Abstract
Zingiberaceae is taxonomically complex family where species are perennial herb. However, lack of chloroplast genomic information severely hinders our understanding of Zingiberaceae species in the research of evolution and phylogenetic relationships. In this study, the complete chloroplast (cp) genomes of fourteen Curcuma species were assembled and characterized using next-generation sequencing. We compared the genome features, repeat sequences, sequence divergence, and constructed the phylogenetic relationships of the 25 Zingiberaceae species. In each Zingiberaceae species, the 25 complete chloroplast genomes ranging from 155,890 bp (Zingiber spectabile) to 164,101 bp (Lanxangia tsaoko) contained 111 genes consisting of 77 protein coding genes, 4 ribosomal RNAs and 30 transfer RNAs. These chloroplast genomes are similar to most angiosperm that consisted of a four-part circular DNA molecules. Moreover, the characteristics of the long repeats sequences and simple sequence repeats (SSRs) were found. Six divergent hotspots regions (matK-trnk, Rps16-trnQ, petN-psbM, rpl32, ndhA, and ycf1) were identified in the 25 Zingiberaceae chloroplast genomes, which could be potential molecular markers. In addition to Wurfbainia longiligularis, the ψycf1 was discovered among the 25 Zingiberaceae species. The shared protein coding genes from 52 Zingiberales plants and four other family species as out groups were used to construct phylogenetic trees distinguished by maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference (BI) and showed that Musaceae was the basal group in Zingiberales, and Curcuma had a close relationship with Stahlianthu. Besides this, Curcuma flaviflora was clustered together with Zingiber. Its distribution area (Southeast Asia) overlaps with the latter. Maybe hybridization occur in related groups within the same region. This may explain why Zingiberaceae species have a complex phylogeny, and more samples and genetic data were necessary to confirm their relationship. This study provide the reliable information and high-quality chloroplast genomes and genome resources for future Zingiberaceae research.
Highlights
Over the past decade, due to the linkage of genetic material existed in the plastome, the whole plastid genomes have been used to assess the phylogenetic relationship and taxonomic significance in some areas
The quadripartite structure included the large single copy (LSC) region and small single copy (SSC) region separated by two inverted repeat (IR) regions (Figure 1)
The LSC of the chloroplast genomes accounted for 53.58–58.27% of the total size and it ranged in size from 86,921 bp (Curcuma wenyujin) to 90,832 bp (Zingiber spectabile); the SSC of the chloroplast genomes accounted for 9.34–11.87% of the total size and it ranged in size from 152,88 bp (Wurfbainia longiligularis) to 185,08 bp (Zingiber spectabile)
Summary
Due to the linkage of genetic material existed in the plastome, the whole plastid genomes have been used to assess the phylogenetic relationship and taxonomic significance in some areas. Chloroplast DNA has the characteristics of haploid inheritance, relatively small genome size and slow mutation rate in plants (Palmer et al, 1988). These chloroplast DNA features were used by scientists through comparing with chloroplast DNA phylogenies, proving to be very useful in understanding of plant phylogenetic studies and clearer taxonomic levels (Alwadani et al, 2019; Gonçalves et al, 2019). The chloroplast DNA genome in complex genome plants has been proved comparatively inexpensive and sequenced (Guo et al, 2017; Saarela et al, 2018)
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