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Liu H, Xie K, Hua D. The complete chloroplast genome of Pyankovia brachiata (amaranthaceae), an annual desert plant in China. Mitochondrial DNA B Resour 2024; 9:1112-1116. [PMID: 39165386 PMCID: PMC11334741 DOI: 10.1080/23802359.2024.2393469] [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: 06/21/2024] [Accepted: 08/12/2024] [Indexed: 08/22/2024] Open
Abstract
Pyankovia brachiata (Pall.) Akhani & Roalson 2007, is an annual plant belonging to the genus Pyankovia, family Amaranthaceae, which is widely distributed in the inland deserts of Northwest China. P. brachiata was previously categorized under the genus Salsola in Salsoleae and has been a long-standing topic of debate. Therefore, the complete chloroplast genome of P. brachiata must be studied to provide a theoretical reference for species classification. In this study, we sequenced P. brachiata samples and determined the species' complete chloroplast genome. The complete chloroplast genome was 149,922 bp in length, with one large single copy (LSC: 83,565 bp), one small single copy (SSC: 18,535 bp), and two inverted repeat regions (IRa and IRb, 23,911 bp each). It contains 132 genes, including 87 protein-coding, eight rRNA, and 37 tRNA genes. The phylogenetic position showed that P. brachiata has the closest relationship with Caroxylon passerinum (accession number: NC057191.1). This study will provide genetic information and be beneficial to understanding the systematic position of P. brachiata within the Amaranthaceae.
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Affiliation(s)
- Huafeng Liu
- College of Life Sciences, China West Normal University, Nanchong, China
| | - Kaiqing Xie
- College of Grassland Science, Xinjiang Agricultural University, Urumqi, China
| | - Donglai Hua
- College of Life Science and Biotechnology, Mianyang Normal University, Mianyang, China
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Wu L, Fan P, Zhou J, Li Y, Xu Z, Lin Y, Wang Y, Song J, Yao H. Gene Losses and Homology of the Chloroplast Genomes of Taxillus and Phacellaria Species. Genes (Basel) 2023; 14:genes14040943. [PMID: 37107701 PMCID: PMC10137875 DOI: 10.3390/genes14040943] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
Research on the chloroplast genome of parasitic plants is limited. In particular, the homology between the chloroplast genomes of parasitic and hyperparasitic plants has not been reported yet. In this study, three chloroplast genomes of Taxillus (Taxillus chinensis, Taxillus delavayi, and Taxillus thibetensis) and one chloroplast genome of Phacellaria (Phacellaria rigidula) were sequenced and analyzed, among which T. chinensis is the host of P. rigidula. The chloroplast genomes of the four species were 119,941-138,492 bp in length. Compared with the chloroplast genome of the autotrophic plant Nicotiana tabacum, all of the ndh genes, three ribosomal protein genes, three tRNA genes and the infA gene were lost in the three Taxillus species. Meanwhile, in P. rigidula, the trnV-UAC gene and the ycf15 gene were lost, and only one ndh gene (ndhB) existed. The results of homology analysis showed that the homology between P. rigidula and its host T. chinensis was low, indicating that P. rigidula grows on its host T. chinensis but they do not share the chloroplast genome. In addition, horizontal gene transfer was not found between P. rigidula and its host T. chinensis. Several candidate highly variable regions in the chloroplast genomes of Taxillus and Phacellaria species were selected for species identification study. Phylogenetic analysis revealed that the species of Taxillus and Scurrula were closely related and supported that Scurrula and Taxillus should be treated as congeneric, while species in Phacellaria had a close relationship with that in Viscum.
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Affiliation(s)
- Liwei Wu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Panhui Fan
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Jianguo Zhou
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Yonghua Li
- Faculty of Pharmacy, Guangxi University of Chinese Medicine, Nanning 530004, China
| | - Zhichao Xu
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Yulin Lin
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Yu Wang
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Jingyuan Song
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Hui Yao
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
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Yu J, Li J, Zuo Y, Qin Q, Zeng S, Rennenberg H, Deng H. Plastome variations reveal the distinct evolutionary scenarios of plastomes in the subfamily Cereoideae (Cactaceae). BMC PLANT BIOLOGY 2023; 23:132. [PMID: 36882685 PMCID: PMC9993602 DOI: 10.1186/s12870-023-04148-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 03/01/2023] [Indexed: 05/27/2023]
Abstract
BACKGROUND The cactus family (Cactaceae) has been reported to have evolved a minimal photosynthetic plastome size, with the loss of inverted-repeat (IR) regions and NDH gene suites. However, there are very limited genomic data on the family, especially Cereoideae, the largest subfamily of cacti. RESULTS In the present study, we assembled and annotated 35 plastomes, 33 of which were representatives of Cereoideae, alongside 2 previously published plastomes. We analyzed the organelle genomes of 35 genera in the subfamily. These plastomes have variations rarely observed in those of other angiosperms, including size differences (with ~ 30 kb between the shortest and longest), dramatic dynamic changes in IR boundaries, frequent plastome inversions, and rearrangements. These results suggested that cacti have the most complex plastome evolution among angiosperms. CONCLUSION These results provide unique insight into the dynamic evolutionary history of Cereoideae plastomes and refine current knowledge of the relationships within the subfamily.
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Affiliation(s)
- Jie Yu
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716 China
- No. 2 Tiansheng Road, Beibei District, Chongqing, 400716 China
| | - Jingling Li
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716 China
| | - Youwei Zuo
- Center for Biodiversity Conservation and Utilization, School of Life Sciences, Southwest University, Chongqing, 400715 China
| | - Qiulin Qin
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716 China
| | - Siyuan Zeng
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716 China
| | - Heinz Rennenberg
- Center of Molecular Ecophysiology, College of Resources and Environment, Southwest University, Chongqing, 400715 China
| | - Hongping Deng
- Center for Biodiversity Conservation and Utilization, School of Life Sciences, Southwest University, Chongqing, 400715 China
- No. 2 Tiansheng Road, Beibei District, Chongqing, 400716 China
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Comparative Analyses of Chloroplast Genomes for Parasitic Species of Santalales in the Light of Two Newly Sequenced Species, Taxillus nigrans and Scurrula parasitica. Genes (Basel) 2023; 14:genes14030560. [PMID: 36980832 PMCID: PMC10048710 DOI: 10.3390/genes14030560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/16/2023] [Accepted: 02/19/2023] [Indexed: 02/26/2023] Open
Abstract
When a flowering plant species changes its life history from self-supply to parasite, its chloroplast genomes may have experienced functional physical reduction, and gene loss. Most species of Santalales are hemiparasitic and few studies focus on comparing the chloroplast genomes of the species from this order. In this study, we collected and compared chloroplast genomes of 12 species of Santalales and sequenced the chloroplast genomes of Taxillus nigrans and Scurrula parasitica for the first time. The chloroplast genomes for these species showed typical quadripartite structural organization. Phylogenetic analysis suggested that these 12 species of Santalales clustered into three clades: Viscum (4 spp.) and Osyris (1 sp.) in the Santalaceae and Champereia (1 sp.) in the Opiliaceae formed one clade, while Taxillus (3 spp.) and Scurrula (1 sp.) in the Loranthaceae and Schoepfia (1 sp.) in the Schoepfiaceae formed another clade. Erythropalum (1 sp.), in the Erythropalaceae, appeared as a third, most distant, clade within the Santalales. In addition, both Viscum and Taxillus are monophyletic, and Scurrula is sister to Taxillus. A comparative analysis of the chloroplast genome showed differences in genome size and the loss of genes, such as the ndh genes, infA genes, partial ribosomal genes, and tRNA genes. The 12 species were classified into six categories by the loss, order, and structure of genes in the chloroplast genome. Each of the five genera (Viscum, Osyris, Champereia, Schoepfia, and Erythropalum) represented an independent category, while the three Taxillus species and Scurrula were classified into a sixth category. Although we found that different genes were lost in various categories, most genes related to photosynthesis were retained in the 12 species. Hence, the genetic information accorded with observations that they are hemiparasitic species. Our comparative genomic analyses can provide a new case for the chloroplast genome evolution of parasitic species.
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Feng J, Xiong Y, Su X, Liu T, Xiong Y, Zhao J, Lei X, Yan L, Gou W, Ma X. Analysis of Complete Chloroplast Genome: Structure, Phylogenetic Relationships of Galega orientalis and Evolutionary Inference of Galegeae. Genes (Basel) 2023; 14:176. [PMID: 36672917 PMCID: PMC9859028 DOI: 10.3390/genes14010176] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/24/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
Galega orientalis, a leguminous herb in the Fabaceae family, is an ecologically and economically important species widely cultivated for its strong stress resistance and high protein content. However, genomic information of Galega orientalis has not been reported, which limiting its evolutionary analysis. The small genome size makes chloroplast relatively easy to obtain genomic sequence for phylogenetic studies and molecular marker development. Here, the chloroplast genome of Galega orientalis was sequenced and annotated. The results showed that the chloroplast genome of G. orientalis is 125,280 bp in length with GC content of 34.11%. A total of 107 genes were identified, including 74 protein-coding genes, 29 tRNAs and four rRNAs. One inverted repeat (IR) region was lost in the chloroplast genome of G. orientalis. In addition, five genes (rpl22, ycf2, rps16, trnE-UUC and pbf1) were lost compared with the chloroplast genome of its related species G. officinalis. A total of 84 long repeats and 68 simple sequence repeats were detected, which could be used as potential markers in the genetic studies of G. orientalis and related species. We found that the Ka/Ks values of three genes petL, rpl20, and ycf4 were higher than one in the pairwise comparation of G. officinalis and other three Galegeae species (Calophaca sinica, Caragana jubata, Caragana korshinskii), which indicated those three genes were under positive selection. A comparative genomic analysis of 15 Galegeae species showed that most conserved non-coding sequence regions and two genic regions (ycf1 and clpP) were highly divergent, which could be used as DNA barcodes for rapid and accurate species identification. Phylogenetic trees constructed based on the ycf1 and clpP genes confirmed the evolutionary relationships among Galegeae species. In addition, among the 15 Galegeae species analyzed, Galega orientalis had a unique 30-bp intron in the ycf1 gene and Tibetia liangshanensis lacked two introns in the clpP gene, which is contrary to existing conclusion that only Glycyrrhiza species in the IR lacking clade (IRLC) lack two introns. In conclusion, for the first time, the complete chloroplast genome of G. orientalis was determined and annotated, which could provide insights into the unsolved evolutionary relationships within the genus Galegeae.
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Affiliation(s)
- Junjie Feng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Sichuan Academy of Grassland Science, Chengdu 611130, China
| | - Yi Xiong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaoli Su
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Tianqi Liu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yanli Xiong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Junming Zhao
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiong Lei
- Sichuan Academy of Grassland Science, Chengdu 611130, China
| | - Lijun Yan
- Sichuan Academy of Grassland Science, Chengdu 611130, China
| | - Wenlong Gou
- Sichuan Academy of Grassland Science, Chengdu 611130, China
| | - Xiao Ma
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
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Turudić A, Liber Z, Grdiša M, Jakše J, Varga F, Šatović Z. Variation in Chloroplast Genome Size: Biological Phenomena and Technological Artifacts. PLANTS (BASEL, SWITZERLAND) 2023; 12:254. [PMID: 36678967 PMCID: PMC9864865 DOI: 10.3390/plants12020254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/31/2022] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
Abstract
The development of bioinformatic solutions is guided by biological knowledge of the subject. In some cases, we use unambiguous biological models, while in others we rely on assumptions. A commonly used assumption for genomes is that related species have similar genome sequences. This is even more obvious in the case of chloroplast genomes due to their slow evolution. We investigated whether the lengths of complete chloroplast sequences are closely related to the taxonomic proximity of the species. The study was performed using all available RefSeq sequences from the asterid and rosid clades. In general, chloroplast length distributions are narrow at both the family and genus levels. In addition, clear biological explanations have already been reported for families and genera that exhibit particularly wide distributions. The main factors responsible for the length variations are parasitic life forms, IR loss, IR expansions and contractions, and polyphyly. However, the presence of outliers in the distribution at the genus level is a strong indication of possible inaccuracies in sequence assembly.
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Affiliation(s)
- Ante Turudić
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska c. 25, 10000 Zagreb, Croatia
- Faculty of Agriculture, University of Zagreb, Svetošimunska c. 25, 10000 Zagreb, Croatia
| | - Zlatko Liber
- Faculty of Agriculture, University of Zagreb, Svetošimunska c. 25, 10000 Zagreb, Croatia
- Faculty of Science, University of Zagreb, Marulićev trg 9a, 10000 Zagreb, Croatia
| | - Martina Grdiša
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska c. 25, 10000 Zagreb, Croatia
- Faculty of Agriculture, University of Zagreb, Svetošimunska c. 25, 10000 Zagreb, Croatia
| | - Jernej Jakše
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Filip Varga
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska c. 25, 10000 Zagreb, Croatia
- Faculty of Agriculture, University of Zagreb, Svetošimunska c. 25, 10000 Zagreb, Croatia
| | - Zlatko Šatović
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska c. 25, 10000 Zagreb, Croatia
- Faculty of Agriculture, University of Zagreb, Svetošimunska c. 25, 10000 Zagreb, Croatia
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Qin L, Lu E, Chen K, Bao R, Liang L, Hu X. The complete chloroplast genome of Striga asiatica (L.) Kuntze 1891 ( Orobanchaceae), a hemiparasitic weed from Guangxi China. Mitochondrial DNA B Resour 2023; 8:497-500. [PMID: 37063239 PMCID: PMC10101682 DOI: 10.1080/23802359.2023.2197089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023] Open
Abstract
Striga asiatica (L.) Kuntze 1891 is a hemiparasitic plant native to Asia and Africa. It is invasive and causes yield losses in crops such as corn, rice and sorghum. Lack of chloroplast genomic data has limited research into its obligate parasitic lifestyle. In this study, the complete chloroplast genome of Striga asiatica was sequenced and characterized. It is a quadripartite structure with a total length of 191,085 bp and a GC content of 37.86%. It has a large single copy region (LSC) of 51,406 bp, a small single copy region (SSC) of 273 bp, and two copies of the reverse repeat sequence (IRA and IRB) of 69,703 bp. A total of 122 protein-coding genes, 8 rRNA genes, and 44 tRNA genes were annotated in the chloroplast genome. There were a lot of ndh gene deletions and pseudogenizations in this chloroplast genome. For example, ndhA, D, E, H, I, and K were all pseudogenes because they were missing the 5' end start codon. ndhB, C, and J had shorter gene lengths than their homologs, and ndhF and ndhG were missing genes. The phylogenetic tree reveals that all Striga species form a clade, and a bootstrap value of 100 indicates that S. asiatica is closely related to Striga hermonthica and Striga sepera. The comprehensive chloroplast genomic resource of S. asiatica would assist researchers in comprehending hemiparasitic mechanisms, molecular markers, and evolutionary patterns of the genus Striga.
