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Zhang L, Zhang E, Wei Y, Zheng G. Phylogenetic analysis and divergence time estimation of Lycium species in China based on the chloroplast genomes. BMC Genomics 2024; 25:569. [PMID: 38844874 PMCID: PMC11155141 DOI: 10.1186/s12864-024-10487-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 05/31/2024] [Indexed: 06/10/2024] Open
Abstract
BACKGROUND Lycium is an economically and ecologically important genus of shrubs, consisting of approximately 70 species distributed worldwide, 15 of which are located in China. Despite the economic and ecological importance of Lycium, its phylogeny, interspecific relationships, and evolutionary history remain relatively unknown. In this study, we constructed a phylogeny and estimated divergence time based on the chloroplast genomes (CPGs) of 15 species, including subspecies, of the genus Lycium from China. RESULTS We sequenced and annotated 15 CPGs in this study. Comparative analysis of these genomes from these Lycium species revealed a typical quadripartite structure, with a total sequence length ranging from 154,890 to 155,677 base pairs (bp). The CPGs was highly conserved and moderately differentiated. Through annotation, we identified a total of 128-132 genes. Analysis of the boundaries of inverted repeat (IR) regions showed consistent positioning: the junctions of the IRb/LSC region were located in rps19 in all Lycium species, IRb/SSC between the ycf1 and ndhF genes, and SSC/IRa within the ycf1 gene. Sequence variation in the SSC region exceeded that in the IR region. We did not detect major expansions or contractions in the IR region or rearrangements or insertions in the CPGs of the 15 Lycium species. Comparative analyses revealed five hotspot regions in the CPG: trnR(UCU), atpF-atpH, ycf3-trnS(GGA), trnS(GGA), and trnL-UAG, which could potentially serve as molecular markers. In addition, phylogenetic tree construction based on the CPG indicated that the 15 Lycium species formed a monophyletic group and were divided into two typical subbranches and three minor branches. Molecular dating suggested that Lycium diverged from its sister genus approximately 17.7 million years ago (Mya) and species diversification within the Lycium species of China primarily occurred during the recent Pliocene epoch. CONCLUSION The divergence time estimation presented in this study will facilitate future research on Lycium, aid in species differentiation, and facilitate diverse investigations into this economically and ecologically important genus.
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Affiliation(s)
- Lei Zhang
- Key Laboratory of Ecological Protection of Agro-Pastoral Ecotones in the Yellow River Basin, College of Biological Science & Engineering, National Ethnic Affairs Commission of the People's Republic of China, North Minzu University, Yinchuan, 750021, China
| | - Erdong Zhang
- Key Laboratory of Ecological Protection of Agro-Pastoral Ecotones in the Yellow River Basin, College of Biological Science & Engineering, National Ethnic Affairs Commission of the People's Republic of China, North Minzu University, Yinchuan, 750021, China
| | - Yuqing Wei
- Key Laboratory of Ecological Protection of Agro-Pastoral Ecotones in the Yellow River Basin, College of Biological Science & Engineering, National Ethnic Affairs Commission of the People's Republic of China, North Minzu University, Yinchuan, 750021, China
| | - Guoqi Zheng
- Key Laboratory of the Ministry of Education for Protection and Utilization of Special Biological Resources in the Western, School of Life Science, Ningxia University, Yinchuan, Ningxia, 750021, China.
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Singh D, Mittal N, Verma S, Singh A, Siddiqui MH. Applications of some advanced sequencing, analytical, and computational approaches in medicinal plant research: a review. Mol Biol Rep 2023; 51:23. [PMID: 38117315 DOI: 10.1007/s11033-023-09057-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 11/27/2023] [Indexed: 12/21/2023]
Abstract
The potential active chemicals found in medicinal plants, which have long been employed as natural medicines, are abundant. Exploring the genes responsible for producing these compounds has given new insights into medicinal plant research. Previously, the authentication of medicinal plants was done via DNA marker sequencing. With the advancement of sequencing technology, several new techniques like next-generation sequencing, single molecule sequencing, and fourth-generation sequencing have emerged. These techniques enshrined the role of molecular approaches for medicinal plants because all the genes involved in the biosynthesis of medicinal compound(s) could be identified through RNA-seq analysis. In several research insights, transcriptome data have also been used for the identification of biosynthesis pathways. miRNAs in several medicinal plants and their role in the biosynthesis pathway as well as regulation of the disease-causing genes were also identified. In several research articles, an in silico study was also found to be effective in identifying the inhibitory effect of medicinal plant-based compounds against virus' gene(s). The use of advanced analytical methods like spectroscopy and chromatography in metabolite proofing of secondary metabolites has also been reported in several recent research findings. Furthermore, advancement in molecular and analytic methods will give new insight into studying the traditionally important medicinal plants that are still unexplored.
