{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,9]],"date-time":"2026-04-09T14:50:35Z","timestamp":1775746235974,"version":"3.50.1"},"reference-count":72,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2022,12,14]],"date-time":"2022-12-14T00:00:00Z","timestamp":1670976000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"FCT\u2014Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"name":"GREEN-IT\u2014Bioresources for Sustainability R&D Unit","award":["UIDB\/04551\/2020"],"award-info":[{"award-number":["UIDB\/04551\/2020"]}]},{"name":"GREEN-IT\u2014Bioresources for Sustainability R&D Unit","award":["UIDP\/04551\/2020"],"award-info":[{"award-number":["UIDP\/04551\/2020"]}]},{"name":"LS4FUTURE Associated Laboratory","award":["LA\/P\/0087\/2020"],"award-info":[{"award-number":["LA\/P\/0087\/2020"]}]},{"name":"FCT","award":["PD\/BD\/114362\/2016"],"award-info":[{"award-number":["PD\/BD\/114362\/2016"]}]},{"name":"FCT","award":["SFRH\/BPD\/86742\/2012"],"award-info":[{"award-number":["SFRH\/BPD\/86742\/2012"]}]},{"name":"FCT","award":["PD\/BD\/128434\/2017"],"award-info":[{"award-number":["PD\/BD\/128434\/2017"]}]},{"name":"CEEC","award":["CEECIND\/03345\/2018"],"award-info":[{"award-number":["CEECIND\/03345\/2018"]}]},{"name":"(Single cell HUB)"},{"name":"ONEIDA"},{"name":"Programa Operacional Regional Lisboa 2020"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,5,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>During sexual reproduction in flowering plants, the two haploid sperm cells (SCs) embedded within the cytoplasm of a growing pollen tube are carried to the embryo sac for double fertilization. Pollen development in flowering plants is a dynamic process that encompasses changes at transcriptome and epigenome levels. While the transcriptome of pollen and SCs in Arabidopsis (Arabidopsis thaliana) is well documented, previous analyses have mostly been based on gene-level expression. In-depth transcriptome analysis, particularly the extent of alternative splicing (AS) at the resolution of SC and vegetative nucleus (VN), is still lacking. Therefore, we performed RNA-seq analysis to generate a spliceome map of Arabidopsis SCs and VN isolated from mature pollen grains. Based on our de novo transcriptome assembly, we identified 58,039 transcripts, including 9,681 novel transcripts, of which 2,091 were expressed in SCs and 3,600 in VN. Four hundred and sixty-eight genes were regulated both at gene and splicing levels, with many having functions in mRNA splicing, chromatin modification, and protein localization. Moreover, a comparison with egg cell RNA-seq data uncovered sex-specific regulation of transcription and splicing factors. Our study provides insights into a gamete-specific AS landscape at unprecedented resolution.<\/jats:p>","DOI":"10.1093\/plphys\/kiac574","type":"journal-article","created":{"date-parts":[[2022,12,14]],"date-time":"2022-12-14T14:52:13Z","timestamp":1671029533000},"page":"85-101","source":"Crossref","is-referenced-by-count":25,"title":["Cell-type-specific alternative splicing in the Arabidopsis germline"],"prefix":"10.1093","volume":"192","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3544-4723","authenticated-orcid":false,"given":"Chandra Shekhar","family":"Misra","sequence":"first","affiliation":[{"name":"Instituto de Tecnologia Qu\u00edmica e Biol\u00f3gica Ant\u00f3nio Xavier, Universidade Nova de Lisboa (ITQB NOVA) , 2780-157 Oeiras , Portugal"},{"name":"Instituto Gulbenkian de Ci\u00eancia , 2780-156 Oeiras , Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4779-6459","authenticated-orcid":false,"given":"Ant\u00f3nio G G","family":"Sousa","sequence":"additional","affiliation":[{"name":"Instituto Gulbenkian de Ci\u00eancia , 2780-156 Oeiras , Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5626-0619","authenticated-orcid":false,"given":"Pedro M","family":"Barros","sequence":"additional","affiliation":[{"name":"Instituto de