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Affiliation(s)
- Liu Qin
- Key Laboratory for Conservation and Utilization of subtropical Bio-Resources Education Department of Guangxi Zhuang Autonomous Region, Yulin Normal University, Yulin, China
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, Yulin Normal University, Yulin, China
| | - Enke Lu
- Key Laboratory for Conservation and Utilization of subtropical Bio-Resources Education Department of Guangxi Zhuang Autonomous Region, Yulin Normal University, Yulin, China
| | - Kexin Chen
- Key Laboratory for Conservation and Utilization of subtropical Bio-Resources Education Department of Guangxi Zhuang Autonomous Region, Yulin Normal University, Yulin, China
| | - Rizhen Bao
- Key Laboratory for Conservation and Utilization of subtropical Bio-Resources Education Department of Guangxi Zhuang Autonomous Region, Yulin Normal University, Yulin, China
| | - Lina Liang
- Key Laboratory for Conservation and Utilization of subtropical Bio-Resources Education Department of Guangxi Zhuang Autonomous Region, Yulin Normal University, Yulin, China
| | - Xiaohu Hu
- Key Laboratory for Conservation and Utilization of subtropical Bio-Resources Education Department of Guangxi Zhuang Autonomous Region, Yulin Normal University, Yulin, China
- CONTACT Xiaohu Hu Key Laboratory for Conservation and Utilization of subtropical Bio-Resources, Education Department of Guangxi Zhuang Autonomous Region, Yulin Normal University, Yulin, China
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López-Barrera A, Santos-Ordóñez E, Pacheco-Coello R, Villao-Uzho L, Miranda M, Gutiérrez Y, Chóez-Guaranda I, Ruiz-Reyes SG. ITS1 Barcode and Phytochemical Analysis by Gas Chromatography-Mass Spectrometry of Corynaea crassa Hook. f (Balanophoraceae) from Ecuador and Peru. Genes (Basel) 2022; 14:genes14010088. [PMID: 36672828 PMCID: PMC9859250 DOI: 10.3390/genes14010088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/13/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022] Open
Abstract
The use of medicinal plants is the basis of traditional healthcare. Recently, the use of herbal medicine has been increasing among consumers due to availability, economy, and less side effect. For instance, the hemiparasite plant Corynaea crassa has medicinal properties and could be found in some regions of America, from Costa Rica to Bolivia. Phytochemical and genetic characterization of medicinal plants is needed for proper identification of metabolites responsible for medicinal properties and for genotyping, respectively. Moreover, characterization of medicinal plants through the use of DNA barcodes is an important tool for phylogenetic analysis and identification of species; furthermore, complemented with phytochemical analysis, both are useful for identification of plant species and quality control of medicinal products. The objective of this study was to analyze the species of C. crassa collected in Ecuador and Peru from the phylogenetic and phytochemical point of view. Polymerase chain reaction (PCR) was performed for amplification of the internal transcribed spacer 1 (ITS1) region after DNA extraction of samples of C. crassa. Blast analysis was performed in the GenBank database with the ITS1 sequences obtained from two accessions of C. crassa from Ecuador (GenBank accession numbers OM471920 and OM471919 for isolates CIBE-17 and CIBE-18, respectively) and three from Peru (GenBank accession numbers OM471921, OM471922, and OM471923 for isolates CIBE-13, CIBE-14, and CIBE-15, respectively). The accessions available in the GenBank were used for phylogenetic analysis. For the phytochemical analysis, hydroalcoholic extracts were obtained by maceration using 80% ethanol as solvent, followed by a derivatization process and analysis by gas chromatography-mass spectrometry. Based on the phylogenetic analysis of the C. crassa samples, the ITS1 sequence could be used to differentiate C. crassa of different locations. The samples of C. crassa from Ecuador and Peru are more similar between them than with other clades including Helosis spp. The phytochemical study revealed differences in the presence and relative abundance of some metabolites; mainly eugenol, 1,4-lactone arabinonic acid, dimethoxyrabelomycin and azelaic acid, which are reported for the first time for the species under study and the genus Corynaea. These results are the first findings on the combined analysis using genetic and phytochemical analysis for C. crassa, which could be used as a useful tool for quality control of the C. crassa species in medicinal products.
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Affiliation(s)
- Alexandra López-Barrera
- Department of Pharmacy, Faculty of Chemical Sciences, Universidad de Guayaquil, Guayaquil 090514, Ecuador
| | - Efrén Santos-Ordóñez
- Facultad de Ciencias de la Vida, Campus Gustavo Galindo, ESPOL Polytechnic University, Escuela Superior Politécnica del Litoral, ESPOL, Guayaquil 090902, Ecuador
- Centro de Investigaciones Biotecnológicas del Ecuador, Campus Gustavo Galindo, ESPOL Polytechnic University, Escuela Superior Politécnica del Litoral, ESPOL, Guayaquil 090902, Ecuador
- Correspondence:
| | - Ricardo Pacheco-Coello
- Centro de Investigaciones Biotecnológicas del Ecuador, Campus Gustavo Galindo, ESPOL Polytechnic University, Escuela Superior Politécnica del Litoral, ESPOL, Guayaquil 090902, Ecuador
| | - Liliana Villao-Uzho
- Centro de Investigaciones Biotecnológicas del Ecuador, Campus Gustavo Galindo, ESPOL Polytechnic University, Escuela Superior Politécnica del Litoral, ESPOL, Guayaquil 090902, Ecuador
| | - Migdalia Miranda
- Facultad de Ciencias Naturales y Matemáticas, ESPOL Polytechnic University, Escuela Superior Politécnica del Litoral, ESPOL, Guayaquil 090902, Ecuador
| | - Yamilet Gutiérrez
- Department of Pharmacy, Institute of Pharmacy and Food, Universidad de La Habana, La Habana 10400, Cuba
| | - Iván Chóez-Guaranda
- Centro de Investigaciones Biotecnológicas del Ecuador, Campus Gustavo Galindo, ESPOL Polytechnic University, Escuela Superior Politécnica del Litoral, ESPOL, Guayaquil 090902, Ecuador
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Fan Y, Zhao Q, Duan H, Bi S, Hao X, Xu R, Bai R, Yu R, Lu W, Bao T, Wuriyanghan H. Large-scale mRNA transfer between Haloxylon ammodendron (Chenopodiaceae) and herbaceous root holoparasite Cistanche deserticola (Orobanchaceae). iScience 2022; 26:105880. [PMID: 36686392 PMCID: PMC9852350 DOI: 10.1016/j.isci.2022.105880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 09/27/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022] Open
Abstract
Exchanges of mRNA were shown between host and stem parasites but not root parasites. Cistanche deserticola (Orobanchaceae) is a holoparasitic herb which parasitizes on the roots of woody plant Haloxylon ammodendron (Chenopodiaceae). We used transcriptome sequencing and bioinformatic analyses to identify nearly ten thousand mobile mRNAs. Transcript abundance appears to be a driving force for transfer event and mRNA exchanges occur through haustorial junction. Mobility of selected mRNAs was confirmed in situ and in sunflower-Orobanche cumana heterologous parasitic system. Four C. deserticola →H. ammodendron mobile mRNAs appear to facilitate haustorium development. Of interest, two mobile mRNAs of putative resistance genes CdNLR1 and CdNLR2 cause root-specific hypersensitive response and retard parasite development, which might contribute to parasitic equilibrium. The present study provides evidence for the large-scale mRNA transfer event between a woody host and a root parasite, and demonstrates the functional relevance of six C. deserticola genes in host-parasite interactions.
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Affiliation(s)
- Yanyan Fan
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Qiqi Zhao
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Huimin Duan
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Shuxin Bi
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Xiaomin Hao
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Rui Xu
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Runyao Bai
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Ruonan Yu
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Wenting Lu
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Tiejun Bao
- Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, Ministry of Education, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China,Corresponding author
| | - Hada Wuriyanghan
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China,Corresponding author
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10
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Hou L, Li G, Chen Q, Zhao J, Pan J, Lin R, Zhu X, Wang P, Wang X. De novo full length transcriptome analysis and gene expression profiling to identify genes involved in phenylethanol glycosides biosynthesis in Cistanche tubulosa. BMC Genomics 2022; 23:698. [PMID: 36209069 PMCID: PMC9548140 DOI: 10.1186/s12864-022-08921-x] [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: 02/19/2022] [Accepted: 09/27/2022] [Indexed: 11/26/2022] Open
Abstract
Background The dried stem of Cistanche, is a famous Chinese traditional medicine. The main active pharmacodynamic components are phenylethanol glycosides (PhGs). Cistanche tubulosa produces higher level of PhGs in its stems than that of Cistanche deserticola. However, the key genes in the PhGs biosynthesis pathway is not clear in C. tubulosa. Results In this study, we performed the full-length transcriptome sequencing and gene expression profiling of C. tubulosa using PacBio combined with BGISEQ-500 RNA-seq technology. Totally, 237,772 unique transcripts were obtained, ranging from 199 bp to 31,857 bp. Among the unique transcripts, 188,135 (79.12%) transcripts were annotated. Interestingly, 1080 transcripts were annotated as 22 enzymes related to PhGs biosynthesis. We measured the content of echinacoside, acteoside and total PhGs at two development stages, and found that the content of PhGs was 46.74% of dry matter in young fleshy stem (YS1) and then decreased to 31.22% at the harvest stage (HS2). To compare with YS1, 13,631 genes were up-regulated, and 15,521 genes were down regulated in HS2. Many differentially expressed genes (DEGs) were identified to be involved in phenylpropanoid biosynthesis pathway, phenylalanine metabolism pathway, and tyrosine metabolism pathway. Conclusions This is the first report of transcriptome study of C. tubulosa which provided the foundation for understanding of PhGs biosynthesis. Based on these results, we proposed a potential model for PhGs biosynthesis in C. tubulosa. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08921-x.
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Affiliation(s)
- Lei Hou
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, China
| | - Guanghui Li
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, China
| | - Qingliang Chen
- Modern Research Center for Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - JinJin Zhao
- Shandong Academy of Grape, Shandong Engineering Research Center for Grape Cultivation and Deep-Processing, Jinan, 250100, China
| | - Jiaowen Pan
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, China
| | - Ruxia Lin
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, China
| | - Xiujin Zhu
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, China
| | - Pengfei Wang
- College of Agronomy, Hebei Agricultural University, Baoding, 071000, China.
| | - Xingjun Wang
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, China.
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11
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Miao Y, Chen H, Xu W, Yang Q, Liu C, Huang L. Structural mutations of small single copy (SSC) region in the plastid genomes of five Cistanche species and inter-species identification. BMC PLANT BIOLOGY 2022; 22:412. [PMID: 36008757 PMCID: PMC9404617 DOI: 10.1186/s12870-022-03682-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 06/08/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Cistanche is an important genus of Orobanchaceae, with critical medicinal, economic, and desertification control values. However, the phylogenetic relationships of Cistanche genus remained obscure. To date, no effective molecular markers have been reported to discriminate effectively the Cistanche closely related species reported here. In this study, we obtained and characterized the plastomes of four Cistanche species from China, to clarify the phylogenetic relationship within the genus, and to develop molecular markers for species discrimination. RESULTS: Four Cistanche species (Cistanche deserticola, Cistanche salsa, Cistanche tubulosa and Cistanche sinensis), were deep-sequenced with Illumina. Their plastomes were assembled using SPAdes and annotated using CPGAVAS2. The plastic genomes were analyzed in detail, finding that all showed the conserved quadripartite structure (LSC-IR-SSC-IR) and with full sizes ranging from 75 to 111 Kbp. We observed a significant contraction of small single copy region (SSC, ranging from 0.4-29 Kbp) and expansion of inverted repeat region (IR, ranging from 6-30 Kbp), with C. deserticola and C. salsa showing the smallest SSCs with only one gene (rpl32). Compared with other Orobanchaceae species, Cistanche species showed extremely high rates of gene loss and pseudogenization, as reported for other parasitic Orobanchaceae species. Furthermore, analysis of sequence divergence on protein-coding genes showed the three genes (rpl22, clpP and ycf2) had undergone positive selection in the Cistanche species under study. In addition, by comparison of all available Cistanche plastomes we found 25 highly divergent intergenic spacer (IGS) regions that were used to predict two DNA barcode markers (Cis-mk01 and Cis-mk02 based on IGS region trnR-ACG-trnN-GUU) and eleven specific DNA barcode markers using Ecoprimer software. Experimental validation showed 100% species discrimination success rate with both type of markers. CONCLUSION Our findings have shown that Cistanche species are an ideal model to investigate the structure variation, gene loss and pseudogenization during the process of plastome evolution in parasitic species, providing new insights into the evolutionary relationships among the Cistanche species. In addition, the developed DNA barcodes markers allow the proper species identification, ensuring the effective and safe use of Cistanche species as medicinal products.
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Affiliation(s)
- Yujing Miao
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
| | - Haimei Chen
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
| | - Wanqi Xu
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
| | - Qiaoqiao Yang
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
| | - Chang Liu
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China.
| | - Linfang Huang
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China.
