Complete chloroplast genomes provide insights into evolution and phylogeny of Zingiber (Zingiberaceae)
Abstract Background The genus Zingiber of the Zingiberaceae is distributed in tropical, subtropical, and in Far East Asia. This genus contains about 100–150 species, with many species valued as important agricultural, medicinal and horticultural resources. However, genomic resources and suitable mol...
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| Format: | Article |
| Language: | English |
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BMC
2023-01-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-023-09115-9 |
| _version_ | 1827900026702004224 |
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| author | Dongzhu Jiang Xiaodong Cai Min Gong Maoqin Xia Haitao Xing Shanshan Dong Shuming Tian Jialin Li Junyao Lin Yiqing Liu Hong-Lei Li |
| author_facet | Dongzhu Jiang Xiaodong Cai Min Gong Maoqin Xia Haitao Xing Shanshan Dong Shuming Tian Jialin Li Junyao Lin Yiqing Liu Hong-Lei Li |
| author_sort | Dongzhu Jiang |
| collection | DOAJ |
| description | Abstract Background The genus Zingiber of the Zingiberaceae is distributed in tropical, subtropical, and in Far East Asia. This genus contains about 100–150 species, with many species valued as important agricultural, medicinal and horticultural resources. However, genomic resources and suitable molecular markers for species identification are currently sparse. Results We conducted comparative genomics and phylogenetic analyses on Zingiber species. The Zingiber chloroplast genome (size range 162,507–163,711 bp) possess typical quadripartite structures that consist of a large single copy (LSC, 86,986–88,200 bp), a small single copy (SSC, 15,498–15,891 bp) and a pair of inverted repeats (IRs, 29,765–29,934 bp). The genomes contain 113 unique genes, including 79 protein coding genes, 30 tRNA and 4 rRNA genes. The genome structures, gene contents, amino acid frequencies, codon usage patterns, RNA editing sites, simple sequence repeats and long repeats are conservative in the genomes of Zingiber. The analysis of sequence divergence indicates that the following genes undergo positive selection (ccsA, ndhA, ndhB, petD, psbA, psbB, psbC, rbcL, rpl12, rpl20, rpl23, rpl33, rpoC2, rps7, rps12 and ycf3). Eight highly variable regions are identified including seven intergenic regions (petA-pabJ, rbcL-accD, rpl32-trnL-UAG, rps16-trnQ-UUG, trnC-GCA-psbM, psbC-trnS-UGA and ndhF-rpl32) and one genic regions (ycf1). The phylogenetic analysis revealed that the sect. Zingiber was sister to sect. Cryptanthium rather than sect. Pleuranthesis. Conclusions This study reports 14 complete chloroplast genomes of Zingiber species. Overall, this study provided a solid backbone phylogeny of Zingiber. The polymorphisms we have uncovered in the sequencing of the genome offer a rare possibility (for Zingiber) of the generation of DNA markers. These results provide a foundation for future studies that seek to understand the molecular evolutionary dynamics or individual population variation in the genus Zingiber. |
| first_indexed | 2024-03-12T23:25:26Z |
| format | Article |
| id | doaj.art-a509650f628b40ff844bc9cb75204b26 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-03-12T23:25:26Z |
| publishDate | 2023-01-01 |
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| series | BMC Genomics |
| spelling | doaj.art-a509650f628b40ff844bc9cb75204b262023-07-16T11:10:32ZengBMCBMC Genomics1471-21642023-01-0124111810.1186/s12864-023-09115-9Complete chloroplast genomes provide insights into evolution and phylogeny of Zingiber (Zingiberaceae)Dongzhu Jiang0Xiaodong Cai1Min Gong2Maoqin Xia3Haitao Xing4Shanshan Dong5Shuming Tian6Jialin Li7Junyao Lin8Yiqing Liu9Hong-Lei Li10College of Landscape Architecture and Life Science, Chongqing University of Arts and SciencesCollege of Horticulture and Gardening, Yangtze UniversityCollege of Landscape Architecture and Life Science, Chongqing University of Arts and SciencesCollege of Landscape