Abstract
Zingiber montanum (Z. montanum) and Zingiber zerumbet (Z. zerumbet) are important medicinal and ornamental herbs in the genus Zingiber and family Zingiberaceae. Chloroplast-derived markers are useful for species identification and phylogenetic studies, but further development is warranted for these two Zingiber species. In this study, we report the complete chloroplast genomes of Z. montanum and Z. zerumbet, which had lengths of 164,464 bp and 163,589 bp, respectively. These genomes had typical quadripartite structures with a large single copy (LSC, 87,856-89,161 bp), a small single copy (SSC, 15,803-15,642 bp), and a pair of inverted repeats (IRa and IRb, 29,393-30,449 bp). We identified 111 unique genes in each chloroplast genome, including 79 protein-coding genes, 28 tRNAs and 4 rRNA genes. We analyzed the molecular structures, gene information, amino acid frequencies, codon usage patterns, RNA editing sites, simple sequence repeats (SSRs) and long repeats from the two chloroplast genomes. A comparison of the Z. montanum and Z. zerumbet chloroplast genomes detected 489 single-nucleotide polymorphisms (SNPs) and 172 insertions/deletions (indels). Thirteen highly divergent regions, including ycf1, rps19, rps18-rpl20, accD-psaI, psaC-ndhE, psbA-trnK-UUU, trnfM-CAU-rps14, trnE-UUC-trnT-UGU, ccsA-ndhD, psbC-trnS-UGA, start-psbA, petA-psbJ, and rbcL-accD, were identified and might be useful for future species identification and phylogeny in the genus Zingiber. Positive selection was observed for ATP synthase (atpA and atpB), RNA polymerase (rpoA), small subunit ribosomal protein (rps3) and other protein-coding genes (accD, clpP, ycf1, and ycf2) based on the Ka/Ks ratios. Additionally, chloroplast SNP-based phylogeny analyses found that Zingiber was a monophyletic sister branch to Kaempferia and that chloroplast SNPs could be used to identify Zingiber species. The genome resources in our study provide valuable information for the identification and phylogenetic analysis of the genus Zingiber and family Zingiberaceae.
Highlights
Zingiber Boehm., belonging to the family Zingiberaceae, consists of between 100 and 150 species, all of which are widely distributed in southern and southeastern Asia, with particular concentrations in Thailand and southern China [1,2,3,4]
The raw Illumina and PacBio chloroplast sequencing data had been submitted to the National Center for Biotechnology Information (NCBI) with SRA numbers SRR8185396 and SRR8184511 for Z. montanum, respectively, and SRA numbers SRR8185094 and SRR8184512 for Z. zerumbet, respectively
Similar to most other angiosperms, the two genomes had typical quadripartite structure circle molecules consisting of a large single copy (LSC) of 87,856 bp in Z. montanum and 89,161 bp in Z. zerumbet, a small single copy (SSC) region of 15,803 bp in Z. montanum and 15,642 bp in Z. zerumbet, and two inverted repeats (IRs) regions of 30,356 bp and 30,449 bp in Z. montanum and each 29,393 bp in Z. zerumbet (Fig 1 and Table 1)
Summary
Zingiber Boehm., belonging to the family Zingiberaceae, consists of between 100 and 150 species, all of which are widely distributed in southern and southeastern Asia, with particular concentrations in Thailand and southern China [1,2,3,4]. Most species have an assemblage of tightly clasped, overlapping bracts that often age to yellow, red, or chestnut brown and are often highly showy and long-lived, leading to the cultivation of a number of species for landscaping and cut-flower uses [2,3,4]. Z. zerumbet, commonly known as “shampoo ginger”, is found across southern China (Guangdong, Guangxi, Hainan and Yunnan provinces), most of Southeast Asia, Myanmar, India, and Sri Lanka [1,2,3,4]. Zerumbone from the Z. zerumbet rhizome has been reported to suppress the phagocytic activity of human neutrophils [9], to prevent and treat tooth decay disease [10], to cure osteoarthritis of the knee [11], and to treat various immune-inflammatory related disorders [12]
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