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Wachananawat B, Kong BL, Shaw P, Bongcheewin B, Sangvirotjanapat S, Prombutara P, Pornputtapong N, Sukrong S. Characterization and phylogenetic analysis of the complete chloroplast genome of Curcuma comosa and C. latifolia. Heliyon 2024; 10:e31248. [PMID: 38813184 PMCID: PMC11133819 DOI: 10.1016/j.heliyon.2024.e31248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 04/23/2024] [Accepted: 05/13/2024] [Indexed: 05/31/2024] Open
Abstract
Members of the Curcuma genus, a crop in the Zingiberaceae, are widely utilized rhizomatous herbs globally. There are two distinct species, C. comosa Roxb. and C. latifolia Roscoe, referred to the same vernacular name "Wan Chak Motluk" in Thai. C. comosa holds economic importance and is extensively used as a Thai traditional medicine due to its phytoestrogenic properties. However, its morphology closely resembles that of C. latifolia, which contains zederone, a compound known for its hepatotoxic effects. They are often confused, which may affect the quality, efficacy and safety of the derived herbal materials. Thus, DNA markers were developed for discriminating C. comosa from C. latifolia. This study focused on analyzing core DNA barcode regions, including rbcL, matK, psbA-trnH spacer and ITS2, of the authentic C. comosa and C. latifolia species. As a result, no variable nucleotides in core DNA barcode regions were observed. The complete chloroplast (cp) genome was introduced to differentiate between the two species. The comparison revealed that the cp genomes of C. comosa and C. latifolia were 162,272 and 162,289 bp, respectively, with a total of 133 identified genes. The phylogenetic analysis revealed that C. comosa and C. latifolia exhibited a very close relationship with other Curcuma species. The cp genome of C. comosa and C. latifolia were identified for the first time, providing valuable insights for species identification and evolutionary research within the Zingiberaceae family.
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Affiliation(s)
- Bussarin Wachananawat
- Center of Excellence in DNA Barcoding of Thai Medicinal Plants, Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Bobby Lim‐Ho Kong
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine and Institute of Chinese Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, N.T., China
| | - Pang‐Chui Shaw
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine and Institute of Chinese Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, N.T., China
| | - Bhanubong Bongcheewin
- Department of Pharmaceutical Botany, Faculty of Pharmacy and Center of Excellence in Herbal Medicine and Natural Products, Faculty of Pharmacy, Mahidol University, Bangkok, 10400, Thailand
- Sireeruckhachati Nature Learning Park, Mahidol University, Nakhon Pathom, 73170, Thailand
| | | | - Pinidphon Prombutara
- Faculty of Science, Omics Science & Bioinformatics Center, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Natapol Pornputtapong
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Suchada Sukrong
- Center of Excellence in DNA Barcoding of Thai Medicinal Plants, Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, 10330, Thailand
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Zhao M, Wu Y, Ren Y. Complete Chloroplast Genome Sequence Structure and Phylogenetic Analysis of Kohlrabi ( Brassica oleracea var. gongylodes L.). Genes (Basel) 2024; 15:550. [PMID: 38790180 PMCID: PMC11120933 DOI: 10.3390/genes15050550] [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: 04/04/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
Kohlrabi is an important swollen-stem cabbage variety belonging to the Brassicaceae family. However, few complete chloroplast genome sequences of this genus have been reported. Here, a complete chloroplast genome with a quadripartite cycle of 153,364 bp was obtained. A total of 132 genes were identified, including 87 protein-coding genes, 37 transfer RNA genes and eight ribosomal RNA genes. The base composition analysis showed that the overall GC content was 36.36% of the complete chloroplast genome sequence. Relative synonymous codon usage frequency (RSCU) analysis showed that most codons with values greater than 1 ended with A or U, while most codons with values less than 1 ended with C or G. Thirty-five scattered repeats were identified and most of them were distributed in the large single-copy (LSC) region. A total of 290 simple sequence repeats (SSRs) were found and 188 of them were distributed in the LSC region. Phylogenetic relationship analysis showed that five Brassica oleracea subspecies were clustered into one group and the kohlrabi chloroplast genome was closely related to that of B. oleracea var. botrytis. Our results provide a basis for understanding chloroplast-dependent metabolic studies and provide new insight for understanding the polyploidization of Brassicaceae species.
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Affiliation(s)
- Mengliang Zhao
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China;
| | - Yanxun Wu
- Qinghai Academy of Agriculture and Forestry Sciences, Xining 810016, China;
| | - Yanjing Ren
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China;
- Qinghai Academy of Agriculture and Forestry Sciences, Xining 810016, China;
- Laboratory of Research and Utilization of Germplasm Resources in Qinghai-Tibet Plateau, Xining 810016, China
- Qinghai Provincial Key Laboratory of Vegetable Genetics and Physiology, Xining 810016, China
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He S, Xu B, Chen S, Li G, Zhang J, Xu J, Wu H, Li X, Yang Z. Sequence characteristics, genetic diversity and phylogenetic analysis of the Cucurbita ficifolia (Cucurbitaceae) chloroplasts genome. BMC Genomics 2024; 25:384. [PMID: 38637729 PMCID: PMC11027378 DOI: 10.1186/s12864-024-10278-2] [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: 11/28/2023] [Accepted: 04/02/2024] [Indexed: 04/20/2024] Open
Abstract
BACKGROUND Curcubita ficifolia Bouché (Cucurbitaceae) has high value as a food crop and medicinal plant, and also has horticultural value as rootstock for other melon species. China is home to many different cultivars, but the genetic diversity of these resources and the evolutionary relationships among them, as well as the differences between C. ficifolia and other Cucurbita species, remain unclear. RESULTS We investigated the chloroplast (cp) genomes of 160 C. ficifolia individuals from 31 populations in Yunnan, a major C. ficifolia production area in China. We found that the cp genome of C. ficifolia is ~151 kb and contains 128 genes, of which 86 are protein coding genes, 34 encode tRNA, and eight encode rRNAs. We also identified 64 SSRs, mainly AT repeats. The cp genome was found to contain a total of 204 SNP and 57 indels, and a total of 21 haplotypes were found in the 160 study individuals. The reverse repeat (IR) region of C. ficifolia contained a few differences compared with this region in the six other Cucurbita species. Sequence difference analysis demonstrated that most of the variable regions were concentrated in the single copy (SC) region. Moreover, the sequences of the coding regions were found to be more similar among species than those of the non-coding regions. The phylogenies reconstructed from the cp genomes of 61 representative species of Cucurbitaceae reflected the currently accepted classification, in which C. ficifolia is sister to the other Cucurbita species, however, different interspecific relationships were found between Cucurbita species. CONCLUSIONS These results will be valuable in the classification of C. ficifolia genetic resources and will contribute to our understanding of evolutionary relationships within the genus Cucurbita.
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Affiliation(s)
- Shuilian He
- College of Landscape and Horticulture, Yunnan Agricultural University, 650201, Kunming, Yunnan, China
- Key Laboratory of Vegetable Biology of Yunnan Province, College of Landscape and Horticulture, Yunnan Agricultural University, 650201, Kunming, Yunnan, China
| | - Bin Xu
- College of Landscape and Horticulture, Yunnan Agricultural University, 650201, Kunming, Yunnan, China
| | - Siyun Chen
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, China
| | - Gengyun Li
- College of Landscape and Horticulture, Yunnan Agricultural University, 650201, Kunming, Yunnan, China
| | - Jie Zhang
- College of Landscape and Horticulture, Yunnan Agricultural University, 650201, Kunming, Yunnan, China
| | - Junqiang Xu
- College of Landscape and Horticulture, Yunnan Agricultural University, 650201, Kunming, Yunnan, China
| | - Hang Wu
- College of Landscape and Horticulture, Yunnan Agricultural University, 650201, Kunming, Yunnan, China
| | - Xuejiao Li
- College of Landscape and Horticulture, Yunnan Agricultural University, 650201, Kunming, Yunnan, China.
| | - Zhengan Yang
- College of Landscape and Horticulture, Yunnan Agricultural University, 650201, Kunming, Yunnan, China.
- Key Laboratory of Vegetable Biology of Yunnan Province, College of Landscape and Horticulture, Yunnan Agricultural University, 650201, Kunming, Yunnan, China.
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Lubna, Asaf S, Jan R, Asif S, Bilal S, Khan AL, Kim KM, Lee IJ, Al-Harrasi A. Plastome diversity and evolution in mosses: Insights from structural characterization, comparative genomics, and phylogenetic analysis. Int J Biol Macromol 2024; 257:128608. [PMID: 38065441 DOI: 10.1016/j.ijbiomac.2023.128608] [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: 05/08/2023] [Revised: 11/09/2023] [Accepted: 11/27/2023] [Indexed: 01/27/2024]
Abstract
Mosses play a significant role in ecology, evolution, and the economy. They belong to the nonvascular plant kingdom and are considered the closest living relatives of the first terrestrial plants. The circular chloroplast DNA molecules (plastomes) of mosses contain all the genetic information essential for chloroplast functions and represent the source of the evolutionary history of these organisms. This study comprehensively analyzed the plastomes of 47 moss species belonging to 14 orders, focusing on their size, GC content, gene loss, gene content, synteny, and evolution. The findings revealed great differences among plastome sizes, with Takakia lepidozioides (Takakiopsida) and Funaria hygrometrica (Funariales) having the largest and smallest plastomes, respectively. Moss plastomes included 69 to 89 protein-coding genes, 8 rRNA genes, and 34 to 42 tRNA genes, resulting in the total number of genes in a plastome ranging between 115 and 138. Various genes have been lost from the plastomes of different moss species, with Atrichum angustatum lacking the highest number of genes. This study also examined plastome synteny and moss evolution using comparative genomics and repeat sequence analysis. The results demonstrated that synteny and similarity levels varied across the 47 moss examined species, with some exhibiting structure similarity and others displaying structural inversions. Maximum likelihood and Bayesian approaches were used to construct a phylogenetic tree using 36 concatenated protein-coding genes, and the results revealed that the genera Sphagnum and Takakia are sister groups to the other mosses. Additionally, it was found that Tetraphidales, Polytrichales, Buxbaumiales, and Diphysciales are closely related. This research describes the evolutionary diversity of mosses and offers guidelines for future studies in this field. The findings also highlight the need for more investigations into the factors regulating plastome size variation in these plants.
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Affiliation(s)
- Lubna
- Natural and Medical Science Research Center, University of Nizwa, 616 Nizwa, Oman
| | - Sajjad Asaf
- Natural and Medical Science Research Center, University of Nizwa, 616 Nizwa, Oman.
| | - Rahmatullah Jan
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Saleem Asif
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Saqib Bilal
- Natural and Medical Science Research Center, University of Nizwa, 616 Nizwa, Oman
| | - Abdul Latif Khan
- Department of Engineering Technology, University of Houston, Sugar Land, TX, 77479, USA
| | - Kyung-Min Kim
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - In-Jung Lee
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea.
| | - Ahmed Al-Harrasi
- Natural and Medical Science Research Center, University of Nizwa, 616 Nizwa, Oman.