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12
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Liu A, Li Y, Wang Q, Zhang X, Xiong J, Li Y, Lei Y, Sun Y. Analysis of microbial diversity and community structure of rhizosphere soil of Cistanche salsa from different host plants. Front Microbiol 2022; 13:971228. [PMID: 36046015 PMCID: PMC9421434 DOI: 10.3389/fmicb.2022.971228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
Host plants influence rhizosphere microorganism composition through root secretions, and rhizosphere associated microorganisms influence Cistanche seeds germination. At present, little is known about effects of different host plants on soil bacteria and fungi in the rhizosphere of Cistanche salsa. High-throughput sequencing was used here to reveal the similarities and differences in the structural composition of the soil microbial community of C. salsa from six host plants (i.e., Halocnemum strobilaceum, Atriplex patens, Kalidium foliatum, Caroxylon passerinum, Anabasis aphylla, Krascheninnikovia ceratoides). We discovered that Krascheninnikovia ceratoides-parasitizing C. salsa (YRCR6) had the highest diversity of rhizosphere bacterial communities, and Anabasis aphylla -parasitizing C. salsa (YRCR5) had the highest diversity of rhizosphere fungal communities. Fungal communities were more influenced by the host plant than bacterial communities. In addition, we discovered certain rhizosphere microorganisms that may be associated with Cistanche seeds germination, including Mortierella, Aspergillus alliaceus, and Cladosporium, which are account for a relatively high proportion in Halocnemum strobilaceum, Atriplex patens and Anabasis aphylla -parasitizing C. salsa. Redundancy analysis results also revealed that AP, HCO3–, pH, Ca2+, SO42–, and K+ had a highly significant impact on the bacterial community structure (P < 0.01), while pH and SO42– had a significant impact on the fungal community structure (P < 0.05). Conclusively, differences were noted in the structure of rhizosphere bacterial and fungal communities of C. salsa parasitizing different plants in the same habit and the difference may be related to the host plant. This result can provide a new ideas for the selection of host plants and the cultivation of C. salsa.
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Affiliation(s)
- Ailing Liu
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Yuxia Li
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Qiqi Wang
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Xinrui Zhang
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Jie Xiong
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Yang Li
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Yonghui Lei
- Department of Plant Protection, College of Agriculture, Shihezi University, Shihezi, China
- *Correspondence: Yanfei Sun,
| | - Yanfei Sun
- College of Life Sciences, Shihezi University, Shihezi, China
- Yonghui Lei,
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13
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Wang M, Zhang L, Tong S, Jiang D, Fu Z. Chromosome-level genome assembly of a xerophytic plant, Haloxylon ammodendron. DNA Res 2022; 29:dsac006. [PMID: 35266513 PMCID: PMC8946665 DOI: 10.1093/dnares/dsac006] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 03/09/2022] [Indexed: 01/30/2023] Open
Abstract
Haloxylon ammodendron is a xerophytic perennial shrub or small tree that has a high ecological value in anti-desertification due to its high tolerance to drought and salt stress. Here, we report a high-quality, chromosome-level genome assembly of H. ammodendron by integrating PacBio's high-fidelity sequencing and Hi-C technology. The assembled genome size was 685.4 Mb, of which 99.6% was assigned to nine pseudochromosomes with a contig N50 value of 23.6 Mb. Evolutionary analysis showed that both the recent substantial amplification of long terminal repeat retrotransposons and tandem gene duplication may have contributed to its genome size expansion and arid adaptation. An ample amount of low-GC genes was closely related to functions that may contribute to the desert adaptation of H. ammodendron. Gene family clustering together with gene expression analysis identified differentially expressed genes that may play important roles in the direct response of H. ammodendron to water-deficit stress. We also identified several genes possibly related to the degraded scaly leaves and well-developed root system of H. ammodendron. The reference-level genome assembly presented here will provide a valuable genomic resource for studying the genome evolution of xerophytic plants, as well as for further genetic breeding studies of H. ammodendron.
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Affiliation(s)
- Mingcheng Wang
- Institute for Advanced Study, Chengdu University, Chengdu 610106, China
| | - Lei Zhang
- Key Laboratory of Ecological Protection of Agro-pastoral Ecotones in the Yellow River Basin, National Ethnic Affairs Commission of the People’s Republic of China, College of Biological Science & Engineering, North Minzu University, Yinchuan 750001, China
| | - Shaofei Tong
- MOE Key Laboratory for Bio-resources and Eco-environment, College of Life Science, Sichuan University, Chengdu 610105, China
| | - Dechun Jiang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Zhixi Fu
- College of Life Sciences, Sichuan Normal University, Chengdu 610101, China
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14
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He P, Li Y, Xu N, Peng C, Meng F. Predicting the suitable habitats of parasitic desert species based on a niche model with Haloxylon ammodendron and Cistanche deserticola as examples. Ecol Evol 2021; 11:17817-17834. [PMID: 35003642 PMCID: PMC8717296 DOI: 10.1002/ece3.8340] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 10/03/2021] [Accepted: 10/25/2021] [Indexed: 01/28/2023] Open
Abstract
Haloxylon ammodendron, an excellent tree species for sand fixation and afforestation in the desert areas of western China, is threatened by climate change and anthropogenic activities. The suitable habitat of this species is shrinking at a remarkable rate, although conservation measures have been implemented. Cistanche deserticola is an entirely parasitic herb that occurs in deserts, is a source of "desert ginseng" worldwide, and has extremely high medicinal value. Little is known about using niche models to simulate habitat suitability and evaluate important environmental variables related to parasitic species. In this study, we modeled the current suitable habitat of H. ammodendron and C. deserticola by MaxEnt based on occurrence record data of the distributions of these two species in China. We grouped H. ammodendron and C. deserticola into three groups according to the characteristics of parasitic species and modeled them with environmental factors. The results showed that bioclimate was the most important environmental parameter affecting the H. ammodendron and C. deserticola distribution. Precipitations, such as annual precipitation, precipitation seasonality, and precipitation in the driest quarter, were identified as the most critical parameters. The slope, diurnal temperature range, water vapor pressure, ground-frost frequency, and solar radiation also substantially contributed to the distribution of the two species. The proportions of the most suitable areas for Groups 1, 2, and 3 were 1.2%, 1.3%, and 1.7%, respectively, in China. When combined with cultural geography, five hot spot conservation areas were determined within the distribution of H. ammodendron and C. deserticola. The comprehensive analysis indicated that by using MaxEnt to model the suitable habitat of parasitic species, we further improved the accuracy of the prediction and coupled the error of the distribution of a single species. This study provides a useful reference for the protection of H. ammodendron forests and the management of C. deserticola plantations.
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Affiliation(s)
- Ping He
- Beijing Key lab of Traditional Chinese Medicine Protection and UtilizationFaculty of Geographical ScienceBeijing Normal UniversityBeijingChina
| | - Yunfeng Li
- Beijing Key lab of Traditional Chinese Medicine Protection and UtilizationFaculty of Geographical ScienceBeijing Normal UniversityBeijingChina
- Engineering Research Center of Natural MedicineMinistry of EducationFaculty of Geographical ScienceBeijing Normal UniversityBeijingChina
- Key Laboratory of research and development of traditional Chinese medicine in Hebei ProvinceDepartment of traditional Chinese MedicineChengde Medical CollegeChengdeChina
| | - Ning Xu
- Beijing Key lab of Traditional Chinese Medicine Protection and UtilizationFaculty of Geographical ScienceBeijing Normal UniversityBeijingChina
- Engineering Research Center of Natural MedicineMinistry of EducationFaculty of Geographical ScienceBeijing Normal UniversityBeijingChina
| | - Cheng Peng
- School of pharmacyChengdu University of TCMChengduChina
| | - Fanyun Meng
- Beijing Key lab of Traditional Chinese Medicine Protection and UtilizationFaculty of Geographical ScienceBeijing Normal UniversityBeijingChina
- Engineering Research Center of Natural MedicineMinistry of EducationFaculty of Geographical ScienceBeijing Normal UniversityBeijingChina
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15
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Comparative and phylogenetic analyses of the chloroplast genomes of species of Paeoniaceae. Sci Rep 2021; 11:14643. [PMID: 34282194 PMCID: PMC8289817 DOI: 10.1038/s41598-021-94137-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 07/06/2021] [Indexed: 11/13/2022] Open
Abstract
Plants belonging to family Paeoniaceae are not only economically important ornamental plants but also medicinal plants used as an important source of traditional Chinese medicine. Owing to the complex network evolution and polyploidy evolution of this family, its systematics and taxonomy are controversial and require a detailed investigation. In this study, three complete chloroplast genomes of sect. Paeonia, one of the sections of Paeonia, were sequenced and then analysed together with 16 other published chloroplast genomes of Paeoniaceae species. The total lengths of the chloroplast genomes of these species were 152,153–154,405 bp. A total of 82–87 protein-coding genes, 31–40 tRNA genes and 8 rRNA genes were annotated. Bioinformatics analysis revealed 61–74 simple sequence repeats (SSRs) in the chloroplast genomes, most of which have A/T base preference. Codon usage analysis showed that A/U-ending codons were more positive than C/G-ending codons, and a slight bias in codon usage was observed in these species. A comparative analysis of these 19 species of Paeoniaceae was then conducted. Fourteen highly variable regions were selected for species relationship study. Phylogenetic analysis revealed that the species of sect. Paeonia gathered in one branch and then divided into different small branches. P. lactiflora, P. anomala, P. anomala subsp. veitchii and P. mairei clustered together. P. intermedia was related to P. obovata and P. obovata subsp. willmottiae. P. emodi was the sister to all other species in the sect. Paeonia.
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16
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Wu L, Cui Y, Wang Q, Xu Z, Wang Y, Lin Y, Song J, Yao H. Identification and phylogenetic analysis of five Crataegus species (Rosaceae) based on complete chloroplast genomes. PLANTA 2021; 254:14. [PMID: 34180013 DOI: 10.1007/s00425-021-03667-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 06/15/2021] [Indexed: 06/13/2023]
Abstract
The chloroplast genomes of the five Crataegus species were shown to have a conserved genome structure. Complete chloroplast genome sequences were more suitable than highly variable regions for the identification and phylogenetic analysis of Crataegus species. Hawthorn, which is commonly used as a traditional Chinese medicine, is one of the most popular sour fruits and has high economic value. Crataegus pinnatifida var. pinnatifida and C. pinnatifida var. major are frequently adulterated with other Crataegus species on the herbal medicine market. However, most Crataegus plants are difficult to identify using traditional morphological methods. Here, we compared five Crataegus chloroplast (CP) genomes comprising two newly sequenced (i.e., C. pinnatifida var. pinnatifida and C. pinnatifida var. major) and three previously published CP genomes. The CP genomes of the five Crataegus species had a conserved genome structure, gene content and codon usage. The total length of the CP genomes was 159,654-159,865 bp. A total of 129-130 genes, including 84-85 protein-coding genes, 37 tRNA genes and 8 rRNA genes, were annotated. Bioinformatics analysis revealed 96-103 simple sequence repeats (SSRs) and 48-70 long repeats in the five CP genomes. Combining the results of mVISTA and nucleotide diversity, five highly variable regions were screened for species identification and relationship studies. Maximum likelihood trees were constructed on the basis of complete CP genome sequences and highly variable regions. The results showed that the former had higher discriminatory power for Crataegus species, indicating that the complete CP genome could be used as a super-barcode to accurately authenticate the five Crataegus species.
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Affiliation(s)
- Liwei Wu
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, 100193, China
| | - Yingxian Cui
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, 100193, China
| | - Qing Wang
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, 100193, China
| | - Zhichao Xu
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, 100193, China
| | - Yu Wang
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
| | - Yulin Lin
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
| | - Jingyuan Song
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, 100193, China
| | - Hui Yao
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China.
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, 100193, China.
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17
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Choi KS, Park S. Complete Plastid and Mitochondrial Genomes of Aeginetia indica Reveal Intracellular Gene Transfer (IGT), Horizontal Gene Transfer (HGT), and Cytoplasmic Male Sterility (CMS). Int J Mol Sci 2021; 22:6143. [PMID: 34200260 PMCID: PMC8201098 DOI: 10.3390/ijms22116143] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/01/2021] [Accepted: 06/05/2021] [Indexed: 11/16/2022] Open
Abstract
Orobanchaceae have become a model group for studies on the evolution of parasitic flowering plants, and Aeginetia indica, a holoparasitic plant, is a member of this family. In this study, we assembled the complete chloroplast and mitochondrial genomes of A. indica. The chloroplast and mitochondrial genomes were 56,381 bp and 401,628 bp long, respectively. The chloroplast genome of A. indica shows massive plastid genes and the loss of one IR (inverted repeat). A comparison of the A. indica chloroplast genome sequence with that of a previous study demonstrated that the two chloroplast genomes encode a similar number of proteins (except atpH) but differ greatly in length. The A. indica mitochondrial genome has 53 genes, including 35 protein-coding genes (34 native mitochondrial genes and one chloroplast gene), 15 tRNA (11 native mitochondrial genes and four chloroplast genes) genes, and three rRNA genes. Evidence for intracellular gene transfer (IGT) and horizontal gene transfer (HGT) was obtained for plastid and mitochondrial genomes. ψndhB and ψcemA in the A. indica mitogenome were transferred from the plastid genome of A. indica. The atpH gene in the plastid of A. indica was transferred from another plastid angiosperm plastid and the atpI gene in mitogenome A. indica was transferred from a host plant like Miscanthus siensis. Cox2 (orf43) encodes proteins containing a membrane domain, making ORF (Open Reading Frame) the most likely candidate gene for CMS development in A. indica.
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Affiliation(s)
- Kyoung-Su Choi
- Institute of Natural Science, Yeungnam Univiersity, Gyeongsan-si 38541, Gyeongbuk-do, Korea;
- Department of Life Sciences, Yeungnam University, Gyeongsan-si 38541, Gyeongbuk-do, Korea
| | - Seonjoo Park
- Department of Life Sciences, Yeungnam University, Gyeongsan-si 38541, Gyeongbuk-do, Korea
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Villanueva-Corrales S, García-Botero C, Garcés-Cardona F, Ramírez-Ríos V, Villanueva-Mejía DF, Álvarez JC. The Complete Chloroplast Genome of Plukenetia volubilis Provides Insights Into the Organelle Inheritance. FRONTIERS IN PLANT SCIENCE 2021; 12:667060. [PMID: 33968119 PMCID: PMC8103035 DOI: 10.3389/fpls.2021.667060] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 03/24/2021] [Indexed: 05/04/2023]
Abstract
Plukenetia volubilis L. (Malpighiales: Euphorbiaceae), also known as Sacha inchi, is considered a promising crop due to its high seed content of unsaturated fatty acids (UFAs), all of them highly valuable for food and cosmetic industries, but the genetic basis of oil biosynthesis of this non-model plant is still insufficient. Here, we sequenced the total DNA of Sacha inchi by using Illumina and Nanopore technologies and approached a de novo reconstruction of the whole nucleotide sequence and the organization of its 164,111 bp length of the chloroplast genome, displaying two copies of an inverted repeat sequence [inverted repeat A (IRA) and inverted repeat B (IRB)] of 28,209 bp, each one separating a small single copy (SSC) region of 17,860 bp and a large single copy (LSC) region of 89,833 bp. We detected two large inversions on the chloroplast genome that were not presented in the previously reported sequence and studied a promising cpDNA marker, useful in phylogenetic approaches. This chloroplast DNA (cpDNA) marker was used on a set of five distinct Colombian cultivars of P. volubilis from different geographical locations to reveal their phylogenetic relationships. Thus, we evaluated if it has enough resolution to genotype cultivars, intending to crossbreed parents and following marker's trace down to the F1 generation. We finally elucidated, by using molecular and cytological methods on cut flower buds, that the inheritance mode of P. volubilis cpDNA is maternally transmitted and proposed that it occurs as long as it is physically excluded during pollen development. This de novo chloroplast genome will provide a valuable resource for studying this promising crop, allowing the determination of the organellar inheritance mechanism of some critical phenotypic traits and enabling the use of genetic engineering in breeding programs to develop new varieties.
