551
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Lin Z, Zhou P, Ma X, Deng Y, Liao Z, Li R, Ming R. Comparative analysis of chloroplast genomes in Vasconcellea pubescens A.DC. and Carica papaya L. Sci Rep 2020; 10:15799. [PMID: 32978465 PMCID: PMC7519098 DOI: 10.1038/s41598-020-72769-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 08/28/2020] [Indexed: 01/12/2023] Open
Abstract
The chloroplast genome is an integral part of plant genomes in a species along with nuclear and mitochondrial genomes, contributing to adaptation, diversification, and evolution of plant lineages. In the family Caricaceae, only the Carica papaya chloroplast genome and its nuclear and mitochondrial genomes were sequenced, and no chloroplast genome-wide comparison across genera was conducted. Here, we sequenced and assembled the chloroplast genome of Vasconcellea pubescens A.DC. using Oxford Nanopore Technology. The size of the genome is 158,712 bp, smaller than 160,100 bp of the C. papaya chloroplast genome. And two structural haplotypes, LSC_IRa_SSCrc_IRb and LSC_IRa_SSC_IRb, were identified in both V. pubescens and C. papaya chloroplast genomes. The insertion-deletion mutations may play an important role in Ycf1 gene evolution in family Caricaceae. Ycf2 is the only one gene positively selected in the V. pubescens chloroplast genome. In the C. papaya chloroplast genome, there are 46 RNA editing loci with an average RNA editing efficiency of 63%. These findings will improve our understanding of the genomes of these two crops in the family Caricaceae and will contribute to crop improvement.
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Affiliation(s)
- Zhicong Lin
- College of Agriculture, Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Ping Zhou
- Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350013, Fujian, China
| | - Xinyi Ma
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Youjin Deng
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Zhenyang Liao
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Ruoyu Li
- College of Agriculture, Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Ray Ming
- College of Agriculture, Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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552
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Zheng S, Poczai P, Hyvönen J, Tang J, Amiryousefi A. Chloroplot: An Online Program for the Versatile Plotting of Organelle Genomes. Front Genet 2020; 11:576124. [PMID: 33101394 PMCID: PMC7545089 DOI: 10.3389/fgene.2020.576124] [Citation(s) in RCA: 118] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 08/28/2020] [Indexed: 11/13/2022] Open
Abstract
Understanding the complexity of genomic structures and their unique architecture is linked with the power of visualization tools used to represent these features. Such tools should be able to provide a realistic and scalable version of genomic content. Here, we present an online organelle plotting tool focused on chloroplasts, which were developed to visualize the exclusive structure of these genomes. The distinguished unique features of this program include its ability to represent the Single Short Copy (SSC) regions in reverse complement, which allows the depiction of the codon usage bias index for each gene, along with the possibility of the minor mismatches between inverted repeat (IR) regions and user-specified plotting layers. The versatile color schemes and diverse functionalities of the program are specifically designed to reflect the accurate scalable representation of the plastid genomes. We introduce a Shiny app website for easy use of the program; a more advanced application of the tool is possible by further development and modification of the downloadable source codes provided online. The software and its libraries are completely coded in R, available at https://irscope.shinyapps.io/chloroplot/.
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Affiliation(s)
- Shuyu Zheng
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Peter Poczai
- Finnish Museum of Natural History (Botany), University of Helsinki, Helsinki, Finland.,Department of Biosciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Jaakko Hyvönen
- Finnish Museum of Natural History (Botany), University of Helsinki, Helsinki, Finland.,Department of Biosciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Jing Tang
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Ali Amiryousefi
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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553
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Nawae W, Yundaeng C, Naktang C, Kongkachana W, Yoocha T, Sonthirod C, Narong N, Somta P, Laosatit K, Tangphatsornruang S, Pootakham W. The Genome and Transcriptome Analysis of the Vigna mungo Chloroplast. PLANTS (BASEL, SWITZERLAND) 2020; 9:plants9091247. [PMID: 32967378 PMCID: PMC7570002 DOI: 10.3390/plants9091247] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/11/2020] [Accepted: 09/17/2020] [Indexed: 05/20/2023]
Abstract
Vigna mungo is cultivated in approximately 5 million hectares worldwide. The chloroplast genome of this species has not been previously reported. In this study, we sequenced the genome and transcriptome of the V. mungo chloroplast. We identified many positively selected genes in the photosynthetic pathway (e.g., rbcL, ndhF, and atpF) and RNA polymerase genes (e.g., rpoC2) from the comparison of the chloroplast genome of V. mungo, temperate legume species, and tropical legume species. Our transcriptome data from PacBio isoform sequencing showed that the 51-kb DNA inversion could affect the transcriptional regulation of accD polycistronic. Using Illumina deep RNA sequencing, we found RNA editing of clpP in the leaf, shoot, flower, fruit, and root tissues of V. mungo. We also found three G-to-A RNA editing events that change guanine to adenine in the transcripts transcribed from the adenine-rich regions of the ycf4 gene. The edited guanine bases were found particularly in the chloroplast genome of the Vigna species. These G-to-A RNA editing events were likely to provide a mechanism for correcting DNA base mutations. The V. mungo chloroplast genome sequence and the analysis results obtained in this study can apply to phylogenetic studies and chloroplast genome engineering.
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Affiliation(s)
- Wanapinun Nawae
- National Omics Center (NOC), National Science and Technology Development Agency, 111 Thailand Science Park, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand; (W.N.); (C.Y.); (C.N.); (W.K.); (T.Y.); (C.S.); (N.N.); (S.T.)
| | - Chutintorn Yundaeng
- National Omics Center (NOC), National Science and Technology Development Agency, 111 Thailand Science Park, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand; (W.N.); (C.Y.); (C.N.); (W.K.); (T.Y.); (C.S.); (N.N.); (S.T.)
| | - Chaiwat Naktang
- National Omics Center (NOC), National Science and Technology Development Agency, 111 Thailand Science Park, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand; (W.N.); (C.Y.); (C.N.); (W.K.); (T.Y.); (C.S.); (N.N.); (S.T.)
| | - Wasitthee Kongkachana
- National Omics Center (NOC), National Science and Technology Development Agency, 111 Thailand Science Park, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand; (W.N.); (C.Y.); (C.N.); (W.K.); (T.Y.); (C.S.); (N.N.); (S.T.)
| | - Thippawan Yoocha
- National Omics Center (NOC), National Science and Technology Development Agency, 111 Thailand Science Park, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand; (W.N.); (C.Y.); (C.N.); (W.K.); (T.Y.); (C.S.); (N.N.); (S.T.)
| | - Chutima Sonthirod
- National Omics Center (NOC), National Science and Technology Development Agency, 111 Thailand Science Park, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand; (W.N.); (C.Y.); (C.N.); (W.K.); (T.Y.); (C.S.); (N.N.); (S.T.)
| | - Nattapol Narong
- National Omics Center (NOC), National Science and Technology Development Agency, 111 Thailand Science Park, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand; (W.N.); (C.Y.); (C.N.); (W.K.); (T.Y.); (C.S.); (N.N.); (S.T.)
| | - Prakit Somta
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom 73140, Thailand; (P.S.); (K.L.)
| | - Kularb Laosatit
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom 73140, Thailand; (P.S.); (K.L.)
| | - Sithichoke Tangphatsornruang
- National Omics Center (NOC), National Science and Technology Development Agency, 111 Thailand Science Park, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand; (W.N.); (C.Y.); (C.N.); (W.K.); (T.Y.); (C.S.); (N.N.); (S.T.)
| | - Wirulda Pootakham
- National Omics Center (NOC), National Science and Technology Development Agency, 111 Thailand Science Park, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand; (W.N.); (C.Y.); (C.N.); (W.K.); (T.Y.); (C.S.); (N.N.); (S.T.)
- Correspondence: or
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554
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Wu Z, Liao R, Yang T, Dong X, Lan D, Qin R, Liu H. Analysis of six chloroplast genomes provides insight into the evolution of Chrysosplenium (Saxifragaceae). BMC Genomics 2020; 21:621. [PMID: 32912155 PMCID: PMC7488271 DOI: 10.1186/s12864-020-07045-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 09/01/2020] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Chrysosplenium L. (Saxifragaceae) is a genus of plants widely distributed in Northern Hemisphere and usually found in moist, shaded valleys and mountain slopes. This genus is ideal for studying plant adaptation to low light conditions. Although some progress has been made in the systematics and biogeography of Chrysosplenium, its chloroplast genome evolution remains to be investigated. RESULTS To fill this gap, we sequenced the chloroplast genomes of six Chrysosplenium species and analyzed their genome structure, GC content, and nucleotide diversity. Moreover, we performed a phylogenetic analysis and calculated non-synonymous (Ka) /synonymous (Ks) substitution ratios using the combined protein-coding genes of 29 species within Saxifragales and two additional species as outgroups, as well as a pair-wise estimation for each gene within Chrysosplenium. Compared with the outgroups in Saxifragaceae, the six Chrysosplenium chloroplast genomes had lower GC contents; they also had conserved boundary regions and gene contents, as only the rpl32 gene was lost in four of the Chrysosplenium chloroplast genomes. Phylogenetic analyses suggested that the Chrysosplenium separated to two major clades (the opposite group and the alternate group). The selection pressure estimation (Ka/Ks ratios) of genes in the Chrysosplenium species showed that matK and ycf2 were subjected to positive selection. CONCLUSION This study provides genetic resources for exploring the phylogeny of Chrysosplenium and sheds light on plant adaptation to low light conditions. The lower average GC content and the lacking gene of rpl32 indicated selective pressure in their unique habitats. Different from results previously reported, our selective pressure estimation suggested that the genes related to photosynthesis (such as ycf2) were under positive selection at sites in the coding region.
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Affiliation(s)
- Zhihua Wu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Sciences, South-Central University for Nationalities, Wuhan, 430074, Hubei, China
| | - Rui Liao
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Sciences, South-Central University for Nationalities, Wuhan, 430074, Hubei, China
| | - Tiange Yang
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Sciences, South-Central University for Nationalities, Wuhan, 430074, Hubei, China
| | - Xiang Dong
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Deqing Lan
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Sciences, South-Central University for Nationalities, Wuhan, 430074, Hubei, China
| | - Rui Qin
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Sciences, South-Central University for Nationalities, Wuhan, 430074, Hubei, China
| | - Hong Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Sciences, South-Central University for Nationalities, Wuhan, 430074, Hubei, China.