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Huang L, Lu Z, Wang J, Bao H, Zhang H, Jiang M. Complete chloroplast genome of Tricyrtis xianjuensis Li, Chen & Ma 2014 (Liliaceae): a species endemic to Zhejiang province, China. Mitochondrial DNA B Resour 2024; 9:60-65. [PMID: 38197054 PMCID: PMC10776049 DOI: 10.1080/23802359.2023.2301021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 12/27/2023] [Indexed: 01/11/2024] Open
Abstract
Tricyrtis xianjuensis Li, Chen & Ma 2014 is a rare and endangered species endemic to Zhejiang province, with fewer than 200 individuals in the wild. In our present study, the complete chloroplast genome of T. xianjuensis was assembled by using high-throughput sequencing data, and its genomic features were described and comparative genomic analyses within Liliaceae family were performed. The complete chloroplast genome of T. xianjuensis was 155,748 bp in length, exhibiting a GC content of 37.3%. This genome structure contained two inverted repeats (IRs), as well as a small single-copy (SSC) and a large single-copy (LSC) region. The IR region measured 26,371 bp, while the SSC and LSC regions were 17,729 bp and 85,277 bp in length, respectively. A total of 137 genes were identified, including 85 protein-coding genes, 38 tRNA genes, eight rRNA genes, and six pseudogenes. Phylogenic analysis revealed T. xianjuensis shared a clade with T. formosana Baker 1879 and T. macropoda Miq. 1867, with a support rate of 100%. The assembly and analysis of T. xianjuensis chloroplast genome provided an insight into further studies on the conservation genetics of this endangered species.
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Affiliation(s)
- Leqin Huang
- College of Life Sciences, Taizhou University, Taizhou, China
| | - Zhenyu Lu
- College of Life Sciences, Taizhou University, Taizhou, China
| | - Junfeng Wang
- Scientific Research Management Center, East China Medicinal Botanical Garden, Lishui, China
| | - Honghua Bao
- Taizhou Municipal Ecology and Environment Bureau, Taizhou, China
| | - Huijuan Zhang
- College of Life Sciences, Taizhou University, Taizhou, China
| | - Ming Jiang
- College of Life Sciences, Taizhou University, Taizhou, China
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Yan M, Dong S, Gong Q, Xu Q, Ge Y. Comparative chloroplast genome analysis of four Polygonatum species insights into DNA barcoding, evolution, and phylogeny. Sci Rep 2023; 13:16495. [PMID: 37779129 PMCID: PMC10543443 DOI: 10.1038/s41598-023-43638-1] [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: 02/28/2023] [Accepted: 09/26/2023] [Indexed: 10/03/2023] Open
Abstract
The Polygonatum genus represents a perennial herb with the Liliaceae family, boasting substantial economic and medicinal significance. The majority of Polygonatum plants exhibit notable similarity while lacking distinctive identifying characteristics, thus resulting in the proliferation of adulterated medicinal materials within the market. Within this study, we conducted an in-depth analysis of the complete chloroplast (cp) genomes of four Polygonatum plants and compared them with four closely akin species. The primary objectives were to unveil structural variations, species divergence, and the phylogenetic interrelations among taxa. The cp genomes of the four Polygonatum species were typified by a conventional quadripartite structure, incorporating a large single copy region (LSC), a small single copy region (SSC), and a pair of inverted repeat regions. In total, we annotated a range of 131 to 133 genes, encompassing 84 to 86 protein-coding genes, 38 transfer RNA (tRNA) genes, 8 ribosomal RNA (rRNA) genes, and 0 to 2 pseudogenes (ycf1, infA). Our comparative analyses unequivocally revealed a remarkable consistency in gene order and GC content within the Polygonatum genus. Furthermore, we predicted a potential 59 to 64 RNA editing sites distributed across 22 protein-coding genes, with the ndhB gene exhibiting the most prominent propensity for RNA editing sites, boasting a tally of 15 sites. Notably, six regions of substantial potential variability were ascertained, characterized by elevated Pi values. Noteworthy, molecular markers for species identification, population genetic scrutiny, and phylogenetic investigations within the genus were identified in the form of the psaJ-rpl33 and trnS + trnT-psaD barcodes. The resultant phylogenetic tree unequivocally depicted the formation of a monophyletic clade comprising species within the evolutionary framework of Liliaceae, demonstrating closer evolutionary affinities with Maianthemum, Dracaeneae, and Asparageae. This comprehensive compendium of findings collectively contributes to the advancement of molecular species identification, elucidation of phylogenetic interrelationships, and the establishment of DNA barcodes tailored to the Polygonatum species.
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Affiliation(s)
- Meixiu Yan
- The First Affiliated Hospital of Zhejiang Chinese Medical University, 54 Youdian Road, Hangzhou, Zhejiang Province, People's Republic of China
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
| | - Shujie Dong
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
| | - Qiuyi Gong
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
| | - Qin Xu
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
| | - Yuqing Ge
- The First Affiliated Hospital of Zhejiang Chinese Medical University, 54 Youdian Road, Hangzhou, Zhejiang Province, People's Republic of China.
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Kurt S, Kaymaz Y, Ateş D, Tanyolaç MB. Complete chloroplast genome of Lens lamottei reveals intraspecies variation among with Lens culinaris. Sci Rep 2023; 13:14959. [PMID: 37696838 PMCID: PMC10495401 DOI: 10.1038/s41598-023-41287-y] [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: 05/28/2023] [Accepted: 08/24/2023] [Indexed: 09/13/2023] Open
Abstract
Lens lamottei is a member of the Fabaceae family and the second gene pool of the genus Lens. The environmental factors that drove the divergence among wild and cultivated species have been studied extensively. Recent research has focused on genomic signatures associated with various phenotypes with the acceleration of next-generation techniques in molecular profiling. Therefore, in this study, we provide the complete sequence of the chloroplast genome sequence in the wild Lens species L. lamottei with a deep coverage of 713 × next-generation sequencing (NGS) data for the first time. Compared to the cultivated species, Lens culinaris, we identified synonymous, and nonsynonymous changes in the protein-coding regions of the genes ndhB, ndhF, ndhH, petA, rpoA, rpoC2, rps3, and ycf2 in L. lamottei. Phylogenetic analysis of chloroplast genomes of various plants under Leguminosae revealed that L. lamottei and L. culinaris are closest to one another than to other species. The complete chloroplast genome of L. lamottei also allowed us to reanalyze previously published transcriptomic data, which showed high levels of gene expression for ATP-synthase, rubisco, and photosystem genes. Overall, this study provides a deeper insight into the diversity of Lens species and the agricultural importance of these plants through their chloroplast genomes.
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Affiliation(s)
- Selda Kurt
- Faculty of Engineering, Department of Bioengineering, Ege University, Izmir, Turkey
| | - Yasin Kaymaz
- Faculty of Engineering, Department of Bioengineering, Ege University, Izmir, Turkey
| | - Duygu Ateş
- Faculty of Engineering, Department of Bioengineering, Ege University, Izmir, Turkey
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Waswa EN, Mkala EM, Odago WO, Amenu SG, Mutinda ES, Muthui SW, Ding SX, Hu GW, Wang QF. Comparative chloroplast genome analysis of Sambucus L. (Viburnaceae): inference for phylogenetic relationships among the closely related Sambucus adnata Wall. ex DC Sambucus javanica Blume. FRONTIERS IN PLANT SCIENCE 2023; 14:1179510. [PMID: 37396648 PMCID: PMC10313135 DOI: 10.3389/fpls.2023.1179510] [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: 03/04/2023] [Accepted: 05/31/2023] [Indexed: 07/04/2023]
Abstract
Sambucus L. is found in the family Viburnaceae (syn. Adoxaceae) and encompasses approximately 29 accepted species. The complex morphology of these species has caused continued confusion concerning their nomenclature, classification, and identification. Despite previous attempts to resolve taxonomic complexities in the Sambucus genus, there are still unclear phylogenetic relationships among several species. In this study, the newly obtained plastome of Sambucus williamsii Hance. as well as the populations of Sambucus canadensis L., Sambucus javanica Blume, and Sambucus adnata Wall. ex DC were sequenced, and their sizes, structural similarity, gene order, gene number, and guanine-cytosine (GC) contents were analyzed. The phylogenetic analyses were conducted using the whole chloroplast genomes and protein-coding genes (PCGs). The findings revealed that the chloroplast genomes of Sambucus species exhibited typical quadripartite double-stranded DNA molecules. Their lengths ranged from 158,012 base pairs (bp) (S. javanica) to 158,716 bp (S. canadensis L). Each genome comprised a pair of inverted repeats (IRs), which separated the large single-copy (LSC) and small single-copy (SSC) regions. In addition, the plastomes contained 132 genes, encompassing 87 protein-coding, 37 tRNA, and four rRNA genes. In the simple sequence repeat (SSR) analysis, A/T mononucleotides had the highest proportion, with the most repetitive sequences observed in S. williamsii. The comparative genome analyses showed high similarities in structure, order, and gene contents. The hypervariable regions in the studied chloroplast genomes were trnT-GGU, trnF-GAA, psaJ, trnL-UAG, ndhF, and ndhE, which may be used as candidate barcodes for species discrimination in Sambucus genus. Phylogenetic analyses supported the monophyly of Sambucus and revealed the separation of S. javanica and S. adnata populations. Sambucus chinensis Lindl. was nested within S. javanica in the same clade, collaborating their conspecific treatment. These outcomes indicate that the chloroplast genome of Sambucus plants is a valuable genetic resource for resolving taxonomic discrepancies at the lower taxonomic levels and can be applied in molecular evolutionary studies.
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Affiliation(s)
- Emmanuel Nyongesa Waswa
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- Botany Department, University of Chinese Academy of Sciences, Beijing, China
| | - Elijah Mbandi Mkala
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- Botany Department, University of Chinese Academy of Sciences, Beijing, China
| | - Wyclif Ochieng Odago
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- Botany Department, University of Chinese Academy of Sciences, Beijing, China
| | - Sara Getachew Amenu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- Botany Department, University of Chinese Academy of Sciences, Beijing, China
| | - Elizabeth Syowai Mutinda
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- Botany Department, University of Chinese Academy of Sciences, Beijing, China
| | - Samuel Wamburu Muthui
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- Botany Department, University of Chinese Academy of Sciences, Beijing, China
| | - Shi-Xiong Ding
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- Botany Department, University of Chinese Academy of Sciences, Beijing, China
| | - Guang-Wan Hu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- Botany Department, University of Chinese Academy of Sciences, Beijing, China
| | - Qing-Feng Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- Botany Department, University of Chinese Academy of Sciences, Beijing, China
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Waswa EN, Mkala EM, Odago WO, Amenu SG, Mutinda ES, Muthui SW, Ding SX, Hu GW, Wang QF. Comparative chloroplast genome analysis of Sambucus L. (Viburnaceae): inference for phylogenetic relationships among the closely related Sambucus adnata Wall. ex DC Sambucus javanica Blume. FRONTIERS IN PLANT SCIENCE 2023; 14. [DOI: https:/doi.org/10.3389/fpls.2023.1179510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Sambucus L. is found in the family Viburnaceae (syn. Adoxaceae) and encompasses approximately 29 accepted species. The complex morphology of these species has caused continued confusion concerning their nomenclature, classification, and identification. Despite previous attempts to resolve taxonomic complexities in the Sambucus genus, there are still unclear phylogenetic relationships among several species. In this study, the newly obtained plastome of Sambucus williamsii Hance. as well as the populations of Sambucus canadensis L., Sambucus javanica Blume, and Sambucus adnata Wall. ex DC were sequenced, and their sizes, structural similarity, gene order, gene number, and guanine–cytosine (GC) contents were analyzed. The phylogenetic analyses were conducted using the whole chloroplast genomes and protein-coding genes (PCGs). The findings revealed that the chloroplast genomes of Sambucus species exhibited typical quadripartite double-stranded DNA molecules. Their lengths ranged from 158,012 base pairs (bp) (S. javanica) to 158,716 bp (S. canadensis L). Each genome comprised a pair of inverted repeats (IRs), which separated the large single-copy (LSC) and small single-copy (SSC) regions. In addition, the plastomes contained 132 genes, encompassing 87 protein-coding, 37 tRNA, and four rRNA genes. In the simple sequence repeat (SSR) analysis, A/T mononucleotides had the highest proportion, with the most repetitive sequences observed in S. williamsii. The comparative genome analyses showed high similarities in structure, order, and gene contents. The hypervariable regions in the studied chloroplast genomes were trnT-GGU, trnF-GAA, psaJ, trnL-UAG, ndhF, and ndhE, which may be used as candidate barcodes for species discrimination in Sambucus genus. Phylogenetic analyses supported the monophyly of Sambucus and revealed the separation of S. javanica and S. adnata populations. Sambucus chinensis Lindl. was nested within S. javanica in the same clade, collaborating their conspecific treatment. These outcomes indicate that the chloroplast genome of Sambucus plants is a valuable genetic resource for resolving taxonomic discrepancies at the lower taxonomic levels and can be applied in molecular evolutionary studies.
