a tool for predicting conserved microRNA targets and target mimics in plants","volume":"34","author":"Ma","year":"2018","journal-title":"Bioinformatics"},{"key":"2023062711304711600_btz038-B42","doi-asserted-by":"crossref","first-page":"e6","DOI":"10.1093\/pcp\/pcu187","article-title":"MOROKOSHI: transcriptome database in Sorghum bicolor","volume":"56","author":"Makita","year":"2015","journal-title":"Plant Cell Physiol"},{"key":"2023062711304711600_btz038-B43","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12864-015-1529-x","article-title":"Transcriptome and hormone profiling reveals Eucalyptus grandis defence responses against Chrysoporthe austroafricana","volume":"16","author":"Mangwanda","year":"2015","journal-title":"BMC Genomics"},{"key":"2023062711304711600_btz038-B44","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1038\/nature11928","article-title":"Circular RNAs are a large class of animal RNAs with regulatory potency","volume":"495","author":"Memczak","year":"2013","journal-title":"Nature"},{"key":"2023062711304711600_btz038-B46","doi-asserted-by":"crossref","first-page":"356","DOI":"10.1038\/nature13308","article-title":"The genome of Eucalyptus grandis","volume":"510","author":"Myburg","year":"2014","journal-title":"Nature"},{"key":"2023062711304711600_btz038-B47","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/gb-2014-15-3-r59","article-title":"Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies","volume":"15","author":"Neale","year":"2014","journal-title":"Genome Biol"},{"key":"2023062711304711600_btz038-B48","doi-asserted-by":"crossref","first-page":"579","DOI":"10.1038\/nature12211","article-title":"The Norway spruce genome sequence and conifer genome evolution","volume":"497","author":"Nystedt","year":"2013","journal-title":"Nature"},{"key":"2023062711304711600_btz038-B49","doi-asserted-by":"crossref","first-page":"1418","DOI":"10.1093\/pcp\/pcv064","article-title":"The transcriptome and terpene profile of Eucalyptus grandis reveals mechanisms of defense against the insect pest, Leptocybe invasa","volume":"56","author":"Oates","year":"2015","journal-title":"Plant Cell Physiol"},{"key":"2023062711304711600_btz038-B50","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1007\/s11103-013-0106-4","article-title":"Diversity in the complexity of phosphate starvation transcriptomes among rice cultivars based on RNA-Seq profiles","volume":"83","author":"Oono","year":"2013","journal-title":"Plant Mol. Biol"},{"key":"2023062711304711600_btz038-B51","doi-asserted-by":"crossref","first-page":"D196","DOI":"10.1093\/nar\/gkp931","article-title":"InParanoid 7: new algorithms and tools for eukaryotic orthology analysis","volume":"38","author":"Ostlund","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"2023062711304711600_btz038-B52","doi-asserted-by":"crossref","first-page":"456","DOI":"10.1038\/ng.2569","article-title":"The draft genome of the fast-growing non-timber forest species moso bamboo (Phyllostachys heterocycla)","volume":"45","author":"Peng","year":"2013","journal-title":"Nat. Genet"},{"key":"2023062711304711600_btz038-B53","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1146\/annurev.arplant.58.032806.103754","article-title":"Alternative splicing of pre-messenger RNAs in plants in the genomic era","volume":"58","author":"Reddy","year":"2007","journal-title":"Annu. Rev. Plant Biol"},{"key":"2023062711304711600_btz038-B54","doi-asserted-by":"crossref","first-page":"875","DOI":"10.1002\/wrna.98","article-title":"Plant serine\/arginine-rich proteins: roles in precursor messenger RNA splicing, plant development, and stress responses","volume":"2","author":"Reddy","year":"2011","journal-title":"Wiley Interdiscipl. Rev. RNA"},{"key":"2023062711304711600_btz038-B55","doi-asserted-by":"crossref","first-page":"1684","DOI":"10.1104\/pp.15.00287","article-title":"Comprehensive tissue-specific transcriptome analysis reveals distinct regulatory programs during early tomato fruit development","volume":"168","author":"Richard","year":"2015","journal-title":"Plant Physiol"},{"key":"2023062711304711600_btz038-B56","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1186\/s12864-015-1731-x","article-title":"Daytime soybean transcriptome fluctuations during water deficit stress","volume":"16","author":"Rodrigues","year":"2015","journal-title":"BMC Genomics"},{"key":"2023062711304711600_btz038-B57","doi-asserted-by":"crossref","first-page":"R4","DOI":"10.1186\/gb-2012-13-1-r4","article-title":"SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data","volume":"13","author":"Rogers","year":"2012","journal-title":"Genome Biol"},{"key":"2023062711304711600_btz038-B58","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0030733","article-title":"Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types","volume":"7","author":"Salzman","year":"2012","journal-title":"PLoS One"},{"key":"2023062711304711600_btz038-B59","doi-asserted-by":"crossref","first-page":"E5593","DOI":"10.1073\/pnas.1419161111","article-title":"rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data","volume":"111","author":"Shen","year":"2014","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023062711304711600_btz038-B60","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1105\/tpc.114.122739","article-title":"Global