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Affiliation(s)
- Dhananjay Singh
- Department of Biosciences, Integral University, Lucknow, Uttar Pradesh, 226026, India
| | - Nishu Mittal
- Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Barabanki, Uttar Pradesh, 225003, India
| | - Swati Verma
- College of Horticulture and Forestry Thunag, Dr. Y. S. Parmar University of Horticulture and Forestry, Nauni, Solan, Himachal Pradesh, 173230, India
| | - Anjali Singh
- Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Barabanki, Uttar Pradesh, 225003, India
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Wei Z, Chen F, Ding H, Liu W, Yang B, Geng J, Chen S, Guo S. Comparative Analysis of Six Chloroplast Genomes in Chenopodium and Its Related Genera ( Amaranthaceae): New Insights into Phylogenetic Relationships and the Development of Species-Specific Molecular Markers. Genes (Basel) 2023; 14:2183. [PMID: 38137004 PMCID: PMC10743295 DOI: 10.3390/genes14122183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/27/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
Species within the genus Chenopodium hold significant research interest due to their nutritional richness and salt tolerance. However, the morphological similarities among closely related species and a dearth of genomic resources have impeded their comprehensive study and utilization. In the present research, we conduct the sequencing and assembly of chloroplast (cp) genomes from six Chenopodium and related species, five of which were sequenced for the first time. These genomes ranged in length from 151,850 to 152,215 base pairs, showcased typical quadripartite structures, and encoded 85 protein-coding genes (PCGs), 1 pseudogene, 37 tRNA genes, and 8 rRNA genes. Compared with the previously published sequences of related species, these cp genomes are relatively conservative, but there are also some interspecific differences, such as inversion and IR region contraction. We discerned 929 simple sequence repeats (SSRs) and a series of highly variable regions across 16 related species, predominantly situated in the intergenic spacer (IGS) region and introns. The phylogenetic evaluations revealed that Chenopodium is more closely related to genera such as Atriplex, Beta, Dysphania, and Oxybase than to other members of the Amaranthaceae family. These lineages shared a common ancestor approximately 60.80 million years ago, after which they diverged into distinct genera. Based on InDels and SNPs between species, we designed 12 pairs of primers for species identification, and experiments confirmed that they could completely distinguish 10 related species.
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Affiliation(s)
- Zixiang Wei
- College of Life Sciences, Yantai University, Yantai 264005, China; (Z.W.); (F.C.); (H.D.); (W.L.); (B.Y.); (J.G.)
| | - Fangjun Chen
- College of Life Sciences, Yantai University, Yantai 264005, China; (Z.W.); (F.C.); (H.D.); (W.L.); (B.Y.); (J.G.)
| | - Hongxia Ding
- College of Life Sciences, Yantai University, Yantai 264005, China; (Z.W.); (F.C.); (H.D.); (W.L.); (B.Y.); (J.G.)
| | - Wenli Liu
- College of Life Sciences, Yantai University, Yantai 264005, China; (Z.W.); (F.C.); (H.D.); (W.L.); (B.Y.); (J.G.)
| | - Bo Yang
- College of Life Sciences, Yantai University, Yantai 264005, China; (Z.W.); (F.C.); (H.D.); (W.L.); (B.Y.); (J.G.)
| | - Jiahui Geng
- College of Life Sciences, Yantai University, Yantai 264005, China; (Z.W.); (F.C.); (H.D.); (W.L.); (B.Y.); (J.G.)
| | - Shihua Chen
- College of Life Sciences, Yantai University, Yantai 264005, China; (Z.W.); (F.C.); (H.D.); (W.L.); (B.Y.); (J.G.)
| | - Shanli Guo
- College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
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Zhou Q, Chen Y, Wang J, Li M, Zeng W, Wang Y, Li Y, Zhao H. A comparative study of the chloroplast genomes of five Lepidium species with high medicinal value. FUNCTIONAL PLANT BIOLOGY : FPB 2023; 50:29-45. [PMID: 36043226 DOI: 10.1071/fp22052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
Plantgenomics is a rapidly developing field in medicinal plant research. This study analysed the relevant information of chloroplasts genome sequences of five medicinal plants from the genus Lepidium . We sequenced the complete chloroplast (cp) genomes of Lepidium apetalum Willd. and Lepidium perfoliatum Linnaeus., and assessed their genetic profiles against the reported profiles of Lepidium sativum Linnaeus., Lepidium meyenii Walp., and Lepidium virginicum Linn. We found that L. apetalum and L. perfoliatum possessed 130 distinct genes that included 85 protein-coding, 37 transfer RNA (tRNA), and eight ribosomal RNA (rRNA) genes. Our repeat analyses revealed that L. apetalum harboured 20 direct repeats, 16 palindrome repeats, 30 tandem repeats, and 87 simple sequence repeats, whereas, L. perfoliatum had 15 direct repeats, 20 palindrome repeats, four reverse repeats, 21 tandem repeats, and 98 simple sequence repeats. Using syntenic analysis, we also revealed a high degree of sequence similarity within the coding regions of Lepidium medicinal plant cp genomes, and a high degree of divergence among the intergenic spacers. Pairwise alignment and single-nucleotide polymorphism (SNP) examinations further revealed certain Lepidium -specific gene fragments. Codon usage analysis showed that codon 14 was the most frequently used codon in the Lepidium coding sequences. Further, correlation investigations suggest that L. apetalum and L. perfoliatum originate from similar genetic backgrounds. Analysis of codon usage bias of Lepidium cp genome was strongly influenced by mutation and natural selection. We showed that L. apetalum and L. perfoliatum will likely enhance breeding, species recognition, phylogenetic evolution, and cp genetic engineering of the Lepidium medicinal plants.