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Affiliation(s)
| | - Camilo García-Botero
- CIBIOP Research Group, Biological Sciences Department, EAFIT University, Medellín, Colombia
| | - Froilán Garcés-Cardona
- CIBIOP Research Group, Biological Sciences Department, EAFIT University, Medellín, Colombia
| | - Viviana Ramírez-Ríos
- CIBIOP Research Group, Biological Sciences Department, EAFIT University, Medellín, Colombia
| | | | - Javier C. Álvarez
- BEC Research Group, Biological Sciences Department, EAFIT University, Medellín, Colombia
- CIBIOP Research Group, Biological Sciences Department, EAFIT University, Medellín, Colombia
- *Correspondence: Javier C. Álvarez,
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Mandakh U, Battseren M, Ganbat D, Ayanga T, Adiya Z, Borjigidai A, Long C. Folk nomenclature of plants in Cistanche deserticola-associated community in South Gobi, Mongolia. PLANT DIVERSITY 2020; 42:434-442. [PMID: 33733011 PMCID: PMC7936101 DOI: 10.1016/j.pld.2020.09.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 08/20/2020] [Accepted: 09/26/2020] [Indexed: 05/15/2023]
Abstract
Cistanche deserticola is an important medicinal plant in Mongolia. Despite its significant role in local healing systems, little traditional knowledge had been reported. The present study investigated folk names of C. deserticola and other species of the same community in Umnugobi Province, South Gobi region of Mongolia, based on ethnobotanical approaches. The high correspondence between folk names and scientific names of plant species occurring in Cistanche-associated community shows the scientific meaning of folk nomenclature and classification in Mongolia. The Mongolian and folk names of plants were formed on the basis of observations and understanding of wild plants including their morphology, phenology and traditional uses as well. Results from this study will support the conservation of C. deserticola itself, a rare and endangered plant species listed in the Monglian Red Data Book. Our documentation of folk nomenclature based on 96 plant species in the Cistanche community, as a part of traditional knowledge associated with biodiversity, will be very helpful for making strategy of plant biodiversity conservation in Mongolia.
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Affiliation(s)
- Urtnasan Mandakh
- College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, China
- Key Laboratory of Ethnomedicine (Minzu University of China), Ministry of Education, Beijing, 100081, China
- Institute of Geography and Geoecology, Mongolian Academy of Sciences, Ulaanbaatar, 15170, Mongolia
| | - Munkhjargal Battseren
- Botanic Garden and Research Institute, Mongolian Academy of Sciences, Ulaanbaatar, 210351, Mongolia
| | - Danzanchadav Ganbat
- Institute of Geography and Geoecology, Mongolian Academy of Sciences, Ulaanbaatar, 15170, Mongolia
- College of Geographical Science, Inner Mongolia Normal University, Hohhot, 010022, China
| | - Turuutuvshin Ayanga
- Institute of Geography and Geoecology, Mongolian Academy of Sciences, Ulaanbaatar, 15170, Mongolia
| | - Zolzaya Adiya
- Institute of Geography and Geoecology, Mongolian Academy of Sciences, Ulaanbaatar, 15170, Mongolia
- Department of Geography, School of Arts and Sciences, National University of Mongolia, Ulaanbaatar, 14201, Mongolia
| | - Almaz Borjigidai
- Key Laboratory of Ethnomedicine (Minzu University of China), Ministry of Education, Beijing, 100081, China
- School of Pharmacy, Minzu University of China, Beijing, 100081, China
- Corresponding author. Key Laboratory of Ethnomedicine (Minzu University of China), Ministry of Education, Beijing 100081, China.
| | - Chunlin Long
- College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, China
- Key Laboratory of Ethnomedicine (Minzu University of China), Ministry of Education, Beijing, 100081, China
- Corresponding author. College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China.
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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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21
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Xu J, Shen X, Liao B, Xu J, Hou D. Comparing and phylogenetic analysis chloroplast genome of three Achyranthes species. Sci Rep 2020; 10:10818. [PMID: 32616875 PMCID: PMC7331806 DOI: 10.1038/s41598-020-67679-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 06/12/2020] [Indexed: 11/29/2022] Open
Abstract
In this study, the chloroplast genome sequencing of the Achyranthes longifolia, Achyranthes bidentata and Achyranthes aspera were performed by Next-generation sequencing technology. The results revealed that there were a length of 151,520 bp (A. longifolia), 151,284 bp (A. bidentata), 151,486 bp (A. aspera), respectively. These chloroplast genome have a highly conserved structure with a pair of inverted repeat (IR) regions (25,150 bp; 25,145 bp; 25,150 bp), a large single copy (LSC) regions (83,732 bp; 83,933 bp; 83,966 bp) and a small single copy (SSC) regions (17,252 bp; 17,263 bp; 17,254 bp) in A. bidentate, A. aspera and A. longifolia. There were 127 genes were annotated, which including 8 rRNA genes, 37 tRNA genes and 82 functional genes. The phylogenetic analysis strongly revealed that Achyranthes is monophyletic, and A. bidentata was the closest relationship with A. aspera and A. longifolia. A. bidentata and A. longifolia were clustered together, the three Achyranthes species had the same origin, then the gunes of Achyranthes is the closest relative to Alternanthera, and that forms a group with Alternanthera philoxeroides. The research laid a foundation and provided relevant basis for the identification of germplasm resources in the future.
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Affiliation(s)
- Jingya Xu
- Agricultural College, Henan University of Science and Technology, Luoyang, China
- The Luoyang Engineering Research Center of Breeding and Utilization of Dao-Di Herbs, Luoyang, China
- Institute of Chinese Materia Medical, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xiaofeng Shen
- Institute of Chinese Materia Medical, China Academy of Chinese Medical Sciences, Beijing, China
| | - Baosheng Liao
- Institute of Chinese Materia Medical, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jiang Xu
- Institute of Chinese Materia Medical, China Academy of Chinese Medical Sciences, Beijing, China.
| | - Dianyun Hou
- Agricultural College, Henan University of Science and Technology, Luoyang, China.
- The Luoyang Engineering Research Center of Breeding and Utilization of Dao-Di Herbs, Luoyang, China.
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22
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Ataei N, Schneeweiss GM, García MA, Krug M, Lehnert M, Valizadeh J, Quandt D. A multilocus phylogeny of the non-photosynthetic parasitic plant Cistanche (Orobanchaceae) refutes current taxonomy and identifies four major morphologically distinct clades. Mol Phylogenet Evol 2020; 151:106898. [PMID: 32585287 DOI: 10.1016/j.ympev.2020.106898] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 05/24/2020] [Accepted: 06/17/2020] [Indexed: 02/09/2023]
Abstract
Phylogenetic relationships of and within non-photosynthetic parasitic lineages are notoriously poorly known, which negatively affects our understanding of parasitic plants. This is also the case for Cistanche (Orobanchaceae), an Old World genus with about two dozen species, whose relationships have not yet been addressed using molecular phylogenetic approaches. Here we infer phylogenetic relationships within the genus, employing a taxonomically and geographically broad sampling covering all previously distinguished infrageneric groups and most of the currently recognized species. A combined matrix of three plastid markers (trnL-trnF, including the trnL intron and the intergenic spacer (IGS), trnS-trnfM IGS and psbA-trnH IGS) and one nuclear marker (ITS) was analyzed using maximum parsimony, maximum likelihood and Bayesian inference. Cistanche falls into four well-supported and geographically differentiated clades: East Asian Clade, Northwest African Clade, Southwest Asian Clade and Widespread Clade. Of those, only the East Asian Clade corresponds to a previously recognized taxonomic section, whereas the others either contain members of two or three sections (Widespread Clade and Southwest Asian Clade, respectively) or have not been taxonomically recognized so far (Northwest African Clade). Whereas the Southwest Asian Clade exhibits strong phylogenetic structure among and partly within species (the East Asian Clade and the Northwest African Clade are monospecific), phylogenetic resolution within the Widespread Clade is often low and hampered by discrepancies between nuclear and plastid markers. Both molecular and morphological data indicate that species diversity in Cistanche is currently underestimated.
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Affiliation(s)
- Najibeh Ataei
- Nees Institute for Biodiversity of Plants, Rheinische Friedrich-Wilhelms-Universität Bonn, Meckenheimer Allee 170, 53115 Bonn, Germany; General Directorate for Agricultural Research Institute of Afghanistan (ARIA), Ministry of Agriculture, Irrigation and Livestock, Badam Bagh, Kabul, Afghanistan
| | - Gerald M Schneeweiss
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria.
| | - Miguel Angel García
- Department of Biology, University of Toronto at Mississauga, 3359 Mississauga, Canada; Real Jardín Botánico, CSIC, Plaza de Murillo 2, 28014 Madrid, Spain
| | - Michael Krug
- Nees Institute for Biodiversity of Plants, Rheinische Friedrich-Wilhelms-Universität Bonn, Meckenheimer Allee 170, 53115 Bonn, Germany
| | - Marcus Lehnert
- Nees Institute for Biodiversity of Plants, Rheinische Friedrich-Wilhelms-Universität Bonn, Meckenheimer Allee 170, 53115 Bonn, Germany
| | - Jafar Valizadeh
- Department of Biology, University of Sistan and Baluchistan, Zahedan, Iran
| | - Dietmar Quandt
- Nees Institute for Biodiversity of Plants, Rheinische Friedrich-Wilhelms-Universität Bonn, Meckenheimer Allee 170, 53115 Bonn, Germany.
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23
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Guo X, Liu C, Zhang G, Su W, Landis JB, Zhang X, Wang H, Ji Y. The Complete Plastomes of Five Hemiparasitic Plants ( Osyris wightiana, Pyrularia edulis, Santalum album, Viscum liquidambaricolum, and V. ovalifolium): Comparative and Evolutionary Analyses Within Santalales. Front Genet 2020; 11:597. [PMID: 32612639 PMCID: PMC7308561 DOI: 10.3389/fgene.2020.00597] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 05/18/2020] [Indexed: 11/27/2022] Open
Abstract
Most species of Santalales (the sandalwood order) are hemiparasites, including both facultative and obligate hemiparasites. Despite its rich diversity, only a small fraction of the species in the sandalwood order have sequenced plastomes. The evolution of parasitism-associated plastome reduction in Santalales remains under-studied. Here, we report the complete plastomes of three facultative hemiparasites (Pyrularia edulis, Cervantesiaceae; Osyris wightiana, and Santalum album, Santalaceae), and two obligate hemiparasites (Viscum liquidambaricolum and Viscum ovalifolium, Viscaceae). Coupled with publicly available data, we investigated the dynamics of plastome degradation in Santalales hemiparasites. Our results indicate that these hemiparasites can be characterized by various degrees of plastome downsizing, structural rearrangement, and gene loss. The loss or pseudogenization of ndh genes was commonly observed in Santalales hemiparasites, which may be correlated to the lifestyle shift from photoautotroph to hemiparasitism. However, the obligate hemiparasites did not exhibit a consistently higher level of gene loss or pseudogenization compared to facultative hemiparasites, which suggests that the degree of plastome reduction is not correlated with the trophic level facultative or obligate hemiparasitism. Instead, closely related taxa tend to possess highly similar plastome size, structure, and gene content. This implies the parasitism-associated plastome degradation in Santalales may evolve in a lineage-specific manner.
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Affiliation(s)
- Xiaorong Guo
- Institute of Ecology and Geobotany, Yunnan University, Kunming, China
| | - Changkun Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Guangfei Zhang
- Institute of Ecology and Geobotany, Yunnan University, Kunming, China
| | - Wenhua Su
- Institute of Ecology and Geobotany, Yunnan University, Kunming, China
| | - Jacob B. Landis
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - Xu Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Hengchang Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Yunheng Ji
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Population, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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24
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Xiong Y, Xiong Y, He J, Yu Q, Zhao J, Lei X, Dong Z, Yang J, Peng Y, Zhang X, Ma X. The Complete Chloroplast Genome of Two Important Annual Clover Species, Trifolium alexandrinum and T. resupinatum: Genome Structure, Comparative Analyses and Phylogenetic Relationships with Relatives in Leguminosae. PLANTS (BASEL, SWITZERLAND) 2020; 9:E478. [PMID: 32283660 PMCID: PMC7238141 DOI: 10.3390/plants9040478] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/03/2020] [Accepted: 04/04/2020] [Indexed: 01/31/2023]
Abstract
Trifolium L., which belongs to the IR lacking clade (IRLC), is one of the largest genera in the Leguminosae and contains several economically important fodder species. Here, we present whole chloroplast (cp) genome sequencing and annotation of two important annual grasses, Trifolium alexandrinum (Egyptian clover) and T. resupinatum (Persian clover). Abundant single nucleotide polymorphisms (SNPs) and insertions/deletions (In/Dels) were discovered between those two species. Global alignment of T. alexandrinum and T. resupinatum to a further thirteen Trifolium species revealed a large amount of rearrangement and repetitive events in these fifteen species. As hypothetical cp open reading frame (ORF) and RNA polymerase subunits, ycf1 and rpoC2 in the cp genomes both contain vast repetitive sequences and observed high Pi values (0.7008, 0.3982) between T. alexandrinum and T. resupinatum. Thus they could be considered as the candidate genes for phylogenetic analysis of Trifolium species. In addition, the divergence time of those IR lacking Trifolium species ranged from 84.8505 Mya to 4.7720 Mya. This study will provide insight into the evolution of Trifolium species.