Tecnologia Qu\u00edmica e Biol\u00f3gica Ant\u00f3nio Xavier, Universidade Nova de Lisboa (ITQB NOVA) , 2780-157 Oeiras , Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1598-9478","authenticated-orcid":false,"given":"Anton","family":"Kermanov","sequence":"additional","affiliation":[{"name":"Instituto de Tecnologia Qu\u00edmica e Biol\u00f3gica Ant\u00f3nio Xavier, Universidade Nova de Lisboa (ITQB NOVA) , 2780-157 Oeiras , Portugal"},{"name":"Instituto Gulbenkian de Ci\u00eancia , 2780-156 Oeiras , Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6845-6122","authenticated-orcid":false,"given":"J\u00f6rg D","family":"Becker","sequence":"additional","affiliation":[{"name":"Instituto de Tecnologia Qu\u00edmica e Biol\u00f3gica Ant\u00f3nio Xavier, Universidade Nova de Lisboa (ITQB NOVA) , 2780-157 Oeiras , Portugal"},{"name":"Instituto Gulbenkian de Ci\u00eancia , 2780-156 Oeiras , Portugal"}]}],"member":"286","published-online":{"date-parts":[[2022,12,14]]},"reference":[{"issue":"4","key":"2023050211440118700_kiac574-B1","doi-asserted-by":"crossref","first-page":"1713","DOI":"10.1104\/pp.109.135806","article-title":"MIKC* MADS domain heterodimers are required for pollen maturation and tube growth in Arabidopsis","volume":"149","author":"Adamczyk","year":"2009","journal-title":"Plant Physiol"},{"issue":"5","key":"2023050211440118700_kiac574-B2","doi-asserted-by":"crossref","first-page":"729","DOI":"10.1111\/tpj.12336","article-title":"Transcriptomes of isolated Oryza sativa gametes characterized by deep sequencing: evidence for distinct sex-dependent chromatin and epigenetic states before fertilization","volume":"76","author":"Anderson","year":"2013","journal-title":"Plant J"},{"key":"2023050211440118700_kiac574-B3","doi-asserted-by":"crossref","first-page":"619404","DOI":"10.3389\/fpls.2020.619404","article-title":"Barley anther and meiocyte transcriptome dynamics in meiotic prophase I","volume":"11","author":"Barakate","year":"2020","journal-title":"Front Plant Sci"},{"issue":"7","key":"2023050211440118700_kiac574-B4","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1038\/nrm.2017.27","article-title":"Alternative splicing as a regulator of development and tissue identity","volume":"18","author":"Baralle","year":"2017","journal-title":"Nat Rev Mol Cell Biol"},{"issue":"1","key":"2023050211440118700_kiac574-B5","doi-asserted-by":"crossref","first-page":"8876","DOI":"10.1038\/s41598-019-45184-1","article-title":"Genome-wide alternative splicing landscapes modulated by biotrophic sugarcane smut pathogen","volume":"9","author":"Bedre","year":"2019","journal-title":"Sci Rep"},{"issue":"1","key":"2023050211440118700_kiac574-B6","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1146\/annurev-arplant-042110-103824","article-title":"Germline specification and function in plants","volume":"62","author":"Berger","year":"2011","journal-title":"Annu Rev Plant Biol"},{"issue":"2","key":"2023050211440118700_kiac574-B7","doi-asserted-by":"crossref","first-page":"534","DOI":"10.1105\/tpc.110.081059","article-title":"The R2R3 MYB transcription factor DUO1 activates a male germline-specific regulon essential for sperm cell differentiation in Arabidopsis","volume":"23","author":"Borg","year":"2011","journal-title":"Plant Cell"},{"issue":"6","key":"2023050211440118700_kiac574-B8","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1038\/s41556-020-0515-y","article-title":"Targeted reprogramming of H3K27me3 resets epigenetic memory in plant paternal chromatin","volume":"22","author":"Borg","year":"2020","journal-title":"Nat Cell Biol"},{"issue":"1","key":"2023050211440118700_kiac574-B9","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1186\/1746-4811-8-44","article-title":"FACS-based purification of Arabidopsis microspores, sperm cells and vegetative nuclei","volume":"8","author":"Borges","year":"2012","journal-title":"Plant