Complete chloroplast genomes provide insights into evolution and phylogeny of Zingiber (Zingiberaceae)

Abstract

Background The genus Zingiber of the Zingiberaceae is distributed in tropical, subtropical, and in Far East Asia. This genus contains about 100–150 species, with many species valued as important agricultural, medicinal and horticultural resources. However, genomic resources and suitable molecular markers for species identification are currently sparse. Results We conducted comparative genomics and phylogenetic analyses on Zingiber species. The Zingiber chloroplast genome (size range 162,507–163,711 bp) possess typical quadripartite structures that consist of a large single copy (LSC, 86,986–88,200 bp), a small single copy (SSC, 15,498–15,891 bp) and a pair of inverted repeats (IRs, 29,765–29,934 bp). The genomes contain 113 unique genes, including 79 protein coding genes, 30 tRNA and 4 rRNA genes. The genome structures, gene contents, amino acid frequencies, codon usage patterns, RNA editing sites, simple sequence repeats and long repeats are conservative in the genomes of Zingiber. The analysis of sequence divergence indicates that the following genes undergo positive selection (ccsA, ndhA, ndhB, petD, psbA, psbB, psbC, rbcL, rpl12, rpl20, rpl23, rpl33, rpoC2, rps7, rps12 and ycf3). Eight highly variable regions are identified including seven intergenic regions (petA-pabJ, rbcL-accD, rpl32-trnL-UAG, rps16-trnQ-UUG, trnC-GCA-psbM, psbC-trnS-UGA and ndhF-rpl32) and one genic regions (ycf1). The phylogenetic analysis revealed that the sect. Zingiber was sister to sect. Cryptanthium rather than sect. Pleuranthesis. Conclusions This study reports 14 complete chloroplast genomes of Zingiber species. Overall, this study provided a solid backbone phylogeny of Zingiber. The polymorphisms we have uncovered in the sequencing of the genome offer a rare possibility (for Zingiber) of the generation of DNA markers. These results provide a foundation for future studies that seek to understand the molecular evolutionary dynamics or individual population variation in the genus Zingiber.

Characterization and phylogenetic analysis of the complete chloroplast genome of Curcuma comosa and C. latifolia

“…In this study, no substantial differences were observed in the total number of genes, protein-coding genes, tRNAs, or rRNAs between C. comosa and C. latifolia . Similar findings were observed in other plant species in Zingiberaceae [ 32 , 33 , [60] , [61] , [62] , [63] , [64] , [65] , [66] , [67] , [68] ]. The frequencies of codon usage for each triplet nucleotide sequence encoding a specific amino acid were analyzed.…”

Phylogenomic Analysis and Dynamic Evolution of Chloroplast Genomes of Clematis nannophylla

“…In this study, we compared the cp genome structure of ve Clematis species using mVISTA (using Clematis fruticosa as a reference) and found that the non-coding region was more prone to mutations than the coding region. Furthermore, the variation in the SC region was higher than that in the IR region, which is similar to the results of previous plant studies [25,51,53]. psbA-atpA, atpI-rpoC2, rpoB-psbD, psbE-petG, clpP, and rpoC2 were the most highly variable regions detected in C. nannophylla.…”

Thirteen complete chloroplast genomes of the costaceae family: insights into genome structure, selective pressure and phylogenetic relationships

“…Lastly, ycf1 encodes unknown proteins and is competent in identification at genus and species level of orchids [ 46 ]. Recent studies have revealed that these eight genes with positive selection in flowering plants are common [ 27 – 31 , 33 , 35 , 47 , 48 ]. For example, ndhF has been reported as a positive selection in the Aroideae species [ 30 ]; clpP and ycf1 have been reported as positive selections in the Polystachya species [ 31 ]; ndhA and clpP have been reported as positive selections in the Hoya species [ 35 ]; ndhA , clpP , rps12 and ycf1 have been reported as positive selections in the Zingiber species [ 33 , 47 ]; and cemA , clpP , ndhF , petB , rps12 and ycf1 have been reported as positive selections in the Dalbergia species [ 48 ].…”

“…Recent studies have revealed that these eight genes with positive selection in flowering plants are common [ 27 – 31 , 33 , 35 , 47 , 48 ]. For example, ndhF has been reported as a positive selection in the Aroideae species [ 30 ]; clpP and ycf1 have been reported as positive selections in the Polystachya species [ 31 ]; ndhA and clpP have been reported as positive selections in the Hoya species [ 35 ]; ndhA , clpP , rps12 and ycf1 have been reported as positive selections in the Zingiber species [ 33 , 47 ]; and cemA , clpP , ndhF , petB , rps12 and ycf1 have been reported as positive selections in the Dalbergia species [ 48 ]. Among the analyzed species of Costaceae, they possessed diversity of ecological habitats, such as shade under the woods, forest margins, moist places in valleys, roadsides and ditch sides [ 1 , 7 ].…”