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555
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Comparative Analysis of Complete Chloroplast Genome Sequences and Insertion-Deletion (Indel) Polymorphisms to Distinguish Five Vaccinium Species. FORESTS 2020. [DOI: 10.3390/f11090927] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
We report the identification of interspecific barcoding InDel regions in Vaccinium species. We compared five complete Vaccinium chloroplast (cp) genomes (V. bracteatum, V. vitis-idaea, V. uliginosum, V. macrocarpon, and V. oldhamii) to identify regions that can be used to distinguish them. Comparative analysis of nucleotide diversity from five cp genomes revealed 25 hotspot coding and noncoding regions, occurring in 65 of a total of 505 sliding windows, that exhibited nucleotide diversity (Pi) > 0.02. PCR validation of 12 hypervariable InDel regions identified seven candidate barcodes with high discriminatory powers: accD-trnT-GGU, rpoB-rpoA, ycf2-trnL-GAA, rps12-ycf15, trnV-GAC, and ndhE-ndhF. Among them, the rpoB-rpoA(2) and ycf2-trnL-CAA sequences clearly showed the intraspecific and interspecific distance among five Vaccinium species by using a K2P technique. In phylogenetic analysis, included five Vaccinium species (n = 19) in the Bayesian and Neighbor-Joining (NJ) analysis revered all species in two major clades and resolved taxonomic position within species groups. These two locus provide comprehensive information that aids the phylogenetics of this genus and increased discriminatory capacity during species authentication.
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556
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Zhang F, Wang T, Shu X, Wang N, Zhuang W, Wang Z. Complete Chloroplast Genomes and Comparative Analyses of L. chinensis, L. anhuiensis, and L. aurea (Amaryllidaceae). Int J Mol Sci 2020; 21:E5729. [PMID: 32785156 PMCID: PMC7461117 DOI: 10.3390/ijms21165729] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/02/2020] [Accepted: 08/03/2020] [Indexed: 11/16/2022] Open
Abstract
The genus Lycoris (about 20 species) includes important medicinal and ornamental plants. Due to the similar morphological features and insufficient genomic resources, germplasm identification and molecular phylogeny analysis are very limited. Here, we sequenced the complete chloroplast genomes of L. chinensis, L. anhuiensis, and L. aurea; they have very similar morphological traits that make it difficult to identify. The full length of their cp genomes was nearly 158k bp with the same guanine-cytosine content of 37.8%. A total of 137 genes were annotated, including 87 protein-coding genes, 42 tRNAs, and eight rRNAs. A comparative analysis revealed the conservation in sequence size, GC content, and gene content. Some variations were observed in repeat structures, gene expansion on the IR-SC (Inverted Repeat-Single-Copy) boundary regions. Together with the cpSSR (chloroplast simple sequence repeats), these genetic variations are useful to develop molecular markers for germplasm identification. Phylogenetic analysis showed that seven Lycoris species were clustered into a monophyletic group, and closed to Narcissus in Amaryllidaceae. L. chinensis, L. anhuiensis, and L. longituba were clustered together, suggesting that they were very likely to be derived from one species, and had the same ancestor with L. squamigera. Our results provided information on the study of genetic diversity, origins or relatedness of native species, and the identification of cultivars.
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Affiliation(s)
- Fengjiao Zhang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing 210014, China; (T.W.); (X.S.); (N.W.); (W.Z.)
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing 210014, China
| | - Tao Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing 210014, China; (T.W.); (X.S.); (N.W.); (W.Z.)
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing 210014, China
| | - Xiaochun Shu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing 210014, China; (T.W.); (X.S.); (N.W.); (W.Z.)
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing 210014, China
| | - Ning Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing 210014, China; (T.W.); (X.S.); (N.W.); (W.Z.)
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing 210014, China
| | - Weibing Zhuang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing 210014, China; (T.W.); (X.S.); (N.W.); (W.Z.)
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing 210014, China
| | - Zhong Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing 210014, China; (T.W.); (X.S.); (N.W.); (W.Z.)
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing 210014, China
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557
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Jiang M, Xu Y, Wang L, Liu J, Yu J, Chen H. High level of intraspecific divergence and low frequency of RNA editing in the chloroplast genome sequence of Tagetes erecta. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:2948-2953. [PMID: 33458014 PMCID: PMC7782230 DOI: 10.1080/23802359.2020.1791001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Tagetes erecta L. is an important commercial and medicinal plant. In this study, we reported the complete chloroplast genome sequence of T. erecta. The genome has a circular structure of 152,076 bp containing a large single-copy region (LSC) of 83,914 bp, a small copy region (SSC) of 18,064 bp, and two inverted repeats (IR) of 25,049 bp by each. It harbors 111 unique genes, including 79 protein-coding genes, 4 ribosomal RNA genes, and 28 transfer RNA genes. A total of 41 microsatellite, 20 tandem, and 37 interspersed repeats were detected in the genome. The phylogenomic analysis shows that T. erecta is a single phylogenetic cluster. The complete chloroplast genome of T. erecta lays the foundation for the phylogenetic, evolutionary, and conservation studies of the genus Tagetes. Furthermore, the intergenic region of atpB-rbcL was variable among the species T. erecta. This suggests that this region might be a mutation hotspot and will be useful for phylogenetic study and the development of molecular markers. At last, we systematically identified the RNA editing sites in the chloroplast genome of T. erecta based on the transcriptome downloaded from the SRA database. This study identified the characteristics of the T. erecta chloroplast genome, SNPs, and RNA editing sites, which will facilitate species identification and phylogenetic analysis within T. erecta.
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Affiliation(s)
- Mei Jiang
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, P. R. China
| | - Yicen Xu
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Liqiang Wang
- College of Pharmacy, Heze University, Heze, Shandong Province, P. R. China
| | - Jingting Liu
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, P. R. China
| | - Jie Yu
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Haimei Chen
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, P. R. China
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558
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Mehmood F, Abdullah, Ubaid Z, Shahzadi I, Ahmed I, Waheed MT, Poczai P, Mirza B. Plastid genomics of Nicotiana (Solanaceae): insights into molecular evolution, positive selection and the origin of the maternal genome of Aztec tobacco ( Nicotiana rustica). PeerJ 2020; 8:e9552. [PMID: 32775052 PMCID: PMC7382938 DOI: 10.7717/peerj.9552] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 06/24/2020] [Indexed: 12/17/2022] Open
Abstract
Species of the genus Nicotiana (Solanaceae), commonly referred to as tobacco plants, are often cultivated as non-food crops and garden ornamentals. In addition to the worldwide production of tobacco leaves, they are also used as evolutionary model systems due to their complex development history tangled by polyploidy and hybridization. Here, we assembled the plastid genomes of five tobacco species: N. knightiana, N. rustica, N. paniculata, N. obtusifolia and N. glauca. De novo assembled tobacco plastid genomes had the typical quadripartite structure, consisting of a pair of inverted repeat (IR) regions (25,323-25,369 bp each) separated by a large single-copy (LSC) region (86,510-86,716 bp) and a small single-copy (SSC) region (18,441-18,555 bp). Comparative analyses of Nicotiana plastid genomes with currently available Solanaceae genome sequences showed similar GC and gene content, codon usage, simple sequence and oligonucleotide repeats, RNA editing sites, and substitutions. We identified 20 highly polymorphic regions, mostly belonging to intergenic spacer regions (IGS), which could be suitable for the development of robust and cost-effective markers for inferring the phylogeny of the genus Nicotiana and family Solanaceae. Our comparative plastid genome analysis revealed that the maternal parent of the tetraploid N. rustica was the common ancestor of N. paniculata and N. knightiana, and the later species is more closely related to N. rustica. Relaxed molecular clock analyses estimated the speciation event between N. rustica and N. knightiana appeared 0.56 Ma (HPD 0.65-0.46). Biogeographical analysis supported a south-to-north range expansion and diversification for N. rustica and related species, where N. undulata and N. paniculata evolved in North/Central Peru, while N. rustica developed in Southern Peru and separated from N. knightiana, which adapted to the Southern coastal climatic regimes. We further inspected selective pressure on protein-coding genes among tobacco species to determine if this adaptation process affected the evolution of plastid genes. These analyses indicate that four genes involved in different plastid functions, including DNA replication (rpoA) and photosynthesis (atpB, ndhD and ndhF), came under positive selective pressure as a result of specific environmental conditions. Genetic mutations in these genes might have contributed to better survival and superior adaptations during the evolutionary history of tobacco species.
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Affiliation(s)
- Furrukh Mehmood
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
- Botany Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Abdullah
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Zartasha Ubaid
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Iram Shahzadi
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Ibrar Ahmed
- Alpha Genomics Private Limited, Islamabad, Pakistan
| | - Mohammad Tahir Waheed
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Peter Poczai
- Botany Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Bushra Mirza
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
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559
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Jang JH, Jung HK, Park H, Lee KM, Kim JK, Hwang TY, Cho HW. Characterization of the complete chloroplast genome of Liriope platyphylla (Asparagaceae: Nolinoideae) isolated in Korea. Mitochondrial DNA B Resour 2020; 5:2874-2875. [PMID: 33457984 PMCID: PMC7782188 DOI: 10.1080/23802359.2020.1787898] [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] [Indexed: 11/08/2022] Open
Abstract
Liriope platyphylla is used as an important medicinal plant for fatigue, cough, and inflammation in South Korea. Here, we report the complete chloroplast genome of L. platyphylla. The total genome size of the chloroplast is 157,076 bp with a large single-copy region (LSC: 85,374 bp), a small single-copy region (SSC: 18,748 bp), and inverted repeat regions (IRa and IRb: 26,477 bp). The GC content of the L. platyphylla chloroplast was 37.6%. The cp genome encoded a set of 129 genes, including 83 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. The phylogenetic tree analysis indicated that L. platyphylla is closely related to L. spicata.