Methods"},{"issue":"2","key":"2023050211440118700_kiac574-B10","doi-asserted-by":"crossref","first-page":"1168","DOI":"10.1104\/pp.108.125229","article-title":"Comparative transcriptomics of Arabidopsis sperm cells","volume":"148","author":"Borges","year":"2008","journal-title":"Plant Physiol"},{"issue":"3","key":"2023050211440118700_kiac574-B11","doi-asserted-by":"crossref","first-page":"e1000430","DOI":"10.1371\/journal.pgen.1000430","article-title":"A plant germline-specific integrator of sperm specification and cell cycle progression","volume":"5","author":"Brownfield","year":"2009","journal-title":"PLoS Genet"},{"issue":"7","key":"2023050211440118700_kiac574-B12","doi-asserted-by":"crossref","first-page":"1940","DOI":"10.1105\/tpc.109.066373","article-title":"Arabidopsis DUO POLLEN3 is a key regulator of male germline development and embryogenesis","volume":"21","author":"Brownfield","year":"2009","journal-title":"Plant Cell"},{"issue":"1","key":"2023050211440118700_kiac574-B13","doi-asserted-by":"crossref","first-page":"194","DOI":"10.1016\/j.cell.2012.09.001","article-title":"Reprogramming of DNA methylation in pollen guides epigenetic inheritance via small RNA","volume":"151","author":"Calarco","year":"2012","journal-title":"Cell"},{"issue":"7","key":"2023050211440118700_kiac574-B14","doi-asserted-by":"crossref","first-page":"1424","DOI":"10.1105\/tpc.18.00177","article-title":"Rapid and dynamic alternative splicing impacts the Arabidopsis cold response transcriptome","volume":"30","author":"Calixto","year":"2018","journal-title":"Plant Cell"},{"key":"2023050211440118700_kiac574-B15","article-title":"Tspex: a tissue-specificity calculator for gene expression data","author":"Camargo","year":"2020","journal-title":"Res Square"},{"issue":"4","key":"2023050211440118700_kiac574-B16","doi-asserted-by":"crossref","first-page":"1163","DOI":"10.1093\/mp\/sst097","article-title":"LlSR28 is involved in pollen germination by affecting filamentous actin dynamics","volume":"6","author":"Cao","year":"2013","journal-title":"Mol Plant"},{"key":"2023050211440118700_kiac574-B17","doi-asserted-by":"crossref","first-page":"708","DOI":"10.3389\/fpls.2019.00708","article-title":"Alternative splicing and protein diversity: plants versus animals","volume":"10","author":"Chaudhary","year":"2019","journal-title":"Front Plant Sci"},{"issue":"9","key":"2023050211440118700_kiac574-B18","doi-asserted-by":"crossref","first-page":"2106","DOI":"10.1105\/tpc.17.00099","article-title":"Zygotic genome activation occurs shortly after fertilization in maize","volume":"29","author":"Chen","year":"2017","journal-title":"Plant Cell"},{"key":"2023050211440118700_kiac574-B19","doi-asserted-by":"crossref","first-page":"789","DOI":"10.1111\/tpj.13415","article-title":"Araport11: a complete reannotation of the Arabidopsis thaliana reference genome","volume":"89","author":"Cheng","year":"2017","journal-title":"Plant J"},{"issue":"6","key":"2023050211440118700_kiac574-B20","doi-asserted-by":"crossref","first-page":"1188","DOI":"10.1101\/gr.849004","article-title":"Weblogo: a sequence logo generator","volume":"14","author":"Crooks","year":"2004","journal-title":"Genome Res"},{"issue":"1","key":"2023050211440118700_kiac574-B21","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"},{"issue":"8","key":"2023050211440118700_kiac574-B22","doi-asserted-by":"crossref","first-page":"e1006360","DOI":"10.1371\/journal.pcbi.1006360","article-title":"Ggsashimi: sashimi plot revised for browser- and annotation-independent splicing visualization","volume":"14","author":"Garrido-Mart\u00edn","year":"2018","journal-title":"PLoS Comput Biol"},{"issue":"3","key":"2023050211440118700_kiac574-B23","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1007\/s00497-021-00411-6","article-title":"A dynamic intron retention program regulates the expression of several hundred genes during pollen meiosis","volume":"34","author":"Golicz","year":"2021","journal-title":"Plant