Characterization and phylogenetic analysis of the complete chloroplast genome of Curcuma zedoaria (Zingiberaceae)

Abstract

The first complete chloroplast genome of Curcuma zedoaria (Zingiberaceae) was reported in this study. The C. zedoaria chloroplast genome was 162,135 bp in length, and consisted of one large single-copy (LSC) region of 86,966 bp, one small single-copy (SSC) region of 15,737 bp, and a pair of inverted repeat (IR) regions 29,716 bp. It encoded 141 genes, including 87 protein-coding genes (79 PCG species), 46 tRNA genes (28 tRNA species), and 8 rRNA genes (4 rRNA species). The phylogenetic analysis based on single nucleotide polymorphisms strongly supported that C. zedoaria, Curcuma roscoeana, Curcuma longa, and Stahlianthus involucratus clustered together in group Curcuma II within the family Zingiberaceae.

Complete chloroplast genomes of Zingiber montanum and Zingiber zerumbet: Genome structure, comparative and phylogenetic analyses

“…zerumbet were 35.75% and 36.27%, respectively ( Table 1 and S1 Table ). Additionally, the GC contents of the two species were the highest (40.46%-41.02%) in the IR regions, the lowest (29.24%-29.64%) in the SSC regions, and moderate (33.63%-34.31%) in the LSC regions ( Table 1 ), which were similar to the chloroplast genomes of other reported species in the family Zingiberaceae [ 15 – 26 ]. Approximately 50.76%-51.37% of the two Zingiber species chloroplast genomes consisted of protein-coding genes (83,496 bp in Z .…”

“…The overall GC contents in the chloroplast genomes of Z. montanum and Z. zerumbet were 35.75% and 36.27%, respectively (Table 1 and S1 Table). Additionally, the GC contents of the two species were the highest (40.46%-41.02%) in the IR regions, the lowest (29.24%-29.64%) in the SSC regions, and moderate (33.63%-34.31%) in the LSC regions (Table 1), which were similar to the chloroplast genomes of other reported species in the family Zingiberaceae [15][16][17][18][19][20][21][22][23][24][25][26]. Approximately 50.76%-51.37% of the two Zingiber species chloroplast genomes consisted of protein-coding genes (83,496 bp in Z. montanum and 84,042 bp in Z. zerumbet), 1.74%-1.75% of tRNAs (2,876 bp Z. montanum and 2,877 bp in Z. zerumbet), and 5.50%-5.52% of rRNAs (9,046 bp in Z. montanum and 9,046 bp in Z. zerumbet) (S1 Table).…”

“…The chloroplast genome sequences provided useful genomic resources for phylogenetic studies [51,52]. Several previous studies have successfully used protein-coding genes, whole chloroplast genome sequences, or chloroplast SNP-based matrices for phylogenetic inference in the family Zingiberaceae [13,[15][16][17][18][19][20][21][22][23][24][25][26]. In the present study, a phylogenetic tree was reconstructed with a chloroplast SNP matrix from 31 chloroplast genomes using the ML method with C. pulverulentus, C. viridis and C. indica as outgroups.…”

“…The complete chloroplast genome contains more effective DNA markers, such as single-nucleotide polymorphisms (SNPs), insertion/deletions (indels) and hotspot variable regions, which can be used for accurate species identification. In recent years, more than 25 complete chloroplast genomes have been sequenced in the family Zingiberaceae [15][16][17][18][19][20][21][22][23][24][25][26]. However, to the best of our knowledge, the chloroplast genomes of Z. montanum and Z. zerumbet have not yet been elucidated.…”

“…Chloroplasts are photosynthetic organelles that can transform light energy into chemical energy in green plants [27][28][29]. These organelles have their own chloroplast genomes that encode 110-130 genes with a size range of 120-180 kb and have a typical quadripartite structure consisting of a large single copy (LSC) region, a small single copy (SSC) region, and two copies of inverted repeats (IRs) [18][19][20][21][22][23][24][25][26]. Whole chloroplast genomes have been widely exploited to resolve plant phylogenies, origin problems and species identification [15-17, 22-26, 30].…”