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Affiliation(s)
- Ji-Hun Jang
- National Development Institute of Korean Medicine, Jangheung-gun, South Korea
| | - Ho-Kyung Jung
- National Development Institute of Korean Medicine, Jangheung-gun, South Korea
| | - Ho Park
- National Development Institute of Korean Medicine, Jangheung-gun, South Korea
| | - Kyung-Min Lee
- National Development Institute of Korean Medicine, Jangheung-gun, South Korea
| | - Ji-Kyung Kim
- National Development Institute of Korean Medicine, Jangheung-gun, South Korea
| | - Tae-Yeon Hwang
- National Development Institute of Korean Medicine, Jangheung-gun, South Korea
| | - Hyun-Woo Cho
- National Development Institute of Korean Medicine, Jangheung-gun, South Korea
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560
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Charr JC, Garavito A, Guyeux C, Crouzillat D, Descombes P, Fournier C, Ly SN, Raharimalala EN, Rakotomalala JJ, Stoffelen P, Janssens S, Hamon P, Guyot R. Complex evolutionary history of coffees revealed by full plastid genomes and 28,800 nuclear SNP analyses, with particular emphasis on Coffea canephora (Robusta coffee). Mol Phylogenet Evol 2020; 151:106906. [PMID: 32653553 DOI: 10.1016/j.ympev.2020.106906] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 06/17/2020] [Accepted: 07/06/2020] [Indexed: 11/16/2022]
Abstract
For decades coffees were associated with the genus Coffea. In 2011, the closely related genus Psilanthus was subsumed into Coffea. However, results obtained in 2017-based on 28,800 nuclear SNPs-indicated that there is not substantial phylogenetic support for this incorporation. In addition, a recent study of 16 plastid full-genome sequences highlighted an incongruous placement of Coffea canephora (Robusta coffee) between maternal and nuclear trees. In this study, similar global features of the plastid genomes of Psilanthus and Coffea are observed. In agreement with morphological and physiological traits, the nuclear phylogenetic tree clearly separates Psilanthus from Coffea (with exception to C. rhamnifolia, closer to Psilanthus than to Coffea). In contrast, the maternal molecular tree was incongruent with both morphological and nuclear differentiation, with four main clades observed, two of which include both Psilanthus and Coffea species, and two with either Psilanthus or Coffea species. Interestingly, Coffea and Psilanthus taxa sampled in West and Central Africa are members of the same group. Several mechanisms such as the retention of ancestral polymorphisms due to incomplete lineage sorting, hybridization leading to homoploidy (without chromosome doubling) and alloploidy (for C. arabica) are involved in the evolutionary history of the coffee species. While sharing similar morphological characteristics, the genetic relationships within C. canephora have shown that some populations are well differentiated and genetically isolated. Given the position of its closely-related species, we may also consider C. canephora to be undergoing a long process of speciation with an intermediate step of (sub-)speciation.
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Affiliation(s)
- Jean-Claude Charr
- Femto-ST Institute, UMR 6174 CNRS, Université de Bourgogne Franche-Comté, France.
| | - Andrea Garavito
- Departamento de Ciencias biológicas, Facultad de Ciencias Exactas y Naturales, Universidad de Caldas, Manizales, Colombia
| | - Christophe Guyeux
- Femto-ST Institute, UMR 6174 CNRS, Université de Bourgogne Franche-Comté, France.
| | | | | | | | - Serigne N Ly
- Institut de Recherche pour le Développement, UMR DIADE, CIRAD, Université de Montpellier, France.
| | | | | | - Piet Stoffelen
- Meise Botanic Garden, Nieuwelaan 38, BE-1860 Meise, Belgium.
| | - Steven Janssens
- Meise Botanic Garden, Nieuwelaan 38, BE-1860 Meise, Belgium.
| | - Perla Hamon
- Institut de Recherche pour le Développement, UMR DIADE, CIRAD, Université de Montpellier, France.
| | - Romain Guyot
- Institut de Recherche pour le Développement, UMR DIADE, CIRAD, Université de Montpellier, France; Department of Electronics and Automatization, Universidad Autónoma de Manizales, Manizales, Colombia.
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561
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Transcriptome and complete chloroplast genome of Glycyrrhiza inflata and comparative analyses with the other two licorice species. Genomics 2020; 112:4179-4188. [PMID: 32650098 DOI: 10.1016/j.ygeno.2020.07.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 06/04/2020] [Accepted: 07/02/2020] [Indexed: 11/20/2022]
Abstract
In this study, we characterized the transcriptome and chloroplast genome of Glycyrrhiza inflata and performed comparative analyses with G. uralensis and G. glabra. 60,541unigenes were obtained from the transcriptome of G. inflata. The results of function annotation revealed a similar distribution of functional categories among three licorice species. By comparing chloroplast genomes of licorice species, it was demonstrated that the structure and the length of genome as well as gene content and gene order were highly similar. The phylogenetic tree, constructed with the mixed data of transcriptome and chloroplast genome, elucidated that G. inflata and G. glabra had a closer relationship than G. uralensis. Six regions were suggested as potential markers for the identification of three licorice species. In each licorice species, two unigenes were homologous to reference flavonol synthase. For G. inflata, 48 and 21 RNA editing sites were detected by PREP-Cp program and RNA-Seq data mapping, respectively.
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562
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Xu W, Chen H, Tian L, Jiang M, Yang Q, Wang L, Ahmad B, Huang L. Extensive gene loss in the plastome of holoparasitic plant Cistanche tubulosa (Orobanchaceae). MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:2679-2681. [PMID: 33457902 PMCID: PMC7782945 DOI: 10.1080/23802359.2020.1787273] [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: 11/25/2022]
Abstract
Extensive photosynthetic gene loss and rapid evolutionary rate occur in the plastomes of parasitic plants. The holoparasitic plant Cistanche tubulosa of Orobanchaceae is an important medicinal resources that are distributed in arid areas. In this study, the complete plastome of C. tubulosa has been sequenced, assembled and analyzed. The total plastome of C. tubulosa was 75,375 bp in length, consisting of a pair of inverted repeats (IRs, 6,593 bp), a large single-copy region (LSC, 32,470 bp) and a small single-copy region (SSC, 29,719 bp). It contained 24 intact protein coding genes, nine pseudogenes, and 44 missing genes. In addition, all the protein-coding genes, which were related to photosynthesis and energy production, were pseudogenised or lost. Four rRNA genes and 24 tRNA genes were intact meanwhile five tRNA genes were missing. Phylogenetic tree indicated that C. tubulosa was closely related to C. phelypaea. Our results may improve understanding of the plastome organization, classification, and evolution of parasitic plants.
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Affiliation(s)
- Wanqi Xu
- Key Research Laboratory of Traditional Chinese Medicine Resources Protection from Ministry of Education, Engineering Research Center of Chinese Medicine Resource, National Administration of Traditional Chinese Medicine, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Haimei Chen
- Key Research Laboratory of Traditional Chinese Medicine Resources Protection from Ministry of Education, Engineering Research Center of Chinese Medicine Resource, National Administration of Traditional Chinese Medicine, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Lixia Tian
- Key Research Laboratory of Traditional Chinese Medicine Resources Protection from Ministry of Education, Engineering Research Center of Chinese Medicine Resource, National Administration of Traditional Chinese Medicine, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Mei Jiang
- Key Research Laboratory of Traditional Chinese Medicine Resources Protection from Ministry of Education, Engineering Research Center of Chinese Medicine Resource, National Administration of Traditional Chinese Medicine, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Qiaoqiao Yang
- Key Research Laboratory of Traditional Chinese Medicine Resources Protection from Ministry of Education, Engineering Research Center of Chinese Medicine Resource, National Administration of Traditional Chinese Medicine, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Liqiang Wang
- Key Research Laboratory of Traditional Chinese Medicine Resources Protection from Ministry of Education, Engineering Research Center of Chinese Medicine Resource, National Administration of Traditional Chinese Medicine, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Bashir Ahmad
- Center for Biotechnology and Microbiology, University of Peshawar, Peshawar, Pakistan
| | - LinFang Huang
- Key Research Laboratory of Traditional Chinese Medicine Resources Protection from Ministry of Education, Engineering Research Center of Chinese Medicine Resource, National Administration of Traditional Chinese Medicine, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
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563
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Tyagi S, Jung JA, Kim JS, Won SY. A comparative analysis of the complete chloroplast genomes of three Chrysanthemum boreale strains. PeerJ 2020; 8:e9448. [PMID: 32685287 PMCID: PMC7337036 DOI: 10.7717/peerj.9448] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 06/09/2020] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Chrysanthemum boreale Makino (Anthemideae, Asteraceae) is a plant of economic, ornamental and medicinal importance. We characterized and compared the chloroplast genomes of three C. boreale strains. These were collected from different geographic regions of Korea and varied in floral morphology. METHODS The chloroplast genomes were obtained by next-generation sequencing techniques, assembled de novo, annotated, and compared with one another. Phylogenetic analysis placed them within the Anthemideae tribe. RESULTS The sizes of the complete chloroplast genomes of the C. boreale strains were 151,012 bp (strain 121002), 151,098 bp (strain IT232531) and 151,010 bp (strain IT301358). Each genome contained 80 unique protein-coding genes, 4 rRNA genes and 29 tRNA genes. Comparative analyses revealed a high degree of conservation in the overall sequence, gene content, gene order and GC content among the strains. We identified 298 single nucleotide polymorphisms (SNPs) and 106 insertions/deletions (indels) in the chloroplast genomes. These variations were more abundant in non-coding regions than in coding regions. Long dispersed repeats and simple sequence repeats were present in both coding and noncoding regions, with greater frequency in the latter. Regardless of their location, these repeats can be used for molecular marker development. Phylogenetic analysis revealed the evolutionary relationship of the species in the Anthemideae tribe. The three complete chloroplast genomes will be valuable genetic resources for studying the population genetics and evolutionary relationships of Asteraceae species.
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Affiliation(s)
- Swati Tyagi
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, Republic of Korea
| | - Jae-A Jung
- Floriculture Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju, Republic of Korea
| | - Jung Sun Kim
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, Republic of Korea
| | - So Youn Won
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, Republic of Korea
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564
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Sa W, Liang J, Shang QH, Liu ML, Wang ML, Li ZH. The complete nucleotide molecular sequence of plastid genome of Zanthoxylum armatum (Rutaceae). Mitochondrial DNA B Resour 2020; 5:3400-3401. [PMID: 33458184 PMCID: PMC7782098 DOI: 10.1080/23802359.2020.1823263] [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: 11/21/2022] Open
Abstract
Zanthoxylum armatum DC. (Rutaceae) is a shrub and/or tree species with the important medicinal and economic values. In this study, the plastid genome of Z. armatum was characterized by Illumina Hiseq 2500 sequencing platform. In total, the plastid genome is 158,557 bp in length, and comprises a large single copy region of 85,752 bp, a small single copy region of 17,605 bp, and two inverted repeat regions of 27,600 bp. The complete plastid genome contains 87 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis suggested that Z. armatum and the congeneric Z. simulans clustered into an evolutionary clade with the high support.
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Affiliation(s)
- Wei Sa
- State Key Laboratory of Plateau Ecology and Agriculture, College of Ecological and Environmental Engineering, Qinghai University, Xining, China
| | - Jian Liang
- State Key Laboratory of Plateau Ecology and Agriculture, College of Ecological and Environmental Engineering, Qinghai University, Xining, China
| | - Qian-Han Shang
- State Key Laboratory of Plateau Ecology and Agriculture, College of Ecological and Environmental Engineering, Qinghai University, Xining, China
| | - Mi-Li Liu
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Ma-Li Wang
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Zhong-Hu Li
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
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565
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Cao T, Ma X, Zhang Y, Su W, Li B, Zhou Q, Zhu Q. The complete chloroplast genome sequence of the Pueraria lobata (Willd.) Ohwi (Leguminosae). Mitochondrial DNA B Resour 2020; 5:3772-3774. [PMID: 33367096 PMCID: PMC7671689 DOI: 10.1080/23802359.2020.1835576] [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: 11/06/2022] Open
Abstract
Pueraria lobata (Willd.) Ohwi is an essential traditional oriental medicine with therapeutic effects. In this study, we assembled the complete chloroplast genome of P. lobata. The total genome size was 153,442 bp in length, containing a large single-copy (LSC) region of 84,162 bp, a small single-copy (SSC) of 17,998 bp, and a pair of inverted repeats (IRs) of 25,641 bp, and possessing 35.41% GC content. In addition, the whole chloroplast genome encodes a total of 129 genes, including 84 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic tree analysis of 48 species in the family Papilionoideae of Leguminosae indicated that P. lobata was belong to Papilionoideae and closely related to the genus, Pachyrhizus, Vigna and Phaseolus.
