Abstract
The Papaver spp. (Papaver rhoeas (Corn poppy) and Papaver nudicaule (Iceland poppy)) genera are ornamental and medicinal plants that are used for the isolation of alkaloid drugs. In this study, we generated 700 Mb of transcriptome sequences with the PacBio platform. They were assembled into 120,926 contigs, and 1185 (82.2%) of the benchmarking universal single-copy orthologs (BUSCO) core genes were completely present in our assembled transcriptome. Furthermore, using 128 Gb of Illumina sequences, the transcript expression was assessed at three stages of Papaver plant development (30, 60, and 90 days), from which we identified 137 differentially expressed transcripts. Furthermore, three co-occurrence heat maps are generated from 51 different plant genomes along with the Papaver transcriptome, i.e., secondary metabolite biosynthesis, isoquinoline alkaloid biosynthesis (BIA) pathway, and cytochrome. Sixty-nine transcripts in the BIA pathway along with 22 different alkaloids (quantified with LC-QTOF-MS/MS) were mapped into the BIA KEGG map (map00950). Finally, we identified 39 full-length cytochrome transcripts and compared them with other genomes. Collectively, this transcriptome data, along with the expression and quantitative metabolite profiles, provides an initial recording of secondary metabolites and their expression related to Papaver plant development. Moreover, these profiles could help to further detail the functional characterization of the various secondary metabolite biosynthesis and Papaver plant development associated problems.
Highlights
Plants in the Papaver genus from Papaveraceae family have been used in traditional medicinal practices for a long time
After filtering out the low-quality reads and adapter contamination according to the technologies that were used (Table 1, section A), a total of 302 Mb high-quality long read sequences were assembled into 120,926 contigs with 3117 bases of N50 (Table 1, section A)
Most of the sequence lengths were between 3000 and 3500 bp (Figure 1A). This representative transcriptome contains 1185 (82.3%) benchmarking universal single-copy orthologs (BUSCO) genes present in the reference transcriptome, and only 180 (12.5%) genes were missing from the representative transcriptome (Table 1, section D)
Summary
Plants in the Papaver genus from Papaveraceae family (commonly known as poppy) have been used in traditional medicinal practices for a long time. A few studies used high-throughput sequencing, such as 454 [8,30,31] and Illumina [29], but this was not sufficient to characterize the gene content in Papaver species With this knowledge, this study was further modeled to capture the transcripts expression patterns and alkaloid accumulation at three different time points in Papaver developmental life cycle, from stage three to five. We have reported the first study on the generation of the transcriptome from long-read sequencing technology and an assessment of differential transcript expressions during the Papaver plant developmental stages These transcripts were compared with 51 closely- and distantly-related plants from monocots and dicots to obtain an overview of the secondary metabolites, with reference to the KEGG database. We have profiled 860 secondary metabolite biosynthesis transcripts, 39 cytochromes, and 69 BIA synthesis transcripts, with their relative expressions from three different plant developmental stages, i.e., from leaf rosette stage to blossom and seed formation stage
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