{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,24]],"date-time":"2026-08-24T10:34:00Z","timestamp":1787567640211,"version":"build-2736575974"},"reference-count":38,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,8,24]],"date-time":"2026-08-24T00:00:00Z","timestamp":1787529600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2026,8,24]],"date-time":"2026-08-24T00:00:00Z","timestamp":1787529600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/100012095","name":"Scottish Government","doi-asserted-by":"crossref","award":["KJHI-B1-1"],"award-info":[{"award-number":["KJHI-B1-1"]}],"id":[{"id":"10.13039\/100012095","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100012095","name":"Scottish Government","doi-asserted-by":"crossref","award":["RESAS projects KJHI-B1-2"],"award-info":[{"award-number":["RESAS projects KJHI-B1-2"]}],"id":[{"id":"10.13039\/100012095","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BB\/S020160\/1"],"award-info":[{"award-number":["BB\/S020160\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Data"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Transcriptome annotations provide essential information on transcript locations, sequences and structures, including transcription start, end sites and splice junctions. They underpin key biological analyses such as gene and transcript quantification, and the study of transcriptional and post-transcriptional regulation, including alternative transcription initiation, polyadenylation and splicing. Accurate characterisation of transcript isoforms is critical for understanding how gene expression relates to functional protein products. However, for many species\u2014including Solanaceae crops such as potato and tomato\u2014current annotations suffer from limited isoform coverage, with tens or hundreds of thousands of splice junctions and transcript isoforms missing. This undermines the completeness and accuracy of transcript-level analyses. Here, by generating Iso-seq and RNA-seq on a range of tissues and samples, we have produced transcriptome annotations for both potato and tomato with improved coverage, diversity, accurate splice junctions, and transcript start and end sites. We have also made these high-quality resources accessible through genome browsers. These enhanced annotations will enable more accurate transcriptome analyses, supporting higher-resolution and novel biological discoveries.<\/jats:p>","DOI":"10.1038\/s41597-026-07792-1","type":"journal-article","created":{"date-parts":[[2026,8,24]],"date-time":"2026-08-24T09:29:46Z","timestamp":1787563786000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["PotatoRTD and TomatoRTD: Comprehensive Reference Transcript Datasets for Accurate Transcriptome Analysis and Isoform Discovery"],"prefix":"10.1038","volume":"13","author":[{"given":"Wenbin","family":"Guo","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Linda","family":"Milne","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sara","family":"Lopez-Gomollon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amanpreet","family":"Kaur","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ingo","family":"Hein","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Baulcombe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Runxuan","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,8,24]]},"reference":[{"key":"7792_CR1","doi-asserted-by":"publisher","first-page":"417","DOI":"10.1038\/nmeth.4197","volume":"14","author":"R Patro","year":"2017","unstructured":"Patro, R., Duggal, G., Love, M. I., Irizarry, R. A. & Kingsford, C. Salmon provides fast and bias-aware quantification of transcript expression. Nature Methods 14, 417\u2013419 (2017).","journal-title":"Nature Methods"},{"key":"7792_CR2","doi-asserted-by":"publisher","first-page":"525","DOI":"10.1038\/nbt.3519","volume":"34","author":"NL Bray","year":"2016","unstructured":"Bray, N. L., Pimentel, H., Melsted, P. & Pachter, L. Near-optimal probabilistic RNA-seq quantification. Nature Biotechnology 34, 525\u2013527 (2016).","journal-title":"Nature Biotechnology"},{"key":"7792_CR3","unstructured":"Soneson, C. et al. A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs. Life Sci. Alliance 2 (2019)."