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Affiliation(s)
- Qian Zhou
- Key Laboratory of Biological Resources and Ecology of Pamirs Plateau in Xinjiang Uygur Autonomous Region, College of Life and Geography Sciences, Kashi University, Kashi, China
| | - Yun Chen
- Key Laboratory of Biological Resources and Ecology of Pamirs Plateau in Xinjiang Uygur Autonomous Region, College of Life and Geography Sciences, Kashi University, Kashi, China
| | - Jilian Wang
- Key Laboratory of Biological Resources and Ecology of Pamirs Plateau in Xinjiang Uygur Autonomous Region, College of Life and Geography Sciences, Kashi University, Kashi, China
| | - Mingyuan Li
- Key Laboratory of Biological Resources and Ecology of Pamirs Plateau in Xinjiang Uygur Autonomous Region, College of Life and Geography Sciences, Kashi University, Kashi, China
| | - Weijun Zeng
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumqi, China
| | - Yuzhou Wang
- Key Laboratory of Biological Resources and Ecology of Pamirs Plateau in Xinjiang Uygur Autonomous Region, College of Life and Geography Sciences, Kashi University, Kashi, China
| | - Yanhong Li
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumqi, China
| | - Huixin Zhao
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumqi, China
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Chen Q, Chen C, Wang B, Wang Z, Xu W, Huang Y, Sun Q. Complete chloroplast genomes of 11 Sabia samples: Genomic features, comparative analysis, and phylogenetic relationship. FRONTIERS IN PLANT SCIENCE 2022; 13:1052920. [PMID: 36589084 PMCID: PMC9800934 DOI: 10.3389/fpls.2022.1052920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 11/18/2022] [Indexed: 06/17/2023]
Abstract
The genus Sabia is a woody climber belonging to the family Sabiaceae, order Proteales. Several species of this genus have been utilized as medicines for treating diseases, such as rheumatic arthritis, traumatism, hepatitis, etc. However, the lack of molecular data has prevented the accurate identification and refinement of taxonomic relationships in this genus. In this study, chloroplast genomes of 11 samples of the genus Sabia were assembled and analyzed. These chloroplast genomes showed a typical quadripartite structure and ranged in length from 160,956 to 162,209 bp. The structure of the genomes was found to be relatively conserved, with 130 genes annotated, including 85 coding genes, 37 tRNA genes, and eight rRNA genes. A total of 78-98 simple sequence repeats and 52-61 interspersed repeats were detected. Sequence alignment revealed 11 highly variable loci in chloroplast genomes. Among these loci, ndhF-ndhD achieved a remarkably higher resolution than the other regions. In addition, phylogenetic analysis indicated that Sect. Pachydiscus and Sect. Sabia of Sabia did not form two separate monophyletic groups. The divergence time calculated based on the Reltime method indicated that the evolutionary branches of Sabia and Meliosma started to form approximately 85.95 million years ago (Mya), and the species within Sabia began to diverge approximately 7.65 Mya. In conclusion, our study provides a basis for comprehensively exploring the phylogenetic relationships of Sabia. It also provides a methodological basis and data support for establishing a standardized and scientific identification system for this genus.
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Affiliation(s)
| | | | | | | | | | - Yuan Huang
- *Correspondence: Yuan Huang, ; Qingwen Sun,
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6
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Ren W, Jiang Z, Zhang M, Kong L, Zhang H, Liu Y, Fu Q, Ma W. The chloroplast genome of Salix floderusii and characterization of chloroplast regulatory elements. FRONTIERS IN PLANT SCIENCE 2022; 13:987443. [PMID: 36092427 PMCID: PMC9459086 DOI: 10.3389/fpls.2022.987443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
Salix floderusii is a rare alpine tree species in the Salix genus. Unfortunately, no extensive germplasm identification, molecular phylogeny, and chloroplast genomics of this plant have been conducted. We sequenced the chloroplast (cp) genome of S. floderusii for the first time using second-generation sequencing technology. The cp genome was 155,540 bp long, including a large single-copy region (LSC, 84,401 bp), a small single-copy region (SSC, 16,221 bp), and inverted repeat regions (IR, 54,918 bp). A total of 131 genes were identified, including 86 protein genes, 37 tRNA genes, and 8 rRNA genes. The S. floderusii cp genome contains 1 complement repeat, 24 forward repeats, 17 palindromic repeats, and 7 reverse repeats. Analysis of the IR borders showed that the IRa and IRb regions of S. floderusii and Salix caprea were shorter than those of Salix cinerea, which may affect plastome evolution. Furthermore, four highly variable regions were found, including the rpl22 coding region, psbM/trnD-GUC non-coding region, petA/psbJ non-coding region, and ycf1 coding region. These high variable regions can be used as candidate molecular markers and as a reference for identifying future Salix species. In addition, phylogenetic analysis indicated that the cp genome of S. floderusii is sister to Salix cupularis and belongs to the Subgenus Vetrix. Genes (Sf-trnI, Sf-PpsbA, aadA, Sf-TpsbA, Sf-trnA) obtained via cloning were inserted into the pBluescript II SK (+) to yield the cp expression vectors, which harbored the selectable marker gene aadA. The results of a spectinomycin resistance test indicated that the cp expression vector had been successfully constructed. Moreover, the aadA gene was efficiently expressed under the regulation of predicted regulatory elements. The present study provides a solid foundation for establishing subsequent S. floderusii cp transformation systems and developing strategies for the genetic improvement of S. floderusii.
