A global survey of the transcriptome of the opium poppy ( Papaver somniferum ) based on single‐molecule long‐read isoform sequencing

Opium poppy (Papaver somniferum), which produces benzylisoquinoline alkaloids (BIAs), is an important medicinal plant. However, due to the 70.9% repetitive content and the whole-genome 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-molecule long-read isoform sequencing (IsoSeq) technology to improve opium poppy genome annotation and identify genome-wide alternative splicing (AS). In total, we identified 410 699 full-length isoforms, correcting 1007 misannotated genes and identifying 10 473 unannotated genes. Notably, the annotations of two BIA metabolism genes, CYP80B1 (PS0533980.1) and BBE (PS1014490.1), were corrected, and a novel copy of CYP80B1 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, 474 169 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-length transcripts, we discovered the tissue- and development-specific 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-related pathways were also enriched among the genes of the RI sites, indicating the post-transcriptional mechanism during the seedling development of opium poppy. Our data provide abundant transcriptome insights into the AS of the opium poppy.