Comparative and Phylogenetic Analyses of Ginger (<i>Zingiber officinale</i>) in the Family Zingiberaceae Based on the Complete Chloroplast Genome
<i>Zingiber officinale</i>, commonly known as ginger, is an important plant of the family Zingiberaceae and is widely used as an herbal medicine and condiment. The lack of chloroplast genomic information hinders molecular research and phylogenetic analysis on ginger. We introduced the co...
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MDPI AG
2019-08-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/8/8/283 |
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| author | Yingxian Cui Liping Nie Wei Sun Zhichao Xu Yu Wang Jing Yu Jingyuan Song Hui Yao |
| author_facet | Yingxian Cui Liping Nie Wei Sun Zhichao Xu Yu Wang Jing Yu Jingyuan Song Hui Yao |
| author_sort | Yingxian Cui |
| collection | DOAJ |
| description | <i>Zingiber officinale</i>, commonly known as ginger, is an important plant of the family Zingiberaceae and is widely used as an herbal medicine and condiment. The lack of chloroplast genomic information hinders molecular research and phylogenetic analysis on ginger. We introduced the complete chloroplast genome of <i>Z. officinale</i> and identified its phylogenetic position in Zingiberaceae. The chloroplast genome of <i>Z. officinale</i> is 162,621 bp with a four-part circular structure and 36.1% GC content. All 113 unique genes were annotated. A total of 78 simple sequence repeats (SSRs) and 42 long repeat sequences, which are potential areas for species authentication, were found. Comparative analysis revealed some highly variable regions, including <i>rps16-trnQ-UUG</i>, <i>atpH-atpI</i>, <i>trnT-UGU-trnL-UAA</i>, <i>ycf1</i>, and <i>psaC-ndhE</i>. Moreover, the small single-copy (SSC) region was the most variable region in all four shared regions, indicating that it may be undergoing rapid nucleotide substitution in the family Zingiberaceae. Phylogenetic analysis based on all available chloroplasts of Zingiberales in the National Center for Biotechnology Information indicated that <i>Zingiber</i> is a sister branch to <i>Kaempferia</i> species. The availability of the <i>Z. officinale</i> chloroplast genome provided invaluable data for species-level authentication and phylogenetic analysis and can thus benefit further investigations on species in the family Zingiberaceae. |
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| spelling | doaj.art-2e21053ad9fd4022b2d25ddef9ca7b072022-12-22T04:09:41ZengMDPI AGPlants2223-77472019-08-018828310.3390/plants8080283plants8080283Comparative and Phylogenetic Analyses of Ginger (<i>Zingiber officinale</i>) in the Family Zingiberaceae Based on the Complete Chloroplast GenomeYingxian Cui0Liping Nie1Wei Sun2Zhichao Xu3Yu Wang4Jing Yu5Jingyuan Song6Hui Yao7Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, ChinaKey Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, ChinaInstitute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, ChinaKey Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, ChinaKey Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, ChinaKey Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, ChinaKey Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, ChinaKey Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China<i>Zingiber officinale</i>, commonly known as ginger, is an important plant of the family Zingiberaceae and is widely used as an herbal medicine and condiment. The lack of chloroplast genomic information hinders molecular research and phylogenetic analysis on ginger. We introduced the complete chloroplast genome of <i>Z. officinale</i> and identified its phylogenetic position in Zingiberaceae. The chloroplast genome of <i>Z. officinale</i> is 162,621 bp with a four-part circular structure and 36.1% GC content. All 113 unique genes were annotated. A total of 78 simple sequence repeats (SSRs) and 42 long repeat sequences, which are potential areas for species authentication, were found. Comparative analysis revealed some highly variable regions, including <i>rps16-trnQ-UUG</i>, <i>atpH-atpI</i>, <i>trnT-UGU-trnL-UAA</i>, <i>ycf1</i>, and <i>psaC-ndhE</i>. Moreover, the small single-copy (SSC) region was the most variable region in all four shared regions, indicating that it may be undergoing rapid nucleotide substitution in the family Zingiberaceae. Phylogenetic analysis based on all available chloroplasts of Zingiberales in the National Center for Biotechnology Information indicated that <i>Zingiber</i> is a sister branch to <i>Kaempferia</i> species. The availability of the <i>Z. officinale</i> chloroplast genome provided invaluable data for species-level authentication and phylogenetic analysis and can thus benefit further investigations on species in the family Zingiberaceae.https://www.mdpi.com/2223-7747/8/8/283<i>Zingiber officinale</i>Zingiberaceaecomplete chloroplast genomecomparative analysisphylogenetic analysis |
| spellingShingle | Yingxian Cui Liping Nie Wei Sun Zhichao Xu Yu Wang Jing Yu Jingyuan Song Hui Yao Comparative and Phylogenetic Analyses of Ginger (<i>Zingiber officinale</i>) in the Family Zingiberaceae Based on the Complete Chloroplast Genome Plants <i>Zingiber officinale</i> Zingiberaceae complete chloroplast genome comparative analysis phylogenetic analysis |
| title | Comparative and Phylogenetic Analyses of Ginger (<i>Zingiber officinale</i>) in the Family Zingiberaceae Based on the Complete Chloroplast Genome |
| title_full | Comparative and Phylogenetic Analyses of Ginger (<i>Zingiber officinale</i>) in the Family Zingiberaceae Based on the Complete Chloroplast Genome |
| title_fullStr | Comparative and Phylogenetic Analyses of Ginger (<i>Zingiber officinale</i>) in the Family Zingiberaceae Based on the Complete Chloroplast Genome |
| title_full_unstemmed | Comparative and Phylogenetic Analyses of Ginger (<i>Zingiber officinale</i>) in the Family Zingiberaceae Based on the Complete Chloroplast Genome |
| title_short | Comparative and Phylogenetic Analyses of Ginger (<i>Zingiber officinale</i>) in the Family Zingiberaceae Based on the Complete Chloroplast Genome |
| title_sort | comparative and phylogenetic analyses of ginger i zingiber officinale i in the family zingiberaceae based on the complete chloroplast genome |
| topic | <i>Zingiber officinale</i> Zingiberaceae complete chloroplast genome comparative analysis phylogenetic analysis |
| url | https://www.mdpi.com/2223-7747/8/8/283 |
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