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Affiliation(s)
- Yanli Xiong
- College of Animal science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.X.); (Y.X.); (Q.Y.); (J.Z.); (X.L.); (Z.D.); (J.Y.); (Y.P.)
| | - Yi Xiong
- College of Animal science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.X.); (Y.X.); (Q.Y.); (J.Z.); (X.L.); (Z.D.); (J.Y.); (Y.P.)
| | - Jun He
- State Key Laboratory of Exploration and Utilization of Crop Gene Resources in 10 Southwest China, Key Laboratory of Biology and Genetic Improvement of Maize in 11 Southwest Region, Ministry of Agriculture, Maize Research Institute of Sichuan 12 Agricultural University, Chengdu 600031, China;
| | - Qingqing Yu
- College of Animal science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.X.); (Y.X.); (Q.Y.); (J.Z.); (X.L.); (Z.D.); (J.Y.); (Y.P.)
| | - Junming Zhao
- College of Animal science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.X.); (Y.X.); (Q.Y.); (J.Z.); (X.L.); (Z.D.); (J.Y.); (Y.P.)
| | - Xiong Lei
- College of Animal science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.X.); (Y.X.); (Q.Y.); (J.Z.); (X.L.); (Z.D.); (J.Y.); (Y.P.)
| | - Zhixiao Dong
- College of Animal science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.X.); (Y.X.); (Q.Y.); (J.Z.); (X.L.); (Z.D.); (J.Y.); (Y.P.)
| | - Jian Yang
- College of Animal science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.X.); (Y.X.); (Q.Y.); (J.Z.); (X.L.); (Z.D.); (J.Y.); (Y.P.)
| | - Yan Peng
- College of Animal science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.X.); (Y.X.); (Q.Y.); (J.Z.); (X.L.); (Z.D.); (J.Y.); (Y.P.)
| | - Xinquan Zhang
- College of Animal science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.X.); (Y.X.); (Q.Y.); (J.Z.); (X.L.); (Z.D.); (J.Y.); (Y.P.)
| | - Xiao Ma
- College of Animal science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.X.); (Y.X.); (Q.Y.); (J.Z.); (X.L.); (Z.D.); (J.Y.); (Y.P.)
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25
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Liu X, Fu W, Tang Y, Zhang W, Song Z, Li L, Yang J, Ma H, Yang J, Zhou C, Davis CC, Wang Y. Diverse trajectories of plastome degradation in holoparasitic Cistanche and genomic location of the lost plastid genes. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:877-892. [PMID: 31639183 DOI: 10.1093/jxb/erz456] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 10/04/2019] [Indexed: 06/10/2023]
Abstract
The plastid genomes (plastomes) of non-photosynthetic plants generally undergo gene loss and pseudogenization. Despite massive plastomes reported in different parasitism types of the broomrape family (Orobanchaceae), more plastomes representing different degradation patterns in a single genus are expected to be explored. Here, we sequence and assemble the complete plastomes of three holoparasitic Cistanche species (C. salsa, C. mongolica, and C. sinensis) and compare them with the available plastomes of Orobanchaceae. We identified that the diverse degradation trajectories under purifying selection existed among three Cistanche clades, showing obvious size differences in the entire plastome, long single copy region, and non-coding region, and different patterns of the retention/loss of functional genes. With few exceptions of putatively functional genes, massive plastid fragments, which have been lost and transferred into the mitochondrial or nuclear genomes, are non-functional. In contrast to the equivalents of the Orobanche species, some plastid-derived genes with diverse genomic locations are found in Cistanche. The early and initially diverged clades in different genera such as Cistanche and Aphyllon possess obvious patterns of plastome degradation, suggesting that such key lineages should be considered prior to comparative analysis of plastome evolution, especially in the same genus.
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Affiliation(s)
- Xiaoqing Liu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Weirui Fu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Yiwei Tang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Wenju Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Zhiping Song
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Linfeng Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Ji Yang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Hong Ma
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Institute of Plant Biology, Center for Evolutionary Biology, Fudan University, Shanghai, China
- Department of Biology, Institute of Molecular Evolutionary Genetics, and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Jianhua Yang
- College of Pharmacy, The First Affiliated Hospital, Xinjiang Medical University, Urumqi, China
| | - Chan Zhou
- Department of Population and Quantitative Health Sciences, Massachusetts General Hospital, 55 Lake Ave, North Worcester, MA, USA
| | - Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Avenue, Cambridge, MA, USA
| | - Yuguo Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
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Nie L, Cui Y, Wu L, Zhou J, Xu Z, Li Y, Li X, Wang Y, Yao H. Gene Losses and Variations in Chloroplast Genome of Parasitic Plant Macrosolen and Phylogenetic Relationships within Santalales. Int J Mol Sci 2019; 20:E5812. [PMID: 31752332 PMCID: PMC6888684 DOI: 10.3390/ijms20225812] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 11/15/2019] [Accepted: 11/17/2019] [Indexed: 11/16/2022] Open
Abstract
Macrosolen plants are parasitic shrubs, several of which are important medicinal plants, that are used as folk medicine in some provinces of China. However, reports on Macrosolen are limited. In this study, the complete chloroplast genome sequences of Macrosolen cochinchinensis, Macrosolen tricolor and Macrosolen bibracteolatus are reported. The chloroplast genomes were sequenced by Illumina HiSeq X. The length of the chloroplast genomes ranged from 129,570 bp (M. cochinchinensis) to 126,621 bp (M. tricolor), with a total of 113 genes, including 35 tRNA, eight rRNA, 68 protein-coding genes, and two pseudogenes (ycf1 and rpl2). The simple sequence repeats are mainly comprised of A/T mononucleotide repeats. Comparative genome analyses of the three species detected the most divergent regions in the non-coding spacers. Phylogenetic analyses using maximum parsimony and maximum likelihood strongly supported the idea that Loranthaceae and Viscaceae are monophyletic clades. The data obtained in this study are beneficial for further investigations of Macrosolen in respect to evolution and molecular identification.
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Affiliation(s)
- Liping Nie
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; (L.N.); (Y.C.); (L.W.); (J.Z.); (Z.X.); (Y.W.)
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing 100193, China
| | - Yingxian Cui
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; (L.N.); (Y.C.); (L.W.); (J.Z.); (Z.X.); (Y.W.)
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing 100193, China
| | - Liwei Wu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; (L.N.); (Y.C.); (L.W.); (J.Z.); (Z.X.); (Y.W.)
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing 100193, China
| | - Jianguo Zhou
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; (L.N.); (Y.C.); (L.W.); (J.Z.); (Z.X.); (Y.W.)
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing 100193, China
| | - Zhichao Xu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; (L.N.); (Y.C.); (L.W.); (J.Z.); (Z.X.); (Y.W.)
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing 100193, China
| | - Yonghua Li
- College of Pharmacy, Guangxi University of Traditional Chinese Medicine, Nanning 530200, China
| | - Xiwen Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China;
| | - Yu Wang
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; (L.N.); (Y.C.); (L.W.); (J.Z.); (Z.X.); (Y.W.)
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing 100193, China
| | - Hui Yao
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; (L.N.); (Y.C.); (L.W.); (J.Z.); (Z.X.); (Y.W.)
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing 100193, China
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Zong D, Gan P, Zhou A, Li J, Xie Z, Duan A, He C. Comparative analysis of the complete chloroplast genomes of seven Populus species: Insights into alternative female parents of Populus tomentosa. PLoS One 2019; 14:e0218455. [PMID: 31216332 PMCID: PMC6583991 DOI: 10.1371/journal.pone.0218455] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Accepted: 06/03/2019] [Indexed: 12/25/2022] Open
Abstract
Populus tomentosa, of section Populus, is distributed mainly in northern China. This species has high resistance to many diseases and insects, and it plays key roles in shelterbelts and urban afforestation in northern China. It has long been suspected to be a hybrid, but its parents remain unknown. In the present study, we report four newly sequenced complete cp genomes from section Populus and comparative genomic analyses of these new sequences and three published cp genome sequences. The seven cp genomes ranged from 155,853 bp (P. tremula var. davidiana) to 156,746 bp (P. adenopoda) in length, and their gene orders, gene numbers and GC contents were similar. We analyzed SNPs, indels, SSRs and repeats among the seven cp genomes, and eight small inversions were detected in the ndhC-trnV, rbcL-accD, petA-psbJ, trnW-trnP, rpl16-rps3, trnL-ycf15, ycf15-trnL, and ndhF-trnL intergenic regions. Furthermore, seven divergent regions (trnH-psbA, matK, psbM-psbD, ndhC-trnV, ycf1, ndhF-ccsA and ccsA-ndhD) were found in more highly variable regions. The phylogenetic tree reveals that P. tomentosa is closely related to P. alba and P. alba var. pyramidalis. Hence, P. alba was involved in the formation of P. tomentosa.
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Affiliation(s)
- Dan Zong
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, Yunnan, China
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, Yunnan, China
| | - Peihua Gan
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, Yunnan, China
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, Yunnan, China
| | - Anpei Zhou
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, Yunnan, China
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, Yunnan, China
| | - Jinyu Li
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, Yunnan, China
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, Yunnan, China
| | - Zhongli Xie
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, Yunnan, China
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, Yunnan, China
| | - Anan Duan
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, Yunnan, China
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, Yunnan, China
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, Yunnan, China
| | - Chengzhong He
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, Yunnan, China
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, Yunnan, China
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, Yunnan, China
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28
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Alwadani KG, Janes JK, Andrew RL. Chloroplast genome analysis of box-ironbark Eucalyptus. Mol Phylogenet Evol 2019; 136:76-86. [PMID: 30954587 DOI: 10.1016/j.ympev.2019.04.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 03/25/2019] [Accepted: 04/01/2019] [Indexed: 11/17/2022]
Abstract
Eucalyptus L'Hérit. (Myrtaceae) is a taxonomically complex and highly speciose genus that dominates much of Australia's woody vegetation. However, very little information is available about the molecular biology and chloroplast diversity of certain groups, such as Eucalyptus section Adnataria, which is found in many woodland habitats of eastern Australia. We report four new complete chloroplast genomes of Eucalyptus, including three genomes from species previously lacking any chloroplast reference sequences. Plastomes of E. albens, E. conica, E. crebra and E. melliodora assembled using a de novo approach were shown to be largely identical to each other, and similar in size and structure to previously published chloroplast genomes from Eucalyptus. A total of 132 genes (114 single-copy genes and 18 duplicated genes in the IR regions) were identified, and shown to be highly conserved in terms of gene order, content and organization. Slightly higher divergence in the intergenic spacers was identified through comparative genomic analyses. Chloroplast sequences of 35 additional individuals representing 12 species were assembled using a reference guided approach. Rates of nucleotide substitution varied among the protein coding genes, with 17 genes under possible positive selection, and 29 invariant genes. Phylogenetic analysis of either the whole reconstructed plastome sequences or the individual genes revealed extreme discordance with expected species boundaries or higher-level relationships. Plastome relationships were better predicted by geography than by nuclear DNA or taxonomic relationships, suggesting a substantial influence of gene flow over and above the effects of incomplete lineage sorting. These results provide resources for future research and valuable insights into the prevalence of interspecific gene flow among Eucalyptus species.
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Affiliation(s)
- Khawla G Alwadani
- School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia; Biology Department, Faculty of Science, Jazan University, Saudi Arabia
| | - Jasmine K Janes
- School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia; Biology Department, Faculty of Science and Technology, Vancouver Island University, British Columbia, Canada
| | - Rose L Andrew
- School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia.
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29
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Schneider AC, Braukmann T, Banerjee A, Stefanovic S. Convergent Plastome Evolution and Gene Loss in Holoparasitic Lennoaceae. Genome Biol Evol 2018; 10:2663-2670. [PMID: 30169817 PMCID: PMC6178340 DOI: 10.1093/gbe/evy190] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2018] [Indexed: 11/15/2022] Open
Abstract
The Lennoaceae, a small monophyletic plant family of root parasites endemic to the Americas, are one of the last remaining independently evolved lineages of parasitic angiosperms lacking a published plastome. In this study, we present the assembled and annotated plastomes of two species spanning the crown node of Lennoaceae, Lennoa madreporoides and Pholisma arenarium, as well as their close autotrophic relative from the sister family Ehretiaceae, Tiquilia plicata. We find that the plastomes of L. madreporoides and P. arenarium are similar in size and gene content, and substantially reduced compared to T. plicata, consistent with trends seen in other holoparasitic lineages. In particular, most plastid genes involved in photosynthesis function have been lost, whereas housekeeping genes (ribosomal protein-coding genes, rRNAs, and tRNAs) are retained. One notable exception is the persistence of a rbcL open reading frame in P. arenarium but not L. madreporoides suggesting a nonphotosynthetic function for this gene. Of the retained coding genes, dN/dS ratios indicate that some remain under purifying selection, whereas others show relaxed selection. Overall, this study supports the mounting evidence for convergent plastome evolution in flowering plants following the shift to heterotrophy.
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Affiliation(s)
- Adam C Schneider
- Department of Biology, University of Toronto Mississauga, Ontario, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada.,Department of Biology, Hendrix College, Conway, AR
| | - Thomas Braukmann
- Centre for Biodiversity Genomics, University of Guelph, Ontario, Canada
| | - Arjan Banerjee
- Department of Biology, University of Toronto Mississauga, Ontario, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada
| | - Saša Stefanovic
- Department of Biology, University of Toronto Mississauga, Ontario, Canada
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30
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Schelkunov MI, Penin AA, Logacheva MD. RNA-seq highlights parallel and contrasting patterns in the evolution of the nuclear genome of fully mycoheterotrophic plants. BMC Genomics 2018; 19:602. [PMID: 30092758 PMCID: PMC6085651 DOI: 10.1186/s12864-018-4968-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 07/30/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND While photosynthesis is the most notable trait of plants, several lineages of plants (so-called full heterotrophs) have adapted to obtain organic compounds from other sources. The switch to heterotrophy leads to profound changes at the morphological, physiological and genomic levels. RESULTS Here, we characterize the transcriptomes of three species representing two lineages of mycoheterotrophic plants: orchids (Epipogium aphyllum and Epipogium roseum) and Ericaceae (Hypopitys monotropa). Comparative analysis is used to highlight the parallelism between distantly related fully heterotrophic plants. In both lineages, we observed genome-wide elimination of nuclear genes that encode proteins related to photosynthesis, while systems associated with protein import to plastids as well as plastid transcription and translation remain active. Genes encoding components of plastid ribosomes that have been lost from the plastid genomes have not been transferred to the nuclear genomes; instead, some of the encoded proteins have been substituted by homologs. The nuclear genes of both Epipogium species accumulated nucleotide substitutions twice as rapidly as their photosynthetic relatives; in contrast, no increase in the substitution rate was observed in H. monotropa. CONCLUSIONS Full heterotrophy leads to profound changes in nuclear gene content. The observed increase in the rate of nucleotide substitutions is lineage specific, rather than a universal phenomenon among non-photosynthetic plants.