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Senapati A, Chetri BK, Mitra S, Shelke RG, Rangan L. Decoding the complete chloroplast genome of Cissus quadrangularis: insights into molecular structure, comparative genome analysis and mining of mutational hotspot regions. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:709-724. [PMID: 37363414 PMCID: PMC10284753 DOI: 10.1007/s12298-023-01312-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/25/2023] [Accepted: 04/24/2023] [Indexed: 06/28/2023]
Abstract
Cissus quadrangularis L., a member of the Vitaceae family, is an important medicinal plant with widespread application in Indian traditional medicines. C. quadrangularis L. whole chloroplast genome of 160,404 bp was assembled using a genome skimming approach from the whole genome library. The assembled chloroplast genome contained a large single-copy region (88,987 bp), a small single-copy region (18,621 bp), and pairs of inverted repeat regions (26,398 bp). It also comprised 133 genes, including 37 tRNAs, eight rRNAs, and 88 protein-coding genes. Aside from that, we annotated three genes atpH, petB, and psbL, as well as one duplicated copy of the ycf1 gene in C. quadrangularis L. that had previously been missing from the annotation of compared Cissus chloroplast genomes. Five divergent hotspot regions such as petA_psbJ (0.1237), rps16_trnQ-UUG (0.0913), psbC_trnS-UGA (0.0847), rps15_ycf1 (0.0788), and rps2_rpoC2 (0.0788) were identified in the investigation that could aid in future species discrimination. Surprisingly, we found the overlapping genes ycf1 and ndhF on the IRb/SSC junction, rarely seen in angiosperms. The results of the phylogenetic study showed that the genomes of the Cissus species under study formed a single distinct clade. The detailed annotations given in this study could be useful in the future for genome annotations of Cissus species. The current findings of the study have the potential to serve as a useful resource for future research in the field of population genetics and the evolutionary relationships in the Cissus genus. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01312-w.
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Affiliation(s)
- Alok Senapati
- Applied Biodiversity Laboratory, O Block, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039 India
| | - Bimal K. Chetri
- School of Agro and Rural Technology, Indian Institute of Technology Guwahati, Guwahati, Assam 781039 India
| | - Sudip Mitra
- School of Agro and Rural Technology, Indian Institute of Technology Guwahati, Guwahati, Assam 781039 India
| | - Rahul G. Shelke
- Applied Biodiversity Laboratory, O Block, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039 India
| | - Latha Rangan
- Applied Biodiversity Laboratory, O Block, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039 India
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Xu Y, Liu Y, Yu Z, Jia X. Complete Chloroplast Genome Sequence of the Long Blooming Cultivar Camellia 'Xiari Qixin': Genome Features, Comparative and Phylogenetic Analysis. Genes (Basel) 2023; 14:460. [PMID: 36833387 PMCID: PMC9956581 DOI: 10.3390/genes14020460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/07/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
The camellia flower is a famous woody plant with a long-cultivated history and high ornamental value. It is extensively planted and utilized around the world and owns a massive germplasm resource. Camellia 'Xiari Qixin' belongs to one of the typical cultivars in the four seasons camellia hybrids series. Due to its long flowering period, this kind of cultivar is identified as a precious resource of camellia flowers. In this study, the complete chloroplast genome sequence of C. 'Xiari Qixin' was first reported. Its whole chloroplast genome is 157,039 bp in length with an overall GC content of 37.30%, composed of a large single copy region (LSC, 86,674 bp), a small single copy region (SSC, 18,281 bp), and a pair of inverted repeat regions (IRs, 26,042 bp each). A total of 134 genes were predicted in this genome, including 8 ribosomal RNA genes, 37 transfer RNA genes, and 89 protein-coding genes. In addition, 50 simple sequence repeats (SSRs) and 36 long repeat sequences were detected. By comparing C. 'Xiari Qixin' and seven Camellia species on the chloroplast genome, seven mutation hotspot regions were identified, including psbK, trnS (GCU)-trnG(GCC), trnG(GCC), petN-psbM, trnF(GAA)-ndhJ, trnP(UGG)-psaJ, and ycf1. Phylogenetic analysis of 30 chloroplast genomes showed that the genetic relationship between C. 'Xiari Qixin' and Camellia azalea is quite close in evolution. These results could not only provide a valuable database for determining the maternal origin of Camellia cultivars, but also contribute to the exploration of the phylogenetic relationship and utilization of germplasm resources for Camellia.
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Affiliation(s)
| | | | | | - Xiaocheng Jia
- Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
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Koo H, Shin AY, Hong S, Kim YM. The complete chloroplast genome of Hibiscus syriacus using long-read sequencing: Comparative analysis to examine the evolution of the tribe Hibisceae. FRONTIERS IN PLANT SCIENCE 2023; 14:1111968. [PMID: 36818825 PMCID: PMC9931742 DOI: 10.3389/fpls.2023.1111968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
Hibiscus syriacus, a member of the tribe Hibisceae, is considered an important ornamental and medicinal plant in east Asian countries. Here, we sequenced and assembled the complete chloroplast genome of H. syriacus var. Baekdansim using the PacBio long-read sequencing platform. A quadripartite structure with 161,026 base pairs was obtained, consisting of a pair of inverted repeats (IRA and IRB) with 25,745 base pairs, separated by a large single-copy region of 89,705 base pairs and a short single-copy region of 19,831 base pairs. This chloroplast genome had 79 protein-coding genes, 30 transfer RNA genes, 4 ribosomal RNA genes, and 109 simple sequence repeat regions. Among them, ndhD and rpoC1, containing traces of RNA-editing events associated with adaptive evolution, were identified by analysis of putative RNA-editing sites. Codon usage analysis revealed a preference for A/U-terminated codons. Furthermore, the codon usage pattern had a clustering tendency similar to that of the phylogenetic analysis of the tribe Hibisceae. This study provides clues for understanding the relationships and refining the taxonomy of the tribe Hibisceae.
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Affiliation(s)
- Hyunjin Koo
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Ah-Young Shin
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Bioinformatics, Korea Research Institute of Bioscience and Biotechnology (KRIBB) School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Seongmin Hong
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Yong-Min Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Bioinformatics, Korea Research Institute of Bioscience and Biotechnology (KRIBB) School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
- Digital Biotech Innovation Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
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Distinctive origin and evolution of endemic thistle of Korean volcanic island: Structural organization and phylogenetic relationships with complete chloroplast genome. PLoS One 2023; 18:e0277471. [PMID: 36913349 PMCID: PMC10010555 DOI: 10.1371/journal.pone.0277471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/28/2022] [Indexed: 03/14/2023] Open
Abstract
Unlike other Cirsium in Korea, Cirsium nipponicum (Island thistle) is distributed only on Ulleung Island, a volcanic island off the east coast of the Korean Peninsula, and a unique thistle with none or very small thorns. Although many researchers have questioned the origin and evolution of C. nipponicum, there is not much genomic information to estimate it. We thus assembled the complete chloroplast of C. nipponicum and reconstructed the phylogenetic relationships within the genus Cirsium. The chloroplast genome was 152,586 bp, encoding 133 genes consisting of 8 rRNA genes, 37 tRNA genes, and 88 protein-coding genes. We found 833 polymorphic sites and eight highly variable regions in chloroplast genomes of six Cirsium species by calculating nucleotide diversity, as well as 18 specific variable regions distinguished C. nipponicum from other Cirsium. As a result of phylogenetic analysis, C. nipponicum was closer to C. arvense and C. vulgare than native Cirsium in Korea: C. rhinoceros and C. japonicum. These results indicate that C. nipponicum is likely introduced through the north Eurasian root, not the mainland, and evolved independently in Ulleung Island. This study contributes to further understanding the evolutionary process and the biodiversity conservation of C. nipponicum on Ulleung Island.
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Yaradua SS, Yessoufou K. The Complete Chloroplast Genome of Hypoestes forskaolii (Vahl) R.Br: Insights into Comparative and Phylogenetic Analyses within the Tribe Justiceae. Genes (Basel) 2022; 13:genes13122259. [PMID: 36553525 PMCID: PMC9778027 DOI: 10.3390/genes13122259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 12/02/2022] Open
Abstract
Hypoestes forskaolii is one of the most important species of the family Acanthaceae, known for its high economic and medicinal importance. It is well distributed in the Arab region as well as on the African continent. Previous studies on ethnomedicine have reported that H. forskaolii has an anti-parasitic effect as well as antimalarial and anthelmintic activities. Previous studies mainly focused on the ethnomedicinal properties, hence, there is no information on the genomic architecture and phylogenetic positions of the species within the tribe Justiceae. The tribe Justicieae is the most taxonomically difficult taxon in Acanthoideae due to its unresolved infratribal classification. Therefore, by sequencing the complete chloroplast genome (cp genome) of H. forskaolii, we explored the evolutionary patterns of the cp genome and reconstructed the phylogeny of Justiceae. The cp genome is quadripartite and circular in structure and has a length of 151,142 bp. There are 130 genes (86 coding for protein, 36 coding for tRNA and 8 coding for rRNA) present in the plastome. Analyses of long repeats showed only three types of repeats: forward, palindromic and reverse were present in the genome. Microsatellites analysis revealed 134 microsatellites in the cp genome with mononucleotides having the highest frequency. Comparative analyses within Justiceae showed that genomes structure and gene contents were highly conserved but there is a slight distinction in the location of the genes in the inverted repeat and single copy junctions. Additionally, it was discovered that the cp genome includes variable hotspots that can be utilized as DNA barcodes and tools for determining evolutionary relationships in the Justiceae. These regions include: atpH-atpI, trnK-rps16, atpB-rbcL, trnT-trnL, psbI-trnS, matK, trnH-psbA, and ndhD. The Bayesian inference phylogenetic tree showed that H. forskaolii is a sister to the Dicliptra clade and belongs to Diclipterinae. The result also confirms the polyphyly of Justicia and inclusion of Diclipterinae within justicioid. This research has revealed the phylogenetic position of H. forskaolii and also reported the resources that can be used for evolutionary and phylogenetic studies of the species and the Justicieae.
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Affiliation(s)
- Samaila Samaila Yaradua
- Department of Geography, Environmental Management and Energy Studies, APK Campus, University of Johannesburg, Johannesburg 2006, South Africa
- Department of Biology, Umaru Musa Yaradua University, Katsina 820102, Nigeria
- Correspondence:
| | - Kowiyou Yessoufou
- Department of Geography, Environmental Management and Energy Studies, APK Campus, University of Johannesburg, Johannesburg 2006, South Africa
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AL-Juhani WS, Alharbi SA, Al Aboud NM, Aljohani AY. Complete chloroplast genome of the desert date (Balanites aegyptiaca (L.) Del. comparative analysis, and phylogenetic relationships among the members of Zygophyllaceae. BMC Genomics 2022; 23:626. [PMID: 36045328 PMCID: PMC9434970 DOI: 10.1186/s12864-022-08850-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 08/18/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Balanites aegyptiaca (L.) Delile, commonly known as desert date, is a thorny evergreen tree belonging to the family Zygophyllaceae and subfamily Tribuloideae that is widespread in arid and semiarid regions. This plant is an important source of food and medicines and plays an important role in conservation strategies for restoring degraded desert ecosystems.