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Affiliation(s)
- Tianxu Cao
- Department of Horticulture, College of Agronomy, Jiangxi Agricultural University, Nanchang, PR China
| | - Xiling Ma
- Department of Horticulture, College of Agronomy, Jiangxi Agricultural University, Nanchang, PR China
| | - Yu Zhang
- Department of Horticulture, College of Agronomy, Jiangxi Agricultural University, Nanchang, PR China
| | - Wenzheng Su
- Department of Horticulture, College of Agronomy, Jiangxi Agricultural University, Nanchang, PR China
| | - Bicong Li
- Department of Horticulture, College of Agronomy, Jiangxi Agricultural University, Nanchang, PR China
| | - Qinghong Zhou
- Department of Horticulture, College of Agronomy, Jiangxi Agricultural University, Nanchang, PR China
| | - Qianglong Zhu
- Department of Horticulture, College of Agronomy, Jiangxi Agricultural University, Nanchang, PR China
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566
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Li J, Jiang M, Chen H, Yu J, Liu C. Intraspecific variations among the chloroplast genomes of Artemisia scoparia (asteraceae) from Pakistan and China. Mitochondrial DNA B Resour 2020. [DOI: 10.1080/23802359.2020.1810167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- Jingling Li
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Mei Jiang
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Haimei Chen
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Jie Yu
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Chang Liu
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
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567
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Zhang Y, Liu X, Yao Y, Luo Y, Yang Q, Zhang C, Chaoqun X, Suo F, Shen G, Guo B. The complete chloroplast genome of Epimedium pudingense (Berberidaceae), a narrowly distributed plant species in China. Mitochondrial DNA B Resour 2020; 5:2631-2633. [PMID: 33457886 PMCID: PMC7782884 DOI: 10.1080/23802359.2020.1781560] [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: 11/24/2022] Open
Abstract
Epimedium L. is the largest herbaceous genus of Berberidaceae which comprises more than 60 species. Epimedium pudingense is a rare plant species only narrowly inhabited in the Puding County in the Guizhou Province of China. Here, we first report the complete chloroplast genome of E. pudingense assembled from Illumina short-read sequencing data. The chloroplast genome of E. pudingense was 157,325 bp in length, with a total GC content of 36.11%. A total of 112 unique genes were identified, among which are 78 protein-coding genes, 30 tRNA genes and four rRNA genes. The phylogenetic analysis revealed that E. pudingense closely related to E. elachyphyllum. Our study will provide useful fundamental data for further phylogenetic and evolutionary studies of the Epimedium genus.
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Affiliation(s)
- Yixin Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Xiang Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
- Chongqing Academy of Chinese Materia Medica, Chongqing, China
| | - Yu Yao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Yanjiao Luo
- College-of-Pharmacy, Shanxi Medical University, Taiyuan, China
| | - Qianru Yang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Cheng Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Xu Chaoqun
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Fengmei Suo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Guoan Shen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Baolin Guo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
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568
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Feng X, Yang Z, Xiu-Rong W, Hong Hong T. Characterization of the complete chloroplast genome of Trachycarpus fortunei. Mitochondrial DNA B Resour 2020; 5:3106-3107. [PMID: 33458075 PMCID: PMC7782514 DOI: 10.1080/23802359.2020.1800432] [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: 12/01/2022] Open
Abstract
Trachycarpus fortunei (Hook.) H. Wendl. (Fam.: Palmae; Gen.: Trachycarpus) is an evergreen tree that is widely distributed in China. In this study, T. fortunei complete chloroplast (cp) genome was assembled. The total cp genome size of T. fortunei was 158,613 bp in length, containing a large single-copy region of 86,422 bp, a small single-copy region of 17,847 bp, and a pair of inverted repeat regions of 27,172 bp. The overall GC-content of T. fortunei cp genome was 37.21%. It encodes a total of 109 unique genes, including 79 protein-coding genes, 26 tRNA genes, four rRNA genes. Twelve genes contain a single intron and 11 genes have two introns. Phylogenetic analysis results reveal that T. fortunei was closely related to Chamaerops humilis.
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Affiliation(s)
- Xiao Feng
- College of Forestry, Guizhou University, Guiyang, PR China
- Institute for Forest Resources & Environment of Guizhou, Guizhou University, Guiyang, PR China
- Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, Guizhou University, Guiyang, PR China
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, PR China
| | - Zhao Yang
- College of Forestry, Guizhou University, Guiyang, PR China
- Institute for Forest Resources & Environment of Guizhou, Guizhou University, Guiyang, PR China
- Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, Guizhou University, Guiyang, PR China
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, PR China
| | - Wang Xiu-Rong
- College of Forestry, Guizhou University, Guiyang, PR China
| | - Tian Hong Hong
- College of Forestry, Guizhou University, Guiyang, PR China
- Institute for Forest Resources & Environment of Guizhou, Guizhou University, Guiyang, PR China
- Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, Guizhou University, Guiyang, PR China
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, PR China
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569
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Li P, Ren M, Zhu Q, Zhang Y, Xu H, Wang Z, Liu S, Cheng Q, Liang B. The complete chloroplast genome of Hippeastrum vittatum (Amaryllidaceae). Mitochondrial DNA B Resour 2020; 5:3521-3523. [PMID: 33458226 PMCID: PMC7781927 DOI: 10.1080/23802359.2020.1827059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Peiling Li
- College of Horticulture, Xinyang Agricultural and Forestry University, Xinyang, China
- Henan Key Laboratory of Tea Comprehensive Utilization in South Henan, Xinyang Agriculture and Forestry University, Xinyang, China
| | - Maofei Ren
- College of Horticulture, Xinyang Agricultural and Forestry University, Xinyang, China
- Henan Key Laboratory of Tea Comprehensive Utilization in South Henan, Xinyang Agriculture and Forestry University, Xinyang, China
| | - Qingsong Zhu
- College of Horticulture, Xinyang Agricultural and Forestry University, Xinyang, China
- Henan Key Laboratory of Tea Comprehensive Utilization in South Henan, Xinyang Agriculture and Forestry University, Xinyang, China
| | - Yan Zhang
- College of Horticulture, Xinyang Agricultural and Forestry University, Xinyang, China
- Henan Key Laboratory of Tea Comprehensive Utilization in South Henan, Xinyang Agriculture and Forestry University, Xinyang, China
| | - Hanbing Xu
- College of Horticulture, Xinyang Agricultural and Forestry University, Xinyang, China
- Henan Key Laboratory of Tea Comprehensive Utilization in South Henan, Xinyang Agriculture and Forestry University, Xinyang, China
| | - Zhiyong Wang
- College of Horticulture, Xinyang Agricultural and Forestry University, Xinyang, China
- Henan Key Laboratory of Tea Comprehensive Utilization in South Henan, Xinyang Agriculture and Forestry University, Xinyang, China
| | - Songhu Liu
- College of Horticulture, Xinyang Agricultural and Forestry University, Xinyang, China
- Henan Key Laboratory of Tea Comprehensive Utilization in South Henan, Xinyang Agriculture and Forestry University, Xinyang, China
| | - Qin Cheng
- College of Horticulture, Xinyang Agricultural and Forestry University, Xinyang, China
- Henan Key Laboratory of Tea Comprehensive Utilization in South Henan, Xinyang Agriculture and Forestry University, Xinyang, China
| | - Benguo Liang
- College of Horticulture, Xinyang Agricultural and Forestry University, Xinyang, China
- Henan Key Laboratory of Tea Comprehensive Utilization in South Henan, Xinyang Agriculture and Forestry University, Xinyang, China
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570
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Mehmood F, Abdullah, Ubaid Z, Bao Y, Poczai P, Mirza B. Comparative Plastomics of Ashwagandha ( Withania, Solanaceae) and Identification of Mutational Hotspots for Barcoding Medicinal Plants. PLANTS (BASEL, SWITZERLAND) 2020; 9:E752. [PMID: 32549379 PMCID: PMC7355740 DOI: 10.3390/plants9060752] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 06/10/2020] [Accepted: 06/12/2020] [Indexed: 01/04/2023]
Abstract
Within the family Solanaceae, Withania is a small genus belonging to the Solanoideae subfamily. Here, we report the de novo assembled chloroplast genome sequences of W. coagulans, W. adpressa, and W. riebeckii. The length of these genomes ranged from 154,162 to 154,364 base pairs (bp). These genomes contained a pair of inverted repeats (IRa and IRb) ranging from 25,029 to 25,071 bp that were separated by a large single-copy (LSC) region of 85,635-85,765 bp and a small single-copy (SSC) region of 18,457-18,469 bp. We analyzed the structural organization, gene content and order, guanine-cytosine content, codon usage, RNA-editing sites, microsatellites, oligonucleotide and tandem repeats, and substitutions of Withania plastomes, which revealed high similarities among the species. Comparative analysis among the Withania species also highlighted 10 divergent hotspots that could potentially be used for molecular marker development, phylogenetic analysis, and species identification. Furthermore, our analyses showed that even three mutational hotspots (rps4-trnT, trnM-atpE, and rps15) were sufficient to discriminate the Withania species included in current study.
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Affiliation(s)
- Furrukh Mehmood
- Department of Biochemistry, Quaid-i-Azam University, Islamabad 45320, Pakistan; (F.M.); (A.); (Z.U.)
- Botany Unit, Finnish Museum of Natural History, University of Helsinki, P.O. Box 7, FI-00014 Helsinki, Finland
| | - Abdullah
- Department of Biochemistry, Quaid-i-Azam University, Islamabad 45320, Pakistan; (F.M.); (A.); (Z.U.)
| | - Zartasha Ubaid
- Department of Biochemistry, Quaid-i-Azam University, Islamabad 45320, Pakistan; (F.M.); (A.); (Z.U.)
| | - Yiming Bao
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China;
- School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peter Poczai
- Botany Unit, Finnish Museum of Natural History, University of Helsinki, P.O. Box 7, FI-00014 Helsinki, Finland
| | - Bushra Mirza
- Department of Biochemistry, Quaid-i-Azam University, Islamabad 45320, Pakistan; (F.M.); (A.); (Z.U.)