dissection of alternative splicing in paleopolyploid soybean","volume":"26","author":"Shen","year":"2014","journal-title":"Plant Cell"},{"key":"2023062711304711600_btz038-B61","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2164-14-233","article-title":"Identification of drought-responsive and novel Populus trichocarpa microRNAs by high-throughput sequencing and their targets using degradome analysis","volume":"14","author":"Shuai","year":"2013","journal-title":"BMC Genomics"},{"key":"2023062711304711600_btz038-B62","doi-asserted-by":"crossref","first-page":"1630","DOI":"10.1101\/gr.094607.109","article-title":"JBrowse: a next-generation genome browser","volume":"19","author":"Skinner","year":"2009","journal-title":"Genome Res"},{"key":"2023062711304711600_btz038-B63","doi-asserted-by":"crossref","first-page":"1848","DOI":"10.1104\/pp.108.133371","article-title":"Alternative splicing studies of the reactive oxygen species gene network in Populus reveal two isoforms of high-isoelectric-point superoxide dismutase","volume":"149","author":"Srivastava","year":"2009","journal-title":"Plant Physiol"},{"key":"2023062711304711600_btz038-B64","doi-asserted-by":"crossref","first-page":"424","DOI":"10.1007\/s11105-014-0759-4","article-title":"Analysis of the drought stress-responsive transcriptome of black cottonwood (Populus trichocarpa) using deep RNA sequencing","volume":"33","author":"Tang","year":"2015","journal-title":"Plant Mol. Biol. Report"},{"key":"2023062711304711600_btz038-B65","doi-asserted-by":"crossref","first-page":"562","DOI":"10.1038\/nprot.2012.016","article-title":"Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks","volume":"7","author":"Trapnell","year":"2012","journal-title":"Nat. Protoc"},{"key":"2023062711304711600_btz038-B66","doi-asserted-by":"crossref","first-page":"1596","DOI":"10.1126\/science.1128691","article-title":"The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)","volume":"313","author":"Tuskan","year":"2006","journal-title":"Science"},{"key":"2023062711304711600_btz038-B67","doi-asserted-by":"crossref","first-page":"11708","DOI":"10.1038\/ncomms11708","article-title":"Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing","volume":"7","author":"Wang","year":"2016","journal-title":"Nat. Commun"},{"key":"2023062711304711600_btz038-B68","doi-asserted-by":"crossref","first-page":"e1002012","DOI":"10.1371\/journal.pgen.1002012","article-title":"miRNA control of vegetative phase change in trees","volume":"7","author":"Wang","year":"2011","journal-title":"PLoS Genet"},{"key":"2023062711304711600_btz038-B69","doi-asserted-by":"crossref","first-page":"e178","DOI":"10.1093\/nar\/gkq622","article-title":"MapSplice: accurate mapping of RNA-seq reads for splice junction discovery","volume":"38","author":"Wang","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"2023062711304711600_btz038-B70","doi-asserted-by":"crossref","first-page":"684","DOI":"10.1111\/tpj.13597","article-title":"Comprehensive profiling of rhizome\u2014associated alternative splicing and alternative polyadenylation in moso bamboo (Phyllostachys edulis)","volume":"91","author":"Wang","year":"2017","journal-title":"Plant J"},{"key":"2023062711304711600_btz038-B71","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2164-12-342","article-title":"Identification of lignin genes and regulatory sequences involved in secondary cell wall formation in Acacia auriculiformis and Acacia mangium via de novo transcriptome sequencing","volume":"12","author":"Wong","year":"2011","journal-title":"BMC Genomics"},{"key":"2023062711304711600_btz038-B72","doi-asserted-by":"crossref","first-page":"W22","DOI":"10.1093\/nar\/gks554","article-title":"PsRobot: a web-based plant small RNA meta-analysis toolbox","volume":"40","author":"Wu","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2023062711304711600_btz038-B73","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1007\/978-1-4939-3578-9_15","article-title":"GMAP and GSNAP for genomic sequence alignment: enhancements to speed, accuracy, and functionality","volume":"1418","author":"Wu","year":"2016","journal-title":"Methods Mol. Biol"},{"key":"2023062711304711600_btz038-B74","doi-asserted-by":"crossref","first-page":"1859","DOI":"10.1093\/bioinformatics\/bti310","article-title":"GMAP: a genomic mapping and alignment program for mRNA and EST sequences","volume":"21","author":"Wu","year":"2005","journal-title":"Bioinformatics"},{"key":"2023062711304711600_btz038-B75","first-page":"msv164","article-title":"Extensive families of miRNAs and PHAS Loci in Norway Spruce demonstrate the origins of complex phasiRNA networks in seed plants","author":"Xia","year":"2015","journal-title":"Mol. Biol. Evol"},{"key":"2023062711304711600_btz038-B76","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1186\/1471-2105-14-33","article-title":"HTQC: a fast quality control toolkit for Illumina sequencing data","volume":"14","author":"Yang","year":"2013","journal-title":"BMC