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

Li, Dongmei; Ye, Yuan-Jun; Xu, Ye-Chun; Liu, Jinmei; Zhu, Genfa

doi:10.1371/journal.pone.0236590

Cited by 22 publications

(33 citation statements)

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“…In the selective pressure analysis, five genes were positively selected, and their selection might reflect the adaptive evolution of these Alpinia species. The results are consistent with the reports that acc D and ycf 1 evolved under positive selection in the Zingiber plastomes [ 37 ]. Particular amino acids were identified to have been positively selected in two genes, acc D, and ycf 1.…”

Section: Discussionsupporting

confidence: 93%

“…Because of the lack of mobility, plants must deal with the challenge of abiotic stresses, such as soil salinity, drought, and extreme temperature. Many genes from plastomes, such as clp P [ 34 ], rbc L [ 35 ], and mat K [ 36 ], ycf 1 and ycf 2 [ 37 ], have been positively selected. The positive selection of the plastome genes may serve as an adaptive evolution for adjusting to environmental changes.…”

Section: Discussionmentioning

confidence: 99%

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Phylogenetic analysis and development of molecular markers for five medicinal Alpinia species based on complete plastome sequences

et al. 2021

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Background Alpinia species are widely used as medicinal herbs. To understand the taxonomic classification and plastome evolution of the medicinal Alpinia species and correctly identify medicinal products derived from Alpinia species, we systematically analyzed the plastome sequences from five Alpinia species. Four of the Alpinia species: Alpinia galanga (L.) Willd., Alpinia hainanensis K.Schum., Alpinia officinarum Hance, and Alpinia oxyphylla Miq., are listed in the Chinese pharmacopeia. The other one, Alpinia nigra (Gaertn.) Burtt, is well known for its medicinal values. Results The four Alpinia species: A. galanga, A. nigra, A. officinarum, and A. oxyphylla, were sequenced using the Next-generation sequencing technology. The plastomes were assembled using Novoplasty and annotated using CPGAVAS2. The sizes of the four plastomes range from 160,590 bp for A. galanga to 164,294 bp for A. nigra, and display a conserved quadripartite structure. Each of the plastomes encodes a total of 111 unique genes, including 79 protein-coding, 28 tRNA, and four rRNA genes. In addition, 293–296 SSRs were detected in the four plastomes, of which the majority are mononucleotides Adenine/Thymine and are found in the noncoding regions. The long repeat analysis shows all types of repeats are contained in the plastomes, of which palindromic repeats occur most frequently. The comparative genomic analyses revealed that the pair of the inverted repeats were less divergent than the single-copy region. Analysis of sequence divergence on protein-coding genes showed that two genes (accD and ycf1) had undergone positive selection. Phylogenetic analysis based on coding sequence of 77 shared plastome genes resolves the molecular phylogeny of 20 species from Zingiberaceae. In particular, molecular phylogeny of four sequenced Alpinia species (A. galanga, A. nigra, A. officinarum, and A. oxyphylla) based on the plastome and nuclear sequences showed congruency. Furthermore, a comparison of the four newly sequenced Alpinia plastomes and one previously reported Alpinia plastomes (accession number: NC_048461) reveals 59 highly divergent intergenic spacer regions. We developed and validated two molecular markers Alpp and Alpr, based on two regions: petN-psbM and psaJ-rpl33, respectively. The discrimination success rate was 100 % in validation experiments. Conclusions The results from this study will be invaluable for ensuring the effective and safe uses of Alpinia medicinal products and for the exploration of novel Alpinia species to improve human health.

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Section: Discussionsupporting

confidence: 93%

Section: Discussionmentioning

confidence: 99%

Phylogenetic analysis and development of molecular markers for five medicinal Alpinia species based on complete plastome sequences

et al. 2021

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“…Among the seven divergent regions, six existed in LSC regions and only rps15/ycf1 was in SSC regions (Figure 8). The nucleotide diversity of two Clethra species shows a lower Pi value compared to other previous analyzed genera [73,74] and indicates evolutionary conservation in the chloroplast genome. The IR regions have lower nucleotide diversity than the LSC and SSC regions similar to other reported results [75][76][77][78] owing to their stability and consistency [79].…”

Section: Analysis Of Simple Sequence Repeats (Ssrs) and Nucleotide Diversitymentioning

confidence: 66%

Complete Chloroplast Genome of Clethra fargesii Franch., an Original Sympetalous Plant from Central China: Comparative Analysis, Adaptive Evolution, and Phylogenetic Relationships

