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Here, we report single-molecule real-time sequencing data from the testis and epididymis of the Banna mini-pig inbred line (BMI), a promising laboratory animal for medical research. We obtained high-quality full-length transcriptomes and identified 9879 isoforms and 8761 isoforms in the BMI testis and epididymis, respectively. Most of the isoforms we identified have novel exon structures that will greatly improve the annotation of testis- and epididymis-expressed genes in pigs. We also found that 3055 genes (over 50%) were shared between BMI testis and epididymis, indicating widespread expression profiles of genes related to reproduction. We characterized extensive alternative splicing events in BMI testis and epididymis and showed that 96 testis-expressed genes and 79 epididymis-expressed genes have more than six isoforms, revealing the complexity of alternative splicing. We accurately defined the transcribed isoforms in BMI testis and epididymis by combining Pacific Biotechnology Isoform-sequencing (PacBio Iso-Seq) and Illumina RNA Sequencing (RNA-seq) techniques. The refined annotation of some key genes governing male reproduction will facilitate further understanding of the molecular mechanisms underlying BMI male sterility. In addition, the high-confident identification of 548 and 669 long noncoding RNAs (lncRNAs) in these two tissues has established a candidate gene set for future functional investigations. Overall, our study provides new insights into the role of the testis and epididymis during BMI reproduction, paving the path for further studies on BMI male infertility.<\/jats:p>","DOI":"10.1093\/biolre\/ioac216","type":"journal-article","created":{"date-parts":[[2022,12,8]],"date-time":"2022-12-08T14:04:28Z","timestamp":1670508268000},"page":"465-478","source":"Crossref","is-referenced-by-count":10,"title":["Transcriptomic analysis of testis and epididymis tissues from Banna mini-pig inbred line boars with single-molecule long-read sequencing"],"prefix":"10.1093","volume":"108","author":[{"given":"Pei","family":"Wang","sequence":"first","affiliation":[{"name":"Yunnan Agricultural University College of Animal Science and Technology, , Kunming, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xia","family":"Zhang","sequence":"additional","affiliation":[{"name":"Lyuliang University College of Life Science, , Lvliang, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hailong","family":"Huo","sequence":"additional","affiliation":[{"name":"Yunnan Vocational and Technical college of Agriculture , Kunming, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Weizhen","family":"Li","sequence":"additional","affiliation":[{"name":"Yunnan Agricultural University College of Veterinary Medicine, , Kunming, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhipeng","family":"Liu","sequence":"additional","affiliation":[{"name":"Yunnan Agricultural University College of Animal Science and Technology, , Kunming, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lina","family":"Wang","sequence":"additional","affiliation":[{"name":"Yunnan Agricultural University College of Animal Science and Technology, , Kunming, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Luogang","family":"Li","sequence":"additional","affiliation":[{"name":"Yunnan Agricultural University College of Animal Science and Technology, , Kunming, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yu H","family":"Sun","sequence":"additional","affiliation":[{"name":"University of Rochester Department of Biology, , Rochester, NY , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jinlong","family":"Huo","sequence":"additional","affiliation":[{"name":"Yunnan Agricultural University College of Animal Science and Technology, , Kunming , China"},{"name":"University of Rochester Department of Biology, , Rochester, NY , 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