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Affiliation(s)
- Weichao Ren
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Zhehui Jiang
- School of Forestry, Northeast Forestry University, Harbin, China
| | - Meiqi Zhang
- School of Forestry, Northeast Forestry University, Harbin, China
| | - Lingyang Kong
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Houliang Zhang
- Yichun Branch of Heilongjiang Academy of Forestry, Yichun, China
| | - Yunwei Liu
- Yichun Branch of Heilongjiang Academy of Forestry, Yichun, China
| | - Qifeng Fu
- Experimental Teaching and Training Center, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Wei Ma
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, China
- Experimental Teaching and Training Center, Heilongjiang University of Chinese Medicine, Harbin, China
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7
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Xu S, Sun M, Mei Y, Gu Y, Huang D, Wang J. The complete chloroplast genome sequence of the medicinal plant Abrus pulchellus subsp. cantoniensis: genome structure, comparative and phylogenetic relationship analysis. JOURNAL OF PLANT RESEARCH 2022; 135:443-452. [PMID: 35338406 DOI: 10.1007/s10265-022-01385-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 02/23/2022] [Indexed: 06/14/2023]
Abstract
Abrus pulchellus subsp. cantoniensis, an endemic medicinal plant in southern China, is clinically used to treat jaundice hepatitis, cholecystitis, stomachache and breast carbuncle. Here, we assembled and analyzed the first complete chloroplast (cp) genome of A. pulchellus subsp. cantoniensis. The A. pulchellus subsp. cantoniensis cp genome size is 156,497 bp with 36.5% GC content. The cp genome encodes 130 genes, including 77 protein-coding genes, 30 tRNA genes and four rRNA genes, of which 19 genes are duplicated in the inverted repeats (IR) regions. A total of 30 codons exhibited codon usage bias with A/U-ending. Moreover, 53 putative RNA editing sites were predicted in 20 genes, all of which were cytidine to thymine transitions. Repeat sequence analysis identified 45 repeat structures and 125 simple-sequence repeats (SSRs) in A. pulchellus subsp. cantoniensis cp genome. In addition, 19 mononucleotides (located in atpB, trnV-UAC, ycf3, atpF, rps16, rps18, clpP, rpl16, trnG-UCC and ndhA) and three compound SSRs (located in ndhA, atpB and rpl16) showed species specificity between A. pulchellus subsp. cantoniensis and Abrus precatorius, which might be informative sources for developing molecular markers for species identification. Furthermore, phylogenetic analysis inferred that A. pulchellus subsp. cantoniensis was closely related to A. precatorius, and the genus Abrus formed a subclade with Canavalia in the Millettioid/Phaseoloid clade. These data provide a valuable resource to facilitate the evolutionary relationship and species identification of this species.
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Affiliation(s)
- Shiqiang Xu
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, No. 18, West Second Street, Jinying Road, Tianhe District, Guangzhou, 510640, Guangdong, China
- Guangdong Provincial Engineering and Technology Research Center for Conservation and Utilization of the Genuine Southern Medicinal Resources, Guangzhou, China
| | - Mingyang Sun
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, No. 18, West Second Street, Jinying Road, Tianhe District, Guangzhou, 510640, Guangdong, China
- Guangdong Provincial Engineering and Technology Research Center for Conservation and Utilization of the Genuine Southern Medicinal Resources, Guangzhou, China
| | - Yu Mei
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, No. 18, West Second Street, Jinying Road, Tianhe District, Guangzhou, 510640, Guangdong, China
- Guangdong Provincial Engineering and Technology Research Center for Conservation and Utilization of the Genuine Southern Medicinal Resources, Guangzhou, China
| | - Yan Gu
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, No. 18, West Second Street, Jinying Road, Tianhe District, Guangzhou, 510640, Guangdong, China
- Guangdong Provincial Engineering and Technology Research Center for Conservation and Utilization of the Genuine Southern Medicinal Resources, Guangzhou, China
| | - Ding Huang
- College of Pharmacy, Guangxi University of Chinese Medicine, 13 Wuhe Avenue, Nanning, 530200, Guangxi Zhuang Autonomous Region, China.
| | - Jihua Wang
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, No. 18, West Second Street, Jinying Road, Tianhe District, Guangzhou, 510640, Guangdong, China.