Ding

Dong

Yang

et al. 2021

Forests

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Clethra fargesii, an essential ecological and endemic woody plant of the genus Clethra in Clethraceae, is widely distributed in Central China. So far, there have been a paucity of studies on its chloroplast genome. In the present study, we sequenced and assembled the complete chloroplast genome of C. fargesii. We also analyzed the chloroplast genome features and compared them to Clethra delavayi and other closely related species in Ericales. The complete chloroplast genome is 157,486 bp in length, including a large single-copy (LSC) region of 87,034 bp and a small single-copy (SSC) region of 18,492 bp, separated by a pair of inverted repeat (IR) regions of 25,980 bp. The GC content of the whole genome is 37.3%, while those in LSC, SSC, and IR regions are 35.4%, 30.7%, and 43.0%, respectively. The chloroplast genome of C. fargesii encodes 132 genes in total, including 87 protein-coding genes (PCGs), 37 tRNA genes, and eight rRNA genes. A total of 26,407 codons and 73 SSRs were identified in C. fargesii chloroplast genome. Additionally, we postulated and demonstrated that the structure of the chloroplast genome in Clethra species may present evolutionary conservation based on the comparative analysis of genome features and genome alignment among eight Ericales species. The low Pi values revealed evolutionary conservation based on the nucleotide diversity analysis of chloroplast genome in two Clethra species. The low selection pressure was shown by a few positively selected genes by adaptive evolution analysis using 80 coding sequences (CDSs) of the chloroplast genomes of two Clethra species. The phylogenetic tree showed that Clethraceae and Ericaceae are sister clades, which reconfirm the previous hypothesis that Clethra is highly conserved in the chloroplast genome using 75 CDSs of chloroplast genome among 40 species. The genome information and analysis results presented in this study are valuable for further study on the intraspecies identification, biogeographic analysis, and phylogenetic relationship in Clethraceae.

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“…In the 10 identified chloroplast genomes that we sequenced, the ndhB gene has the highest number of potential editing sites (11), followed by the ndhD gene (9) (Table S 6 ). Similar to other Zingiberaceae species, such as K. galanga [ 18 ], A. pumila [ 19 ], and Z. zerumbet [ 26 ], the ndhB gene contains the highest number of editing sites. All of these editing sites are C-to-T transitions that occur at the first or second positions of the codons.…”

Section: Resultsmentioning

confidence: 99%

“…Compared to traditional chloroplast markers, complete chloroplast genomes provide high resolution for relationship reconstruction within the Alpinia , Amomum , Curcuma and Zingiber genera, which allows an exploration of their phylogenetic positions in family Zingiberaceae [ 12 – 18 ]. Moreover, chloroplast single nucleotide polymorphism (SNP)-based phylogenetic analyses improve the phylogenetic resolution within the Alpinia , Amomum , Curcuma, Hedychium , Kaempferia , Stahlianthus and Zingiber genera in family Zingiberaceae [ 19 – 26 ]. However, because of the lack of complete chloroplast genomic data for the genus Globba , no studies have focused on the structural or mutational dynamics of the chloroplast genomes among the four genera of Globba , Hedychium , Kaempferia and Zingiber in subfamily Zingiberoideae.…”

Section: Introductionmentioning

confidence: 99%

Molecular evolution of chloroplast genomes in subfamily Zingiberoideae (Zingiberaceae)

Wang

et al. 2021

BMC Plant Biol

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Background Zingiberoideae is a large and diverse subfamily of the family Zingiberaceae. Four genera in subfamily Zingiberoideae each possess 50 or more species, including Globba (100), Hedychium (> 80), Kaempferia (50) and Zingiber (150). Despite the agricultural, medicinal and horticultural importance of these species, genomic resources and suitable molecular markers for them are currently sparse. Results Here, we have sequenced, assembled and analyzed ten complete chloroplast genomes from nine species of subfamily Zingiberoideae: Globba lancangensis, Globba marantina, Globba multiflora, Globba schomburgkii, Globba schomburgkii var. angustata, Hedychium coccineum, Hedychium neocarneum, Kaempferia rotunda ‘Red Leaf’, Kaempferia rotunda ‘Silver Diamonds’ and Zingiber recurvatum. These ten chloroplast genomes (size range 162,630–163,968 bp) possess typical quadripartite structures that consist of a large single copy (LSC, 87,172–88,632 bp), a small single copy (SSC, 15,393–15,917 bp) and a pair of inverted repeats (IRs, 29,673–29,833 bp). The genomes contain 111–113 different genes, including 79 protein coding genes, 28–30 tRNAs and 4 rRNA genes. The dynamics of the genome structures, gene contents, amino acid frequencies, codon usage patterns, RNA editing sites, simple sequence repeats and long repeats exhibit similarities, with slight differences observed among the ten genomes. Further comparative analysis of seventeen related Zingiberoideae species, 12 divergent hotspots are identified. Positive selection is observed in 14 protein coding genes, including accD, ccsA, ndhA, ndhB, psbJ, rbcL, rpl20, rpoC1, rpoC2, rps12, rps18, ycf1, ycf2 and ycf4. Phylogenetic analyses, based on the complete chloroplast-derived single-nucleotide polymorphism data, strongly support that Globba, Hedychium, and Curcuma I + “the Kaempferia clade” consisting of Curcuma II, Kaempferia and Zingiber, form a nested evolutionary relationship in subfamily Zingiberoideae. Conclusions Our study provides detailed information on ten complete Zingiberoideae chloroplast genomes, representing a valuable resource for future studies that seek to understand the molecular evolutionary dynamics in family Zingiberaceae. The identified divergent hotspots can be used for development of molecular markers for phylogenetic inference and species identification among closely related species within four genera of Globba, Hedychium, Kaempferia and Zingiber in subfamily Zingiberoideae.

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

Cited by 22 publications

References 45 publications

Phylogenetic analysis and development of molecular markers for five medicinal Alpinia species based on complete plastome sequences

Phylogenetic analysis and development of molecular markers for five medicinal Alpinia species based on complete plastome sequences

Complete Chloroplast Genome of Clethra fargesii Franch., an Original Sympetalous Plant from Central China: Comparative Analysis, Adaptive Evolution, and Phylogenetic Relationships

Molecular evolution of chloroplast genomes in subfamily Zingiberoideae (Zingiberaceae)

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