- Vice Chancellor of Lahore College for Women University, Lahore 54000, Pakistan
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571
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Zhu Q, Cai L, Li H, Zhang Y, Su W, Zhou Q. The complete chloroplast genome sequence of the Canna edulis Ker Gawl. (Cannaceae). Mitochondrial DNA B Resour 2020; 5:2427-2428. [PMID: 33457814 PMCID: PMC7782134 DOI: 10.1080/23802359.2020.1775512] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Canna edulis Ker Gawl. is an essential traditional tuber crop used for fresh consumption and to isolate starch in some tropical and semitropical regions. The complete chloroplast genome sequence of C. edulis has been determined in this study. The total genome size is 164,650 bp in length and contains a pair of inverted repeats (IRs) of 27,278 bp, which were separated by large single-copy (LSC) and small single-copy (SSC) of 91,421 bp and 18,673 bp, respectively. A total of 131 genes were predicted including 86 protein-coding genes, 8 rRNA genes and 37 tRNA genes. Further, maximum-likelihood phylogenetic analysis revealed that C. edulis belongs to Cannaceae in Zingiberales. The chloroplast genome of C. edulis is first complete genome sequence in Cannaceae and would play a significant role in the development of molecular markers in plant phylogenetic and population genetic studies.
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Affiliation(s)
- Qianglong Zhu
- Department of Horticulture, College of Agronomy, Jiangxi Agricultural University, Nanchang, P.R. China
| | - Lijuan Cai
- Nanchang Business college, Jiangxi Agricultural University, Nanchang, P.R. China
| | - Huiying Li
- Department of Horticulture, College of Agronomy, Jiangxi Agricultural University, Nanchang, P.R. China
| | - Yu Zhang
- Department of Horticulture, College of Agronomy, Jiangxi Agricultural University, Nanchang, P.R. China
| | - Wenzhen Su
- Department of Horticulture, College of Agronomy, Jiangxi Agricultural University, Nanchang, P.R. China
| | - Qinghong Zhou
- Department of Horticulture, College of Agronomy, Jiangxi Agricultural University, Nanchang, P.R. China
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572
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Zhang R, Zhang YX, Liu W, Hui C. The complete chloroplast genome of Dendrocalamus hamiltonii (Poaceae, Bambuseae). MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:2320-2321. [PMID: 33457774 PMCID: PMC7782895 DOI: 10.1080/23802359.2020.1772696] [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: 12/03/2022]
Abstract
Dendrocalamus hamiltonii is one of the best bamboo species with bamboo shoots, and has higher economic value. The chloroplast genome is a circular molecule of 139404 bp in length, consisting of a 82938 bp large single copy region (LSC), a 12876 bp small single copy region (SSC), and a pair of inverted repeats region (IRa and IRb: 21795 bp each). The GC content of chloroplast genome is 38.9%. The cp genome contains a total of 133 genes, including 86 protein-coding genes, 8 rRNA genes, and 39 tRNA genes. Moreover, phylogenomic analysis showed that D. hamiltonii and D. brandisii clustered together in one branch.
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Affiliation(s)
- Ruli Zhang
- Sympodial Bamboos Technological and Engineering Research Center (SymBTERC) National Forestry and Grassland Administration (NFGA), Southwest Forestry University, Kunming, China.,Institute of Bamboo and Rattan, Southwest Forestry University, Kunming, China
| | - Yu-Xiao Zhang
- Sympodial Bamboos Technological and Engineering Research Center (SymBTERC) National Forestry and Grassland Administration (NFGA), Southwest Forestry University, Kunming, China.,Yunnan Academy of Biodiversity, Southwest Forestry University, Kunming, China
| | - Weiyi Liu
- Sympodial Bamboos Technological and Engineering Research Center (SymBTERC) National Forestry and Grassland Administration (NFGA), Southwest Forestry University, Kunming, China.,Institute of Bamboo and Rattan, Southwest Forestry University, Kunming, China
| | - Chaomao Hui
- Sympodial Bamboos Technological and Engineering Research Center (SymBTERC) National Forestry and Grassland Administration (NFGA), Southwest Forestry University, Kunming, China.,Institute of Bamboo and Rattan, Southwest Forestry University, Kunming, China
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573
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Li X, Xu T, Yao Y, Yang Q, Xu C, Suo F, Zhang C, Shen G, Guo B, Liu X, Wei S. The complete chloroplast genome of Epimedium enshiense B. L. Guo et Hsiao (Berberidaceae). MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:2045-2046. [PMID: 33457736 PMCID: PMC7782069 DOI: 10.1080/23802359.2020.1730269] [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: 10/30/2022]
Abstract
The genus of Epimedium belongs to Berberidaceae family, which is famous for their medicinal and ornamental value. In recent years, Epimedium has attracted increasing attention due to their medicinal and nutritive value. In this research, we reported the complete chloroplast (cp) genome of Epimedium enshiense. The complete chloroplast of this species is 157,076 bp in length, including a pair of invert repeat regions (IRS) (25,833 bp) that is divided by a large single copy area (LSC) (88,340 bp) and a small single copy area (SSC) (17,070 bp). The circular chloroplast genome of E. enshiense contains 112 unique genes, composing of 78 protein-coding genes, 30 tRNA, and four rRNA genes. Phylogenetic analysis indicates that E. enshiense has a closer relationship with E. dolichostmon.
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Affiliation(s)
- Xiaoming Li
- School of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang, China.,Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Tianrong Xu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China.,College of Pharmacy, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Yu Yao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Qianru Yang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Chaoqun Xu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Fengmei Suo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Cheng Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Guoan Shen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Baolin Guo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Xiang Liu
- Chongqing Key Laboratory of Traditional Chinese Medicine Resource, Chongqing Academy of Chinese Materia Medica, Chongqing, China
| | - Shenghua Wei
- School of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang, China
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574
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Tyagi S, Jung JA, Kim JS, Won SY. Comparative Analysis of the Complete Chloroplast Genome of Mainland Aster spathulifolius and Other Aster Species. PLANTS (BASEL, SWITZERLAND) 2020; 9:E568. [PMID: 32365609 PMCID: PMC7285121 DOI: 10.3390/plants9050568] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/25/2020] [Accepted: 04/27/2020] [Indexed: 11/16/2022]
Abstract
Aster spathulifolius, a common ornamental and medicinal plant, is widely distributed in Korea and Japan, and is genetically classified into mainland and island types. Here, we sequenced the whole chloroplast genome of mainland A. spathulifolius and compared it with those of the island type and other Aster species. The chloroplast genome of mainland A. spathulifolius is 152,732 bp with a conserved quadripartite structure, has 37.28% guanine-cytosine (GC) content, and contains 114 non-redundant genes. Comparison of the chloroplast genomes between the two A. spathulifolius lines and the other Aster species revealed that their sequences, GC contents, gene contents and orders, and exon-intron structure were well conserved; however, differences were observed in their lengths, repeat sequences, and the contraction and expansion of the inverted repeats. The variations were mostly in the single-copy regions and non-coding regions, which, together with the detected simple sequence repeats, could be used for the development of molecular markers to distinguish between these plants. All Aster species clustered into a monophyletic group, but the chloroplast genome of mainland A. spathulifolius was more similar to the other Aster species than to that of the island A. spathulifolius. The accD and ndhF genes were detected to be under positive selection within the Aster lineage compared to other related taxa. The complete chloroplast genome of mainland A. spathulifolius presented in this study will be helpful for species identification and the analysis of the genetic diversity, evolution, and phylogenetic relationships in the Aster genus and the Asteraceae.
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Affiliation(s)
- Swati Tyagi
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (S.T.); (J.S.K.)
| | - Jae-A Jung
- Floriculture Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Korea;
| | - Jung Sun Kim
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (S.T.); (J.S.K.)
| | - So Youn Won
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (S.T.); (J.S.K.)
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575
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Omelchenko DO, Makarenko MS, Kasianov AS, Schelkunov MI, Logacheva MD, Penin AA. Assembly and Analysis of the Complete Mitochondrial Genome of Capsella bursa-pastoris. PLANTS (BASEL, SWITZERLAND) 2020; 9:E469. [PMID: 32276324 PMCID: PMC7238199 DOI: 10.3390/plants9040469] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 03/24/2020] [Accepted: 04/04/2020] [Indexed: 12/11/2022]
Abstract
Shepherd's purse (Capsella bursa-pastoris) is a cosmopolitan annual weed and a promising model plant for studying allopolyploidization in the evolution of angiosperms. Though plant mitochondrial genomes are a valuable source of genetic information, they are hard to assemble. At present, only the complete mitogenome of C. rubella is available out of all species of the genus Capsella. In this work, we have assembled the complete mitogenome of C. bursa-pastoris using high-precision PacBio SMRT third-generation sequencing technology. It is 287,799 bp long and contains 32 protein-coding genes, 3 rRNAs, 25 tRNAs corresponding to 15 amino acids, and 8 open reading frames (ORFs) supported by RNAseq data. Though many repeat regions have been found, none of them is longer than 1 kbp, and the most frequent structural variant originated from these repeats is present in only 4% of the mitogenome copies. The mitochondrial DNA sequence of C. bursa-pastoris differs from C. rubella, but not from C. orientalis, by two long inversions, suggesting that C. orientalis could be its maternal progenitor species. In total, 377 C to U RNA editing sites have been detected. All genes except cox1 and atp8 contain RNA editing sites, and most of them lead to non-synonymous changes of amino acids. Most of the identified RNA editing sites are identical to corresponding RNA editing sites in A. thaliana.
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Affiliation(s)
- Denis O. Omelchenko
- Institute for Information Transmission Problems of the Russian Academy of Sciences, 127051 Moscow, Russia; (A.S.K.); (M.I.S.); (M.D.L.); (A.A.P.)
| | - Maxim S. Makarenko
- Institute for Information Transmission Problems of the Russian Academy of Sciences, 127051 Moscow, Russia; (A.S.K.); (M.I.S.); (M.D.L.); (A.A.P.)
| | - Artem S. Kasianov
- Institute for Information Transmission Problems of the Russian Academy of Sciences, 127051 Moscow, Russia; (A.S.K.); (M.I.S.); (M.D.L.); (A.A.P.)
| | - Mikhail I. Schelkunov
- Institute for Information Transmission Problems of the Russian Academy of Sciences, 127051 Moscow, Russia; (A.S.K.); (M.I.S.); (M.D.L.); (A.A.P.)
- Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
| | - Maria D. Logacheva
- Institute for Information Transmission Problems of the Russian Academy of Sciences, 127051 Moscow, Russia; (A.S.K.); (M.I.S.); (M.D.L.); (A.A.P.)
- Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
| | - Aleksey A. Penin
- Institute for Information Transmission Problems of the Russian Academy of Sciences, 127051 Moscow, Russia; (A.S.K.); (M.I.S.); (M.D.L.); (A.A.P.)