- Guangdong Provincial Engineering and Technology Research Center for Conservation and Utilization of the Genuine Southern Medicinal Resources, Guangzhou, China.
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Yu X, Wang W, Yang H, Zhang X, Wang D, Tian X. Transcriptome and Comparative Chloroplast Genome Analysis of Vincetoxicum versicolor: Insights Into Molecular Evolution and Phylogenetic Implication. Front Genet 2021; 12:602528. [PMID: 33747039 PMCID: PMC7970127 DOI: 10.3389/fgene.2021.602528] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 01/25/2021] [Indexed: 11/13/2022] Open
Abstract
Vincetoxicum versicolor (Bunge) Decne is the original plant species of the Chinese herbal medicine Cynanchi Atrati Radix et Rhizoma. The lack of information on the transcriptome and chloroplast genome of V. versicolor hinders its evolutionary and taxonomic studies. Here, the V. versicolor transcriptome and chloroplast genome were assembled and functionally annotated. In addition, the comparative chloroplast genome analysis was conducted between the genera Vincetoxicum and Cynanchum. A total of 49,801 transcripts were generated, and 20,943 unigenes were obtained from V. versicolor. One thousand thirty-two unigenes from V. versicolor were classified into 73 functional transcription factor families. The transcription factors bHLH and AP2/ERF were the most significantly abundant, indicating that they should be analyzed carefully in the V. versicolor ecological adaptation studies. The chloroplast genomes of Vincetoxicum and Cynanchum exhibited a typical quadripartite structure with highly conserved gene order and gene content. They shared an analogous codon bias pattern in which the codons of protein-coding genes had a preference for A/U endings. The natural selection pressure predominantly influenced the chloroplast genes. A total of 35 RNA editing sites were detected in the V. versicolor chloroplast genome by RNA sequencing (RNA-Seq) data, and one of them restored the start codon in the chloroplast ndhD of V. versicolor. Phylogenetic trees constructed with protein-coding genes supported the view that Vincetoxicum and Cynanchum were two distinct genera.
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Affiliation(s)
- Xiaolei Yu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Wenxiu Wang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Hongxia Yang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xiaoying Zhang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Dan Wang
- Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xiaoxuan Tian
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
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Daniell H, Jin S, Zhu X, Gitzendanner MA, Soltis DE, Soltis PS. Green giant-a tiny chloroplast genome with mighty power to produce high-value proteins: history and phylogeny. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:430-447. [PMID: 33484606 PMCID: PMC7955891 DOI: 10.1111/pbi.13556] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/11/2021] [Accepted: 01/16/2021] [Indexed: 05/04/2023]
Abstract
Free-living cyanobacteria were entrapped by eukaryotic cells ~2 billion years ago, ultimately giving rise to chloroplasts. After a century of debate, the presence of chloroplast DNA was demonstrated in the 1960s. The first chloroplast genomes were sequenced in the 1980s, followed by ~100 vegetable, fruit, cereal, beverage, oil and starch/sugar crop chloroplast genomes in the past three decades. Foreign genes were expressed in isolated chloroplasts or intact plant cells in the late 1980s and stably integrated into chloroplast genomes, with typically maternal inheritance shown in the 1990s. Since then, chloroplast genomes conferred the highest reported levels of tolerance or resistance to biotic or abiotic stress. Although launching products with agronomic traits in important crops using this concept has been elusive, commercial products developed include enzymes used in everyday life from processing fruit juice, to enhancing water absorption of cotton fibre or removal of stains as laundry detergents and in dye removal in the textile industry. Plastid genome sequences have revealed the framework of green plant phylogeny as well as the intricate history of plastid genome transfer events to other eukaryotes. Discordant historical signals among plastid genes suggest possible variable constraints across the plastome and further understanding and mitigation of these constraints may yield new opportunities for bioengineering. In this review, we trace the evolutionary history of chloroplasts, status of autonomy and recent advances in products developed for everyday use or those advanced to the clinic, including treatment of COVID-19 patients and SARS-CoV-2 vaccine.