},{"key":"7792_CR4","unstructured":"Hsieh, P. H., Oyang, Y. J. & Chen, C. Y. Effect of transcriptome assembly on transcript quantification. Scientific Reports 9, 8304 (2019)."},{"key":"7792_CR5","doi-asserted-by":"publisher","first-page":"589","DOI":"10.1016\/j.cels.2019.10.005","volume":"9","author":"C Ma","year":"2019","unstructured":"Ma, C. & Kingsford, C. Detecting, Categorizing, and Correcting Coverage Anomalies of RNA-Seq Quantification. Cell Syst 9, 589\u2013599.e7 (2019).","journal-title":"Cell Syst"},{"key":"7792_CR6","unstructured":"Mays, A. D. et al. Single-Molecule Real-Time (SMRT) Full-Length RNA-Sequencing Reveals Novel and Distinct mRNA Isoforms in Human Bone Marrow Cell Subpopulations. Genes (Basel). 10 (2019)."},{"key":"7792_CR7","doi-asserted-by":"publisher","DOI":"10.1186\/s13068-018-1167-z","volume":"11","author":"C Zuo","year":"2018","unstructured":"Zuo, C. et al. Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing. Biotechnology for Biofuels 11, 170 (2018).","journal-title":"Biotechnology for Biofuels"},{"key":"7792_CR8","doi-asserted-by":"publisher","unstructured":"Reese, F. et al. The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity. bioRxiv 2023.05.15.540865, https:\/\/doi.org\/10.1101\/2023.05.15.540865 (2023).","DOI":"10.1101\/2023.05.15.540865"},{"key":"7792_CR9","doi-asserted-by":"publisher","first-page":"511","DOI":"10.1038\/nbt.1621","volume":"28","author":"C Trapnell","year":"2010","unstructured":"Trapnell, C. et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnology 28, 511\u2013515 (2010).","journal-title":"Nature Biotechnology"},{"key":"7792_CR10","doi-asserted-by":"publisher","first-page":"290","DOI":"10.1038\/nbt.3122","volume":"33","author":"M Pertea","year":"2015","unstructured":"Pertea, M. et al. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nature Biotechnology 33, 290\u2013295 (2015).","journal-title":"Nature Biotechnology"},{"key":"7792_CR11","doi-asserted-by":"publisher","first-page":"1167","DOI":"10.1038\/nbt.4020","volume":"35","author":"M Shao","year":"2017","unstructured":"Shao, M. & Kingsford, C. Accurate assembly of transcripts through phase-preserving graph decomposition. Nature Biotechnology 35, 1167\u20131169 (2017).","journal-title":"Nature Biotechnology"},{"key":"7792_CR12","doi-asserted-by":"publisher","first-page":"1177","DOI":"10.1038\/nmeth.2714","volume":"10","author":"T Steijger","year":"2013","unstructured":"Steijger, T. et al. Assessment of transcript reconstruction methods for RNA-seq. Nature Methods 10, 1177\u20131184 (2013).","journal-title":"Nature Methods"},{"key":"7792_CR13","doi-asserted-by":"publisher","first-page":"3938","DOI":"10.1093\/bioinformatics\/btv488","volume":"31","author":"KE Hayer","year":"2015","unstructured":"Hayer, K. E., Pizarro, A., Lahens, N. F., Hogenesch, J. B. & Grant, G. R. Benchmark analysis of algorithms for determining and quantifying full-length mRNA splice forms from RNA-seq data. Bioinformatics 31, 3938\u20133945 (2015).","journal-title":"Bioinformatics"},{"key":"7792_CR14","doi-asserted-by":"publisher","first-page":"96","DOI":"10.1111\/nph.13545","volume":"208","author":"R Zhang","year":"2015","unstructured":"Zhang, R. et al. AtRTD - a comprehensive reference transcript dataset resource for accurate quantification of transcript-specific expression in Arabidopsis thaliana. New Phytologist 208, 96\u2013101 (2015).","journal-title":"New Phytologist"},{"key":"7792_CR15","doi-asserted-by":"publisher","first-page":"5061","DOI":"10.1093\/nar\/gkx267","volume":"45","author":"R Zhang","year":"2017","unstructured":"Zhang, R. et al. A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing. Nucleic Acids Res 45, 5061\u20135073 (2017).","journal-title":"Nucleic Acids Res"},{"key":"7792_CR16","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-022-02711-0","volume":"23","author":"R Zhang","year":"2022","unstructured":"Zhang, R. et al. A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis. Genome Biology 23, 149 (2022).","journal-title":"Genome Biology"},{"key":"7792_CR17","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-019-6243-7","volume":"20","author":"P Rapazote-Flores","year":"2019","unstructured":"Rapazote-Flores, P. et al. BaRTv1.0: an improved barley reference transcript dataset to determine accurate changes in the barley transcriptome using RNA-seq. BMC Genomics 20, 968 (2019).","journal-title":"BMC Genomics"},{"key":"7792_CR18","doi-asserted-by":"publisher","first-page":"1183","DOI":"10.1111\/tpj.15871","volume":"111","author":"M Coulter","year":"2022","unstructured":"Coulter, M. et al. BaRTv2: a highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification. Plant Journal 111, 1183\u20131202 (2022).","journal-title":"Plant Journal"},{"key":"7792_CR19","doi-asserted-by":"publisher","first-page":"370","DOI":"10.1111\/tpj.16978","volume":"120","author":"MF Kara","year":"2024","unstructured":"Kara, M. F., Guo, W., Zhang, R. & Denby, K. LsRTDv1, a reference transcript dataset for accurate transcript-specific expression analysis in lettuce. Plant Journal 120, 370\u2013386 (2024).","journal-title":"Plant Journal"},{"key":"7792_CR20","doi-asserted-by":"publisher","unstructured":"Campbell, R. et al. TheMetabolic and Developmental Roles of Carotenoid Cleavage Dioxygenase4 from Potato. Plant Physiol. 154, 656\u2013664, https:\/\/doi.org\/10.1104\/pp.110.158733 (2010).","DOI":"10.1104\/pp.110.158733"},{"key":"7792_CR21","doi-asserted-by":"publisher","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","volume":"34","author":"S Chen","year":"2018","unstructured":"Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884\u2013i890 (2018).","journal-title":"Bioinformatics"},{"key":"7792_CR22","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","volume":"29","author":"A Dobin","year":"2013","unstructured":"Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15\u201321 (2013).","journal-title":"Bioinformatics"},{"key":"7792_CR23","doi-asserted-by":"publisher","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","volume":"34","author":"H Li","year":"2018","unstructured":"Li, H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094\u20133100 (2018).","journal-title":"Bioinformatics"},{"key":"7792_CR24","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-020-07123-7","volume":"21","author":"RI Kuo","year":"2020","unstructured":"Kuo, R. I. et al. Illuminating the dark side of the human transcriptome with long read transcript sequencing. BMC Genomics 21, 751 (2020).","journal-title":"BMC Genomics"},{"key":"7792_CR25","doi-asserted-by":"publisher","unstructured":"Entizne, J. C. et al. TranSuite: a software suite for accurate translation and characterization of transcripts. bioRxiv 2020.12.15.422989, https:\/\/doi.org\/10.1101\/2020.12.15.422989 (2020).","DOI":"10.1101\/2020.12.15.422989"},{"key":"7792_CR26","doi-asserted-by":"publisher","first-page":"1236","DOI":"10.1093\/bioinformatics\/btu031","volume":"30","author":"P Jones","year":"2014","unstructured":"Jones, P. et al. InterProScan 5: genome-scale protein function classification. Bioinformatics 30, 1236\u20131240 (2014).","journal-title":"Bioinformatics"},{"key":"7792_CR27","doi-asserted-by":"publisher","first-page":"118","DOI":"10.1002\/pro.4193","volume":"31","author":"P T\u00f6r\u00f6nen","year":"2022","unstructured":"T\u00f6r\u00f6nen, P. & Holm, L. PANNZER\u2014A practical tool for protein function prediction. Protein Science 31, 118\u2013128 (2022).","journal-title":"Protein Science"},{"key":"7792_CR28","unstructured":"NCBI Sequence Read Archive: SRP665952. https:\/\/identifiers.org\/ncbi\/insdc.sra:SRP665952 (2026)."