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Affiliation(s)
- Mikhail I Schelkunov
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.
| | - Aleksey A Penin
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.,A.N Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.,Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Maria D Logacheva
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia. .,Skolkovo Institute of Science and Technology, Moscow, Russia. .,Extreme Biology Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia.
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31
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Shin HW, Lee NS. Understanding plastome evolution in Hemiparasitic Santalales: Complete chloroplast genomes of three species, Dendrotrophe varians, Helixanthera parasitica, and Macrosolen cochinchinensis. PLoS One 2018; 13:e0200293. [PMID: 29975758 PMCID: PMC6033455 DOI: 10.1371/journal.pone.0200293] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 06/22/2018] [Indexed: 01/31/2023] Open
Abstract
Santalales is a large order, with over 2200 species, most of which are root or aerial (stem) hemiparasites. In this study, we report the newly assembled chloroplast genome of Dendrotrophe varians (140,666 bp) in the family Amphorogynaceae and the cp genomes of Helixanthera parasitica (124,881 bp) and Macrosolen cochinchinensis (122,986 bp), both in the family Loranthaceae. We compared the cp genomes of 11 Santalales including eight currently available cp genomes. Santalales cp genomes are slightly or not reduced in size (119-147 kb), similar to other hemiparasitic species, when compared with typical angiosperm cp genomes (120-170 kb). In a phylogeny examining gene content, the NADH dehydrogenase gene group is the only one among eight functional gene groups that lost complete functionally in all examined Santalales. This supports the idea that the functional loss of ndh genes is the initial stage in the evolution of the plastome of parasitic plants, but the loss has occurred independently multiple times in angiosperms, while they are not found in some parasites. This suggests that the functional loss of ndh genes is not essential for the transition from autotroph to parasite. We additionally examined the correlation between gene content and type of parasitism (obligate/facultative and stem/root parasites) of all hemiparasitic species in which cp genomes have been reported to date. Correlation was not found in any types of parasitism.
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Affiliation(s)
- Hye Woo Shin
- Interdisciplinary Program of EcoCreative, The Graduate School, Ewha Womans University, Seoul, Korea
| | - Nam Sook Lee
- Department of Life Science, Ewha Womans University, Seoul, Korea
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32
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Barrett CF, Wicke S, Sass C. Dense infraspecific sampling reveals rapid and independent trajectories of plastome degradation in a heterotrophic orchid complex. THE NEW PHYTOLOGIST 2018; 218:1192-1204. [PMID: 29502351 PMCID: PMC5902423 DOI: 10.1111/nph.15072] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 01/23/2018] [Indexed: 05/08/2023]
Abstract
Heterotrophic plants provide excellent opportunities to study the effects of altered selective regimes on genome evolution. Plastid genome (plastome) studies in heterotrophic plants are often based on one or a few highly divergent species or sequences as representatives of an entire lineage, thus missing important evolutionary-transitory events. Here, we present the first infraspecific analysis of plastome evolution in any heterotrophic plant. By combining genome skimming and targeted sequence capture, we address hypotheses on the degree and rate of plastome degradation in a complex of leafless orchids (Corallorhiza striata) across its geographic range. Plastomes provide strong support for relationships and evidence of reciprocal monophyly between C. involuta and the endangered C. bentleyi. Plastome degradation is extensive, occurring rapidly over a few million years, with evidence of differing rates of genomic change among the two principal clades of the complex. Genome skimming and targeted sequence capture differ widely in coverage depth overall, with depth in targeted sequence capture datasets varying immensely across the plastome as a function of GC content. These findings will help to fill a knowledge gap in models of heterotrophic plastid genome evolution, and have implications for future studies in heterotrophs.
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Affiliation(s)
- Craig F. Barrett
- Department of Biology, West Virginia University, 5218 Life Sciences Building, 53 Campus Drive, Morgantown, WV 26501, USA
| | - Susann Wicke
- Institute for Evolution and Biodiversity, University of Muenster, Huefferstr. 1, 48149 Muenster, Germany
| | - Chodon Sass
- Department of Plant and Microbial Biology, University of California, Berkeley, 431 Koshland Hall, Berkeley, California 94720, USA
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Characterization and Comparative Analysis of the Complete Chloroplast Genome of the Critically Endangered Species Streptocarpus teitensis (Gesneriaceae). BIOMED RESEARCH INTERNATIONAL 2018; 2018:1507847. [PMID: 29770326 PMCID: PMC5889905 DOI: 10.1155/2018/1507847] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 12/27/2017] [Accepted: 01/28/2018] [Indexed: 11/28/2022]
Abstract
Streptocarpus teitensis (Gesneriaceae) is an endemic species listed as critically endangered in the International Union for Conservation of Nature (IUCN) red list of threatened species. However, the sequence and genome information of this species remains to be limited. In this article, we present the complete chloroplast genome structure of Streptocarpus teitensis and its evolution inferred through comparative studies with other related species. S. teitensis displayed a chloroplast genome size of 153,207 bp, sheltering a pair of inverted repeats (IR) of 25,402 bp each split by small and large single-copy (SSC and LSC) regions of 18,300 and 84,103 bp, respectively. The chloroplast genome was observed to contain 116 unique genes, of which 80 are protein-coding, 32 are transfer RNAs, and four are ribosomal RNAs. In addition, a total of 196 SSR markers were detected in the chloroplast genome of Streptocarpus teitensis with mononucleotides (57.1%) being the majority, followed by trinucleotides (33.2%) and dinucleotides and tetranucleotides (both 4.1%), and pentanucleotides being the least (1.5%). Genome alignment indicated that this genome was comparable to other sequenced members of order Lamiales. The phylogenetic analysis suggested that Streptocarpus teitensis is closely related to Lysionotus pauciflorus and Dorcoceras hygrometricum.
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Pogoda CS, Keepers KG, Lendemer JC, Kane NC, Tripp EA. Reductions in complexity of mitochondrial genomes in lichen-forming fungi shed light on genome architecture of obligate symbioses. Mol Ecol 2018; 27:1155-1169. [DOI: 10.1111/mec.14519] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 12/21/2017] [Accepted: 01/19/2018] [Indexed: 01/28/2023]
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35
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Chen H, Shao J, Zhang H, Jiang M, Huang L, Zhang Z, Yang D, He M, Ronaghi M, Luo X, Sun B, Wu W, Liu C. Sequencing and Analysis of Strobilanthes cusia (Nees) Kuntze Chloroplast Genome Revealed the Rare Simultaneous Contraction and Expansion of the Inverted Repeat Region in Angiosperm. FRONTIERS IN PLANT SCIENCE 2018; 9:324. [PMID: 29593773 PMCID: PMC5861152 DOI: 10.3389/fpls.2018.00324] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 02/27/2018] [Indexed: 05/06/2023]
Abstract
Ban-Lan-Gen, the root tissues derived from several morphologically indistinguishable plant species, have been used widely in traditional Chinese medicines for numerous years. The identification of reliable markers to distinguish various source plant species is critical for the effective and safe use of products containing Ban-Lan-Gen. Here, we analyzed and characterized the complete chloroplast (cp) genome sequence of Strobilanthes cusia (Nees) Kuntze to identify high-resolution markers for the species determination of Southern Ban-Lan-Gen. Total DNA was extracted and subjected to next-generation sequencing. The cp genome was then assembled, and the gaps were filled using PCR amplification and Sanger sequencing. Genome annotation was conducted using CpGAVAS web server. The genome was 144,133 bp in length, presenting a typical quadripartite structure of large (LSC; 91,666 bp) and small (SSC; 17,328 bp) single-copy regions separated by a pair of inverted repeats (IRs; 17,811 bp). The genome encodes 113 unique genes, including 79 protein-coding, 30 transfer RNA, and 4 ribosomal RNA genes. A total of 20 tandem, 2 forward, and 6 palindromic repeats were detected in the genome. A phylogenetic analysis based on 65 protein-coding genes showed that S. cusia was closely related to Andrographis paniculata and Ruellia breedlovei, which belong to the same family, Acanthaceae. One interesting feature is that the IR regions apparently undergo simultaneous contraction and expansion, resulting in the presence of single copies of rps19, rpl2, rpl23, and ycf2 in the LSC region and the duplication of psbA and trnH genes in the IRs. This study provides the first complete cp genome in the genus Strobilanthes, containing critical information for the classification of various Strobilanthes species in the future. This study also provides the foundation for precisely determining the plant sources of Ban-Lan-Gen.
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Affiliation(s)
- Haimei Chen
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Junjie Shao
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hui Zhang
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Mei Jiang
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Linfang Huang
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhao Zhang
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Dan Yang
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Molly He
- Illumina, Inc., San Diego, CA, United States
| | | | - Xi Luo
- Illumina, Inc., San Diego, CA, United States
| | - Botao Sun
- Illumina, Inc., San Diego, CA, United States
| | - Wuwei Wu
- Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Chang Liu
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Wang N, Ji S, Zhang H, Mei S, Qiao L, Jin X. Herba Cistanches: Anti-aging. Aging Dis 2017; 8:740-759. [PMID: 29344414 PMCID: PMC5758349 DOI: 10.14336/ad.2017.0720] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 07/20/2017] [Indexed: 12/11/2022] Open
Abstract
The Cistanche species ("Rou Cong Rong" in Chinese) is an endangered wild species growing in arid or semi-arid areas. The dried fleshy stem of Cistanches has been used as a tonic in China for many years. Modern pharmacological studies have since demonstrated that Herba Cistanches possesses broad medicinal functions, especially for use in anti-senescence, anti-oxidation, neuroprotection, anti-inflammation, hepatoprotection, immunomodulation, anti-neoplastic, anti-osteoporosis and the promotion of bone formation. This review summarizes the up-to-date and comprehensive information on Herba Cistanches covering the aspects of the botany, traditional uses, phytochemistry and pharmacology, to lay ground for fully elucidating the potential mechanisms of Herba Cistanches' anti-aging effect and promote its clinical application as an anti-aging herbal medicine.
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Affiliation(s)
- Ningqun Wang
- Department of Traditional Chinese Medicine, Xuanwu Hospital, Capital Medical University, Beijing 100053, China.
| | - Shaozhen Ji
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing 100053, China.
| | - Hao Zhang
- Department of Radiology, Dongfang Hospital of Beijing University of Chinese Medicine, Beijing 100078, China
| | - Shanshan Mei
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing 100053, China.
| | - Lumin Qiao
- Department of Emergency, Traditional Chinese Medicine Hospital of Yinchuan, Ningxia Hui Nationality Autonomous Region 750001, China.
| | - Xianglan Jin
- Department of Neurology, Dongfang Hospital of Beijing University of Chinese Medicine, Beijing 100078, China.
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37
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Kim HT, Chase MW. Independent degradation in genes of the plastid ndh gene family in species of the orchid genus Cymbidium (Orchidaceae; Epidendroideae). PLoS One 2017; 12:e0187318. [PMID: 29140976 PMCID: PMC5695243 DOI: 10.1371/journal.pone.0187318] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 10/17/2017] [Indexed: 11/23/2022] Open
Abstract
In this paper, we compare ndh genes in the plastid genome of many Cymbidium species and three closely related taxa in Orchidaceae looking for evidence of ndh gene degradation. Among the 11 ndh genes, there were frequently large deletions in directly repeated or AT-rich regions. Variation in these degraded ndh genes occurs between individual plants, apparently at population levels in these Cymbidium species. It is likely that ndh gene transfers from the plastome to mitochondrial genome (chondriome) occurred independently in Orchidaceae and that ndh genes in the chondriome were also relatively recently transferred between distantly related species in Orchidaceae. Four variants of the ycf1-rpl32 region, which normally includes the ndhF genes in the plastome, were identified, and some Cymbidium species contained at least two copies of that region in their organellar genomes. The four ycf1-rpl32 variants seem to have a clear pattern of close relationships. Patterns of ndh degradation between closely related taxa and translocation of ndh genes to the chondriome in Cymbidium suggest that there have been multiple bidirectional intracellular gene transfers between two organellar genomes, which have produced different levels of ndh gene degradation among even closely related species.
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Affiliation(s)
- Hyoung Tae Kim
- College of Agriculture and Life Sciences, Kyungpook University, Daegu, Korea
| | - Mark W. Chase
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, United Kingdom
- * E-mail:
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38
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Li Y, Zhou JG, Chen XL, Cui YX, Xu ZC, Li YH, Song JY, Duan BZ, Yao H. Gene losses and partial deletion of small single-copy regions of the chloroplast genomes of two hemiparasitic Taxillus species. Sci Rep 2017; 7:12834. [PMID: 29026168 PMCID: PMC5638910 DOI: 10.1038/s41598-017-13401-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 09/22/2017] [Indexed: 11/17/2022] Open
Abstract
Numerous variations are known to occur in the chloroplast genomes of parasitic plants. We determined the complete chloroplast genome sequences of two hemiparasitic species, Taxillus chinensis and T. sutchuenensis, using Illumina and PacBio sequencing technologies. These species are the first members of the family Loranthaceae to be sequenced. The complete chloroplast genomes of T. chinensis and T. sutchuenensis comprise circular 121,363 and 122,562 bp-long molecules with quadripartite structures, respectively. Compared with the chloroplast genomes of Nicotiana tabacum and Osyris alba, all ndh genes as well as three ribosomal protein genes, seven tRNA genes, four ycf genes, and the infA gene of these two species have been lost. The results of the maximum likelihood and neighbor-joining phylogenetic trees strongly support the theory that Loranthaceae and Viscaceae are monophyletic clades. This research reveals the effect of a parasitic lifestyle on the chloroplast structure and genome content of T. chinensis and T. sutchuenensis, and enhances our understanding of the discrepancies in terms of assembly results between Illumina and PacBio.