Results
In the present study, we sequenced the complete plastome of B. aegyptiaca. The chloroplast genome was 155,800 bp, with a typical four-region structure: a large single copy (LSC) region of 86,562 bp, a small single copy (SSC) region of 18,102 bp, and inverted repeat regions (IRa and IRb) of 25,568 bp each. The GC content was 35.5%. The chloroplast genome of B. aegyptiaca contains 107 genes, 75 of which coding proteins, 28 coding tRNA, and 4 coding rRNA.
We did not observe a large loss in plastid genes or a reduction in the genome size in B. aegyptiaca, as found previously in some species belonging to the family Zygophyllaceae. However, we noticed a divergence in the location of certain genes at the IR-LSC and IR-SSC boundaries and loss of ndh genes relative to other species. Furthermore, the phylogenetic tree constructed from the complete chloroplast genome data broadly supported the taxonomic classification of B. aegyptiaca as belonging to the Zygophyllaceae family. The plastome of B. aegyptiaca was found to be rich in single sequence repeats (SSRs), with a total of 240 SSRs.
Conclusions
The genomic data available from this study could be useful for developing molecular markers to evaluate population structure, investigate genetic variation, and improve production programs for B. aegyptiaca. Furthermore, the current data will support future investigation of the evolution of the family Zygophyllaceae.
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Zhang L, Zhang Y, Jia Y, Ding F, Wang F, Yu G, Wu Y. Characterization of the complete chloroplast genome of Clematoclethra scandens subsp. actinidioides (Actinidiaceae). Mitochondrial DNA B Resour 2022; 7:1548-1549. [PMID: 36081829 PMCID: PMC9448431 DOI: 10.1080/23802359.2022.2110532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Clematoclethra scandens subsp. actinidioides (Actinidiaceae) is an endemic medicinal species in China. Here, we first sequenced and characterized the complete chloroplast genome of C. scandens subsp. actinidioides. The chloroplast genome was 159,341 bp in length, containing a large single-copy of 88,351 bp and a small single-copy of 21,580 bp separated by a pair of identical inverted repeat regions of 24,705 bp each. A total of 131 genes were identified, including 84 protein-coding genes, 39 tRNA, and eight rRNA genes. The phylogenetic analysis of C. scandens subsp. actinidioides showed a relatively close relationship with Clematoclethra scandens subsp. hemsleyi.
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Affiliation(s)
- Lei Zhang
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi’an, China
- Xi’an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), Xi’an, China
| | - Ying Zhang
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi’an, China
- Xi’an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), Xi’an, China
| | - Yun Jia
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi’an, China
- Xi’an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), Xi’an, China
| | - Fangbing Ding
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi’an, China
- Xi’an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), Xi’an, China
| | - Fengwei Wang
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi’an, China
- Xi’an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), Xi’an, China
| | - Gang Yu
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi’an, China
- Xi’an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), Xi’an, China
| | - Yongpeng Wu
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi’an, China
- Xi’an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), Xi’an, China
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Complete chloroplast genome of the medicinal plant Cleome paradoxa R.Br. ex DC: Comparative Analysis, and Phylogenetic Relationships among the members of Cleomaceae. Gene 2022; 845:146851. [DOI: 10.1016/j.gene.2022.146851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 08/21/2022] [Accepted: 08/25/2022] [Indexed: 11/21/2022]
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Gene Losses and Plastome Degradation in the Hemiparasitic Species Plicosepalus acaciae and Plicosepalus curviflorus: Comparative Analyses and Phylogenetic Relationships among Santalales Members. PLANTS 2022; 11:plants11141869. [PMID: 35890506 PMCID: PMC9317152 DOI: 10.3390/plants11141869] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 06/18/2022] [Accepted: 07/07/2022] [Indexed: 11/22/2022]
Abstract
The Plicosepalus genus includes hemiparasitic mistletoe and belongs to the Loranthaceae family, and it has several medicinal uses. In the present study, we sequenced the complete plastomes of two species, Plicosepalus acaciae and Plicosepalus curviflorus, and compared them with the plastomes of photosynthetic species (hemiparasites) and nonphotosynthetic species (holoparasites) in the order Santalales. The complete chloroplast genomes of P. acaciae and P. curviflorus are circular molecules with lengths of 120,181 bp and 121,086 bp, respectively, containing 106 and 108 genes and 63 protein-coding genes, including 25 tRNA and 4 rRNA genes for each species. We observed a reduction in the genome size of P. acaciae and P. curviflorus and the loss of certain genes, although this reduction was less than that in the hemiparasite and holoparasitic cp genomes of the Santalales order. Phylogenetic analysis supported the taxonomic state of P. acaciae and P. curviflorus as members of the family Loranthaceae and tribe Lorantheae; however, the taxonomic status of certain tribes of Loranthaceae must be reconsidered and the species that belong to it must be verified. Furthermore, available chloroplast genome data of parasitic plants could help to strengthen efforts in weed management and encourage biotechnology research to improve host resistance.
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Comparative analysis of chloroplast genomes reveals phylogenetic relationships and intraspecific variation in the medicinal plant Isodon rubescens. PLoS One 2022; 17:e0266546. [PMID: 35385539 PMCID: PMC8985940 DOI: 10.1371/journal.pone.0266546] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 03/22/2022] [Indexed: 11/20/2022] Open
Abstract
Isodon rubescens (Hemsley) H. Hara (Lamiaceae) is a traditional Chinese medicine plant that has been used to treat various human diseases and conditions such as inflammation, respiratory and gastrointestinal bacterial infections, and malignant tumors. However, the contents of the main active components of I. rubescens from different origins differ significantly, which greatly affected its quality. Therefore, a molecular method to identify and classify I. rubescens is needed. Here, we report the DNA sequence of the chloroplast genome of I. rubescens collected from Lushan, Henan province. The genome is 152,642 bp in length and has a conserved structure that includes a pair of IR regions (25,726 bp), a LSC region (83,527 bp) and a SSC region (17,663 bp). The chloroplast genome contains 113 unique genes, four rRNA genes, 30 tRNA genes, and 79 protein-coding genes, 23 of which contain introns. The protein-coding genes account for a total of 24,412 codons, and most of them are A/T biased usage. We identified 32 simple sequence repeats (SSRs) and 48 long repeats. Furthermore, we developed valuable chloroplast molecular resources by comparing chloroplast genomes from three Isodon species, and both mVISTA and DnaSP analyses showed that rps16-trnQ, trnS-trnG, and ndhC-trnM are candidate regions that will allow the identification of intraspecific differences within I. rubescens. Also 14 candidate fragments can be used to identify interspecific differences between species in Isodon. A phylogenetic analysis of the complete chloroplast genomes of 24 species in subfamily Nepetoideae was performed using the maximum likelihood method, and shows that I. rubescens clustered closer to I. serra than I. lophanthoides. Interestingly, our analysis showed that I. rubescens (MW018469.1) from Xianyang, Shaanxi Province (IR-X), is closer to I. serra than to the other two I. rubescens accessions. These results strongly indicate that intraspecific diversity is present in I. rubescens. Therefore, our results provide further insight into the phylogenetic relationships and interspecific diversity of species in the genus Isodon.
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He X, Dong S, Gao C, Wang Q, Zhou M, Cheng R. The complete chloroplast genome of Carpesium abrotanoides L. (Asteraceae): structural organization, comparative analysis, mutational hotspots and phylogenetic implications within the tribe Inuleae. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01038-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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21
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Zhang Z, Tao M, Shan X, Pan Y, Sun C, Song L, Pei X, Jing Z, Dai Z. Characterization of the complete chloroplast genome of Brassica oleracea var. italica and phylogenetic relationships in Brassicaceae. PLoS One 2022; 17:e0263310. [PMID: 35202392 PMCID: PMC8870505 DOI: 10.1371/journal.pone.0263310] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 01/18/2022] [Indexed: 11/23/2022] Open
Abstract
Broccoli (Brassica oleracea var. italica) is an important B. oleracea cultivar, with high economic and agronomic value. However, comparative genome analyses are still needed to clarify variation among cultivars and phylogenetic relationships within the family Brassicaceae. Herein, the complete chloroplast (cp) genome of broccoli was generated by Illumina sequencing platform to provide basic information for genetic studies and to establish phylogenetic relationships within Brassicaceae. The whole genome was 153,364 bp, including two inverted repeat (IR) regions of 26,197 bp each, separated by a small single copy (SSC) region of 17,834 bp and a large single copy (LSC) region of 83,136 bp. The total GC content of the entire chloroplast genome accounts for 36%, while the GC content in each region of SSC,LSC, and IR accounts for 29.1%, 34.15% and 42.35%, respectively. The genome harbored 133 genes, including 88 protein-coding genes, 37 tRNAs, and 8 rRNAs, with 17 duplicates in IRs. The most abundant amino acid was leucine and the least abundant was cysteine. Codon usage analyses revealed a bias for A/T-ending codons. A total of 35 repeat sequences and 92 simple sequence repeats were detected, and the SC-IR boundary regions were variable between the seven cp genomes. A phylogenetic analysis suggested that broccoli is closely related to Brassica oleracea var. italica MH388764.1, Brassica oleracea var. italica MH388765.1, and Brassica oleracea NC_0441167.1. Our results are expected to be useful for further species identification, population genetics analyses, and biological research on broccoli.
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Affiliation(s)
- Zhenchao Zhang
- Department of Vegetables and Flowers, Zhenjiang Institute of Agricultural Sciences, Jurong, China
| | - Meiqi Tao
- Department of Vegetables and Flowers, Zhenjiang Institute of Agricultural Sciences, Jurong, China
| | - Xi Shan
- Department of Vegetables and Flowers, Zhenjiang Institute of Agricultural Sciences, Jurong, China
| | - Yongfei Pan
- Department of Vegetables and Flowers, Zhenjiang Institute of Agricultural Sciences, Jurong, China
| | - Chunqing Sun
- Department of Vegetables and Flowers, Zhenjiang Institute of Agricultural Sciences, Jurong, China
| | - Lixiao Song
- Department of Vegetables, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xuli Pei
- College of Agriculture and Life Science, Kunming University, Kunming, China
| | - Zange Jing
- College of Agriculture and Life Science, Kunming University, Kunming, China
| | - Zhongliang Dai
- Department of Vegetables and Flowers, Zhenjiang Institute of Agricultural Sciences, Jurong, China
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22
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Comparative Analysis of Chloroplast Genomes of Four Medicinal Capparaceae Species: Genome Structures, Phylogenetic Relationships and Adaptive Evolution. PLANTS 2021; 10:plants10061229. [PMID: 34204211 PMCID: PMC8234754 DOI: 10.3390/plants10061229] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 05/25/2021] [Accepted: 05/31/2021] [Indexed: 12/12/2022]
Abstract
This study presents for the first time the complete chloroplast genomes of four medicinal species in the Capparaceae family belonging to two different genera, Cadaba and Maerua (i.e., C. farinosa, C. glandulosa, M. crassifolia and M. oblongifolia), to investigate their evolutionary process and to infer their phylogenetic positions. The four species are considered important medicinal plants, and are used in the treatment of many diseases. In the genus Cadaba, the chloroplast genome ranges from 156,481 bp to 156,560 bp, while that of Maerua ranges from 155,685 bp to 155,436 bp. The chloroplast genome of C. farinosa, M. crassifolia and M. oblongifolia contains 138 genes, while that of C. glandulosa contains 137 genes, comprising 81 protein-coding genes, 31 tRNA genes and 4 rRNA genes. Out of the total genes, 116–117 are unique, while the remaining 19 are replicated in inverted repeat regions. The psbG gene, which encodes for subunit K of NADH dehydrogenase, is absent in C. glandulosa. A total of 249 microsatellites were found in the chloroplast genome of C. farinosa, 251 in C. glandulosa, 227 in M. crassifolia and 233 in M. oblongifolia, the majority of which are mononucleotides A/T found in the intergenic spacer. Comparative analysis revealed variable hotspot regions (atpF, rpoC2, rps19 and ycf1), which can be used as molecular markers for species authentication and as regions for inferring phylogenetic relationships among them, as well as for evolutionary studies. The monophyly of Capparaceae and other families under Brassicales, as well as the phylogenetic positions of the studied species, are highly supported by all the relationships in the phylogenetic tree. The cp genomes reported in this study will provide resources for studying the genetic diversity of Capparaceae, as well as resolving phylogenetic relationships within the family.