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Affiliation(s)
- Henry Daniell
- Department of Basic and Translational SciencesSchool of Dental MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Xin‐Guang Zhu
- State Key Laboratory for Plant Molecular Genetics and Center of Excellence for Molecular Plant SciencesChinese Academy of SciencesShanghaiChina
| | | | - Douglas E. Soltis
- Florida Museum of Natural History and Department of BiologyUniversity of FloridaGainesvilleFLUSA
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFLUSA
| | - Pamela S. Soltis
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFLUSA
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Xu J, Shen X, Liao B, Xu J, Hou D. Comparing and phylogenetic analysis chloroplast genome of three Achyranthes species. Sci Rep 2020; 10:10818. [PMID: 32616875 PMCID: PMC7331806 DOI: 10.1038/s41598-020-67679-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 06/12/2020] [Indexed: 11/29/2022] Open
Abstract
In this study, the chloroplast genome sequencing of the Achyranthes longifolia, Achyranthes bidentata and Achyranthes aspera were performed by Next-generation sequencing technology. The results revealed that there were a length of 151,520 bp (A. longifolia), 151,284 bp (A. bidentata), 151,486 bp (A. aspera), respectively. These chloroplast genome have a highly conserved structure with a pair of inverted repeat (IR) regions (25,150 bp; 25,145 bp; 25,150 bp), a large single copy (LSC) regions (83,732 bp; 83,933 bp; 83,966 bp) and a small single copy (SSC) regions (17,252 bp; 17,263 bp; 17,254 bp) in A. bidentate, A. aspera and A. longifolia. There were 127 genes were annotated, which including 8 rRNA genes, 37 tRNA genes and 82 functional genes. The phylogenetic analysis strongly revealed that Achyranthes is monophyletic, and A. bidentata was the closest relationship with A. aspera and A. longifolia. A. bidentata and A. longifolia were clustered together, the three Achyranthes species had the same origin, then the gunes of Achyranthes is the closest relative to Alternanthera, and that forms a group with Alternanthera philoxeroides. The research laid a foundation and provided relevant basis for the identification of germplasm resources in the future.
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Affiliation(s)
- Jingya Xu
- Agricultural College, Henan University of Science and Technology, Luoyang, China
- The Luoyang Engineering Research Center of Breeding and Utilization of Dao-Di Herbs, Luoyang, China
- Institute of Chinese Materia Medical, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xiaofeng Shen
- Institute of Chinese Materia Medical, China Academy of Chinese Medical Sciences, Beijing, China
| | - Baosheng Liao
- Institute of Chinese Materia Medical, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jiang Xu
- Institute of Chinese Materia Medical, China Academy of Chinese Medical Sciences, Beijing, China.
| | - Dianyun Hou
- Agricultural College, Henan University of Science and Technology, Luoyang, China.
- The Luoyang Engineering Research Center of Breeding and Utilization of Dao-Di Herbs, Luoyang, China.
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11
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Wang Y, Zhao Y, Wang K, Wang L, Feng Y, Qi L, Luo Y, Ji Y, Gong X. The complete chloroplast genome of Catalpa ovata (Bignoniaceae): an important ornamental and medicinal plant. Mitochondrial DNA B Resour 2020. [DOI: 10.1080/23802359.2020.1742226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
- Yan Wang
- Department of Agricultural Sciences, Hebei North University, Zhangjiakou City, Hebei Province, P. R. China
| | - Yue Zhao
- Department of Agricultural Sciences, Hebei North University, Zhangjiakou City, Hebei Province, P. R. China
| | - Kuan Wang
- Department of Agricultural Sciences, Hebei North University, Zhangjiakou City, Hebei Province, P. R. China
| | - Lei Wang
- Department of Agricultural Sciences, Hebei North University, Zhangjiakou City, Hebei Province, P. R. China
| | - Yan Feng
- Department of Agricultural Sciences, Hebei North University, Zhangjiakou City, Hebei Province, P. R. China
| | - Lipan Qi
- Department of Agricultural Sciences, Hebei North University, Zhangjiakou City, Hebei Province, P. R. China
| | - Yating Luo
- Department of Agricultural Sciences, Hebei North University, Zhangjiakou City, Hebei Province, P. R. China
| | - Yihong Ji
- Department of Agricultural Sciences, Hebei North University, Zhangjiakou City, Hebei Province, P. R. China
| | - Xuechen Gong
- Department of Agricultural Sciences, Hebei North University, Zhangjiakou City, Hebei Province, P. R. China
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12
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Liu Z, Yu X, Cui P, Tian X. The complete chloroplast genome of Iris tectorum (Iridaceae). MITOCHONDRIAL DNA PART B 2020. [DOI: 10.1080/23802359.2020.1742599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Zhenzhen Liu
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xiaolei Yu
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Pengdi Cui
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xiaoxuan Tian
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
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13
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Zhang RS, Yang J, Hu HL, Xia RX, Li YP, Su JF, Li Q, Liu YQ, Qin L. A high level of chloroplast genome sequence variability in the Sawtooth Oak Quercus acutissima. Int J Biol Macromol 2020; 152:340-348. [PMID: 32109476 DOI: 10.1016/j.ijbiomac.2020.02.201] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 02/17/2020] [Accepted: 02/18/2020] [Indexed: 11/18/2022]
Abstract
The Sawtooth Oak, Quercus acutissima Carruth., is an economically and ecologically important tree species in the family Fagaceae with a wide distribution in China. Here, we examined its intraspecific chloroplast (cp) genome variability using available and a newly sequenced genome. The new cp genome comes from a Q. acutissima individual collected from Shenyang (Northeast China; "Q. acutissima Shenyang" in the following), and then is compared with two recently published cp genomes from Tongchuan (Northwest China) and Nanjing (East China). The cp genome of Q. acutissima Shenyang exhibits a slightly larger genome size than the other two individuals, although each encodes 86 protein-coding genes, 40 tRNA genes and eight rRNA genes. We also found the length difference for the IR/SC boundary region among the three cp genomes. Sequence comparison revealed a high intraspecific genetic divergence: the three cp genomes differ by 332 sequence patterns including 77 single nucleotide polymorphisms, and 255 indels (each gap considered) scattering across 67 regions. Phylogenetic analyses based on the cp genome recovered the split between the subgenus Cerris and the subgenus Quercus, but revealed that three Q. acutissima individuals did not cluster together, indicating that even complete cp genome data fail to reproduce species boundaries in Asian members of section Cerris. Our results show that more complete plastomes covering remote ranges needs to be sequenced to provide a solid backbone for future population-scale in-depth studies and phylogenetic analysis of section Cerris.