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Affiliation(s)
- Ying Li
- The Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Jian-Guo Zhou
- The Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Xin-Lian Chen
- The Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Ying-Xian Cui
- The Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Zhi-Chao Xu
- The Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Yong-Hua Li
- Department of Pharmacy, Guangxi Traditional Chinese Medicine University, Nanning, 530200, Guangxi, China
| | - Jing-Yuan Song
- The Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Bao-Zhong Duan
- College of Pharmaceutical Science, Dali University, Dali, 671000, Yunnan, China
| | - Hui Yao
- The Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China.
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Reductive evolution of chloroplasts in non-photosynthetic plants, algae and protists. Curr Genet 2017; 64:365-387. [DOI: 10.1007/s00294-017-0761-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 09/22/2017] [Accepted: 10/04/2017] [Indexed: 11/24/2022]
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40
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Zhou J, Chen X, Cui Y, Sun W, Li Y, Wang Y, Song J, Yao H. Molecular Structure and Phylogenetic Analyses of Complete Chloroplast Genomes of Two Aristolochia Medicinal Species. Int J Mol Sci 2017; 18:E1839. [PMID: 28837061 PMCID: PMC5618488 DOI: 10.3390/ijms18091839] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 08/15/2017] [Accepted: 08/20/2017] [Indexed: 12/13/2022] Open
Abstract
The family Aristolochiaceae, comprising about 600 species of eight genera, is a unique plant family containing aristolochic acids (AAs). The complete chloroplast genome sequences of Aristolochia debilis and Aristolochia contorta are reported here. The results show that the complete chloroplast genomes of A. debilis and A. contorta comprise circular 159,793 and 160,576 bp-long molecules, respectively and have typical quadripartite structures. The GC contents of both species were 38.3% each. A total of 131 genes were identified in each genome including 85 protein-coding genes, 37 tRNA genes, eight rRNA genes and one pseudogene (ycf1). The simple-sequence repeat sequences mainly comprise A/T mononucletide repeats. Phylogenetic analyses using maximum parsimony (MP) revealed that A. debilis and A. contorta had a close phylogenetic relationship with species of the family Piperaceae, as well as Laurales and Magnoliales. The data obtained in this study will be beneficial for further investigations on A. debilis and A. contorta from the aspect of evolution, and chloroplast genetic engineering.
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Affiliation(s)
- Jianguo Zhou
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China.
| | - Xinlian Chen
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China.
| | - Yingxian Cui
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China.
| | - Wei Sun
- Institute of Chinese Materia Medica, China Academy of Chinese Medicinal Sciences, Beijing 100700, China.
| | - Yonghua Li
- Department of Pharmacy, Guangxi Traditional Chinese Medicine University, Nanning 530200, China.
| | - Yu Wang
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China.
| | - Jingyuan Song
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China.
| | - Hui Yao
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China.
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Yu J, Wang C, Gong X. Degeneration of photosynthetic capacity in mixotrophic plants, Chimaphila japonica and Pyrola decorata (Ericaceae). PLANT DIVERSITY 2017; 39:80-88. [PMID: 30159495 PMCID: PMC6112300 DOI: 10.1016/j.pld.2016.11.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 11/17/2016] [Accepted: 11/21/2016] [Indexed: 05/25/2023]
Abstract
The evolution of photosynthesis is an important feature of mixotrophic plants. Previous inferences proposed that mixotrophic taxa tend to retain most genes relating to photosynthetic functions but vary in plastid gene content. However, no sequence data are available to test this hypothesis in Ericaceae. To investigate changes in plastid genomes that may result from a transition from autotrophy to mixotrophy, the plastomes of two mixotrophic plants, Pyrola decorata and Chimaphila japonica, were sequenced at Illumina's Genome Analyzer and compared to the published plastome of the autotrophic plant Rhododendron simsii, which also belongs to Ericaceae. The greatest discrepancy between mixotrophic and autotrophic plants was that ndh genes for both P. decorata and C. japonica plastomes have nearly all become pseudogenes. P. decorata and C. japonica also retained all genes directly involved in photosynthesis under strong selection. The calculated rate of nonsynonymous nucleotide substitutions and synonymous substitutions of protein-coding genes (dN/dS) showed that substitution rates in shade plants were apparently higher than those in sunlight plants. The two mixotrophic plastomes were generally very similar to that of non-parasitic plants, although ndh genes were largely pseudogenized. Photosynthesis genes under strong selection were retained in the two mixotrophs, however, with greatly increased substitution rates. Further research is needed to gain a clearer understanding of the evolution of autotrophy and mixotrophy in Ericaceae.
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Affiliation(s)
- Jiaojun Yu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, PR China
- Yunnan Key Laboratory for Wild Plant Resources, Kunming 650201, PR China
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Kunming, PR China
| | - Chaobo Wang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, PR China
- Yunnan Key Laboratory for Wild Plant Resources, Kunming 650201, PR China
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Kunming, PR China
| | - Xun Gong
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, PR China
- Yunnan Key Laboratory for Wild Plant Resources, Kunming 650201, PR China
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Kunming, PR China
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Kang JS, Lee BY, Kwak M. The complete chloroplast genome sequences of Lychnis wilfordii and Silene capitata and comparative analyses with other Caryophyllaceae genomes. PLoS One 2017; 12:e0172924. [PMID: 28241056 PMCID: PMC5328339 DOI: 10.1371/journal.pone.0172924] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 02/10/2017] [Indexed: 11/18/2022] Open
Abstract
The complete chloroplast genomes of Lychnis wilfordii and Silene capitata were determined and compared with ten previously reported Caryophyllaceae chloroplast genomes. The chloroplast genome sequences of L. wilfordii and S. capitata contain 152,320 bp and 150,224 bp, respectively. The gene contents and orders among 12 Caryophyllaceae species are consistent, but several microstructural changes have occurred. Expansion of the inverted repeat (IR) regions at the large single copy (LSC)/IRb and small single copy (SSC)/IR boundaries led to partial or entire gene duplications. Additionally, rearrangements of the LSC region were caused by gene inversions and/or transpositions. The 18 kb inversions, which occurred three times in different lineages of tribe Sileneae, were thought to be facilitated by the intermolecular duplicated sequences. Sequence analyses of the L. wilfordii and S. capitata genomes revealed 39 and 43 repeats, respectively, including forward, palindromic, and reverse repeats. In addition, a total of 67 and 56 simple sequence repeats were discovered in the L. wilfordii and S. capitata chloroplast genomes, respectively. Finally, we constructed phylogenetic trees of the 12 Caryophyllaceae species and two Amaranthaceae species based on 73 protein-coding genes using both maximum parsimony and likelihood methods.
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Affiliation(s)
- Jong-Soo Kang
- Plant Resources Division, National Institute of Biological Resources, Incheon, Republic of Korea
| | - Byoung Yoon Lee
- Plant Resources Division, National Institute of Biological Resources, Incheon, Republic of Korea
| | - Myounghai Kwak
- Plant Resources Division, National Institute of Biological Resources, Incheon, Republic of Korea
- * E-mail:
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Cauz-Santos LA, Munhoz CF, Rodde N, Cauet S, Santos AA, Penha HA, Dornelas MC, Varani AM, Oliveira GCX, Bergès H, Vieira MLC. The Chloroplast Genome of Passiflora edulis (Passifloraceae) Assembled from Long Sequence Reads: Structural Organization and Phylogenomic Studies in Malpighiales. FRONTIERS IN PLANT SCIENCE 2017; 8:334. [PMID: 28344587 PMCID: PMC5345083 DOI: 10.3389/fpls.2017.00334] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 02/27/2017] [Indexed: 05/20/2023]
Abstract
The family Passifloraceae consists of some 700 species classified in around 16 genera. Almost all its members belong to the genus Passiflora. In Brazil, the yellow passion fruit (Passiflora edulis) is of considerable economic importance, both for juice production and consumption as fresh fruit. The availability of chloroplast genomes (cp genomes) and their sequence comparisons has led to a better understanding of the evolutionary relationships within plant taxa. In this study, we obtained the complete nucleotide sequence of the P. edulis chloroplast genome, the first entirely sequenced in the Passifloraceae family. We determined its structure and organization, and also performed phylogenomic studies on the order Malpighiales and the Fabids clade. The P. edulis chloroplast genome is characterized by the presence of two copies of an inverted repeat sequence (IRA and IRB) of 26,154 bp, each separating a small single copy region of 13,378 bp and a large single copy (LSC) region of 85,720 bp. The annotation resulted in the identification of 105 unique genes, including 30 tRNAs, 4 rRNAs, and 71 protein coding genes. Also, 36 repetitive elements and 85 SSRs (microsatellites) were identified. The structure of the complete cp genome of P. edulis differs from that of other species because of rearrangement events detected by means of a comparison based on 22 members of the Malpighiales. The rearrangements were three inversions of 46,151, 3,765 and 1,631 bp, located in the LSC region. Phylogenomic analysis resulted in strongly supported trees, but this could also be a consequence of the limited taxonomic sampling used. Our results have provided a better understanding of the evolutionary relationships in the Malpighiales and the Fabids, confirming the potential of complete chloroplast genome sequences in inferring evolutionary relationships and the utility of long sequence reads for generating very accurate biological information.
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Affiliation(s)
- Luiz A. Cauz-Santos
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, PiracicabaBrazil
| | - Carla F. Munhoz
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, PiracicabaBrazil
| | - Nathalie Rodde
- Institut National de la Recherche Agronomique, French Plant Genomic Resource Center, Castanet-TolosanFrance
| | - Stephane Cauet
- Institut National de la Recherche Agronomique, French Plant Genomic Resource Center, Castanet-TolosanFrance
| | - Anselmo A. Santos
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, PiracicabaBrazil
- FuturaGene Brasil Tecnologia Ltda., São PauloBrazil
| | - Helen A. Penha
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, PiracicabaBrazil
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, JaboticabalBrazil
| | - Marcelo C. Dornelas
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, CampinasBrazil
| | - Alessandro M. Varani
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, JaboticabalBrazil
| | - Giancarlo C. X. Oliveira
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, PiracicabaBrazil
| | - Hélène Bergès
- Institut National de la Recherche Agronomique, French Plant Genomic Resource Center, Castanet-TolosanFrance
| | - Maria Lucia C. Vieira
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, PiracicabaBrazil
- *Correspondence: Maria Lucia C. Vieira,
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Fan W, Zhu A, Kozaczek M, Shah N, Pabón-Mora N, González F, Mower JP. Limited mitogenomic degradation in response to a parasitic lifestyle in Orobanchaceae. Sci Rep 2016; 6:36285. [PMID: 27808159 PMCID: PMC5093741 DOI: 10.1038/srep36285] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 10/13/2016] [Indexed: 01/25/2023] Open
Abstract
In parasitic plants, the reduction in plastid genome (plastome) size and content is driven predominantly by the loss of photosynthetic genes. The first completed mitochondrial genomes (mitogenomes) from parasitic mistletoes also exhibit significant degradation, but the generality of this observation for other parasitic plants is unclear. We sequenced the complete mitogenome and plastome of the hemiparasite Castilleja paramensis (Orobanchaceae) and compared them with additional holoparasitic, hemiparasitic and nonparasitic species from Orobanchaceae. Comparative mitogenomic analysis revealed minimal gene loss among the seven Orobanchaceae species, indicating the retention of typical mitochondrial function among Orobanchaceae species. Phylogenetic analysis demonstrated that the mobile cox1 intron was acquired vertically from a nonparasitic ancestor, arguing against a role for Orobanchaceae parasites in the horizontal acquisition or distribution of this intron. The C. paramensis plastome has retained nearly all genes except for the recent pseudogenization of four subunits of the NAD(P)H dehydrogenase complex, indicating a very early stage of plastome degradation. These results lend support to the notion that loss of ndh gene function is the first step of plastome degradation in the transition to a parasitic lifestyle.
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Affiliation(s)
- Weishu Fan
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA.,Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583, USA
| | - Andan Zhu
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA.,Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583, USA
| | - Melisa Kozaczek
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
| | - Neethu Shah
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA.,Department of Computer Sciences and Engineering, University of Nebraska, Lincoln, NE 68588, USA
| | - Natalia Pabón-Mora
- Instituto de Biología, Universidad de Antioquia, Apartado 1226, Medellín, Colombia
| | - Favio González
- Facultad de Ciencias, Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Apartado 7495, Sede Bogotá, Colombia
| | - Jeffrey P Mower
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA.,Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583, USA
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Moreira PA, Mariac C, Scarcelli N, Couderc M, Rodrigues DP, Clement CR, Vigouroux Y. Chloroplast sequence of treegourd ( Crescentia cujete, Bignoniaceae) to study phylogeography and domestication. APPLICATIONS IN PLANT SCIENCES 2016; 4:apps1600048. [PMID: 27785381 PMCID: PMC5077280 DOI: 10.3732/apps.1600048] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 08/30/2016] [Indexed: 05/07/2023]
Abstract
PREMISE OF THE STUDY Crescentia cujete (Bignoniaceae) fruit rinds are traditionally used for storage vessels and handicrafts. We assembled its chloroplast genome and identified single-nucleotide polymorphisms (SNPs). METHODS AND RESULTS Using a genome skimming approach, the whole chloroplast of C. cujete was assembled using 3,106,928 sequence reads of 150 bp. The chloroplast is 154,662 bp in length, structurally divided into a large single copy region (84,788 bp), a small single copy region (18,299 bp), and two inverted repeat regions (51,575 bp) with 88 genes annotated. By resequencing the whole chloroplast, we identified 66 SNPs in C. cujete (N = 30) and 68 SNPs in C. amazonica (N = 6). Nucleotide diversity was estimated at 1.1 × 10-3 and 3.5 × 10-3 for C. cujete and C. amazonica, respectively. CONCLUSIONS This broadened C. cujete genetic toolkit will be important to study the origin, domestication, diversity, and phylogeography of treegourds in the Neotropics.
