Characterization of the Dicranostigma leptopodum chloroplast genome and comparative analysis within subfamily Papaveroideae

Abstract

Background Dicranostigma leptopodum (Maxim.) Fedde is a perennial herb with bright yellow flowers, well known as "Hongmao Cao" for its medicinal properties, and is an excellent early spring flower used in urban greening. However, its molecular genomic information remains largely unknown. Here, we sequenced and analyzed the chloroplast genome of D. leptopodum to discover its genome structure, organization, and phylogenomic position within the subfamily Papaveroideae. Results The chloroplast genome size of D. leptopodum was 162,942 bp, and D. leptopodum exhibited a characteristic circular quadripartite structure, with a large single-copy (LSC) region (87,565 bp), a small single-copy (SSC) region (18,759 bp) and a pair of inverted repeat (IR) regions (28,309 bp). The D. leptopodum chloroplast genome encoded 113 genes, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. The dynamics of the genome structures, genes, IR contraction and expansion, long repeats, and single sequence repeats exhibited similarities, with slight differences observed among the eight Papaveroideae species. In addition, seven interspace regions and three coding genes displayed highly variable divergence, signifying their potential to serve as molecular markers for phylogenetic and species identification studies. Molecular evolution analyses indicated that most of the genes were undergoing purifying selection. Phylogenetic analyses revealed that D. leptopodum formed a clade with the tribe Chelidonieae. Conclusions Our study provides detailed information on the D. leptopodum chloroplast genome, expanding the available genomic resources that may be used for future evolution and genetic diversity studies.

Phylogenomic analysis of Bupleurum in Western Sichuan, China, including an overlooked new species

“…The rpl32-trnL, petA-psbJ gene have also been reported to show very high nucleotide per site diversity in several genera (Dong et al,FIGURE 4 Comparison of the six Bupleurum species cp genomes using the mVISTA alignment program, with B. chinense as a reference. Chao et al 10.3389/fpls.2023.1294670 Frontiers in Plant Science frontiersin.org Tan et al, 2020;Wang et al, 2022;Niu et al, 2023), and indeed the Pi values of the rpl32-trnL spacer regions of these six Bupleurum species were also much higher than the other regions in the present study, so rpl32-trnL together with petA-psbJ, trnK-rps16, and ycf1 were considered as having potential to be used as high-resolution DNA barcodes to identify species of Bupleurum.…”

“…There is evidence supporting the ycf 1 gene as one of the core plastid DNA barcodes in land plants ( Neubig et al., 2009 ; Franck et al., 2012 ; Dong et al., 2015 ). The rpl 32- trn L, pet A- psb J gene have also been reported to show very high nucleotide per site diversity in several genera ( Dong et al., 2012 ; Tan et al., 2020 ; Wang et al., 2022 ; Niu et al., 2023 ), and indeed the Pi values of the rpl 32- trn L spacer regions of these six Bupleurum species were also much higher than the other regions in the present study, so rpl 32- trn L together with pet A- psb J, trn K- rps 16, and ycf 1 were considered as having potential to be used as high-resolution DNA barcodes to identify species of Bupleurum .…”

Extreme Reconfiguration of Plastid Genomes in Papaveraceae: Rearrangements, Gene Loss, Pseudogenization, IR Expansion, and Repeats

“…The six sampled Corydalis species covered all three subgenera and six major clades that were previously recognized [50]. Although a large number of plastomes were reported in previous studies [38][39][40][41][42]50], to eliminate the potential assembly result deviation induced by diverse sequencing methods or software employed by different scholars, we independently sequenced and assembled for a portion of species. In total, thirteen species were newly sequenced, while another ten species, including one outgroup (Euptelea pleiosperma), were directly downloaded from the GenBank database (https://www.ncbi.nlm.nih.gov/, accessed on 1 December 2023) or retrieved from our previous studies [51] (Table S1).…”

“…Moreover, the plastomes of Fumaria also showed signatures of structural rearrangement and loss of the accD gene [41]. In contrast, the plastomes of Papaveroideae appeared more conserved, with no structure rearrangements and gene losses detected, despite the release of plastomes from several genera [42]. For other closely related Ranunculales taxa, Sun et al [43] reported plastid rearrangements of Circaeasteraceae, and found an inversion of approximately 49 kb and 3.5 kb in the LSC region, with pseudogenizations or losses of the accD and ndh genes.…”

CPJSdraw: analysis and visualization of junction sites of chloroplast genomes

“…Multiple examples of IR expansion or contraction have been reported in plants, where entire genes are moved from the single-copy region to the IR region and vice versa during evolution, resulting in the diversification of the chloroplast genomes of related species, suggesting that IR boundary shifts are dynamic ( Zhu et al, 2016 ). For example, analyses of single-copy and IR boundaries indicated that the IR regions of chloroplast genomes from Arecaceae ( Chen et al, 2022 ), Salicaceae ( He et al, 2022 ), and other families ( Wang et al, 2022 ) underwent expansion or contraction.…”