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Wanga VO, Dong X, Oulo MA, Mkala EM, Yang JX, Onjalalaina GE, Gichua MK, Kirika PM, Gituru RW, Hu GW, Wang QF. Complete Chloroplast Genomes of Acanthochlamys bracteata (China) and Xerophyta (Africa) (Velloziaceae): Comparative Genomics and Phylogenomic Placement. FRONTIERS IN PLANT SCIENCE 2021; 12:691833. [PMID: 34194461 PMCID: PMC8238049 DOI: 10.3389/fpls.2021.691833] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 05/19/2021] [Indexed: 05/15/2023]
Abstract
Acanthochlamys P.C. Kao is a Chinese endemic monotypic genus, whereas Xerophyta Juss. is a genus endemic to Africa mainland, Arabian Peninsula and Madagascar with ca.70 species. In this recent study, the complete chloroplast genome of Acanthochlamys bracteata was sequenced and its genome structure compared with two African Xerophyta species (Xerophyta spekei and Xerophyta viscosa) present in the NCBI database. The genomes showed a quadripartite structure with their sizes ranging from 153,843 bp to 155,498 bp, having large single-copy (LSC) and small single-copy (SSC) regions divided by a pair of inverted repeats (IR regions). The total number of genes found in A. bracteata, X. spekei and X. viscosa cp genomes are 129, 130, and 132, respectively. About 50, 29, 28 palindromic, forward and reverse repeats and 90, 59, 53 simple sequence repeats (SSRs) were found in the A. bracteata, X. spekei, and X. viscosa cp genome, respectively. Nucleotide diversity analysis in all species was 0.03501, Ka/Ks ratio average score was calculated to be 0.26, and intergeneric K2P value within the Order Pandanales was averaged to be 0.0831. Genomic characterization was undertaken by comparing the genomes of the three species of Velloziaceae and it revealed that the coding regions were more conserved than the non-coding regions. However, key variations were noted mostly at the junctions of IRs/SSC regions. Phylogenetic analysis suggests that A. bracteata species has a closer genetic relationship to the genus Xerophyta. The present study reveals the complete chloroplast genome of A. bracteata and gives a genomic comparative analysis with the African species of Xerophyta. Thus, can be useful in developing DNA markers for use in the study of genetic variabilities and evolutionary studies in Velloziaceae.
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Affiliation(s)
- Vincent Okelo Wanga
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Xiang Dong
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Millicent Akinyi Oulo
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Elijah Mbandi Mkala
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Jia-Xin Yang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Guy Eric Onjalalaina
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Moses Kirega Gichua
- Botany Department, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | | | - Robert Wahiti Gituru
- Botany Department, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Guang-Wan Hu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Qing-Feng Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
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Ping J, Feng P, Li J, Zhang R, Su Y, Wang T. Molecular evolution and SSRs analysis based on the chloroplast genome of Callitropsis funebris. Ecol Evol 2021; 11:4786-4802. [PMID: 33976848 PMCID: PMC8093713 DOI: 10.1002/ece3.7381] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 12/13/2022] Open
Abstract
Chloroplast genome sequences have been used to understand evolutionary events and to infer efficiently phylogenetic relationships. Callitropsis funebris (Cupressaceae) is an endemic species in China. Its phylogenetic position is controversial due to morphological characters similar to those of Cupressus, Callitropsis, and Chamaecyparis. This study used next-generation sequencing technology to sequence the complete chloroplast genome of Ca. funebris and then constructed the phylogenetic relationship between Ca. funebris and its related species based on a variety of data sets and methods. Simple sequence repeats (SSRs) and adaptive evolution analysis were also conducted. Our results showed that the monophyletic branch consisting of Ca. funebris and Cupressus tonkinensis is a sister to Cupressus, while Callitropsis is not monophyletic; Ca. nootkatensis and Ca. vietnamensis are nested in turn at the base of the monophyletic group Hesperocyparis. The statistical results of SSRs supported the closest relationship between Ca. funebris and Cupressus. By performing adaptive evolution analysis under the phylogenetic background of Cupressales, the Branch model detected three genes and the Site model detected 10 genes under positive selection; and the Branch-Site model uncovered that rpoA has experienced positive selection in the Ca. funebries branch. Molecular analysis from the chloroplast genome highly supported that Ca. funebris is at the base of Cupressus. Of note, SSR features were found to be able to shed some light on phylogenetic relationships. In short, this chloroplast genomic study has provided new insights into the phylogeny of Ca. funebris and revealed multiple chloroplast genes possibly undergoing adaptive evolution.
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Affiliation(s)
- Jingyao Ping
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Peipei Feng
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Jinye Li
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Rongjing Zhang
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Yingjuan Su
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
- Research Institute of Sun Yat‐sen University in ShenzhenShenzhenChina
| | - Ting Wang
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
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Alzahrani D, Albokhari E, Yaradua S, Abba A. Complete chloroplast genome sequences of Dipterygium glaucum and Cleome chrysantha and other Cleomaceae Species, comparative analysis and phylogenetic relationships. Saudi J Biol Sci 2021; 28:2476-2490. [PMID: 33911961 PMCID: PMC8071925 DOI: 10.1016/j.sjbs.2021.01.049] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/17/2021] [Accepted: 01/21/2021] [Indexed: 11/29/2022] Open
Abstract
This current study presents, for the first time, the complete chloroplast genome of two Cleomaceae species: Dipterygium glaucum and Cleome chrysantha in order to evaluate the evolutionary relationship. The cp genome is 158,576 bp in length with 35.74% GC content in D. glaucum and 158,111 bp with 35.96% GC in C. chrysantha. Inverted repeats IR 26,209 bp, 26,251 bp each, LSC of 87,738 bp, 87,184 bp and SSC of 18,420 bp, 18,425 bp respectively. There are 136 genes in the genome, which includes 80 protein coding genes, 31 tRNA genes and four rRNA genes were observed in both chloroplast genomes. 117 genes are unique while the remaining 19 genes are duplicated in IR regions. The analysis of repeats shows that the cp genome includes all types of repeats with more frequent occurrences of palindromic; Also, this analysis indicates that the total number of simple sequence repeats (SSR) were 323 in D. glaucum, and 313 in C. chrysantha, of which the majority of the SSRs in these plastid genomes were mononucleotide repeats A/T which are located in the intergenic spacer. Moreover, the comparative analysis of the four cp sequences revealed four hotspot genes (atpF, rpoC2, rps19, and ycf1), these variable regions could be used as molecular makers for the species authentication as well as resources for inferring phylogenetic relationships of the species. All the relationships in the phylogenetic tree are with high support, this indicate that the complete chloroplast genome is a useful data for inferring phylogenetic relationship within the Cleomaceae and other families. The simple sequence repeats identified will be useful for identification, genetic diversity, and other evolutionary studies of the species. This study reported the first cp genome of the genus Dipterygium and Cleome. The finding of this study will be beneficial for biological disciplines such as evolutionary and genetic diversity studies of the species within the core Cleomaceae.
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Affiliation(s)
- Dhafer Alzahrani
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Enas Albokhari
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
- Department of Biological Sciences, Faculty of Applied Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Samaila Yaradua
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
- Centre for Biodiversity and Conservation, Department of Biology, Umaru Musa Yaradua University, Katsina, Nigeria
| | - Abidina Abba
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
- Department of Biological Sciences, Faculty of Sciences, Federal University Lokoja, Kogi State, Nigeria
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Alanazi KM, Ali MA, Kim SY, Rahman MO, Farah MA, Alhemaid F, Elangbam M, Gurung AB, Lee J. The cp genome characterization of Adenium obesum: Gene content, repeat organization and phylogeny. Saudi J Biol Sci 2021; 28:3768-3775. [PMID: 34220230 PMCID: PMC8241589 DOI: 10.1016/j.sjbs.2021.03.048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 11/01/2022] Open
Abstract
Adenium obesum (Forssk.) Roem. & Schult. belonging to the family Apocynaceae, is remarkable for its horticultural and ornamental values, poisonous nature, and medicinal uses. In order to have understanding of cp genome characterization of highly valued medicinal plant, and the evolutionary and systematic relationships, the complete plastome / chloroplast (cp) genome of A. obesum was sequenced. The assembled cp genome of A. obesum was found to be 154,437 bp, with an overall GC content of 38.1%. A total of 127 unique coding genes were annotated including 96 protein-coding genes, 28 tRNA genes, and 3 rRNA genes. The repeat structures were found to comprise of only mononucleotide repeats. The SSR loci are compososed of only A/T bases. The phylogenetic analysis of cp genomes revealed its proximity with Nerium oleander.
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Affiliation(s)
- Khalid Mashay Alanazi
- Genetics Laboratory, Department of Zoology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mohammad Ajmal Ali
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Soo-Yong Kim
- International Biological Material Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahangno, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - M Oliur Rahman
- Department of Botany, University of Dhaka, Dhaka 1000, Bangladesh
| | - Mohammad Abul Farah
- Genetics Laboratory, Department of Zoology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Fahad Alhemaid
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Meena Elangbam
- Genetics Laboratory, Centre of Advanced Studies in Life Sciences, Manipur University, Canchipur 795 003, India
| | - Arun Bahadur Gurung
- Department of Basic Sciences and Social Sciences, North-Eastern Hill University, Shillong - 793022, Meghalaya, India
| | - Joongku Lee
- Department of Environment and Forest Resources, Chungnam National University, Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
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27
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Dan Q, Li Q, Li X, Suonan R, Dongzhi D, Guo X. Characterization of the complete chloroplast genome of the prickly blue poppy Meconopsis horridula Hook. f. & Thomson (Ranunculales: Papaveraceae). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:792-793. [PMID: 33763580 PMCID: PMC7954420 DOI: 10.1080/23802359.2021.1882902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The prickly blue poppy (Meconopsis horridula Hook. f. & Thomson) is a traditional Tibetan medicinal herb with high values. In this study, its chloroplast genome was determined to be 153,761 bp in length with an A + T-biased base composition, and comprises a pair of inverted repeat (IR) regions (26,030 bp), separated by a large single-copy (LSC) region (83,803 bp) and a small single-copy (SSC) region (17,898 bp). A total of 113 gene species were annotated, with 20 of them being completely or partially duplicated and 18 of them harboring one or two introns. Phylogenetic analysis suggests that M. horridula is closely related to Meconopsis racemosa Maxim.