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Affiliation(s)
- Priscila Ambrósio Moreira
- Post-Graduate Program in Botany, Instituto Nacional de Pesquisas da Amazônia (INPA), Av. André Araújo 2936, Petrópolis, 69067-375 Manaus, Amazonas, Brazil
- Authors for correspondence: ;
| | - Cédric Mariac
- UMR DIADE, Institut de Recherche pour le Développement (IRD), 393 Avenue Agropolis, Montpellier, Cedex 5, France
| | - Nora Scarcelli
- UMR DIADE, Institut de Recherche pour le Développement (IRD), 393 Avenue Agropolis, Montpellier, Cedex 5, France
| | - Marie Couderc
- UMR DIADE, Institut de Recherche pour le Développement (IRD), 393 Avenue Agropolis, Montpellier, Cedex 5, France
| | - Doriane Picanço Rodrigues
- Post-Graduate Program in Botany, Instituto Nacional de Pesquisas da Amazônia (INPA), Av. André Araújo 2936, Petrópolis, 69067-375 Manaus, Amazonas, Brazil
- Laboratório de Evolução Aplicada, Universidade Federal do Amazonas (UFAM), 69077-000 Manaus, Amazonas, Brazil
| | - Charles R. Clement
- Post-Graduate Program in Botany, Instituto Nacional de Pesquisas da Amazônia (INPA), Av. André Araújo 2936, Petrópolis, 69067-375 Manaus, Amazonas, Brazil
- Coordenação de Tecnologia e Inovação, INPA, Manaus, Amazonas, Brazil
| | - Yves Vigouroux
- UMR DIADE, Institut de Recherche pour le Développement (IRD), 393 Avenue Agropolis, Montpellier, Cedex 5, France
- Authors for correspondence: ;
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Roquet C, Coissac É, Cruaud C, Boleda M, Boyer F, Alberti A, Gielly L, Taberlet P, Thuiller W, Van Es J, Lavergne S. Understanding the evolution of holoparasitic plants: the complete plastid genome of the holoparasite Cytinus hypocistis (Cytinaceae). ANNALS OF BOTANY 2016; 118:885-896. [PMID: 27443299 PMCID: PMC5055816 DOI: 10.1093/aob/mcw135] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 04/09/2016] [Accepted: 05/12/2016] [Indexed: 05/19/2023]
Abstract
Background and Aims Plant plastid genomes are highly conserved in size, gene content and structure; however, parasitic plants are a noticeable exception to this evolutionary stability. Although the evolution of parasites could help to better understand plastome evolution in general, complete plastomes of parasites have been sequenced only for some lineages so far. Here we contribute to filling this gap by providing and analysing the complete plastome sequence of Cytinus hypocistis, the first parasite sequenced for Malvales and a species suspected to have an extremely small genome. Methods We sequenced and assembled de novo the plastid genome of Cytinus hypocistis using a shotgun approach on genomic DNA. Phylogenomic analyses based on coding regions were performed on Malvidae. For each coding region present in Cytinus, we tested for relaxation or intensification of selective pressures in the Cytinus lineage compared with autotrophic Malvales. Key Results Cytinus hypocistis has an extremely divergent genome that is among the smallest sequenced to date (19·4 kb), with only 23 genes and no inverted repeat regions. Phylogenomic analysis confirmed the position of Cytinus within Malvales. All coding regions of Cytinus plastome presented very high substitution rates compared with non-parasitic Malvales. Conclusions Some regions were inferred to be under relaxed negative selection in Cytinus, suggesting that further plastome reduction is occurring due to relaxed purifying selection associated with the loss of photosynthetic activity. On the other hand, increased selection intensity and strong positive selection were detected for rpl22 in the Cytinus lineage, which might indicate an evolutionary role in the host-parasite arms race, a point that needs further research.
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Affiliation(s)
- Cristina Roquet
- Laboratoire d’Ecologie Alpine, Université Grenoble Alpes, BP 53, FR-38000 Grenoble, France
- Laboratoire d’Ecologie Alpine, CNRS, BP 53, FR-38000 Grenoble, France
- *For correspondence. E-mail
| | - Éric Coissac
- Laboratoire d’Ecologie Alpine, Université Grenoble Alpes, BP 53, FR-38000 Grenoble, France
- Laboratoire d’Ecologie Alpine, CNRS, BP 53, FR-38000 Grenoble, France
| | - Corinne Cruaud
- CEA-Institut de Génomique, Genoscope, Centre National de Séquençage, FR-91057 Evry Cedex, France
| | - Martí Boleda
- Laboratoire d’Ecologie Alpine, Université Grenoble Alpes, BP 53, FR-38000 Grenoble, France
- Laboratoire d’Ecologie Alpine, CNRS, BP 53, FR-38000 Grenoble, France
| | - Frédéric Boyer
- Laboratoire d’Ecologie Alpine, Université Grenoble Alpes, BP 53, FR-38000 Grenoble, France
- Laboratoire d’Ecologie Alpine, CNRS, BP 53, FR-38000 Grenoble, France
| | - Adriana Alberti
- CEA-Institut de Génomique, Genoscope, Centre National de Séquençage, FR-91057 Evry Cedex, France
| | - Ludovic Gielly
- Laboratoire d’Ecologie Alpine, Université Grenoble Alpes, BP 53, FR-38000 Grenoble, France
- Laboratoire d’Ecologie Alpine, CNRS, BP 53, FR-38000 Grenoble, France
| | - Pierre Taberlet
- Laboratoire d’Ecologie Alpine, Université Grenoble Alpes, BP 53, FR-38000 Grenoble, France
- Laboratoire d’Ecologie Alpine, CNRS, BP 53, FR-38000 Grenoble, France
| | - Wilfried Thuiller
- Laboratoire d’Ecologie Alpine, Université Grenoble Alpes, BP 53, FR-38000 Grenoble, France
- Laboratoire d’Ecologie Alpine, CNRS, BP 53, FR-38000 Grenoble, France
| | - Jérémie Van Es
- Conservatoire Botanique National Alpin, Domaine de Charance, FR-05000 Gap, France
| | - Sébastien Lavergne
- Laboratoire d’Ecologie Alpine, Université Grenoble Alpes, BP 53, FR-38000 Grenoble, France
- Laboratoire d’Ecologie Alpine, CNRS, BP 53, FR-38000 Grenoble, France
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Liu TJ, Zhang CY, Yan HF, Zhang L, Ge XJ, Hao G. Complete plastid genome sequence of Primula sinensis (Primulaceae): structure comparison, sequence variation and evidence for accD transfer to nucleus. PeerJ 2016; 4:e2101. [PMID: 27375965 PMCID: PMC4928469 DOI: 10.7717/peerj.2101] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 05/10/2016] [Indexed: 11/22/2022] Open
Abstract
Species-rich genus Primula L. is a typical plant group with which to understand genetic variance between species in different levels of relationships. Chloroplast genome sequences are used to be the information resource for quantifying this difference and reconstructing evolutionary history. In this study, we reported the complete chloroplast genome sequence of Primula sinensis and compared it with other related species. This genome of chloroplast showed a typical circular quadripartite structure with 150,859 bp in sequence length consisting of 37.2% GC base. Two inverted repeated regions (25,535 bp) were separated by a large single-copy region (82,064 bp) and a small single-copy region (17,725 bp). The genome consists of 112 genes, including 78 protein-coding genes, 30 tRNA genes and four rRNA genes. Among them, seven coding genes, seven tRNA genes and four rRNA genes have two copies due to their locations in the IR regions. The accD and infA genes lacking intact open reading frames (ORF) were identified as pseudogenes. SSR and sequence variation analyses were also performed on the plastome of Primula sinensis, comparing with another available plastome of P. poissonii. The four most variable regions, rpl36–rps8, rps16–trnQ, trnH–psbA and ndhC–trnV, were identified. Phylogenetic relationship estimates using three sub-datasets extracted from a matrix of 57 protein-coding gene sequences showed the identical result that was consistent with previous studies. A transcript found from P. sinensis transcriptome showed a high similarity to plastid accD functional region and was identified as a putative plastid transit peptide at the N-terminal region. The result strongly suggested that plastid accD has been functionally transferred to the nucleus in P. sinensis.
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Affiliation(s)
- Tong-Jian Liu
- College of Life Sciences, South China Agricultural University , Guangzhou , China
| | - Cai-Yun Zhang
- College of Life Sciences, South China Agricultural University , Guangzhou , China
| | - Hai-Fei Yan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences , Guangzhou , China
| | - Lu Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences , Guangzhou , China
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences , Guangzhou , China
| | - Gang Hao
- College of Life Sciences, South China Agricultural University , Guangzhou , China
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48
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Lim GS, Barrett CF, Pang CC, Davis JI. Drastic reduction of plastome size in the mycoheterotrophic Thismia tentaculata relative to that of its autotrophic relative Tacca chantrieri. AMERICAN JOURNAL OF BOTANY 2016; 103:1129-37. [PMID: 27335389 DOI: 10.3732/ajb.1600042] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 05/06/2016] [Indexed: 05/23/2023]
Abstract
PREMISE OF THE STUDY Heterotrophic angiosperms tend to have reduced plastome sizes relative to those of their autotrophic relatives because genes that code for proteins involved in photosynthesis are lost. However, some plastid-encoded proteins may have vital nonphotosynthetic functions, and the plastome therefore may be retained after the loss of photosynthesis. METHODS We sequenced the plastome of the mycoheterotrophic species Thismia tentaculata and a representative of its sister genus, Tacca chantrieri, using next-generation technology, and we compared sequences and structures of genes and genomes of these species. KEY RESULTS The plastome of Tacca chantrieri is similar to those of other autotrophic taxa of Dioscoreaceae, except in a few local rearrangements and one gene loss. The plastome of Thismia tentaculata is ca. 16 kbp long with a quadripartite structure and is among the smallest known plastomes. Synteny is minimal between the plastomes of Tacca chantrieri and Thismia tentaculata. The latter includes only 12 candidate genes, with all except accD involved in protein synthesis. Of the 12 genes, trnE, trnfM, and accD are frequently among the few that remain in depauperate plastomes. CONCLUSIONS The plastome of Thismia tentaculata, like those of most other heterotrophic plants, includes a small number of genes previously suggested to be essential to plastome survival.
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Affiliation(s)
- Gwynne S Lim
- The New York Botanical Garden, Pfizer Plant Research Laboratory, 2900 Southern Boulevard, Bronx, New York 10458 USA L. H. Bailey Hortorium, Section of Plant Biology, 412 Mann Library Building, Cornell University, Ithaca, New York 14853 USA
| | - Craig F Barrett
- Department of Biology, Life Sciences Building, PO Box 6057, Morgantown, West Virginia 26506 USA
| | - Chun-Chiu Pang
- School of Biological Sciences, Kadoorie Biological Sciences Building, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Jerrold I Davis
- L. H. Bailey Hortorium, Section of Plant Biology, 412 Mann Library Building, Cornell University, Ithaca, New York 14853 USA
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Cusimano N, Wicke S. Massive intracellular gene transfer during plastid genome reduction in nongreen Orobanchaceae. THE NEW PHYTOLOGIST 2016; 210:680-93. [PMID: 26671255 DOI: 10.1111/nph.13784] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Accepted: 10/28/2015] [Indexed: 05/10/2023]
Abstract
Plastid genomes (plastomes) of nonphotosynthetic plants experience extensive gene losses and an acceleration of molecular evolutionary rates. Here, we inferred the mechanisms and timing of reductive genome evolution under relaxed selection in the broomrape family (Orobanchaceae). We analyzed the plastomes of several parasites with a major focus on the genus Orobanche using genome-descriptive and Bayesian phylogenetic-comparative methods. Besides this, we scanned the parasites' other cellular genomes to trace the fate of all genes that were purged from their plastomes. Our analyses indicate that the first functional gene losses occurred within 10 Myr of the transition to obligate parasitism in Orobanchaceae, and that the physical plastome reduction proceeds by small deletions that accumulate over time. Evolutionary rate shifts coincide with the genomic reduction process in broomrapes, suggesting that the shift of selectional constraints away from photosynthesis to other molecular processes alters the plastid rate equilibrium. Most of the photosynthesis-related genes or fragments of genes lost from the plastomes of broomrapes have survived in their nuclear or mitochondrial genomes as the results of multiple intracellular transfers and subsequent fragmentation. Our findings indicate that nonessential DNA is eliminated much faster in the plastomes of nonphotosynthetic parasites than in their other cellular genomes.
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Affiliation(s)
- Natalie Cusimano
- Department of Biology, Ludwig Maximilian University of Munich, Menzinger Street 67, Munich, 80638, Germany
| | - Susann Wicke
- Institute for Evolution and Biodiversity, University of Muenster, Huefferstr. 1, Muenster, 48149, Germany
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Samigullin TH, Logacheva MD, Penin AA, Vallejo-Roman CM. Complete Plastid Genome of the Recent Holoparasite Lathraea squamaria Reveals Earliest Stages of Plastome Reduction in Orobanchaceae. PLoS One 2016; 11:e0150718. [PMID: 26934745 PMCID: PMC4775063 DOI: 10.1371/journal.pone.0150718] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 02/18/2016] [Indexed: 11/29/2022] Open
Abstract
Plants from the family Orobanchaceae are widely used as a model to study different aspects of parasitic lifestyle including host–parasite interactions and physiological and genomic adaptations. Among the latter, the most prominent are those that occurred due to the loss of photosynthesis; they include the reduction of the photosynthesis-related gene set in both nuclear and plastid genomes. In Orobanchaceae, the transition to non-photosynthetic lifestyle occurred several times independently, but only one lineage has been in the focus of evolutionary studies. These studies included analysis of plastid genomes and transcriptomes and allowed the inference of patterns and mechanisms of genome reduction that are thought to be general for parasitic plants. Here we report the plastid genome of Lathraea squamaria, a holoparasitic plant from Orobanchaceae, clade Rhinantheae. We found that in this plant the degree of plastome reduction is the least among non-photosynthetic plants. Like other parasites, Lathraea possess a plastome with elevated absolute rate of nucleotide substitution. The only gene lost is petL, all other genes typical for the plastid genome are present, but some of them–those encoding photosystem components (22 genes), cytochrome b6/f complex proteins (4 genes), plastid-encoded RNA polymerase subunits (2 genes), ribosomal proteins (2 genes), ccsA and cemA–are pseudogenized. Genes for cytochrome b6/f complex and photosystems I and II that do not carry nonsense or frameshift mutations have an increased ratio of non-synonymous to synonymous substitution rates, indicating the relaxation of purifying selection. Our divergence time estimates showed that transition to holoparasitism in Lathraea lineage occurred relatively recently, whereas the holoparasitic lineage Orobancheae is about two times older.
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Affiliation(s)
- Tahir H. Samigullin
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- * E-mail:
| | - Maria D. Logacheva
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Aleksey A. Penin
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Department of Genetics, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Carmen M. Vallejo-Roman
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
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