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Affiliation(s)
- Ru-Song Zhang
- Department of Sericulture, College of Bioscience and Biotechnology, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
| | - Jian Yang
- Department of Sericulture, College of Bioscience and Biotechnology, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
| | - Hua-Lei Hu
- Department of Sericulture, College of Bioscience and Biotechnology, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
| | - Run-Xi Xia
- Department of Sericulture, College of Bioscience and Biotechnology, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
| | - Yu-Ping Li
- Department of Sericulture, College of Bioscience and Biotechnology, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
| | - Jun-Fang Su
- Center for Experimental Teaching, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Qun Li
- Department of Sericulture, College of Bioscience and Biotechnology, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China.
| | - Yan-Qun Liu
- Department of Sericulture, College of Bioscience and Biotechnology, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China.
| | - Li Qin
- Department of Sericulture, College of Bioscience and Biotechnology, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
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Li DM, Zhu GF, Xu YC, Ye YJ, Liu JM. Complete Chloroplast Genomes of Three Medicinal Alpinia Species: Genome Organization, Comparative Analyses and Phylogenetic Relationships in Family Zingiberaceae. PLANTS (BASEL, SWITZERLAND) 2020; 9:E286. [PMID: 32102387 PMCID: PMC7076362 DOI: 10.3390/plants9020286] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 02/18/2020] [Accepted: 02/20/2020] [Indexed: 12/17/2022]
Abstract
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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Affiliation(s)
- Dong-Mei Li
- Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (Y.-C.X.); (Y.-J.Y.)
| | - Gen-Fa Zhu
- Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (Y.-C.X.); (Y.-J.Y.)
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15
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Complete chloroplast genome of Sophora alopecuroides (Papilionoideae): molecular structures, comparative genome analysis and phylogenetic analysis. J Genet 2020. [DOI: 10.1007/s12041-019-1173-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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16
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Zha X, Wang X, Li J, Gao F, Zhou Y. Complete chloroplast genome of Sophora alopecuroides (Papilionoideae): molecular structures, comparative genome analysis and phylogenetic analysis. J Genet 2020; 99:13. [PMID: 32089532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Sophora alopecuroides belongs to the genus Sophora of the family Papilionoideae. It is mainly distributed in the desert and semidesert areas of northern China, and has high medicinal value and ecological function. Previous studies have reported the chemical composition and ecological functions of S. alopecuroides. However, only a few reports are available on the genomic information of S. alopecuroides, especially the chloroplast genome, which greatly limits the study of the evolutionary relationship between other species of Papilionoideae. Here, we report the complete chloroplast genome of S. alopecuroides. The size of the chloroplast genome is 155,207 bp, and the GC content is 36.44%. The S. alopecuroides chloroplast genome consists of 132 genes, including 83 protein-coding genes, 41 transfer RNA (tRNA) genes,and eight ribosomal RNA (rRNA) genes. Phylogenetic analysis revealed the taxonomic position of S. alopecuroides in Papilionoideae, and the genus Sophora and the genus Ammopiptanthus were highly related. Comparative genomics analysis revealed the gene rearrangement in the evolution of S. alopecuroides. The comparison between S. alopecuroides and the species of the Papilionoideae identified a novel 23 kb inversion between the trnC-GCA and trnF-GAA which occurred before the divergence of Sophora and Ammopiptanthus of Thermopsideae. This study provided an essential data for the understanding of phylogenetic status of S. alopecuroides.
