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Here, we employed long\u2010read sequencing technology, Oxford Nanopore Technology, to annotate the pig transcriptome across 17 tissues from two Yorkshire littermate pigs. More than 9.8\u00a0million reads were obtained from a single flow cell, and 69\u2009781 unique transcripts at 50\u2009108 loci were identified. Of these transcripts, 16\u2009255 were found to be novel isoforms, and 22\u2009344 were found at loci that were novel and unannotated in the Ensembl (release 102) and NCBI (release 106) annotations. Novel transcripts were mostly expressed in cerebellum, followed by lung, liver, spleen, and hypothalamus. By comparing the unannotated transcripts to existing databases, there were 21\u2009285 (95.3%) transcripts matched to the NT database (v5) and 13\u2009676 (61.2%) matched to the NR database (v5). Moreover, there were 4324 (19.4%) transcripts matched to the SwissProt database (v5), corresponding to 11\u2009356 proteins. Tissue\u2010specific gene expression analyses showed that 9749 transcripts were highly tissue\u2010specific, and cerebellum contained the most tissue\u2010specific transcripts. As the same samples were used for the annotation of <jats:italic>cis<\/jats:italic>\u2010regulatory elements in the pig genome, the transcriptome annotation generated by this study provides an additional and complementary annotation resource for the Functional Annotation of Animal Genomes effort to comprehensively annotate the pig genome.<\/jats:p>","DOI":"10.1111\/age.13274","type":"journal-article","created":{"date-parts":[[2022,11,17]],"date-time":"2022-11-17T03:14:57Z","timestamp":1668654897000},"page":"35-44","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Transcriptome annotation of 17 porcine tissues using nanopore sequencing technology"],"prefix":"10.1111","volume":"54","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4854-2613","authenticated-orcid":false,"given":"Jinghui","family":"Li","sequence":"first","affiliation":[{"name":"Department of Animal Science University of California Davis  Davis California USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dailu","family":"Guan","sequence":"additional","affiliation":[{"name":"Department of Animal Science University of California Davis  Davis California USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michelle M.","family":"Halstead","sequence":"additional","affiliation":[{"name":"Department of Animal Science University of California Davis  Davis California USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alma D.","family":"Islas\u2010Trejo","sequence":"additional","affiliation":[{"name":"Department of Animal Science University of California Davis  Davis California USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel E.","family":"Goszczynski","sequence":"additional","affiliation":[{"name":"Department of Animal Science University of California Davis  Davis California USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2833-0995","authenticated-orcid":false,"given":"Catherine W.","family":"Ernst","sequence":"additional","affiliation":[{"name":"Department of Animal Science Michigan State University  East Lansing Michigan USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hao","family":"Cheng","sequence":"additional","affiliation":[{"name":"Department of Animal Science University of California Davis  Davis California USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pablo","family":"Ross","sequence":"additional","affiliation":[{"name":"Department of Animal Science University of California Davis  Davis California USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6023-9521","authenticated-orcid":false,"given":"Huaijun","family":"Zhou","sequence":"additional","affiliation":[{"name":"Department of Animal Science University of California Davis  Davis California USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2022,11,16]]},"reference":[{"key":"e_1_2_8_2_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu638"},{"key":"e_1_2_8_3_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-015-0622-4"},{"key":"e_1_2_8_4_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-019-5709-y"},{"key":"e_1_2_8_5_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-020-02197-8"},{"key":"e_1_2_8_6_1","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giab008"},{"key":"e_1_2_8_7_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty149"},{"key":"e_1_2_8_8_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1105136"},{"key":"e_1_2_8_9_1","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.59929"},{"key":"e_1_2_8_10_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4577"},{"key":"e_1_2_8_11_1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-animal-020518-114913"},{"key":"e_1_2_8_12_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-022-05035-y"},{"key":"e_1_2_8_13_1","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2021.664260"},{"key":"e_1_2_8_14_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.humimm.2021.02.012"},{"key":"e_1_2_8_15_1","doi-asserted-by":"publisher","DOI":"10.1038\/nprot.2008.211"},{"key":"e_1_2_8_16_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkn923"},{"key":"e_1_2_8_17_1","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giw018"},{"key":"e_1_2_8_18_1","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.4060"},{"key":"e_1_2_8_19_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-23560-8"},{"key":"e_1_2_8_20_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.1001328"},{"key":"e_1_2_8_21_1","doi-asserted-by":"crossref","unstructured":"Kaplow I.M. 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