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Affiliation(s)
- Quehu Dan
- Tibetan Medicine Research Center, Tibetan Medical College, Qinghai University, Xining, PR China
| | - Qien Li
- Tibetan Medicine Research Center, Tibetan Medical College, Qinghai University, Xining, PR China.,State Key Laboratory of Tibetan Medicine Research and Development, Xining, PR China
| | - XianJia Li
- Tibetan Medicine Research Center, Tibetan Medical College, Qinghai University, Xining, PR China.,State Key Laboratory of Tibetan Medicine Research and Development, Xining, PR China
| | - Renqian Suonan
- Tibetan Medical Hospital of Qinghai Province, Xining, PR China
| | - Duojie Dongzhi
- State Key Laboratory of Tibetan Medicine Research and Development, Xining, PR China
| | - Xiao Guo
- Tibetan Medicine Research Center, Tibetan Medical College, Qinghai University, Xining, PR China.,State Key Laboratory of Tibetan Medicine Research and Development, Xining, PR China
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28
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Comparative analysis and phylogenetic investigation of Hong Kong Ilex chloroplast genomes. Sci Rep 2021; 11:5153. [PMID: 33664414 PMCID: PMC7933167 DOI: 10.1038/s41598-021-84705-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 02/19/2021] [Indexed: 11/29/2022] Open
Abstract
Ilex is a monogeneric plant group (containing approximately 600 species) in the Aquifoliaceae family and one of the most commonly used medicinal herbs. However, its taxonomy and phylogenetic relationships at the species level are debatable. Herein, we obtained the complete chloroplast genomes of all 19 Ilex types that are native to Hong Kong. The genomes are conserved in structure, gene content and arrangement. The chloroplast genomes range in size from 157,119 bp in Ilex graciliflora to 158,020 bp in Ilex kwangtungensis. All these genomes contain 125 genes, of which 88 are protein-coding and 37 are tRNA genes. Four highly varied sequences (rps16-trnQ, rpl32-trnL, ndhD-psaC and ycf1) were found. The number of repeats in the Ilex genomes is mostly conserved, but the number of repeating motifs varies. The phylogenetic relationship among the 19 Ilex genomes, together with eight other available genomes in other studies, was investigated. Most of the species could be correctly assigned to the section or even series level, consistent with previous taxonomy, except Ilex rotunda var. microcarpa, Ilex asprella var. tapuensis and Ilex chapaensis. These species were reclassified; I. rotunda was placed in the section Micrococca, while the other two were grouped with the section Pseudoaquifolium. These studies provide a better understanding of Ilex phylogeny and refine its classification.
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29
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Alzahrani DA. Complete Chloroplast Genome of Abutilon fruticosum: Genome Structure, Comparative and Phylogenetic Analysis. PLANTS 2021; 10:plants10020270. [PMID: 33573201 PMCID: PMC7911161 DOI: 10.3390/plants10020270] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/23/2021] [Accepted: 01/24/2021] [Indexed: 12/30/2022]
Abstract
Abutilon fruticosum is one of the endemic plants with high medicinal and economic value in Saudi Arabia and belongs to the family Malvaceae. However, the plastome sequence and phylogenetic position have not been reported until this study. In this research, the complete chloroplast genome of A. fruticosum was sequenced and assembled, and comparative and phylogenetic analyses within the Malvaceae family were conducted. The chloroplast genome (cp genome) has a circular and quadripartite structure with a total length of 160,357 bp and contains 114 unique genes (80 protein-coding genes, 30 tRNA genes and 4 rRNA genes). The repeat analyses indicate that all the types of repeats (palindromic, complement, forward and reverse) were present in the genome, with palindromic occurring more frequently. A total number of 212 microsatellites were identified in the plastome, of which the majority are mononucleotides. Comparative analyses with other species of Malvaceae indicate a high level of resemblance in gene content and structural organization and a significant level of variation in the position of genes in single copy and inverted repeat borders. The analyses also reveal variable hotspots in the genomes that can serve as barcodes and tools for inferring phylogenetic relationships in the family: the regions include trnH-psbA, trnK-rps16, psbI-trnS, atpH-atpI, trnT-trnL, matK, ycf1 and ndhH. Phylogenetic analysis indicates that A. fruticosum is closely related to Althaea officinalis, which disagrees with the previous systematic position of the species. This study provides insights into the systematic position of A. fruticosum and valuable resources for further phylogenetic and evolutionary studies of the species and the Malvaceae family to resolve ambiguous issues within the taxa.
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Affiliation(s)
- Dhafer A Alzahrani
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
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30
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Yu X, Tan W, Gao H, Miao L, Tian X. Development of a Specific Mini-Barcode From Plastome and its Application for Qualitative and Quantitative Identification of Processed Herbal Products Using DNA Metabarcoding Technique: A Case Study on Senna. Front Pharmacol 2021; 11:585687. [PMID: 33390955 PMCID: PMC7773718 DOI: 10.3389/fphar.2020.585687] [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: 07/21/2020] [Accepted: 11/26/2020] [Indexed: 01/04/2023] Open
Abstract
Herbal products play an important role globally in the pharmaceutical and healthcare industries. However, some specific groups of herbal products are easily adulterated by confused materials on the market, which seriously reduces the products’ quality. Universal conventional DNA barcodes would function poorly since the processed herbal products generally suffer from varying degrees of DNA degradation and DNA mixing during processing or manufacturing. For quality control purposes, an accurate and effective method should be provided for species identification of these herbal products. Here, we provided a strategy of developing the specific mini-barcode using Senna as an example, and by coupling with the metabarcoding technique, it realized the qualitative and quantitative identification of processed herbal products. The plastomes of Senna obtusifolia (L.) H.S.Irwin & Barneby and Senna occidentalis (L.) Link were newly assembled, and the hypervariable coding-regions were identified by comparing their genomes. Then, the specific mini-barcodes were developed based on the identified hypervariable regions. Finally, we applied the DNA metabarcoding technique to the developed mini-barcodes. Results showed that the lengths of plastomes of S. obtusifolia and S. occidentalis were 162,426 and 159,993 bp, respectively. Four hypervariable coding-regions ycf1, rpl23, petL, and matK were identified. Two specific mini-barcodes were successfully developed from matK, and the mini-barcode of primer 647F-847R was proved to be able to qualitatively and quantitatively identify these two processed Senna seeds. Overall, our study established a valuable way to develop the specific mini-barcode, which may provide a new idea for the quality control of processed herbal products.
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Affiliation(s)
- Xiaolei Yu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Wei Tan
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Han Gao
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Lin Miao
- State Key Laboratory of Component-based Chinese Medicine, 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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31
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The Complete Plastid Genome of Artocarpus camansi: A High Degree of Conservation of the Plastome Structure in the Family Moraceae. FORESTS 2020. [DOI: 10.3390/f11111179] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Understanding the plastid genome is extremely important for the interpretation of the genetic mechanisms associated with essential physiological and metabolic functions, the identification of possible marker regions for phylogenetic or phylogeographic analyses, and the elucidation of the modes through which natural selection operates in different regions of this genome. In the present study, we assembled the plastid genome of Artocarpus camansi, compared its repetitive structures with Artocarpus heterophyllus, and searched for evidence of synteny within the family Moraceae. We also constructed a phylogeny based on 56 chloroplast genes to assess the relationships among three families of the order Rosales, that is, the Moraceae, Rhamnaceae, and Cannabaceae. The plastid genome of A. camansi has 160,096 bp, and presents the typical circular quadripartite structure of the Angiosperms, comprising a large single copy (LSC) of 88,745 bp and a small single copy (SSC) of 19,883 bp, separated by a pair of inverted repeat (IR) regions each with a length of 25,734 bp. The total GC content was 36.0%, which is very similar to Artocarpus heterophyllus (36.1%) and other moraceous species. A total of 23,068 codons and 80 SSRs were identified in the A. camansi plastid genome, with the majority of the SSRs being mononucleotide (70.0%). A total of 50 repeat structures were observed in the A. camansi plastid genome, in contrast with 61 repeats in A. heterophyllus. A purifying selection signal was found in 70 of the 79 protein-coding genes, indicating that they have all been highly conserved throughout the evolutionary history of the genus. The comparative analysis of the structural characteristics of the chloroplast among different moraceous species found a high degree of similarity in the sequences, which indicates a highly conserved evolutionary model in these plastid genomes. The phylogenetic analysis also recovered a high degree of similarity between the chloroplast genes of A. camansi and A. heterophyllus, and reconfirmed the hypothesis of the intense conservation of the plastome in the family Moraceae.
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Tan W, Gao H, Jiang W, Zhang H, Yu X, Liu E, Tian X. The complete chloroplast genome of Gleditsia sinensis and Gleditsia japonica: genome organization, comparative analysis, and development of taxon specific DNA mini-barcodes. Sci Rep 2020; 10:16309. [PMID: 33005000 PMCID: PMC7529812 DOI: 10.1038/s41598-020-73392-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 09/07/2020] [Indexed: 11/09/2022] Open
Abstract
Chloroplast genomes have been widely considered an informative and valuable resource for molecular marker development and phylogenetic reconstruction in plant species. This study evaluated the complete chloroplast genomes of the traditional Chinese medicine Gleditsia sinensis and G. japonica, an adulterant of the former. The complete chloroplast genomes of G. sinensis and G. japonica were found to be of sizes 163,175 bp and 162,391 bp, respectively. A total of 111 genes were identified in each chloroplast genome, including 77 coding sequences, 30 tRNA, and 4 rRNA genes. Comparative analysis demonstrated that the chloroplast genomes of these two species were highly conserved in genome size, GC contents, and gene organization. Additionally, nucleotide diversity analysis of the two chloroplast genomes revealed that the two short regions of ycf1b were highly diverse, and could be treated as mini-barcode candidate regions. The mini-barcode of primers ZJ818F-1038R was proven to precisely discriminate between these two species and reflect their biomass ratio accurately. Overall, the findings of our study will shed light on the genetic evolution and guide species identification of G. sinensis and G. japonica.
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Affiliation(s)
- Wei Tan
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Poyang Lake Road 10, Tianjin, 301617, China
| | - Han Gao
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Poyang Lake Road 10, Tianjin, 301617, China
| | - Weiling Jiang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Poyang Lake Road 10, Tianjin, 301617, China
| | - Huanyu Zhang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Poyang Lake Road 10, Tianjin, 301617, China
| | - Xiaolei Yu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Poyang Lake Road 10, Tianjin, 301617, China
| | - Erwei Liu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Poyang Lake Road 10, Tianjin, 301617, China.
| | - Xiaoxuan Tian
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Poyang Lake Road 10, Tianjin, 301617, China.
