Complete chloroplast genome sequence of <i>Hedychium coronarium</i>

Li, Dong-Mei; Zhao, Chenkai; Zhu, Genfa; Xu, Yue-Chun

doi:10.1080/23802359.2019.1659114

Cited by 7 publications

(16 citation statements)

References 4 publications

(8 reference statements)

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“…In the genus Alpinia, two accessions of A. oxyphylla clustered together with high statistical support values (bootstrap values ≥ 99%), which was subsequently sister to A. pumila; A. zerumbet and A. katsumadai clustered together (bootstrap values ≥ 99%) was another sister to A. pumila (Figure 9 and Figure S1). Both ML and MP trees confirmed the previously known phylogenetic relationships in the family Zingiberaceae based on earlier studies [12,20,[23][24][25][31][32][33][34], while unexpected relationships and positions of certain taxa were also revealed in this study. The reconfirmation of previously known relationships included (1) the monophyletic genera of Amomum, Alpinia, Kaempferia, Zingiber and Hedychium and their relationships to the rest of family Zingiberaceae, (2) the paraphyletic genus Curcuma in family Zingiberaceae, (3) relationships between two genera of Curcuma and Stahlianthus.…”

Section: Phylogenetic Analysessupporting

confidence: 90%

“…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].…”

Section: The Chloroplast Genome Features Of Alpinia Speciessupporting

confidence: 89%

“…There were 536 SNPs and 107 indels between K. galanga and K. elegans [23]. Moreover, the SNPs obtained from chloroplast genomes had been successfully used for phylogenetic studies in several Zingiberaceae species, such as in K. galanga and K. elegans [23], S. involucratus [31], H. coronarium [32] and C. longa [33]. Therefore, these SNPs and indels in Alpinia here would be potential genetic markers to facilitate phylogenetic analysis and species identification in the family Zingiberaceae.…”

Section: Interspecific Analyses Of Alpinia Chloroplast Genomesmentioning

confidence: 99%

“…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].…”

Section: Introductionmentioning

confidence: 99%

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

Zhu

et al. 2020

Plants

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Alpinia katsumadai (A. katsumadai), Alpinia oxyphylla (A. oxyphylla) and Alpinia pumila (A. pumila), which belong to the family Zingiberaceae, exhibit multiple medicinal properties. The chloroplast genome of a non-model plant provides valuable information for species identification and phylogenetic analysis. Here, we sequenced three complete chloroplast genomes of A. katsumadai, A. oxyphylla sampled from Guangdong and A. pumila, and analyzed the published chloroplast genomes of Alpinia zerumbet (A. zerumbet) and A. oxyphylla sampled from Hainan to retrieve useful chloroplast molecular resources for Alpinia. The five Alpinia chloroplast genomes possessed typical quadripartite structures comprising of a large single copy (LSC, 87,248–87,667 bp), a small single copy (SSC, 15,306–18,295 bp) and a pair of inverted repeats (IR, 26,917–29,707 bp). They had similar gene contents, gene orders and GC contents, but were slightly different in the numbers of small sequence repeats (SSRs) and long repeats. Interestingly, fifteen highly divergent regions (rpl36, ycf1, rps15, rpl22, infA, psbT-psbN, accD-psaI, petD-rpoA, psaC-ndhE, ccsA-ndhD, ndhF-rpl32, rps11-rpl36, infA-rps8, psbC-psbZ, and rpl32-ccsA), which could be suitable for species identification and phylogenetic studies, were detected in the Alpinia chloroplast genomes. Comparative analyses among the five chloroplast genomes indicated that 1891 mutational events, including 304 single nucleotide polymorphisms (SNPs) and 118 insertion/deletions (indels) between A. pumila and A. katsumadai, 367 SNPs and 122 indels between A. pumila and A. oxyphylla sampled from Guangdong, 331 SNPs and 115 indels between A. pumila and A. zerumbet, 371 SNPs and 120 indels between A. pumila and A. oxyphylla sampled from Hainan, and 20 SNPs and 23 indels between the two accessions of A. oxyphylla, were accurately located. Additionally, phylogenetic relationships based on SNP matrix among 28 whole chloroplast genomes showed that Alpinia was a sister branch to Amomum in the family Zingiberaceae, and that the five Alpinia accessions were divided into three groups, one including A. pumila, another including A. zerumbet and A. katsumadai, and the other including two accessions of A. oxyphylla. In conclusion, the complete chloroplast genomes of the three medicinal Alpinia species in this study provided valuable genomic resources for further phylogeny and species identification in the family Zingiberaceae.

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Section: Phylogenetic Analysessupporting

confidence: 90%

Section: The Chloroplast Genome Features Of Alpinia Speciessupporting

confidence: 89%

Section: Interspecific Analyses Of Alpinia Chloroplast Genomesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Zhu

et al. 2020

Plants

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“…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.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2020

PLoS ONE

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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.

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The complete chloroplast genome sequence of Zingiber teres S. Q. Tong & Y. M. Xia (Zingiberaceae)

Wang

Tian

Wang

et al. 2023

Mitochondrial DNA Part B

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Here, the complete chloroplast genome sequence of Zingiber teres is described using MGI paired-end sequencing. The genome is 163,428 bp in length and contains a small single-copy region (SSC) of 15,782 bp, a large single-copy region (LSC) of 88,142 bp, and two inverted repeat (IR) regions of 29,752 bp. The overall GC content is 36.1%, and the GC content of the IR regions is 41.1%, which is higher than that of both the LSC region (33.8%) and SSC region (29.5%). The genome of Z. teres contains 133 complete genes, including 88 protein-coding genes (79 protein-coding gene species), 38 tRNA genes (28 tRNA species), and 8 rRNA genes (four rRNA species). Maximum likelihood phylogenetic analysis yielded a well-resolved tree of the genus Zingiber , and Z. teres and Zingiber mioga were sister species in this tree. The development of DNA barcodes could aid the identification of Zingiber species.

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Complete chloroplast genome sequence of Hedychium coronarium

Cited by 7 publications

References 4 publications

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

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

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

The complete chloroplast genome sequence of Zingiber teres S. Q. Tong & Y. M. Xia (Zingiberaceae)

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