Reprod"},{"issue":"11","key":"2023050211440118700_kiac574-B24","doi-asserted-by":"crossref","first-page":"1574","DOI":"10.1080\/15476286.2020.1858253","article-title":"3D RNA-seq: a powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists","volume":"18","author":"Guo","year":"2021","journal-title":"RNA Biol"},{"issue":"11","key":"2023050211440118700_kiac574-B25","doi-asserted-by":"crossref","first-page":"R85","DOI":"10.1186\/gb-2004-5-11-r85","article-title":"Transcriptome analysis of haploid male gametophyte development in Arabidopsis","volume":"5","author":"Honys","year":"2004","journal-title":"Genome Biol"},{"issue":"10","key":"2023050211440118700_kiac574-B26","doi-asserted-by":"crossref","first-page":"e74183","DOI":"10.1371\/journal.pone.0074183","article-title":"High-throughput RNA sequencing of pseudomonas-infected Arabidopsis reveals hidden transcriptome complexity and novel splice variants","volume":"8","author":"Howard","year":"2013","journal-title":"PLoS One"},{"issue":"10","key":"2023050211440118700_kiac574-B27","doi-asserted-by":"crossref","first-page":"1470","DOI":"10.1016\/j.molp.2020.07.007","article-title":"Phytophthora effectors modulate genome-wide alternative splicing of host mRNAs to reprogram plant immunity","volume":"13","author":"Huang","year":"2020","journal-title":"Mol Plant"},{"issue":"24","key":"2023050211440118700_kiac574-B28","doi-asserted-by":"crossref","first-page":"1907","DOI":"10.1016\/j.cub.2008.11.057","article-title":"A tip-localized RhoGAP controls cell polarity by globally inhibiting Rho GTPase at the cell apex","volume":"18","author":"Hwang","year":"2008","journal-title":"Curr Biol"},{"issue":"6100","key":"2023050211440118700_kiac574-B29","doi-asserted-by":"crossref","first-page":"1360","DOI":"10.1126\/science.1224839","article-title":"Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes","volume":"337","author":"Ibarra","year":"2012","journal-title":"Science"},{"issue":"D1","key":"2023050211440118700_kiac574-B30","doi-asserted-by":"crossref","first-page":"D1040","DOI":"10.1093\/nar\/gkw982","article-title":"PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants","volume":"45","author":"Jin","year":"2017","journal-title":"Nucleic Acids Res"},{"issue":"8","key":"2023050211440118700_kiac574-B31","doi-asserted-by":"crossref","first-page":"1143","DOI":"10.1038\/s41477-021-00958-2","article-title":"Comparative transcriptomic analysis reveals conserved programmes underpinning organogenesis and reproduction in land plants","volume":"7","author":"Julca","year":"2021","journal-title":"Nat Plants"},{"key":"2023050211440118700_kiac574-B32","first-page":"205","article-title":"Alternative splicing in tomato pollen in response to heat stress","volume":"24","author":"Keller","year":"2017","journal-title":"DNA Res"},{"issue":"8","key":"2023050211440118700_kiac574-B33","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1038\/s41587-019-0201-4","article-title":"Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype","volume":"37","author":"Kim","year":"2019","journal-title":"Nat Biotechnol"},{"issue":"2","key":"2023050211440118700_kiac574-B34","doi-asserted-by":"crossref","first-page":"280","DOI":"10.1111\/j.1365-313X.2011.04592.x","article-title":"Members of the RKD transcription factor family induce an egg cell-like gene expression program","volume":"67","author":"K\u0151szegi","year":"2011","journal-title":"Plant J"},{"key":"2023050211440118700_kiac574-B35","doi-asserted-by":"crossref","first-page":"dev186742","DOI":"10.1242\/dev.186742","article-title":"PRP8A and PRP8B spliceosome subunits act coordinately to control pollen tube attraction in Arabidopsis thaliana","volume":"147","author":"Kulichov\u00e1","year":"2020","journal-title":"Development"},{"issue":"5","key":"2023050211440118700_kiac574-B36","doi-asserted-by":"crossref","first-page":"829","DOI":"10.1093\/mp\/sst175","article-title":"Single-nucleotide resolution mapping of the Gossypium raimondii transcriptome reveals a new mechanism for