Bioinformatics"},{"key":"2023062711304711600_btz038-B77","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1111\/j.1365-313X.2011.04882.x","article-title":"Alternative mRNA processing increases the complexity of microRNA-based gene regulation in Arabidopsis","volume":"70","author":"Yang","year":"2012","journal-title":"Plant J"},{"key":"2023062711304711600_btz038-B78","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1111\/nph.13585","article-title":"Widespread noncoding circular RNAs in plants","volume":"208","author":"Ye","year":"2015","journal-title":"New Phytol"},{"key":"2023062711304711600_btz038-B79","doi-asserted-by":"crossref","first-page":"743","DOI":"10.3389\/fpls.2014.00743","article-title":"Genome-wide identification of non-coding RNAs interacted with microRNAs in soybean","volume":"5","author":"Ye","year":"2014","journal-title":"Front Plant Sci"},{"key":"2023062711304711600_btz038-B80","doi-asserted-by":"crossref","first-page":"1055","DOI":"10.1080\/15476286.2016.1245268","article-title":"Full-length sequence assembly reveals circular RNAs with diverse non-GT\/AG splicing signals in rice","volume":"14","author":"Ye","year":"2017","journal-title":"RNA Biol"},{"key":"2023062711304711600_btz038-B81","article-title":"AtCircDB: a tissue-specific database for Arabidopsis circular RNAs","author":"Ye","year":"2017","journal-title":"Brief Bioinform"},{"key":"2023062711304711600_btz038-B82","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1016\/j.postharvbio.2017.10.013","article-title":"Identification of circular RNAs and their targets during tomato fruit ripening","volume":"136","author":"Yin","year":"2018","journal-title":"Postharvest Biol. Technol"},{"key":"2023062711304711600_btz038-B83","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1186\/1471-2164-14-19","article-title":"Transcriptome analysis of rice root heterosis by RNA-Seq","volume":"14","author":"Zhai","year":"2013","journal-title":"BMC Genomics"},{"key":"2023062711304711600_btz038-B84","doi-asserted-by":"crossref","first-page":"646","DOI":"10.1101\/gr.100677.109","article-title":"Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome","volume":"20","author":"Zhang","year":"2010","journal-title":"Genome Res"},{"key":"2023062711304711600_btz038-B85","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1111\/php.12680","article-title":"Light regulation of alternative pre-mRNA splicing in plants","volume":"93","author":"Zhang","year":"2017","journal-title":"Photochem. Photobiol"},{"key":"2023062711304711600_btz038-B86","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/database\/bax089","article-title":"PlantCircNet: a database for plant circRNA\u2013miRNA\u2013mRNA regulatory networks","volume":"2017","author":"Zhang","year":"2017","journal-title":"Database"},{"key":"2023062711304711600_btz038-B87","doi-asserted-by":"crossref","first-page":"23173","DOI":"10.1038\/srep23173","article-title":"Spatiotemporal transcriptome provides insights into early fruit development of tomato (Solanum lycopersicum)","volume":"6","author":"Zhang","year":"2016","journal-title":"Sci. Rep"},{"key":"2023062711304711600_btz038-B88","doi-asserted-by":"crossref","first-page":"1277","DOI":"10.1101\/gr.202895.115","article-title":"Diverse alternative back-splicing and alternative splicing landscape of circular RNAs","volume":"26","author":"Zhang","year":"2016","journal-title":"Genome Res"},{"key":"2023062711304711600_btz038-B89","first-page":"bau006","article-title":"BambooGDB: a bamboo genome database with functional annotation and an analysis platform","volume":"2014","author":"Zhao","year":"2014","journal-title":"Database J. Biol. Databases Curat"},{"key":"2023062711304711600_btz038-B90","doi-asserted-by":"crossref","first-page":"765","DOI":"10.1104\/pp.113.231134","article-title":"Intron-mediated alternative splicing of WOOD-ASSOCIATED NAC TRANSCRIPTION FACTOR1B regulates cell wall thickening during fiber development in Populus species","volume":"164","author":"Zhao","year":"2014","journal-title":"Plant Physiol"},{"key":"2023062711304711600_btz038-B91","doi-asserted-by":"crossref","first-page":"5636","DOI":"10.1038\/s41598-017-05922-9","article-title":"Genome-wide identification and characterization of circular RNAs by high throughput sequencing in soybean","volume":"7","author":"Zhao","year":"2017","journal-title":"Sci. Rep"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/17\/3119\/50719766\/bioinformatics_35_17_3119.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/17\/3119\/50719766\/bioinformatics_35_17_3119.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,27]],"date-time":"2023-06-27T11:34:34Z","timestamp":1687865674000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/35\/17\/3119\/5299997"}},"subtitle":[],"editor":[{"given":"Janet","family":"Kelso","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2019,1,24]]},"references-count":90,"journal-issue":{"issue":"17","published-print":{"date-parts":[[2019,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btz038","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2019,9,1]]},"published":{"date-parts":[[2019,1,24]]}}}