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33
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Li C, Zhao Y, Xu Z, Yang G, Peng J, Peng X. Initial Characterization of the Chloroplast Genome of Vicia sepium, an Important Wild Resource Plant, and Related Inferences About Its Evolution. Front Genet 2020; 11:73. [PMID: 32153639 PMCID: PMC7044246 DOI: 10.3389/fgene.2020.00073] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 01/22/2020] [Indexed: 01/29/2023] Open
Abstract
Lack of complete genomic information concerning Vicia sepium (Fabaceae: Fabeae) precludes investigations of evolution and populational diversity of this perennial high-protein forage plant suitable for cultivation in extreme conditions. Here, we present the complete and annotated chloroplast genome of this important wild resource plant. V. sepium chloroplast genome includes 76 protein-coding genes, 29 tRNA genes, 4 rRNA genes, and 1 pseudogene. Its 124,095 bp sequence has a loss of one inverted repeat (IR). The GC content of the whole genome, the protein-coding, intron, tRNA, rRNA, and intergenic spacer regions was 35.0%, 36.7%, 34.6%, 52.3%, 54.2%, and 29.2%, respectively. Comparative analyses with plastids from related genera belonging to Fabeae demonstrated that the greatest variation in the V. sepium genome length occurred in protein-coding regions. In these regions, some genes and introns were lost or gained; for example, ycf4, clpP intron, and rpl16 intron deletions and rpl20 and ORF292 insertions were observed. Twelve highly divergent regions, 66 simple sequence repeats (SSRs) and 27 repeat sequences were also found in these regions. Detailed evolutionary rate analysis of protein-coding genes showed that Vicia species exhibit additional interesting characteristics including positive selection of ccsA, clpP, rpl32, rpl33, rpoC1, rps15, rps2, rps4, and rps7, and the evolutionary rates of atpA, accD, and rps2 in Vicia are significantly accelerated. These genes are important candidate genes for understanding the evolutionary strategies of Vicia and other genera in Fabeae. The phylogenetic analysis showed that Vicia and Lens are included in the same clade and that Vicia is paraphyletic. These results provide evidence regarding the evolutionary history of the chloroplast genome.
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Affiliation(s)
- Chaoyang Li
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, China
| | - Yunlin Zhao
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, China
| | - Zhenggang Xu
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, China
- Hunan Urban and Rural Ecological Planning and Restoration Engineering Research Center, Hunan City University, Yiyang, China
| | - Guiyan Yang
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, China
| | - Jiao Peng
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, China
| | - Xiaoyun Peng
- Hunan Urban and Rural Ecological Planning and Restoration Engineering Research Center, Hunan City University, Yiyang, China
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Analysis of complete chloroplast genomes of Curcuma and the contribution to phylogeny and adaptive evolution. Gene 2020; 732:144355. [PMID: 31935501 DOI: 10.1016/j.gene.2020.144355] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 01/07/2020] [Accepted: 01/08/2020] [Indexed: 01/13/2023]
Abstract
Curcuma is an important member of Zingiberaceae. Many species of this genus are widely used in traditional medicine and have important cultural value in East Asia. Among them, C. longa is considered to be the main source of curcumin and has a very wide range of uses. The rapid development of molecular phylogeny has deepened our understanding of taxonomy and evolution of Curcuma. However, little is known about the chloroplast genome phylogeny and the genetic bases of adaptative evolution. In this work, we sequenced the complete chloroplast genome of 4 Curcuma species. Curcuma chloroplast genomes showed highly conserved structures and the length ranged from 159,423 bp to 152,723 bp. A total of 133 genes were observed. Multiple repeats and simple sequence repeats (SSRs) were detected. By comparing with related species, 7 highly variable regions were identified as potential specific DNA barcodes for species identification. Phylogenetic analysis of complete plastome sequences and specific data sets revealed discordance with expected genus boundary. Chloroplast phylogenetic relationships were better predicted by geography than by morphological and nuclear DNA, indicating a substantial existence of introgression. 9 genes were proved to have high posteriori probability in positive selection analysis, and 4 of them (psbA, psbD, PetA and rbcL) closely related to photosynthesis, implying that chloroplast genes may had undergone positive selection pressure in evolution. These results are of great significance for us to understand the genetic basis, phylogeny and adaptive evolution of Curcuma chloroplast.
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Du X, Zeng T, Feng Q, Hu L, Luo X, Weng Q, He J, Zhu B. The complete chloroplast genome sequence of yellow mustard (Sinapis alba L.) and its phylogenetic relationship to other Brassicaceae species. Gene 2020; 731:144340. [PMID: 31923575 DOI: 10.1016/j.gene.2020.144340] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 12/09/2019] [Accepted: 01/06/2020] [Indexed: 12/20/2022]
Abstract
As a member of the large Brassicaceae family, yellow mustard (Sinapis alba L.) has been used as an important gene pool for the genetic improvement of cash crops in Brassicaceae. Understanding the phylogenetic relationship between Sinapis alba (S. alba) and other Brassicaceae crops can provide guidance on the introgression of its favorable alleles into related species. The chloroplast (cp) genome is an ideal model for assessing genome evolution and the phylogenetic relationships of complex angiosperm families. Herein, we de novo assembled the complete cp genome of S. alba by integrating the PacBio and Illumina sequencing platforms. A 153,760 bp quadripartite cycle without any gap was obtained, including a pair of inverted repeats (IRa and IRb) of 26,221 bp, separated by a large single copy (LSC) region of 83,506 bp and a small single copy (SSC) region of 17,821 bp. A total of 78 protein-coding genes, 30 tRNA genes, and four rRNA genes were identified in this cp genome, as were 89 simple sequence repeat (SSR) loci of 18 types. The codon usage analysis revealed a preferential use of the Leu codon with the A/U ending. The phylogenetic analysis using 82 Brassicaceae species demonstrated that S. alba had a close relationship with important Brassica and Raphanus species; moreover, it likely originated from a separate evolutionary pathway compared with the congeneric Sinapis arvensis. The synonymous (Ks) and non-synonymous (Ks) substitution rate analysis showed that genes encoding "Subunits of cytochrome b/f complex" were under the lowest purifying selection pressure, whereas those associated with "Maturase", "Subunit of acetyl-CoA", and "Subunits of NADH-dehydrogenase" underwent relatively higher purifying selection pressures. Our results provide valuable information for fully utilizing the S. alba cp genome as a potential genetic resource for the genetic improvement of Brassica and Raphanus species.
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Affiliation(s)
- Xuye Du
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China
| | - Tuo Zeng
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China; Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qun Feng
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China
| | - Lijuan Hu
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China
| | - Xi Luo
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China
| | - Qingbei Weng
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China
| | - Jiefang He
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China.
| | - Bin Zhu
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China.
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Zhang X, Wu Q, Zhao Y, Yang X. Decaisnea insignis Seed Oil Inhibits Trimethylamine- N-oxide Formation and Remodels Intestinal Microbiota to Alleviate Liver Dysfunction in l-Carnitine Feeding Mice. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:13082-13092. [PMID: 31671940 DOI: 10.1021/acs.jafc.9b05383] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Elevated circulating level of the intestinal microbiota-derived l-carnitine metabolite trimethylamine-N-oxide (TMAO) has recently been linked to many chronic diseases. The purpose of our study was to investigate the effects of omega-7-enriched Decaisnea insignis seed oil (DISO) on reducing TMAO formation to prevent the l-carnitine-induced hepatic damage in mice. Feeding of mice with 3% l-carnitine in drinking water clearly increased the serum and urinary levels of TMAO (p < 0.05 vs Normal), whereas the serum and urinary TMAO formation was sharply reduced by DISO administration (p < 0.05). Meanwhile, DISO resulted in strong inhibition against the elevation of hepatic injury marker (AST, ALT, and ALP) activities and dyslipidemia (TC, TG, LDL-C, and HDL-C), as well as liver inflammatory cytokine (IL-1, IL-6, TNF-α, and TNF-β) release in l-carnitine-fed mice (p < 0.05). As revealed by 16S rDNA gene sequencing, DISO significantly inhibited the l-carnitine-induced elevations in the abundance of Firmicutes, Proteobacteria, and Erysipelotrichaceae and the increases in the proportion of Lactobacillus and Akkermansia, revealing that DISO attenuated the l-carnitine-caused gut dysbiosis. These findings suggested that DISO could alleviate liver dysfunction in l-carnitine-fed mice, which might be due to the protection against TMAO formation by modulating the gut microbiota.
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Complete Chloroplast Genomes of Ampelopsis humulifolia and Ampelopsis japonica: Molecular Structure, Comparative Analysis, and Phylogenetic Analysis. PLANTS 2019; 8:plants8100410. [PMID: 31614980 PMCID: PMC6843361 DOI: 10.3390/plants8100410] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 10/06/2019] [Accepted: 10/11/2019] [Indexed: 02/05/2023]
Abstract
Ampelopsis humulifolia (A. humulifolia) and Ampelopsis japonica (A. japonica), which belong to the family Vitaceae, are valuably used as medicinal plants. The chloroplast (cp) genomes have been recognized as a convincing data for marker selection and phylogenetic studies. Therefore, in this study we reported the complete cp genome sequences of two Ampelopsis species. Results showed that the cp genomes of A. humulifolia and A. japonica were 161,724 and 161,430 bp in length, respectively, with 37.3% guanine-cytosine (GC) content. A total of 114 unique genes were identified in each cp genome, comprising 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. We determined 95 and 99 small sequence repeats (SSRs) in A. humulifolia and A. japonica, respectively. The location and distribution of long repeats in the two cp genomes were identified. A highly divergent region of psbZ (Photosystem II reaction center protein Z) -trnG (tRNA-Glycine) was found and could be treated as a potential marker for Vitaceae, and then the corresponding primers were designed. Additionally, phylogenetic analysis showed that Vitis was closer to Tetrastigma than Ampelopsis. In general, this study provides valuable genetic resources for DNA barcoding marker identification and phylogenetic analyses of Ampelopsis.
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Liu X, Zhao K, Yang X, Zhao Y. Gut Microbiota and Metabolome Response of Decaisnea insignis Seed Oil on Metabolism Disorder Induced by Excess Alcohol Consumption. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:10667-10677. [PMID: 31483636 DOI: 10.1021/acs.jafc.9b04792] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
This study investigated the modulatory effects of Decaisnea insignis seed oil (DISO), which was rich in palmitoleic acid (55.25%), palmitic acid (12.25%), and oleic acid (28.74%), on alcohol-induced metabolism disorder in mice. Fifty mice were orally administered with 38% alcohol (0.4 mL/day) and without or with DISO (3, 6, and 12 g/kg) for consecutive 12 weeks. DISO inhibited the alcohol-induced weight loss and liver function abnormality (p < 0.01) and shifted the profiles of cecal microbiome: elevating the abundance of Lactobacillus, Ruminoccoceae_UCG_004 (p < 0.05) and decreasing abundance of Parabacteroides (p < 0.05). This treatment also regulated metabolome response of amino acid and lipid metabolism in cecal content: upregulating 5-hydroxyindole-3-acetic acid (p < 0.05), 6-hydroxynicotinic acid, 5-methoxytryptamine, nicotinamide, and nicotinic acid (p < 0.1) and downregulating androsterone, tryptophan, and indole-3-acetamide (p < 0.05). DISO protected against alcoholic liver injury and gut microbiota dysbiosis by enriching the relative abundance of Lactobacillus, which was positively associated with the improvement of intestinal permeability and tryptophan metabolism.