alternative splicing of introns","volume":"7","author":"Li","year":"2014","journal-title":"Mol Plant"},{"issue":"2","key":"2023050211440118700_kiac574-B37","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1111\/tpj.14041","article-title":"Transcriptomics analyses reveal the molecular roadmap and long non-coding RNA landscape of sperm cell lineage development","volume":"96","author":"Liu","year":"2018","journal-title":"Plant J"},{"issue":"2","key":"2023050211440118700_kiac574-B38","doi-asserted-by":"crossref","first-page":"1092","DOI":"10.1104\/pp.112.211441","article-title":"RNA-seq of Arabidopsis pollen uncovers novel transcription and alternative splicing","volume":"162","author":"Loraine","year":"2013","journal-title":"Plant Physiol"},{"issue":"1","key":"2023050211440118700_kiac574-B39","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1105\/tpc.114.133991","article-title":"Genome-wide analysis of alternative splicing landscapes modulated during plant\u2013virus interactions in Brachypodium distachyon","volume":"27","author":"Mandadi","year":"2015","journal-title":"Plant Cell"},{"issue":"6","key":"2023050211440118700_kiac574-B40","doi-asserted-by":"crossref","first-page":"1184","DOI":"10.1101\/gr.134106.111","article-title":"Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis","volume":"22","author":"Marquez","year":"2012","journal-title":"Genome Res"},{"issue":"1","key":"2023050211440118700_kiac574-B41","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1186\/s13059-020-02258-y","article-title":"Alternative splicing landscapes in Arabidopsis thaliana across tissues and stress conditions highlight major functional differences with animals","volume":"22","author":"Mart\u00edn","year":"2021","journal-title":"Genome Biol"},{"issue":"1","key":"2023050211440118700_kiac574-B42","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1007\/s00497-018-00355-4","article-title":"Transcriptomics of Arabidopsis sperm cells at single-cell resolution","volume":"32","author":"Misra","year":"2019","journal-title":"Plant Reprod"},{"issue":"1","key":"2023050211440118700_kiac574-B43","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1186\/s13578-017-0153-7","article-title":"Control of gene expression through the nonsense-mediated RNA decay pathway","volume":"7","author":"Nickless","year":"2017","journal-title":"Cell Biosci"},{"issue":"12","key":"2023050211440118700_kiac574-B44","doi-asserted-by":"crossref","first-page":"1413","DOI":"10.1038\/ng.259","article-title":"Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing","volume":"40","author":"Pan","year":"2008","journal-title":"Nat Genet"},{"key":"2023050211440118700_kiac574-B45","doi-asserted-by":"crossref","first-page":"569","DOI":"10.3389\/fpls.2019.00569","article-title":"Arabidopsis U2AF65 regulates flowering time and the growth of pollen tubes","volume":"10","author":"Park","year":"2019","journal-title":"Front Plant Sci"},{"issue":"4","key":"2023050211440118700_kiac574-B46","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1038\/nmeth.4197","article-title":"Salmon provides fast and bias-aware quantification of transcript expression","volume":"14","author":"Patro","year":"2017","journal-title":"Nat Methods"},{"issue":"9","key":"2023050211440118700_kiac574-B47","doi-asserted-by":"crossref","first-page":"1650","DOI":"10.1038\/nprot.2016.095","article-title":"Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown","volume":"11","author":"Pertea","year":"2016","journal-title":"Nat Protoc"},{"issue":"3","key":"2023050211440118700_kiac574-B48","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1038\/nbt.3122","article-title":"Stringtie enables improved reconstruction of a transcriptome from RNA-seq reads","volume":"33","author":"Pertea","year":"2015","journal-title":"Nat Biotechnol"},{"issue":"2","key":"2023050211440118700_kiac574-B49","doi-asserted-by":"crossref","first-page":"744","DOI":"10.1104\/pp.104.057935","article-title":"Gene