Architecture and Life Science, Chongqing University of Arts and SciencesCollege of Landscape Architecture and Life Science, Chongqing University of Arts and SciencesFairylake Botanical Garden, Shenzhen & Chinese Academy of SciencesCollege of Landscape Architecture and Life Science, Chongqing University of Arts and SciencesCollege of Landscape Architecture and Life Science, Chongqing University of Arts and SciencesCollege of Landscape Architecture and Life Science, Chongqing University of Arts and SciencesCollege of Landscape Architecture and Life Science, Chongqing University of Arts and SciencesCollege of Landscape Architecture and Life Science, Chongqing University of Arts and SciencesAbstract Background The genus Zingiber of the Zingiberaceae is distributed in tropical, subtropical, and in Far East Asia. This genus contains about 100–150 species, with many species valued as important agricultural, medicinal and horticultural resources. However, genomic resources and suitable molecular markers for species identification are currently sparse. Results We conducted comparative genomics and phylogenetic analyses on Zingiber species. The Zingiber chloroplast genome (size range 162,507–163,711 bp) possess typical quadripartite structures that consist of a large single copy (LSC, 86,986–88,200 bp), a small single copy (SSC, 15,498–15,891 bp) and a pair of inverted repeats (IRs, 29,765–29,934 bp). The genomes contain 113 unique genes, including 79 protein coding genes, 30 tRNA and 4 rRNA genes. The genome structures, gene contents, amino acid frequencies, codon usage patterns, RNA editing sites, simple sequence repeats and long repeats are conservative in the genomes of Zingiber. The analysis of sequence divergence indicates that the following genes undergo positive selection (ccsA, ndhA, ndhB, petD, psbA, psbB, psbC, rbcL, rpl12, rpl20, rpl23, rpl33, rpoC2, rps7, rps12 and ycf3). Eight highly variable regions are identified including seven intergenic regions (petA-pabJ, rbcL-accD, rpl32-trnL-UAG, rps16-trnQ-UUG, trnC-GCA-psbM, psbC-trnS-UGA and ndhF-rpl32) and one genic regions (ycf1). The phylogenetic analysis revealed that the sect. Zingiber was sister to sect. Cryptanthium rather than sect. Pleuranthesis. Conclusions This study reports 14 complete chloroplast genomes of Zingiber species. Overall, this study provided a solid backbone phylogeny of Zingiber. The polymorphisms we have uncovered in the sequencing of the genome offer a rare possibility (for Zingiber) of the generation of DNA markers. These results provide a foundation for future studies that seek to understand the molecular evolutionary dynamics or individual population variation in the genus Zingiber.https://doi.org/10.1186/s12864-023-09115-9ZingiberChloroplast GenomePhylogenyComparative genomics |
| spellingShingle | Dongzhu Jiang Xiaodong Cai Min Gong Maoqin Xia Haitao Xing Shanshan Dong Shuming Tian Jialin Li Junyao Lin Yiqing Liu Hong-Lei Li Complete chloroplast genomes provide insights into evolution and phylogeny of Zingiber (Zingiberaceae) BMC Genomics Zingiber Chloroplast Genome Phylogeny Comparative genomics |
| title | Complete chloroplast genomes provide insights into evolution and phylogeny of Zingiber (Zingiberaceae) |
| title_full | Complete chloroplast genomes provide insights into evolution and phylogeny of Zingiber (Zingiberaceae) |
| title_fullStr | Complete chloroplast genomes provide insights into evolution and phylogeny of Zingiber (Zingiberaceae) |
| title_full_unstemmed | Complete chloroplast genomes provide insights into evolution and phylogeny of Zingiber (Zingiberaceae) |
| title_short | Complete chloroplast genomes provide insights into evolution and phylogeny of Zingiber (Zingiberaceae) |
| title_sort | complete chloroplast genomes provide insights into evolution and phylogeny of zingiber zingiberaceae |
| topic | Zingiber Chloroplast Genome Phylogeny Comparative genomics |
| url | https://doi.org/10.1186/s12864-023-09115-9 |
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