Genome and transcriptome of Papaver somniferum Chinese landrace CHM indicates that massive genome expansion contributes to high benzylisoquinoline alkaloid biosynthesis

Abstract

Opium poppy (Papaver somniferum) is a source of morphine, codeine, and semisynthetic derivatives, including oxycodone and naltrexone. Here, we report the de novo assembly and genomic analysis of P. somniferum traditional landrace ‘Chinese Herbal Medicine’. Variations between the 2.62 Gb CHM genome and that of the previously sequenced high noscapine 1 (HN1) variety were also explored. Among 79,668 protein-coding genes, we functionally annotated 88.9%, compared to 68.8% reported in the HN1 genome. Gene family and 4DTv comparative analyses with three other Papaveraceae species revealed that opium poppy underwent two whole-genome duplication (WGD) events. The first of these, in ancestral Ranunculales, expanded gene families related to characteristic secondary metabolite production and disease resistance. The more recent species-specific WGD mediated by transposable elements resulted in massive genome expansion. Genes carrying structural variations and large-effect variants associated with agronomically different phenotypes between CHM and HN1 that were identified through our transcriptomic comparison of multiple organs and developmental stages can enable the development of new varieties. These genomic and transcriptomic analyses will provide a valuable resource that informs future basic and agricultural studies of the opium poppy.

A phylotranscriptome study using silica gel-dried leaf tissues produces an updated robust phylogeny of Ranunculaceae

“…The first event occurred in the Ranunculales ancestor at around 110 Mya, as previous studies had also suggested (Pabón-Mora et al, 2013;One Thousand Plant Transcriptomes Initiatives, 2019;Pei et al, 2021). After that, we detected another WGD event around 80 Mya after the divergence of Hydrastideae, but before the divergence of…”

New insights into the evolution of SPX gene family from algae to legumes; a focus on soybean

“…The number of whole-genome duplications is correlated with gene family size [47,50], which is consistent with our results, since P. somniferum and G. max with two WGD events had the largest sizes of SPX family [51,52]. The expansion of SPX family in these two plants is mostly affected by WGD duplication type, while segmental/local duplication type was the main contributor of expansion in S. moellendorffii, the species with third greatest SPX family, which might explain its unique classes.…”

The chromosome-level reference genome of Coptis chinensis provides insights into genomic evolution and berberine biosynthesis

“…Additionally, LTR annotation was performed to estimate the assembly genome quality. Compared with Aquilegia oxysepala (16.7) 21 and Aquilegia coerulea (12.6) 22 in the family Ranunculaceae, a high LAI score of 17.86 showed that the assembly of C. chinensis yielded high sequence continuity and met the reference quality 23 . Overall, the assembled C. chinensis genome contains 595.32 Mb (62.13%) of repetitive sequences, most of which are transposable elements (581.03 Mb; 60.63%).…”

“…To confirm this, we determined Ks rates between C. chinensis and N. nucifera , finding that the mean Ks was larger than that between M. cordata and N. nucifera . Then, we adjusted the Ks distributions of M. cordata according to the ratio of the Ks value of the orthologous gene pairs between C. chinensis-N. nucifera and M. cordata - N. nucifera according to the method of Paterson et al 26 and Pei et al 22 . The adjusted result showed that C. chinensis , A. coerulea and M. cordata occupied almost the same position, strongly implying that they shared a common WGD event (Fig.…”