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Yaradua SS, Alzahrani DA, Albokhary EJ, Abba A, Bello A. Complete Chloroplast Genome Sequence of Justicia flava: Genome Comparative Analysis and Phylogenetic Relationships among Acanthaceae. BIOMED RESEARCH INTERNATIONAL 2019; 2019:4370258. [PMID: 31467890 PMCID: PMC6699374 DOI: 10.1155/2019/4370258] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 06/26/2019] [Indexed: 01/08/2023]
Abstract
The complete chloroplast genome of J. flava, an endangered medicinal plant in Saudi Arabia, was sequenced and compared with cp genome of three Acanthaceae species to characterize the cp genome, identify SSRs, and also detect variation among the cp genomes of the sampled Acanthaceae. NOVOPlasty was used to assemble the complete chloroplast genome from the whole genome data. The cp genome of J. flava was 150, 888bp in length with GC content of 38.2%, and has a quadripartite structure; the genome harbors one pair of inverted repeat (IRa and IRb 25, 500bp each) separated by large single copy (LSC, 82, 995 bp) and small single copy (SSC, 16, 893 bp). There are 132 genes in the genome, which includes 80 protein coding genes, 30 tRNA, and 4 rRNA; 113 are unique while the remaining 19 are duplicated in IR regions. The repeat analysis indicates that the genome contained all types of repeats with palindromic occurring more frequently; the analysis also identified total number of 98 simple sequence repeats (SSR) of which majority are mononucleotides A/T and are found in the intergenic spacer. The comparative analysis with other cp genomes sampled indicated that the inverted repeat regions are conserved than the single copy regions and the noncoding regions show high rate of variation than the coding region. All the genomes have ndhF and ycf1 genes in the border junction of IRb and SSC. Sequence divergence analysis of the protein coding genes showed that seven genes (petB, atpF, psaI, rpl32, rpl16, ycf1, and clpP) are under positive selection. The phylogenetic analysis revealed that Justiceae is sister to Ruellieae. This study reported the first cp genome of the largest genus in Acanthaceae and provided resources for studying genetic diversity of J. flava as well as resolving phylogenetic relationships within the core Acanthaceae.
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Affiliation(s)
- Samaila S. Yaradua
- Department of Biology, King Abdulaziz University, Jeddah, Saudi Arabia
- Centre for Biodiversity and Conservation, Department of Biology, Umaru Musa Yaradua University, Katsina, Nigeria
| | | | - Enas J. Albokhary
- Department of Biology, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Abidina Abba
- Department of Biology, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Abubakar Bello
- Centre for Biodiversity and Conservation, Department of Biology, Umaru Musa Yaradua University, Katsina, Nigeria
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Ye X, Hu D, Guo Y, Sun R. Complete chloroplast genome of Castanopsis sclerophylla (Lindl.) Schott: Genome structure and comparative and phylogenetic analysis. PLoS One 2019; 14:e0212325. [PMID: 31361757 PMCID: PMC6667119 DOI: 10.1371/journal.pone.0212325] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Accepted: 07/17/2019] [Indexed: 11/19/2022] Open
Abstract
Castanopsis sclerophylla (Lindl.) Schott is an important species of evergreen broad-leaved tree in subtropical areas and has high ecological and economic value. However, there are few studies on its chloroplast genome. In this study, the complete chloroplast genome sequence of C. sclerophylla was determined using the Illumina HiSeq 2500 platform. The complete chloroplast genome of C. sclerophylla is 160,497 bp long, including a pair of inverted repeat (IR) regions (25,675 bp) separated by a large single-copy (LSC) region of 90,255 bp and a small single-copy (SSC) region of 18,892 bp. The overall GC content of the chloroplast genome is 36.82%. A total of 131 genes were found; of these, 111 genes are unique and annotated, including 79 protein-coding genes, 27 transfer RNA genes (tRNAs), and four ribosomal RNA genes (rRNAs). Twenty-one genes were found to be duplicated in the IR regions. Comparative analysis indicated that IR contraction might be the reason for the smaller chloroplast genome of C. sclerophylla compared to three congeneric species. Sequence analysis indicated that the LSC and SSC regions are more divergent than IR regions within Castanopsis; furthermore, greater divergence was found in noncoding regions than in coding regions. The maximum likelihood phylogenetic analysis showed that four species of the genus Castanopsis form a monophyletic clade and that C. sclerophylla is closely related to Castanopsis hainanensis with strong bootstrap values. These results not only provide a basic understanding of Castanopsis chloroplast genomes, but also illuminate Castanopsis species evolution within the Fagaceae family. Furthermore, these findings will be valuable for future studies of genetic diversity and enhance our understanding of the phylogenetic evolution of Castanopsis.
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Affiliation(s)
- Xuemin Ye
- Jiangxi Provincial Key Laboratory of Silviculture, College of Forestry, Jiangxi Agricultural University, Nanchang, China
| | - Dongnan Hu
- Jiangxi Provincial Key Laboratory of Silviculture, College of Forestry, Jiangxi Agricultural University, Nanchang, China
| | - Yangping Guo
- Jiangxi Provincial Key Laboratory of Silviculture, College of Forestry, Jiangxi Agricultural University, Nanchang, China
| | - Rongxi Sun
- Jiangxi Provincial Key Laboratory of Silviculture, College of Forestry, Jiangxi Agricultural University, Nanchang, China
- * E-mail:
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Comparison of Four Complete Chloroplast Genomes of Medicinal and Ornamental Meconopsis Species: Genome Organization and Species Discrimination. Sci Rep 2019; 9:10567. [PMID: 31332227 PMCID: PMC6646306 DOI: 10.1038/s41598-019-47008-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 07/08/2019] [Indexed: 11/26/2022] Open
Abstract
High-throughput sequencing of chloroplast genomes has been used to gain insight into the evolutionary relationships of plant species. In this study, we sequenced the complete chloroplast genomes of four species in the Meconopsis genus: M. racemosa, M. integrifolia (Maxim.) Franch, M. horridula and M. punicea. These plants grow in the wild and are recognized as having important medicinal and ornamental applications. The sequencing results showed that the size of the Meconopsis chloroplast genome ranges from 151864 to 153816 bp. A total of 127 genes comprising 90 protein-coding genes, 37 tRNA genes and 8 rRNA genes were observed in all four chloroplast genomes. Comparative analysis of the four chloroplast genomes revealed five hotspot regions (matK, rpoC2, petA, ndhF, and ycf1), which could potentially be used as unique molecular markers for species identification. In addition, the ycf1 gene may also be used as an effective molecular marker to distinguish Papaveraceae and determine the evolutionary relationships among plant species in the Papaveraceae family. Futhermore, these four genomes can provide valuable genetic information for other related studies.
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Comprehensive Analysis of Rhodomyrtus tomentosa Chloroplast Genome. PLANTS 2019; 8:plants8040089. [PMID: 30987338 PMCID: PMC6524380 DOI: 10.3390/plants8040089] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 03/26/2019] [Accepted: 03/29/2019] [Indexed: 11/16/2022]
Abstract
In the last decade, several studies have relied on a small number of plastid genomes to deduce deep phylogenetic relationships in the species-rich Myrtaceae. Nevertheless, the plastome of Rhodomyrtus tomentosa, an important representative plant of the Rhodomyrtus (DC.) genera, has not yet been reported yet. Here, we sequenced and analyzed the complete chloroplast (CP) genome of R. tomentosa, which is a 156,129-bp-long circular molecule with 37.1% GC content. This CP genome displays a typical quadripartite structure with two inverted repeats (IRa and IRb), of 25,824 bp each, that are separated by a small single copy region (SSC, 18,183 bp) and one large single copy region (LSC, 86,298 bp). The CP genome encodes 129 genes, including 84 protein-coding genes, 37 tRNA genes, eight rRNA genes and three pseudogenes (ycf1, rps19, ndhF). A considerable number of protein-coding genes have a universal ATG start codon, except for psbL and ndhD. Premature termination codons (PTCs) were found in one protein-coding gene, namely atpE, which is rarely reported in the CP genome of plants. Phylogenetic analysis revealed that R. tomentosa has a sister relationship with Eugenia uniflora and Psidium guajava. In conclusion, this study identified unique characteristics of the R. tomentosa CP genome providing valuable information for further investigations on species identification and the phylogenetic evolution between R. tomentosa and related species.
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Huang HM, Zhao KK, Wang HX, Zhu ZX, Wang HF. Complete plastome sequence of Stauntonia obovatifoliola subsp. urophylla (Lardizabalaceae). Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1617071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Hua-Min Huang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, China
| | - Kun-Kun Zhao
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, China
| | - Hong-Xin Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, China
| | - Zhi-Xin Zhu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, China
| | - Hua-Feng Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, China
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Meng J, Li X, Li H, Yang J, Wang H, He J. Comparative Analysis of the Complete Chloroplast Genomes of Four Aconitum Medicinal Species. Molecules 2018; 23:molecules23051015. [PMID: 29701675 PMCID: PMC6102581 DOI: 10.3390/molecules23051015] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 04/23/2018] [Accepted: 04/24/2018] [Indexed: 11/20/2022] Open
Abstract
Aconitum (Ranunculaceae) consists of approximately 400 species distributed in the temperate regions of the northern hemisphere. Many species are well-known herbs, mainly used for analgesia and anti-inflammatory purposes. This genus is well represented in China and has gained widespread attention for its toxicity and detoxification properties. In southwestern China, several Aconitum species, called ‘Dula’ in the Yi Nationality, were often used to control the poisonous effects of other Aconitum plants. In this study, the complete chloroplast (cp) genomes of these species were determined for the first time through Illumina paired-end sequencing. Our results indicate that their cp genomes ranged from 151,214 bp (A. episcopale) to 155,769 bp (A. delavayi) in length. A total of 111–112 unique genes were identified, including 85 protein-coding genes, 36–37 tRNA genes and eight ribosomal RNA genes (rRNA). We also analyzed codon usage, IR expansion or contraction and simple sequence repeats in the cp genomes. Eight variable regions were identified and these may potentially be useful as specific DNA barcodes for species identification of Aconitum. Phylogenetic analysis revealed that all five studied species formed a new clade and were resolved with 100% bootstrap support. This study will provide genomic resources and potential plastid markers for DNA barcoding, further taxonomy and germplasm exploration of Aconitum.
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Affiliation(s)
- Jing Meng
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming 650201, China.
| | - Xuepei Li
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming 650201, China.
| | - Hongtao Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
| | - Junbo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
| | - Hong Wang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
| | - Jun He
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
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Saina JK, Li ZZ, Gichira AW, Liao YY. The Complete Chloroplast Genome Sequence of Tree of Heaven (Ailanthus altissima (Mill.) (Sapindales: Simaroubaceae), an Important Pantropical Tree. Int J Mol Sci 2018; 19:E929. [PMID: 29561773 PMCID: PMC5979363 DOI: 10.3390/ijms19040929] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 03/15/2018] [Accepted: 03/16/2018] [Indexed: 12/17/2022] Open
Abstract
Ailanthus altissima (Mill.) Swingle (Simaroubaceae) is a deciduous tree widely distributed throughout temperate regions in China, hence suitable for genetic diversity and evolutionary studies. Previous studies in A. altissima have mainly focused on its biological activities, genetic diversity and genetic structure. However, until now there is no published report regarding genome of this plant species or Simaroubaceae family. Therefore, in this paper, we first characterized A. altissima complete chloroplast genome sequence. The tree of heaven chloroplast genome was found to be a circular molecule 160,815 base pairs (bp) in size and possess a quadripartite structure. The A. altissima chloroplast genome contains 113 unique genes of which 79 and 30 are protein coding and transfer RNA (tRNA) genes respectively and also 4 ribosomal RNA genes (rRNA) with overall GC content of 37.6%. Microsatellite marker detection identified A/T mononucleotides as majority SSRs in all the seven analyzed genomes. Repeat analyses of seven Sapindales revealed a total of 49 repeats in A. altissima, Rhus chinensis, Dodonaea viscosa, Leitneria floridana, while Azadirachta indica, Boswellia sacra, and Citrus aurantiifolia had a total of 48 repeats. The phylogenetic analysis using protein coding genes revealed that A. altissima is a sister to Leitneria floridana and also suggested that Simaroubaceae is a sister to Rutaceae family. The genome information reported here could be further applied for evolution and invasion, population genetics, and molecular studies in this plant species and family.
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Affiliation(s)
- Josphat K Saina
- Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen 518004, China.
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China.
| | - Zhi-Zhong Li
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Andrew W Gichira
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China.
| | - Yi-Ying Liao
- Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen 518004, China.
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