family analysis of the Arabidopsis pollen transcriptome reveals biological implications for cell growth, division control, and gene expression regulation","volume":"138","author":"Pina","year":"2005","journal-title":"Plant Physiol"},{"issue":"W1","key":"2023050211440118700_kiac574-B50","doi-asserted-by":"crossref","first-page":"W191","DOI":"10.1093\/nar\/gkz369","article-title":"G:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update)","volume":"47","author":"Raudvere","year":"2019","journal-title":"Nucleic Acids Res"},{"issue":"9","key":"2023050211440118700_kiac574-B51","doi-asserted-by":"crossref","first-page":"2725","DOI":"10.1105\/tpc.20.00244","article-title":"Nonsense-mediated RNA decay factor UPF1 is critical for posttranscriptional and translational gene regulation in Arabidopsis","volume":"32","author":"Raxwal","year":"2020","journal-title":"Plant Cell"},{"issue":"2","key":"2023050211440118700_kiac574-B52","doi-asserted-by":"crossref","first-page":"e31917","DOI":"10.1371\/journal.pone.0031917","article-title":"A role for nonsense-mediated mRNA decay in plants: pathogen responses are induced in Arabidopsis thaliana NMD mutants","volume":"7","author":"Rayson","year":"2012","journal-title":"PLoS One"},{"issue":"10","key":"2023050211440118700_kiac574-B53","doi-asserted-by":"crossref","first-page":"3657","DOI":"10.1105\/tpc.113.117523","article-title":"Complexity of the alternative splicing landscape in plants","volume":"25","author":"Reddy","year":"2013","journal-title":"Plant Cell"},{"issue":"3","key":"2023050211440118700_kiac574-B54","doi-asserted-by":"crossref","first-page":"244","DOI":"10.1016\/j.cub.2005.01.013","article-title":"A novel class of MYB factors controls sperm-cell formation in plants","volume":"15","author":"Rotman","year":"2005","journal-title":"Curr Biol"},{"issue":"2","key":"2023050211440118700_kiac574-B55","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1007\/s00497-015-0261-7","article-title":"A decade of pollen transcriptomics","volume":"28","author":"Rutley","year":"2015","journal-title":"Plant Reprod"},{"key":"2023050211440118700_kiac574-B56","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1007\/978-1-4939-7286-9_16","volume-title":"Plant Germline Development: Methods and Protocols","author":"Santos","year":"2017"},{"issue":"3","key":"2023050211440118700_kiac574-B57","doi-asserted-by":"crossref","first-page":"1345","DOI":"10.1093\/nar\/gku1392","article-title":"Detection of recurrent alternative splicing switches in tumor samples reveals novel signatures of cancer","volume":"43","author":"Sebesty\u00e9n","year":"2015","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"2023050211440118700_kiac574-B58","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"},{"issue":"3","key":"2023050211440118700_kiac574-B59","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1016\/j.cell.2008.12.038","article-title":"Epigenetic reprogramming and small RNA silencing of transposable elements in pollen","volume":"136","author":"Slotkin","year":"2009","journal-title":"Cell"},{"issue":"10","key":"2023050211440118700_kiac574-B60","doi-asserted-by":"crossref","first-page":"3640","DOI":"10.1105\/tpc.113.113803","article-title":"Alternative splicing at the intersection of biological timing, development, and stress responses","volume":"25","author":"Staiger","year":"2013","journal-title":"Plant Cell"},{"issue":"1","key":"2023050211440118700_kiac574-B61","doi-asserted-by":"crossref","first-page":"586","DOI":"10.1104\/pp.15.01267","article-title":"Genome-wide analysis of alternative splicing during development and drought stress in maize","volume":"170","author":"Thatcher","year":"2016","journal-title":"Plant Physiol"},{"issue":"9","key":"2023050211440118700_kiac574-B62","doi-asserted-by":"crossref","first-page":"3472","DOI":"10.1105\/tpc.114.130773","article-title":"Genome-wide analysis of alternative splicing in Zea mays: landscape and genetic