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576
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Wei X, He M, Jin X. The first complete chloroplast genome of a mangrove fern, Acrostichum speciosum. Mitochondrial DNA B Resour 2020. [DOI: 10.1080/23802359.2020.1735964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
- Xianya Wei
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, China
- Chengdu Agricultural College, Chengdu, China
| | - Meng He
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Xiang Jin
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, China
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577
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Chen Z, Yu J, Li L, Sun Y, Peng Y, Ai Q, Liu C. The complete plastid genome of a drought-tolerant moss, Anomodon attenuatus (Hedw.) hüb. Mitochondrial DNA B Resour 2020. [DOI: 10.1080/23802359.2020.1736956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
- Ziqiang Chen
- Cultivation Base of State Key Laboratory for Ecological Restoration and Ecosystem Management, College of Chinese Medicine Materials, Jilin Agricultural University, Changchun, China
- BGI, Shenzhen, China
- Fairy Lake Botanical Garden, Shenzhen, China
| | | | | | - Yingxin Sun
- Cultivation Base of State Key Laboratory for Ecological Restoration and Ecosystem Management, College of Chinese Medicine Materials, Jilin Agricultural University, Changchun, China
| | - Yang Peng
- Fairy Lake Botanical Garden, Shenzhen, China
| | - Qiang Ai
- Cultivation Base of State Key Laboratory for Ecological Restoration and Ecosystem Management, College of Chinese Medicine Materials, Jilin Agricultural University, Changchun, China
| | - Cuijing Liu
- Cultivation Base of State Key Laboratory for Ecological Restoration and Ecosystem Management, College of Chinese Medicine Materials, Jilin Agricultural University, Changchun, China
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578
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Win PP, Li X, Chen LQ, Tan YH, Yu WB. Complete plastid genome of two Dalbergia species (Fabaceae), and their significance in conservation and phylogeny. Mitochondrial DNA B Resour 2020. [DOI: 10.1080/23802359.2020.1756487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
- Pyae Pyae Win
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
- University of Chinese Academy of Sciences, Beijing, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, China
| | - Xin Li
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
- University of Chinese Academy of Sciences, Beijing, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, China
| | - Li-Qiong Chen
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
- University of Chinese Academy of Sciences, Beijing, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, China
| | - Yun-Hong Tan
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Myanmar
| | - Wen-Bin Yu
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Myanmar
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579
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Shen G, Liu X, He C, Yao Y, Yang Q, Luo Y, Zhang C, Xu C, Suo F, Guo B. The complete chloroplast genome of Epimedium rhizomatosum (Berberidaceae), an endemic plant species to China. Mitochondrial DNA B Resour 2020. [DOI: 10.1080/23802359.2020.1753592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
- Guoan Shen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Xiang Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
- Chongqing Key Laboratory of Traditional Chinese Medicine Resource, Chongqing Academy of Chinese Materia Medica, Chongqing, China
| | - Congfen He
- Beijing Key Lab of Plant Resource Research and Development, Beijing Technology and Business University, Beijing, China
| | - Yu Yao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Qianru Yang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Yanjiao Luo
- Shanxi University of Chinese Medicine, Taiyuan, China
| | - Cheng Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Chaoqun Xu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Fengmei Suo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Baolin Guo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
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580
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Complete Chloroplast Genome Sequence and Phylogenetic Inference of the Canary Islands Dragon Tree (Dracaena draco L.). FORESTS 2020. [DOI: 10.3390/f11030309] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Dracaena draco, which belongs to the genus Dracaena, is an endemic succulent of the Canary Islands. Although it is one of the most popular and widely grown ornamental plants in the world, little is known about its genomic variability. Next generation sequencing, especially in combination with advanced bioinformatics analysis, is a new standard in taxonomic and phylogenetic research. Therefore, in this study, the complete D. draco chloroplast genome (cp) was sequenced and analyzed in order to provide new genomic information and to elucidate phylogenetic relationships, particularly within the genus Dracaena. The D. draco chloroplast genome is 155,422 bp, total guanine-cytosine (GC) content is 37.6%, and it has a typical quadripartite plastid genome structure with four separate regions, including one large single copy region of 83,942 bp length and one small single copy region of 18,472 bp length, separated by two inverted repeat regions, each 26,504 bp in length. One hundred and thirty-two genes were identified, 86 of which are protein-coding genes, 38 are transfer RNAs, and eight are ribosomal RNAs. Seventy-seven simple sequence repeats were also detected. Comparative analysis of the sequence data of various members of Asparagales revealed mutational hotspots potentially useful for their genetic identification. Phylogenetic inference based on 16 complete chloroplast genomes of Asparagales strongly suggested that Dracaena species form one monophyletic group, and that close relationships exist between D. draco, D. cochinchinensis and D. cambodiana. This study provides new and valuable data for further taxonomic, evolutionary and phylogenetic studies within the Dracaena genus.
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581
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Mehmood F, Abdullah, Shahzadi I, Ahmed I, Waheed MT, Mirza B. Characterization of Withania somnifera chloroplast genome and its comparison with other selected species of Solanaceae. Genomics 2020; 112:1522-1530. [DOI: 10.1016/j.ygeno.2019.08.024] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/19/2019] [Accepted: 08/26/2019] [Indexed: 01/04/2023]
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582
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Zhou Q, Li J, Jiang M, Wang L, Liu C, Wang Y. The complete chloroplast genome of Aristolochia kwangsiensi. MITOCHONDRIAL DNA PART B 2020. [DOI: 10.1080/23802359.2020.1731343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Qiang Zhou
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin, P. R. China
| | - Jingling Li
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, P. R. China
| | - Mei Jiang
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Liqiang Wang
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Chang Liu
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Yuhua Wang
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin, P. R. China
- College of Pharmacy, Inner Mongolia Medical University, Hohhot, China
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583
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He M, Wang X, Zhuang Y, Jin X. The complete chloroplast genome of Bougainvillea glabra. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:889-890. [PMID: 33366799 PMCID: PMC7748614 DOI: 10.1080/23802359.2020.1718028] [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: 11/23/2022]
Abstract
Bougainvillea glabra is one of the most popular ornamental and landscaping plants planted in tropical and subtropical regions. The brightly colored bracts, long florescence and strong stress resistance make B. glabra perfect ornamental horticulture plant. Bougainvillea plants have been frequently hybridized, resulting in more than 400 varieties. To investigate the chloroplast genome will help us to understand the biological diversity and stress resistance of Bougainvillea plants better. Here, we report the complete chloroplast genome of B. glabra, which is 154,542 bp in length, including a large single copy (LSC) region of 85,695 bp and a small single copy (SSC) region of 18,077 bp, separated by a pair of identical inverted repeat regions (IRs) of 25,385 bp each. A total of 128 genes were identified, including 83 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis based on 12 chloroplast genomes showed that B. glabra, accompanied with its sister species B. spectabilis, formed a base clade in Nyctaginaceae which was close to Pisonia aculeata. This study will be helpful for better understanding of the genetic diversity and stress resistance of Bougainvillea plants.
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Affiliation(s)
- Meng He
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Xihao Wang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Yangtao Zhuang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Xiang Jin
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, China
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584
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Yao Y, Liu X, Yang Q, Luo Y, Zhang C, Xu C, Suo F, Shen G, Guo B. The complete chloroplast genome of Epimedium brevicornu (Berberidaceae), a traditional Chinese medicinal herb. Mitochondrial DNA B Resour 2020; 5:887-888. [PMID: 33366798 PMCID: PMC7748714 DOI: 10.1080/23802359.2020.1718027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Epimedii Folium has been used as a common traditional Chinese medicine for more than 2000 years in China. In this study, we assembled the complete chloroplast (cp) genome of Epimedium brevicornu. The whole cp genome of E. brevicornu is 158,658 bp in length, comprising a pair of inverted repeat (IR) regions (27,699 bp) separated by a large single copy (LSC) region (86,558 bp) and a small single copy (SSC) region (16,702bp). The E. brevicornu cp genome contains 129 genes, of which 84 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis shows that E. brevicornu is closely clustered with E. wushanense, E. lishihchenii, and E. sagittatum. The published E. brevicornu chloroplast genome will provide useful information for the phylogenetic and evolutionary study on Epimedium family of Berberidaceae.
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Affiliation(s)
- Yu Yao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Xiang Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China.,Chongqing Academy of Chinese Materia Medica, Chongqing, China
| | - Qianru Yang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Yanjiao Luo
- College of Pharmacy, Shanxi Medical University, Taiyuan, China
| | - Cheng Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Chaoqun Xu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Fengmei Suo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Guoan Shen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Baolin Guo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
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585
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Cao T, Zhu Q, Chen X, Wang P, Shan N, Zhou Q, Huang Y. The complete chloroplast genome sequence of the Dioscorea persimilis Prain et Burkill (Dioscoreaceae). MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:451-452. [PMID: 33366597 PMCID: PMC7748837 DOI: 10.1080/23802359.2019.1704645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Dioscorea persimilis belongs to Dioscorea genus, which is considered as one of the most popular food and traditional folk medicine in China. The complete chloroplast genome of D. persimilis was determined in this study. The total genome size was 153,219 bp in length, containing a pair of inverted repeats (IRs) of 25,477 bp, which were separated by large single copy (LSC) and small single copy (SSC) of 83,448 bp and 18,817 bp, respectively. The GC content is 37.01%. A total of 129 genes were predicted including 84 protein-coding genes, eight rRNA genes and 37 tRNA genes. Phylogenetic tree analysis of 24 species in the genus Dioscorea indicated that D. persimilis was closer to Chinese yam, but has remote phylogenetic relationship with Guinea yam.
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Affiliation(s)
- Tianxu Cao
- Ministry of Education of the P.R. China, Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, Nanchang, China.,College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Qianglong Zhu
- College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Xin Chen
- College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Putao Wang
- College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Nan Shan
- College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Qionghong Zhou
- College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Yingjin Huang
- Ministry of Education of the P.R. China, Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, Nanchang, China.,College of Agronomy, Jiangxi Agricultural University, Nanchang, China
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586
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Yang Q, Liu X, Zhang C, Yao Y, Luo Y, Shen G, Guo B. The complete chloroplast genome of Epimedium davidii Franch. (Berberidaceae). Mitochondrial DNA B Resour 2020; 5:445-446. [PMID: 33366594 PMCID: PMC7748688 DOI: 10.1080/23802359.2019.1704641] [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] [Indexed: 10/25/2022] Open
Abstract
Epimedium davidii, which belongs to Berberidaceae, is mainly distributed in the southwest of China. In this study, the complete chloroplast genome of E. davidii was sequenced and assembled. The circular genome is 159,715 bp in length, which comprises a large single-copy region (LSC, 85,862 bp), a small single-copy region (SSC, 17,081 bp), and a pair of inverted repeat regions (IRa and IRb, 28,386 bp). The chloroplast genome of E. davidii contains 112 unique genes, of which 78 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Phylogenetic analysis indicated that E. davidii was closely related to Epimedium acuminatum.
