Complete chloroplast genomes of three important species, Abelmoschus moschatus, A. manihot and A. sagittifolius: Genome structures, mutational hotspots, comparative and phylogenetic analysis in Malvaceae

Abstract

Abelmoschus is an economically and phylogenetically valuable genus in the family Malvaceae. Owing to coexistence of wild and cultivated form and interspecific hybridization, this genus is controversial in systematics and taxonomy and requires detailed investigation. Here, we present whole chloroplast genome sequences and annotation of three important species: A. moschatus, A. manihot and A. sagittifolius, and compared with A. esculentus published previously. These chloroplast genome sequences ranged from 163121 bp to 163453 bp in length and contained 132 genes with 87 protein-coding genes, 37 transfer RNA and 8 ribosomal RNA genes. Comparative analyses revealed that amino acid frequency and codon usage had similarity among four species, while the number of repeat sequences in A. esculentus were much lower than other three species. Six categories of simple sequence repeats (SSRs) were detected, but A. moschatus and A. manihot did not contain hexanucleotide SSRs. Single nucleotide polymorphisms (SNPs) of A/T, T/A and C/T were the largest number type, and the ratio of transition to transversion was from 0.37 to 0.55. Abelmoschus species showed relatively independent inverted-repeats (IR) boundary traits with different boundary genes compared with the other related Malvaceae species. The intergenic spacer regions had more polymorphic than protein-coding regions and intronic regions, and thirty mutational hotpots (≥200 bp) were identified in Abelmoschus, such as start-psbA, atpB-rbcL, petD-exon2-rpoA, clpP-intron1 and clpP-exon2.These mutational hotpots could be used as polymorphic markers to resolve taxonomic discrepancies and biogeographical origin in genus Abelmoschus. Moreover, phylogenetic analysis of 33 Malvaceae species indicated that they were well divided into six subfamilies, and genus Abelmoschus was a well-supported clade within genus Hibiscus.

Genome and transcriptome architecture of allopolyploid okra (Abelmoschus esculentus)

“…Other well-known species in the Malvaceae are cocoa (Theobroma cacao), cotton (Gossypium hirsutum), and Tilia species like lime tree, the mangrove Heritiera species and durian (Durio zibethinus). The genus Abelmoschus contains 11 species, four subspecies and five varieties (Li et al, 2020) of which most members have economic value.…”

A Potent Antioxidant Sesquiterpene, Abelsaginol, from Abelmoschus sagittifolius: Experimental and Theoretical Insights

“… 18 We also observed that coupling constant between H-3 and H-4 of 1 was 4.0 Hz, while it was only 1.2 Hz in the case of 2β,7,3β-trihydroxycalamenene 3- O -β- d -glucoside. 8 Thus, 1 was assigned as a new natural compound, as illustrated in Figure 1 , and named abelsaginol ( AS ).…”

“…Chinese scientists have reported the isolation of sesquiterpenes, lignans, phenolic, and amide constituents from A. sagittifolius . 8 − 10 Several isolated compounds showed moderate cytotoxicities against HepG-2 and Hela cancer cell lines. 9 , 10 These limited data suggest that this traditional medicine does indeed contain potent natural products that can be isolated and tested for their activity.…”

Development of Genomic Resources From Crossostephium Chinense (Asteraceae) Based on Genome Skimming Data

“…Nevertheless, both sequences have harbored 19 highly variable loci (Table 2) that might serve the potential mutational hotspots. Comprehensive mutational hotspot markers screening from the whole chloroplast genome is useful in polymorphism sites identi cation to elucidate the evolutionary and resolving controversial in phylogenetic relationships, hybridization issues, and biogeography [26,27]. For instance, 20 mutational hotspots were respectively recognized for Artemisia scoparia [28], A. maritima and A. absinthium [29].…”

“…Among the cpSSRs markers, three primer sets of which rpoC2-rps2 (cpSSR2), atpA-trnR (cpSSR4), and ycf1 (cpSSR9) were also suggested for mutational hotspots (Table 1). Repeat sequences have been proven crucial in chloroplast genome arrangement and sequence variation [27]. Further, the variable repeat sequences between lineages allow it signi cances used as microsatellites markers for genetic diversity, and population genetics studies of plant species [28,33].…”