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Affiliation(s)
- Xi Zha
- College of Life and Environmental Sciences, Minzu University of China, #27, Zhongguancun South Street, Haidian, Beijing 100081, People's Republic of China. ,
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Chloroplast Genome Sequence of Artemisia scoparia: Comparative Analyses and Screening of Mutational Hotspots. PLANTS 2019; 8:plants8110476. [PMID: 31698805 PMCID: PMC6918244 DOI: 10.3390/plants8110476] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/14/2019] [Accepted: 10/29/2019] [Indexed: 02/07/2023]
Abstract
Artemisia L. is among the most diverse and medicinally important genera of the plant family Asteraceae. Discrepancies arise in the taxonomic classification of Artemisia due to the occurrence of multiple polyploidy events in separate lineages and its complex morphology. The discrepancies could be resolved by increasing the genomic resources. A. scoparia is one of the most medicinally important species in Artemisia. In this paper, we report the complete chloroplast genome sequence of Artemisia scoparia. The genome was 151,060 bp (base pairs), comprising a large single copy (82,834 bp) and small single copy (18,282 bp), separated by a pair of long inverted repeats (IRa and IRb: 24,972 bp each). We identified 114 unique genes, including four ribosomal RNAs, 30 transfer RNAs, and 80 protein-coding genes. We analysed the chloroplast genome features, including oligonucleotide repeats, microsatellites, amino acid frequencies, RNA editing sites, and codon usage. Transversion substitutions were twice as frequent as transition substitutions. Mutational hotspot loci included ccsA-ndhD, trnH-psbA, ndhG-ndhI, rps18-rpl20, and rps15-ycf1. These loci can be used to develop cost-effective and robust molecular markers for resolving the taxonomic discrepancies. The reconstructed phylogenetic tree supported previous findings of Artemisia as a monophyletic genus, sister to the genus Chrysanthemum, whereby A. scoparia appeared as sister to A. capillaris.
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Ding H, Zhu R, Dong J, Bi D, Jiang L, Zeng J, Huang Q, Liu H, Xu W, Wu L, Kan X. Next-Generation Genome Sequencing of Sedum plumbizincicola Sheds Light on the Structural Evolution of Plastid rRNA Operon and Phylogenetic Implications within Saxifragales. PLANTS (BASEL, SWITZERLAND) 2019; 8:E386. [PMID: 31569538 PMCID: PMC6843225 DOI: 10.3390/plants8100386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 09/27/2019] [Accepted: 09/28/2019] [Indexed: 01/21/2023]
Abstract
The genus Sedum, with about 470 recognized species, is classified in the family Crassulaceae of the order Saxifragales. Phylogenetic relationships within the Saxifragales are still unresolved and controversial. In this study, the plastome of S. plumbizincicola was firstly presented, with a focus on the structural analysis of rrn operon and phylogenetic implications within the order Saxifragaceae. The assembled complete plastome of S. plumbizincicola is 149,397 bp in size, with a typical circular, double-stranded, and quadripartite structure of angiosperms. It contains 133 genes, including 85 protein-coding genes (PCGs), 36 tRNA genes, 8 rRNA genes, and four pseudogenes (one ycf1, one rps19, and two ycf15). The predicted secondary structure of S. plumbizincicola 16S rRNA includes three main domains organized in 74 helices. Further, our results confirm that 4.5S rRNA of higher plants is associated with fragmentation of 23S rRNA progenitor. Notably, we also found the sequence of putative rrn5 promoter has some evolutionary implications within the order Saxifragales. Moreover, our phylogenetic analyses suggested that S. plumbizincicola had a closer relationship with S. sarmentosum than S. oryzifolium, and supported the taxonomic revision of Phedimus. Our findings of the present study will be useful for further investigation of the evolution of plastid rRNA operon and phylogenetic relationships within Saxifragales.
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Affiliation(s)
- Hengwu Ding
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China.
- The Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, Wuhu 241000, Anhui, China.
| | - Ran Zhu
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China.
| | - Jinxiu Dong
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China.
| | - De Bi
- National Engineering Laboratory of Soil Pollution Control and Remediation Technologies, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, Jiangsu, China.
| | - Lan Jiang
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China.
| | - Juhua Zeng
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China.
| | - Qingyu Huang
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China.
| | - Huan Liu
- National Engineering Laboratory of Soil Pollution Control and Remediation Technologies, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, Jiangsu, China.
| | - Wenzhong Xu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
| | - Longhua Wu
- National Engineering Laboratory of Soil Pollution Control and Remediation Technologies, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, Jiangsu, China.
| | - Xianzhao Kan
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China.
- The Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, Wuhu 241000, Anhui, China.
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Comparative and Phylogenetic Analyses of Ginger ( Zingiber officinale) in the Family Zingiberaceae Based on the Complete Chloroplast Genome. PLANTS 2019; 8:plants8080283. [PMID: 31409043 PMCID: PMC6724139 DOI: 10.3390/plants8080283] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 08/07/2019] [Accepted: 08/11/2019] [Indexed: 11/21/2022]
Abstract
Zingiber officinale, 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 Z. officinale and identified its phylogenetic position in Zingiberaceae. The chloroplast genome of Z. officinale 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 rps16-trnQ-UUG, atpH-atpI, trnT-UGU-trnL-UAA, ycf1, and psaC-ndhE. 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 Zingiber is a sister branch to Kaempferia species. The availability of the Z. officinale 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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