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Affiliation(s)
- Qianru Yang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, PR China;
| | - Xiang Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, PR China; ,Chongqing Academy of Chinese Materia Medica, Chongqing, PR China;
| | - Cheng Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, PR China;
| | - Yu Yao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, PR China;
| | | | - Guoan Shen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, PR China; ,Guoan Shen Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, No. 151 MaLianWa North Road, Haidian District, Beijing, 100193, PR China
| | - Baolin Guo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, PR China; ,CONTACT Baolin Guo ;
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587
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Luo Y, Liu X, Yu Y, Yang Q, Guo B, Xu C, Suo F, Zhang C, Shen G, Chen A. The complete chloroplast genome of Epimedium qingchengshanense G. Y. Zhong et B. L. Guo (Berberidaceae), an endangered species endemic to China. Mitochondrial DNA B Resour 2020; 5:796-797. [PMID: 33366755 PMCID: PMC7748797 DOI: 10.1080/23802359.2020.1715295] [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: 11/10/2022] Open
Abstract
Epimedium qingchengshanense G. Y. Zhong & B. L. Guo is an endangered species with high ornamental value and medicinal value in China. In this study, we reported the first complete chloroplast (cp) genome of E. qingchengshanense. The whole cp genome of E. qingchengshanense is 159,087 bp in length, comprising a pair of inverted repeat regions (IRs) (27,709 bp) that are separated by a large single-copy (LSC) region (86,607 bp) and a small single-copy (SSC) region (17,062 bp). The circular genome contains 112 unique genes, of which 78 are protein-coding genes, 30 tRNA, and 4 rRNA genes. Phylogenetic analysis shows that E. qingchengshanense has a closer relationship with other Epimedium species.
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Affiliation(s)
- Yanjiao Luo
- College of Pharmacy, Shanxi Medical University, Taiyuan, China
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Xiang Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
- Chongqing Academy of Chinese Materia Medica, Chongqing, China
| | - Yao Yu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Qianru Yang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Baolin Guo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Chaoqun Xu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Fengmei Suo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Cheng Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Guoan Shen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Anjia Chen
- College of Pharmacy, Shanxi Medical University, Taiyuan, China
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588
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Liu J, Jiang M, Wang L, Huang L, Chen H, Liu C. The complete chloroplast genome sequence of the medicinal plant Siegesbeckia orientalis L., the first in the genus Siegesbeckia. Mitochondrial DNA B Resour 2020; 5:145-146. [PMID: 33366460 PMCID: PMC7721004 DOI: 10.1080/23802359.2019.1698355] [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: 11/03/2022] Open
Abstract
Siegesbeckia orientalis L. is a plant with important medicinal and economic values. We reported the first complete chloroplast genome sequence of S. orientalis. This genome is 151,821 bp in length and comprises a large single-copy region of 83,540 bp, a small single-copy region of 18,225 bp and a pair of inverted repeat regions of 25,028 bp each. It encodes 138 genes, including 79 protein-coding genes, 27 tRNA genes, and 4 rRNA genes. The phylogenomic analysis showed that S. orientalis and Guizotia abyssinia were clustered together. This genomewill lay the foundation for the molecular discovery and phylogenomic study of this genus.
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Affiliation(s)
- Jingting Liu
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Mei Jiang
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Liqiang Wang
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Linfang Huang
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Haimei Chen
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Chang Liu
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
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589
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Wen C, Liu X, Yao Y, Luo Y, Liu T, Yang Q, Guo B, Xu C, Suo F, Shen G, Ge F. The complete chloroplast genome of Epimedium mikinorii Stearn. (Berberidaceae). Mitochondrial DNA B Resour 2020; 5:806-807. [PMID: 33366760 PMCID: PMC7748847 DOI: 10.1080/23802359.2020.1715863] [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: 11/25/2022] Open
Abstract
Epimedium mikinorii is a vulnerable species in the Epimedium genus of Berberaceae. Here, we sequenced the complete chloroplast genome of E. mikinorii, which is 157,136 bp in length, and is a typical quadripartite circular molecule composed of two inverted repeats (IRs) of 25,896 bp for each, a large single-copy region (LSC) of 88,395 bp, and a small single-copy region (SSC) of 16,949 bp. The complete chloroplast genome of E. mikinorii contains 134 genes, including 83 protein-coding genes, 38 tRNA genes, 8 rRNA genes, and 5 pseudogenes. Phylogenetic analysis showed that E. mikinorii was closely related to E. dolichostemon.
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Affiliation(s)
- Chunmei Wen
- School of Pharmacy, Jiangxi University of Traditional Chinese Medicine, Nanchang, China
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Xiang Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
- Chongqing Academy of Chinese Materia Medica, Chongqing, China
| | - Yu Yao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Yanjiao Luo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
- School of Pharmacy, Shanxi Medical University, Taiyuan, China
| | - Ting Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
- College of Traditional Chinese Medicine, Shanxi University of Chinese Medicine, Jinzhong, China
| | - Qianru Yang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Baolin Guo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Chaoqun Xu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Fengmei Suo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Guoan Shen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Fei Ge
- School of Pharmacy, Jiangxi University of Traditional Chinese Medicine, Nanchang, China
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590
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Liu T, Liu X, Luo Y, Yao Y, Wen C, Yang Q, Shen G, Guo B. The complete chloroplast genome of Epimedium wushanense T. S. Ying. (Berberidaceae), a traditional Chinese medicinal herb. Mitochondrial DNA B Resour 2020; 5:817-818. [PMID: 33366765 PMCID: PMC7748643 DOI: 10.1080/23802359.2020.1715877] [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: 12/03/2022] Open
Abstract
Epimedium wushanense is a well-known medicinal plant in Berberidaceae in China. In this study, we sequenced the complete chloroplast (cp) genome of E. wushanense. The results showed that the cp genome of E. wushanense was 157,283 bp in length, which is composed of a large single-copy region (LSC, 88,579 bp) and a small single-copy region (SSC, 17,082 bp) that were separated by a pair of inverted repeat regions (IRa and IRb, 25,811 bp). The chloroplast genome of E. wushanense contains 112 unique genes, of which are 78 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. The overall GC content was 38.78%. The phylogenetic tree analysis showed that E. wushanense was closely related to E. pseudowushanense, E. lishihchenii, and E. sagittatum.
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Affiliation(s)
- Ting Liu
- College of Traditional Chinese Medicine, Shanxi University of Chinese Medicine, Jinzhong, China
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Xiang Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
- Chongqing Academy of Chinese Materia Medica, Chongqing, China
| | - Yanjiao Luo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
- College of pharmacy, Shanxi Medical University, Taiyuan, China
| | - Yu Yao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Chunmei Wen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
- School of Pharmacy, Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| | - Qianru Yang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Guoan Shen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Baolin Guo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
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591
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Suo F, Liu X, Zhang C, Xu C, Sheng G, Guo B. The complete chloroplast genome of Epimedium elachyphyllum Stearn (Berberidaceae), an endangered species endemic to China. Mitochondrial DNA B Resour 2020; 5:1027-1028. [PMID: 33366859 PMCID: PMC7748844 DOI: 10.1080/23802359.2020.1721357] [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: 11/17/2022] Open
Abstract
Epimedium elachyphyllum, which belongs to Berberidaceae, is only distributed in Guizhou province of China. In this study, the complete chloroplast (cp)genome of E. elachyphyllum was sequenced and assembled. The circular genome is 157,201 bp in length, which comprises of a large single-copy region (LSC, 88,519 bp), a small single-copy region (SSC, 17,042 bp), and a pair of inverted repeat regions (IRa and IRb, 25,820 bp). The genome of E. elachyphyllum contains 112 unique genes, of which 78 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic analysis based on 18 complete cp genome sequences indicated that E. elachyphyllum was closely related to E. dolichostemon.
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Affiliation(s)
- Fengmei Suo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, People’s Republic of China
| | - Xiang Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, People’s Republic of China
- Chongqing Academy of Chinese Materia Medica, Chongqing, People’s Republic of China
| | - Cheng Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, People’s Republic of China
| | - Chaoqun Xu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, People’s Republic of China
| | - Guoan Sheng
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, People’s Republic of China
| | - Baolin Guo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, People’s Republic of China
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592
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Wang Y, Liu X, Zhang C, Xu C, Suo F, Shen G, Guo B. The complete chloroplast genome of Epimedium xichangense Y. J. Zhang (Berberidaceae). Mitochondrial DNA B Resour 2020; 5:1035-1037. [PMID: 33366862 PMCID: PMC7748833 DOI: 10.1080/23802359.2020.1721353] [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: 11/29/2022] Open
Abstract
Epimedium xichangense, a critically endangered herb with limited population, mainly distributes in Sichuan province, China. In our study, we obtained the complete chloroplast genome of E. xichangense with a length of 158,955 bp, including a large single copy region of 86,478 bp, small single copy region of 17,027 bp, and a pair of inverted repeat regions of 27,725 bp. The GC content in the whole chloroplast genome of E. xichangense is 38.81%. Among the 112 unique genes in the circular genome, 30 tRNA, four rRNA and 78 protein-coding genes were successfully annotated. We constructed the Maximum likelihood (ML) tree with 26 species, and came to the conclusion that E. xichangense was phylogenetically closely related to E. acuminatum and E. chlorandrum.
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Affiliation(s)
- Yuanyue Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Xiang Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
- Chongqing Academy of Chinese Materia Medica, Chongqing, China
| | - Cheng Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Chaoqun Xu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Fengmei Suo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Guoan Shen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Baolin Guo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
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593
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Zhang Y, Liu X, Zhang C, Guo B, Xu C, Shen G, Zhang L. The complete chloroplast genome of Epimedium tianmenshanense (Berberidaceae). Mitochondrial DNA B Resour 2020; 5:1007-1008. [PMID: 33366849 PMCID: PMC7748789 DOI: 10.1080/23802359.2020.1720547] [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: 11/03/2022] Open
Abstract
In this study, the complete chloroplast (cp) genome of Epimedium tianmenshanense was sequenced and assembled. The circular genome is 157,066 bp in size. The whole chloroplast genome of E. tianmenshanense contains 112 unique genes, of which 78 protein-coding genes, 30 tRNA genes, and four rRNA genes. The phylogenetic analysis based on 17 complete chloroplast genomes demonstrated a closer relationship between E. tianmenshanense and E. lishihchenii.
