Comparative and Phylogenetic Analyses of Ginger (Zingiber officinale) in the Family Zingiberaceae Based on the Complete Chloroplast Genome

Abstract

Zingiber officinale, commonly known as ginger, is an important plant of the family Zingiberaceae and is widely used as an herbal medicine and condiment. The lack of chloroplast genomic information hinders molecular research and phylogenetic analysis on ginger. We introduced the complete chloroplast genome of Z. officinale and identified its phylogenetic position in Zingiberaceae. The chloroplast genome of Z. officinale is 162,621 bp with a four-part circular structure and 36.1% GC content. All 113 unique genes were annotated. A total of 78 simple sequence repeats (SSRs) and 42 long repeat sequences, which are potential areas for species authentication, were found. Comparative analysis revealed some highly variable regions, including rps16-trnQ-UUG, atpH-atpI, trnT-UGU-trnL-UAA, ycf1, and psaC-ndhE. Moreover, the small single-copy (SSC) region was the most variable region in all four shared regions, indicating that it may be undergoing rapid nucleotide substitution in the family Zingiberaceae. Phylogenetic analysis based on all available chloroplasts of Zingiberales in the National Center for Biotechnology Information indicated that Zingiber is a sister branch to Kaempferia species. The availability of the Z. officinale chloroplast genome provided invaluable data for species-level authentication and phylogenetic analysis and can thus benefit further investigations on species in the family Zingiberaceae.

Complete Chloroplast Genomes of Three Medicinal Alpinia Species: Genome Organization, Comparative Analyses and Phylogenetic Relationships in Family Zingiberaceae

“…Additionally, the AT content was the highest (70.18-70.38%) in the SSC region, the lowest (50.48%-50.79%) in the IR regions, and moderate (66.14%-66.18%) in the LSC region (Table S1). These genomic structures were consistent with most other published chloroplast genomes of family Zingiberaceae, such as two Kaempferia species [23], three Amomum species [24], Zingiber officinale [25], Stahlianthus involucratus [31], Hedychium coronarium [32] and Curcuma longa [33].…”

“…Of the 27,427-27,669 codons, leucine (Leu) was the most abundant amino acid, with a frequency of 10.34%-10.38%, then isoleucine (Ile) with a frequency of 8.74%-8.80%, while cysteine (Cys) was the least common one with a proportion of 1.12%-1.13% ( Figure 2 and Table S4). This phenomenon was consistent with other land plants' chloroplast genomes, such as Z. officinale [25], Ailanthus altissima [35], Lycium chinense [36], Symplocarpus renifolius [37], and Epipremnum aureum [38]. Due to the value of relative synonymous codon usage (RSCU) >1, thirty codons showed the codon usage bias in the chloroplast genes of all the three Alpinia species (Table S4).…”

“…Typical chloroplast genomes of angiosperms have a generally conserved quadripartite circular structure, which consists of a large single copy (LSC) region, a small single copy (SSC) region, and two copies of inverted repeats (IRs) [16][17][18]. With the rapid development of high-throughput sequencing technologies, such as Illumina and PacBio sequencing platforms, it is now convenient to acquire complete chloroplast genome sequences [19][20][21][22][23][24][25][26][27][28][29][30][31][32][33][34]. The chloroplast genomes have been widely utilized for species identification, the reconstruction of phylogenetic relationships, the resolution of origin problems, and the development of molecular markers [19][20][21][22][23][24][25][26][27][28][29][30].…”

Complete Chloroplast Genomes of Chlorophytum comosum and Chlorophytum gallabatense: Genome Structures, Comparative and Phylogenetic Analysis

“…The Pi values of the seven Asparagales species ranged from 0 to 0.15897 ( Figure 6). This indicates that the species in the order Asparagales could be undergoing rapid nucleotide substitution [36]. The IR regions, as predicted, had a much lower nucleotide variability than the SSC and LSC regions.…”

“…If the relative value of synonymous codon usage (RSCU) is equal to one, the codon usage is not preferred (not biased), but highly preferred if the value is greater than one [36], indicating that the codon is used more often than expected [48] and less preferred with values of less than one. Almost all of the amino acid codons in C. comosum and C. gallabatense, cp genomes have preferences, which is due to the amino acid activity preventing error all through the transcription process, other than tryptophan (UGG) and methionine (AUG), which did not have a bias (RSCU values equal to one) ( Table S1).…”