The plastid genomes (plastomes) of angiosperms are typically highly conserved, with extreme reconfiguration being uncommon, although reports of such events have emerged in some lineages. In this study, we conducted a comprehensive comparison of the complete plastomes from twenty-two species, covering seventeen genera from three subfamilies (Fumarioideae, Hypecooideae, and Papaveroideae) of Papaveraceae. Our results revealed a high level of variability in the plastid genome size of Papaveraceae, ranging from 151,864 bp to 219,144 bp in length, which might be triggered by the expansion of the IR region and a large number of repeat sequences. Moreover, we detected numerous large-scale rearrangements, primarily occurring in the plastomes of Fumarioideae and Hypecooideae. Frequent gene loss or pseudogenization were also observed for ndhs, accD, clpP, infA, rpl2, rpl20, rpl32, rps16, and several tRNA genes, particularly in Fumarioideae and Hypecooideae, which might be associated with the structural variation in their plastomes. Furthermore, we found that the plastomes of Fumarioideae exhibited a higher GC content and more repeat sequences than those of Papaveroideae. Our results showed that Papaveroideae generally displayed a relatively conserved plastome, with the exception of Eomecon chionantha, while Fumarioideae and Hypecooideae typically harbored highly reconfigurable plastomes, showing high variability in the genome size, gene content, and gene order. This study provides insights into the plastome evolution of Papaveraceae and may contribute to the development of effective molecular markers.

Corydalis DC., the largest genus of Papaveraceae, was recognized as one of the most taxonomically challenging plant taxa. Due to the lack of genetic information used in previous studies, species discrimination and taxonomic assignment in Corydalis have not been fully solved. Here, the complete chloroplast genomes were reported for Corydalis edulis Maxim. and Corydalis shensiana Liden, with their genome sizes being 154,395 and 155,938 bp, respectively. Both of the chloroplast genomes comprise two inverted repeat (IR) regions, separated by a large single-copy (LSC) region and a small single-copy (SSC) region, and encode 130 genes, including 85 protein-coding genes, 8 ribosomal RNA genes, 37 transfer RNA genes. Our study will provide novel insight into the molecular phylogeny and classification of Corydalis.

Corydalis DC. is the largest and most diverse genus of Papaveraceae, which has undergone rapid diversification. Corydalis is notable for its diverse benzylisoquinoline alkaloids (BIAs). However, limited genomic resources hinder the understanding of its evolution and BIA diversity. Here, we report a high-quality genome of Corydalis sheareri and provide a comparative analysis of Corydalis genomes. Genome survey shows that the genome of C. sheareri might be an autotetraploid. De novo assembly yields a single homolog genome of 282 Mb, with a contig N50 of 11.39 Mb. Repetitive DNA accounts for 44.47% of the genome, and a total of 26,287 protein-coding genes are predicted. When comparing this genome with the previously reported diploid genome of C. tomentella, large-scale structural variations are detected, which might have dramatic effects on the evolution of Corydalis. Furthermore, a total of 172 candidate genes involved in benzylisoquinoline alkaloids (BIAs) biosynthesis are identified in the genome of C. sheareri. Duplication and phylogenetic analyses indicate that tandem duplications play a prominent role in the evolution of the BIA biosynthesis genes, and might be associated with the BIA diversity in Corydalis.Our study provides more insights into the genome evolution and secondary metabolites diversity of Corydalis, and will accelerate genomic and evolutionary radiation study of species-rich plant genera.

Tragopogon dubius Scopoli is native to Europe and western Asia and is considered an invasive plant in China. In this study, the complete chloroplast genome of T. dubius was obtained using high-throughput next-generation sequencing technology. The whole chloroplast genome was 153,017 bp long with a GC content of 38% and comprised 130 genes (86 protein-coding genes, 36 tRNA genes, and 8 rRNA genes). Phylogenetic analysis based on the concatenated chloroplast protein-coding sequences showed that T. dubius is most closely related to Tragopogon pratensis. This study provides valuable genetic data for further phylogenetic analysis and molecular identification of species in the genus Tragopogon.