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However, due to the 70.9% repetitive content and the whole\u2010genome duplication event of the opium poppy genome, it is difficult to generate accurate and comprehensive gene annotations. To overcome this problem, we used the PacBio single\u2010molecule long\u2010read isoform sequencing (IsoSeq) technology to improve opium poppy genome annotation and identify genome\u2010wide alternative splicing (AS). In total, we identified 410\u2009699 full\u2010length isoforms, correcting 1007 misannotated genes and identifying 10\u2009473 unannotated genes. Notably, the annotations of two BIA metabolism genes, <jats:italic>CYP80B1<\/jats:italic> (<jats:italic>PS0533980.1<\/jats:italic>) and <jats:italic>BBE<\/jats:italic> (<jats:italic>PS1014490.1<\/jats:italic>), were corrected, and a novel copy of <jats:italic>CYP80B1<\/jats:italic> was discovered. In addition, we found current opium poppy genome annotation was biased on GC content and exon number, leading to missing of some younger genes. Furthermore, 474\u2005169 novel splicing junctions were identified, revealing splicing sites characteristics difference of genes originating from different phylostratums. Based on the splicing junctions identified by the full\u2010length transcripts, we discovered the tissue\u2010 and development\u2010specific AS modes. More specifically, we found the percentage of retained introns (RIs) in the petal and stamen decreased, correlating with the lower GC content of the transcriptome. Also, there was a decrease in the percentage of splicing (PSI) at RI sites after cotyledon growth. The development\u2010related pathways were also enriched among the genes of the RI sites, indicating the post\u2010transcriptional mechanism during the seedling development of opium poppy. Our data provide abundant transcriptome insights into the AS of the opium poppy.<\/jats:p>","DOI":"10.1111\/tpj.15689","type":"journal-article","created":{"date-parts":[[2022,1,29]],"date-time":"2022-01-29T18:08:31Z","timestamp":1643479711000},"page":"607-620","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["A global survey of the transcriptome of the opium poppy (<i>Papaver somniferum<\/i>) based on single\u2010molecule long\u2010read isoform sequencing"],"prefix":"10.1111","volume":"110","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3194-1834","authenticated-orcid":false,"given":"Tun","family":"Xu","sequence":"first","affiliation":[{"name":"School of Automation Science and Engineering Faculty of Electronic and Information Engineering, Xi'an Jiaotong University  Xi'an China"},{"name":"MOE Key Lab for Intelligent Networks &amp; Networks Security, Faculty of Electronic and Information Engineering Xi'an Jiaotong 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