regulation","volume":"26","author":"Thatcher","year":"2014","journal-title":"Plant Cell"},{"issue":"1","key":"2023050211440118700_kiac574-B63","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1186\/s13059-018-1417-1","article-title":"SUPPA2: fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions","volume":"19","author":"Trincado","year":"2018","journal-title":"Genome Biol"},{"issue":"11","key":"2023050211440118700_kiac574-B64","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/gb-2007-8-11-r249","article-title":"MADS-complexes regulate transcriptome dynamics during pollen maturation","volume":"8","author":"Verelst","year":"2007","journal-title":"Genome Biol"},{"issue":"7221","key":"2023050211440118700_kiac574-B65","doi-asserted-by":"crossref","first-page":"470","DOI":"10.1038\/nature07509","article-title":"Alternative isoform regulation in human tissue transcriptomes","volume":"456","author":"Wang","year":"2008","journal-title":"Nature"},{"issue":"6","key":"2023050211440118700_kiac574-B66","doi-asserted-by":"crossref","first-page":"506","DOI":"10.1016\/j.cub.2010.01.051","article-title":"Arabidopsis female gametophyte gene expression map reveals similarities between plant and animal gametes","volume":"20","author":"Wuest","year":"2010","journal-title":"Curr Biol"},{"issue":"17","key":"2023050211440118700_kiac574-B67","doi-asserted-by":"crossref","first-page":"3754","DOI":"10.1093\/nar\/gkf492","article-title":"Genome-wide detection of tissue-specific alternative splicing in the human transcriptome","volume":"30","author":"Xu","year":"2002","journal-title":"Nucleic Acids Res"},{"issue":"10","key":"2023050211440118700_kiac574-B68","doi-asserted-by":"crossref","first-page":"R74","DOI":"10.1186\/gb-2004-5-10-r74","article-title":"Variation in alternative splicing across human tissues","volume":"5","author":"Yeo","year":"2004","journal-title":"Genome Biol"},{"issue":"9","key":"2023050211440118700_kiac574-B69","doi-asserted-by":"crossref","first-page":"5061","DOI":"10.1093\/nar\/gkx267","article-title":"A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing","volume":"45","author":"Zhang","year":"2017","journal-title":"Nucleic Acids Res"},{"issue":"5","key":"2023050211440118700_kiac574-B70","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"},{"issue":"1","key":"2023050211440118700_kiac574-B71","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1186\/s13059-022-02711-0","article-title":"A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of iso-seq analysis","volume":"23","author":"Zhang","year":"2022","journal-title":"Genome Biol"},{"issue":"6","key":"2023050211440118700_kiac574-B72","doi-asserted-by":"crossref","first-page":"882","DOI":"10.1016\/j.devcel.2019.04.016","article-title":"Two-step maternal-to-zygotic transition with two-phase parental genome contributions","volume":"49","author":"Zhao","year":"2019","journal-title":"Dev Cell"}],"container-title":["Plant Physiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/plphys\/advance-article-pdf\/doi\/10.1093\/plphys\/kiac574\/48835353\/kiac574.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/plphys\/article-pdf\/192\/1\/85\/50168321\/kiac574.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/plphys\/article-pdf\/192\/1\/85\/50168321\/kiac574.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,2]],"date-time":"2023-05-02T11:53:51Z","timestamp":1683028431000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/plphys\/article\/192\/1\/85\/6901502"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,12,14]]},"references-count":72,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2022,12,14]]},"published-print":{"date-parts":[[2023,5,2]]}},"URL":"https:\/\/doi.org\/10.1093\/plphys\/kiac574","relation":{},"ISSN":["0032-0889","1532-2548"],"issn-type":[{"value":"0032-0889","type":"print"},{"value":"1532-2548","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,5,1]]},"published":{"date-parts":[[2022,12,14]]}}}