},{"key":"7792_CR29","unstructured":"NCBI Sequence Read Archive: SRP665181. https:\/\/identifiers.org\/ncbi\/insdc.sra:SRP665181 (2026)."},{"key":"7792_CR30","doi-asserted-by":"publisher","unstructured":"Guo, W. et al. PotatoRTD and TomatoRTD. Preprint at https:\/\/doi.org\/10.5281\/zenodo.20160822 (2026).","DOI":"10.5281\/zenodo.20160822"},{"key":"7792_CR31","doi-asserted-by":"publisher","first-page":"449","DOI":"10.1146\/annurev.biochem.72.121801.161520","volume":"72","author":"ST Smale","year":"2003","unstructured":"Smale, S. T. & Kadonaga, J. T. The RNA polymerase II core promoter. Annu. Rev. Biochem. 72, 449\u2013479 (2003).","journal-title":"Annu. Rev. Biochem."},{"key":"7792_CR32","doi-asserted-by":"publisher","unstructured":"Kozak, M. Compilation and analysis of sequencesupstream from the translational start site in eukaryotic mRNAs. Nucleic Acids Research 12(2), 857\u2013872, https:\/\/doi.org\/10.1093\/nar\/12.2.857 (1984).","DOI":"10.1093\/nar\/12.2.857"},{"key":"7792_CR33","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-8-67","volume":"8","author":"YY Yamamoto","year":"2007","unstructured":"Yamamoto, Y. Y. et al. Identification of plant promoter constituents by analysis of local distribution of short sequences. BMC Genomics 8, 67 (2007).","journal-title":"BMC Genomics"},{"key":"7792_CR34","doi-asserted-by":"publisher","first-page":"1467","DOI":"10.1016\/S1097-2765(03)00453-2","volume":"12","author":"KM Brown","year":"2003","unstructured":"Brown, K. M. & Gilmartin, G. M. A Mechanism for the Regulation of Pre-mRNA 3\u2032 Processing by Human Cleavage Factor Im. Mol. Cell 12, 1467\u20131476 (2003).","journal-title":"Mol. Cell"},{"key":"7792_CR35","doi-asserted-by":"publisher","first-page":"1770","DOI":"10.1101\/gad.17268411","volume":"25","author":"NJ Proudfoot","year":"2011","unstructured":"Proudfoot, N. J. Ending the message: poly(A) signals then and now. Genes Dev. 25, 1770\u20131782 (2011).","journal-title":"Genes Dev."},{"key":"7792_CR36","doi-asserted-by":"publisher","DOI":"10.1111\/tpj.70186","volume":"122","author":"R Campbell","year":"2025","unstructured":"Campbell, R. et al. GERMIN3 regulates tuber initiation and axillary bud activation by facilitating plasmodesmatal gating. Plant Journal 122, e70186 (2025).","journal-title":"Plant Journal"},{"key":"7792_CR37","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1016\/j.cj.2024.09.013","volume":"13","author":"A Kaur","year":"2025","unstructured":"Kaur, A. et al. Transcriptional profiling during infection of potato NLRs and Phytophthora infestans effectors using cDNA enrichment sequencing. Crop J. 13, 31\u201340 (2025).","journal-title":"Crop J."},{"key":"7792_CR38","doi-asserted-by":"publisher","first-page":"1574","DOI":"10.1080\/15476286.2020.1858253","volume":"18","author":"W Guo","year":"2021","unstructured":"Guo, W. et al. 3D RNA-seq: a powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists. RNA Biol. 18, 1574\u20131587 (2021).","journal-title":"RNA Biol."}],"container-title":["Scientific Data"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41597-026-07792-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41597-026-07792-1","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41597-026-07792-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,24]],"date-time":"2026-08-24T09:29:47Z","timestamp":1787563787000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41597-026-07792-1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,24]]},"references-count":38,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["7792"],"URL":"https:\/\/doi.org\/10.1038\/s41597-026-07792-1","relation":{},"ISSN":["2052-4463"],"issn-type":[{"value":"2052-4463","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,24]]},"assertion":[{"value":"26 February 2026","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"29 June 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"24 August 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Ethics"}}],"article-number":"1222"}}