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Affiliation(s)
- Yue Zhang
- Tianjin University of Traditional Chinese Medicine, Tianjin, PR China
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Xiang Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
- Chongqing Academy of Chinese Materia Medica, Chongqing, PR China
| | - Cheng Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Baolin Guo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Chaoqun Xu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Guoan Shen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Lijuan Zhang
- Tianjin University of Traditional Chinese Medicine, Tianjin, PR China
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594
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Zheng S, Poczai P, Hyvönen J, Tang J, Amiryousefi A. Chloroplot: An Online Program for the Versatile Plotting of Organelle Genomes. Front Genet 2020. [PMID: 33101394 DOI: 10.3389/fgene.576124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
Understanding the complexity of genomic structures and their unique architecture is linked with the power of visualization tools used to represent these features. Such tools should be able to provide a realistic and scalable version of genomic content. Here, we present an online organelle plotting tool focused on chloroplasts, which were developed to visualize the exclusive structure of these genomes. The distinguished unique features of this program include its ability to represent the Single Short Copy (SSC) regions in reverse complement, which allows the depiction of the codon usage bias index for each gene, along with the possibility of the minor mismatches between inverted repeat (IR) regions and user-specified plotting layers. The versatile color schemes and diverse functionalities of the program are specifically designed to reflect the accurate scalable representation of the plastid genomes. We introduce a Shiny app website for easy use of the program; a more advanced application of the tool is possible by further development and modification of the downloadable source codes provided online. The software and its libraries are completely coded in R, available at https://irscope.shinyapps.io/chloroplot/.
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Affiliation(s)
- Shuyu Zheng
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Peter Poczai
- Finnish Museum of Natural History (Botany), University of Helsinki, Helsinki, Finland
- Department of Biosciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Jaakko Hyvönen
- Finnish Museum of Natural History (Botany), University of Helsinki, Helsinki, Finland
- Department of Biosciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Jing Tang
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Ali Amiryousefi
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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595
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Yan-Xiong G, Yao-Hua T, Jiang N, Yu WB. Complete plastome sequence of Acorus tatarinowii (Acoraceae), a traditional Chinese medicinal plant from Xishuangbanna, Yunnan, China. MITOCHONDRIAL DNA PART B-RESOURCES 2019; 5:226-228. [PMID: 33366498 PMCID: PMC7720961 DOI: 10.1080/23802359.2019.1694852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
The complete plastome of Acorus tatarinowii is 153,296 bp in length, with two long inverted repeats (25,752 bp for each) separating by a large single-copy (83,533 bp) and a small single-copy (18,240 bp). The plastome contained 112 unique genes, including 78 protein-coding genes, 30 transfer RNAs, and 4 ribosomal RNAs. Phylogenetic analyses showed that A. tatarinowii was closely related to A. gramineus.
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Affiliation(s)
| | - Tian Yao-Hua
- Yunnan Institute of Tropical Crops, Jinghong, China
| | - Nan Jiang
- Center for Integrative Conservation and Southeast Asia Biodiversity Research Institute, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
| | - Wen-Bin Yu
- Center for Integrative Conservation and Southeast Asia Biodiversity Research Institute, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, China
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596
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Chen H, Jiang M, Wang L, You J, Liu C. Complete plastome of Leucanthemum maximum, the first in genus Leucanthemum. Mitochondrial DNA B Resour 2019; 5:19-20. [PMID: 33366402 PMCID: PMC7721026 DOI: 10.1080/23802359.2019.1693922] [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: 11/01/2019] [Accepted: 11/09/2019] [Indexed: 11/04/2022] Open
Abstract
Leucanthemum maximum is a perennial herb widely used in landscaping. Here, we reported the complete plastome of L. maximum. The plastome was 151,865 bp long, containing a large single-copy region of 84,369 bp, a small single-copy region of 18,450 bp, and two inverted repeats of 24,523 bp each. It encoded 112 unique genes, including 79 protein-coding, 4 rRNA, and 29 tRNA genes. The protein sequence of infA was distinctly truncated compared with those from other Anthemideae species. Phylogenetic analysis showed that the species is closely related to the genus Ismelia. This study provided a high-quality reference for future studies.
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Affiliation(s)
- Haimei Chen
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Mei Jiang
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Liqiang Wang
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Jinwen You
- Institute of Chinese Herbal Medicine, Hubei Academy of Agricultural Sciences, Enshi, Hubei, P. R. China
| | - Chang Liu
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
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597
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Jiang M, Chen H, Wang L, You J, Liu C. The complete chloroplast genome sequence of Cosmos bipinnatus, the first of the genu s Cosmos. MITOCHONDRIAL DNA PART B-RESOURCES 2019; 4:4204-4206. [PMID: 33366384 PMCID: PMC7707777 DOI: 10.1080/23802359.2019.1693298] [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: 11/24/2022]
Abstract
Cosmos bipinnatus has been used widely in traditional medicines. Here, we sequenced and assembled the complete chloroplast genome of C. bipinnatus. This genome is 150,356 bp in size with a pair of inverted repeats (IRs) of 25,082 bp, a large single-copy (LSC) region of 83,003 bp, and a small single-copy region (SSC) of 18,397 bp. It contains 112 unique genes, including 80 protein-coding, 4 rRNA, and 28 tRNA genes. The phylogenomic analysis showed the C. bipinnatus and species belonging to the Madieae, Millerieae, Heliantheae, and Eupatorieae tribes were clustered together. The availability of chloroplast genome provided valuable information for future conservation, taxonomy, evolution, and differentiation studies of C. bipinnatus.
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Affiliation(s)
- Mei Jiang
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Haimei Chen
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Liqiang Wang
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Jinwen You
- Institute of Chinese Herbal Medicine, Hubei Academy of Agricultural Sciences, Enshi, Hubei, P. R. China
| | - Chang Liu
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
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598
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Kahraman K, Lucas SJ. Comparison of different annotation tools for characterization of the complete chloroplast genome of Corylus avellana cv Tombul. BMC Genomics 2019; 20:874. [PMID: 31747873 PMCID: PMC6865063 DOI: 10.1186/s12864-019-6253-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 10/31/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Several bioinformatics tools have been designed for assembly and annotation of chloroplast (cp) genomes, making it difficult to decide which is most useful and applicable to a specific case. The increasing number of plant genomes provide an opportunity to accurately obtain cp genomes from whole genome shotgun (WGS) sequences. Due to the limited genetic information available for European hazelnut (Corylus avellana L.) and as part of a genome sequencing project, we analyzed the complete chloroplast genome of the cultivar 'Tombul' with multiple annotation tools. RESULTS Three different annotation strategies were tested, and the complete cp genome of C. avellana cv Tombul was constructed, which was 161,667 bp in length, and had a typical quadripartite structure. A large single copy (LSC) region of 90,198 bp and a small single copy (SSC) region of 18,733 bp were separated by a pair of inverted repeat (IR) regions of 26,368 bp. In total, 125 predicted functional genes were annotated, including 76 protein-coding, 25 tRNA, and 4 rRNA unique genes. Comparative genomics indicated that the cp genome sequences were relatively highly conserved in species belonging to the same order. However, there were still some variations, especially in intergenic regions, that could be used as molecular markers for analyses of phylogeny and plant identification. Simple sequence repeat (SSR) analysis showed that there were 83 SSRs in the cp genome of cv Tombul. Phylogenetic analysis suggested that C. avellana cv Tombul had a close affinity to the sister group of C. fargesii and C. chinensis, and then a closer evolutionary relationship with Betulaceae family than other species of Fagales. CONCLUSION In this study, the complete cp genome of Corylus avellana cv Tombul, the most widely cultivated variety in Turkey, was obtained and annotated, and additionally phylogenetic relationships were predicted among Fagales species. Our results suggest a very accurate assembly of chloroplast genome from next generation whole genome shotgun (WGS) sequences. Enhancement of taxon sampling in Corylus species provide genomic insights into phylogenetic analyses. The nucleotide sequences of cv Tombul cp genomes can provide comprehensive genetic insight into the evolution of genus Corylus.
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Affiliation(s)
- Kadriye Kahraman
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956, Istanbul, Turkey
- Sabanci University Nanotechnology Research and Application Centre (SUNUM), Sabanci University, 34956, Istanbul, Turkey
| | - Stuart James Lucas
- Sabanci University Nanotechnology Research and Application Centre (SUNUM), Sabanci University, 34956, Istanbul, Turkey.
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Zhang F, Tong H, Yang H, Wang T, Zhuang W, Shu X, Wang Z. Characterisation of the complete chloroplast genome of Lycoris longituba (Amaryllidaceae). Mitochondrial DNA B Resour 2019; 4:3782-3783. [PMID: 33366189 PMCID: PMC7707485 DOI: 10.1080/23802359.2019.1681324] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 10/13/2019] [Indexed: 01/03/2023] Open
Abstract
Lycoris longituba is a species in the Amaryllidaceae with high ornamental and medicinal value. It is also an endangered species in East China due to the narrow distribution. Here, we assembled and characterised the complete chloroplast (cp) genome of this species using high throughput sequencing and bioinformatics analysis. As a result, the whole cp genome size is 158,484 bp, including two inverted repeat (IR) regions of 26,765 bp, large single-copy region (LSC) of 86,458 bp and small single-copy region (SSC) of 18,496 bp. A total of 137 genes were identified, including 87 protein-coding genes, 42 tRNA genes, and eight rRNA genes. Phylogenomic analysis was carried out using complete cp genome of 18 species in five families, supporting the closer relationship between L. longituba and L. squamigera than L. radiata and L. sprengeri in Amaryllidaceae.
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Affiliation(s)
- Fengjiao Zhang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, China
| | - Haiying Tong
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, China
| | - Hong Yang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, China
| | - Tao Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, China
| | - Weibing Zhuang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, China
| | - Xiaochun Shu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, China
| | - Zhong Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, China
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Zhang F, Zhuang W, Shu X, Wang T, Wang Z. Complete chloroplast genome of Lycoris sprengeri (Amaryllidaceae) and genetic comparison. Mitochondrial DNA B Resour 2019; 4:3577-3578. [PMID: 33366093 PMCID: PMC7707319 DOI: 10.1080/23802359.2019.1676673] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 09/23/2019] [Indexed: 10/27/2022] Open
Abstract
Lycoris sprengeri is native to China and has various variations. It belongs to the Amaryllidaceae family, which contains abundant alkaloids for medical use and also was planted as garden bulbous flowers. In this study, we assembled the complete chloroplast (cp) genome of L. sprengeri by DNA sequencing, which will improve the complete cp genomic information for analysis of phylogenetic relationships and germplasm identification in Lycoris. The whole cp genome is 158,687 bp, which contained a large single-copy region (LSC) of 86,489 bp, a small single-copy region (SSC) of 18,540 bp, and a pair of inverted repeats (IRs) of 26,829 bp. A total of 137 genes were annotated, including 87 protein coding genes (PCGs), 42 tRNA, and 8 rRNA genes. Phylogenetic tree analysis revealed that the close relationship of three species of Lycoris (L. sprengeri, L. radiate, and L. squamigera) in the Amaryllidaceae family.
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Affiliation(s)
- Fengjiao Zhang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, PR China
| | - Weibing Zhuang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, PR China
| | - Xiaochun Shu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, PR China
| | - Tao Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, PR China
| | - Zhong Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, PR China
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