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Savov S, Marinova B, Teofanova D, Savov M, Odjakova M, Zagorchev L. Parasitic Plants-Potential Vectors of Phytopathogens. Pathogens 2024; 13:484. [PMID: 38921782 PMCID: PMC11207070 DOI: 10.3390/pathogens13060484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 06/02/2024] [Accepted: 06/05/2024] [Indexed: 06/27/2024] Open
Abstract
Parasitic plants represent a peculiar group of semi- or fully heterotrophic plants, possessing the ability to extract water, minerals, and organic compounds from other plants. All parasitic plants, either root or stem, hemi- or holoparasitic, establish a vascular connection with their host plants through a highly specialized organ called haustoria. Apart from being the organ responsible for nutrient extraction, the haustorial connection is also a highway for various macromolecules, including DNA, proteins, and, apparently, phytopathogens. At least some parasitic plants are considered significant agricultural pests, contributing to enormous yield losses worldwide. Their negative effect is mainly direct, by the exhaustion of host plant fitness and decreasing growth and seed/fruit formation. However, they may pose an additional threat to agriculture by promoting the trans-species dispersion of various pathogens. The current review aims to summarize the available information and to raise awareness of this less-explored problem. We further explore the suitability of certain phytopathogens to serve as specific and efficient methods of control of parasitic plants, as well as methods for control of the phytopathogens.
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Affiliation(s)
| | | | | | | | | | - Lyuben Zagorchev
- Department of Biochemistry, Faculty of Biology, Sofia University “St. Kliment Ohridski”, 8 Dragan Tsankov blvd., 1164 Sofia, Bulgaria; (S.S.); (B.M.); (D.T.); (M.S.); (M.O.)
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Chen LQ, Li X, Yao X, Li DZ, Barrett C, dePamphilis CW, Yu WB. Variations and reduction of plastome are associated with the evolution of parasitism in Convolvulaceae. PLANT MOLECULAR BIOLOGY 2024; 114:40. [PMID: 38622367 DOI: 10.1007/s11103-024-01440-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 03/09/2024] [Indexed: 04/17/2024]
Abstract
Parasitic lifestyle can often relax the constraint on the plastome, leading to gene pseudogenization and loss, and resulting in diverse genomic structures and rampant genome degradation. Although several plastomes of parasitic Cuscuta have been reported, the evolution of parasitism in the family Convolvulaceae which is linked to structural variations and reduction of plastome has not been well investigated. In this study, we assembled and collected 40 plastid genomes belonging to 23 species representing four subgenera of Cuscuta and ten species of autotrophic Convolvulaceae. Our findings revealed nine types of structural variations and six types of inverted repeat (IR) boundary variations in the plastome of Convolvulaceae spp. These structural variations were associated with the shift of parasitic lifestyle, and IR boundary shift, as well as the abundance of long repeats. Overall, the degradation of Cuscuta plastome proceeded gradually, with one clade exhibiting an accelerated degradation rate. We observed five stages of gene loss in Cuscuta, including NAD(P)H complex → PEP complex → Photosynthesis-related → Ribosomal protein subunits → ATP synthase complex. Based on our results, we speculated that the shift of parasitic lifestyle in early divergent time promoted relaxed selection on plastomes, leading to the accumulation of microvariations, which ultimately resulted in the plastome reduction. This study provides new evidence towards a better understanding of plastomic evolution, variation, and reduction in the genus Cuscuta.
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Affiliation(s)
- Li-Qiong Chen
- Center for Integrative Conservation & Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
| | - Xin Li
- Center for Integrative Conservation & Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
- Division of BiologicalScience, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Xin Yao
- Center for Integrative Conservation & Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
| | - De-Zhu Li
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Craig Barrett
- Department of Biology, West Virginia University, Morgantown, West Virginia, 26506, USA
| | - Claude W dePamphilis
- Department of Biology, The Pennsylvania State University, University Park, State College, Pennsylvania, 16802, USA
| | - Wen-Bin Yu
- Center for Integrative Conservation & Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China.
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China.
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Yuan S, Nie C, Jia S, Liu T, Zhao J, Peng J, Kong W, Liu W, Gou W, Lei X, Xiong Y, Xiong Y, Yu Q, Ling Y, Ma X. Complete chloroplast genomes of three wild perennial Hordeum species from Central Asia: genome structure, mutation hotspot, phylogenetic relationships, and comparative analysis. FRONTIERS IN PLANT SCIENCE 2023; 14:1170004. [PMID: 37554563 PMCID: PMC10405828 DOI: 10.3389/fpls.2023.1170004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 07/05/2023] [Indexed: 08/10/2023]
Abstract
Hordeum L. is widely distributed in mountain or plateau of subtropical and warm temperate regions around the world. Three wild perennial Hordeum species, including H. bogdanii, H. brevisubulatum, and H. violaceum, have been used as forage and for grassland ecological restoration in high-altitude areas in recent years. To date, the degree of interspecies sequence variation in the three Hordeum species within existing gene pools is still not well-defined. Herein, we sequenced and assembled chloroplast (cp) genomes of the three species. The results revealed that the cp genome of H. bogdanii showed certain sequence variations compared with the cp genomes of the other two species (H. brevisubulatum and H. violaceum), and the latter two were characterized by a higher relative affinity. Parity rule 2 plot (PR2) analysis illuminated that most genes of all ten Hordeum species were concentrated in nucleotide T and G. Numerous single nucleotide polymorphism (SNP) and insertion/deletion (In/Del) events were detected in the three Hordeum species. A series of hotspots regions (tRNA-GGU ~ tRNA-GCA, tRNA-UGU ~ ndhJ, psbE ~ rps18, ndhF ~ tRNA-UAG, etc.) were identified by mVISTA procedures, and the five highly polymorphic genes (tRNA-UGC, tRNA-UAA, tRNA-UUU, tRNA-UAC, and ndhA) were proved by the nucleotide diversity (Pi). Although the distribution and existence of cp simple sequence repeats (cpSSRs) were predicted in the three Hordeum cp genomes, no rearrangement was found between them. A similar phenomenon has been found in the cp genome of the other seven Hordeum species, which has been published so far. In addition, evolutionary relationships were reappraised based on the currently reported cp genome of Hordeum L. This study offers a framework for gaining a better understanding of the evolutionary history of Hordeum species through the re-examination of their cp genomes, and by identifying highly polymorphic genes and hotspot regions that could provide important insights into the genetic diversity and differentiation of these species.
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Affiliation(s)
- Shuai Yuan
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
- Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Cong Nie
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Shangang Jia
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Tianqi Liu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Junming Zhao
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jinghan Peng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Weixia Kong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Wei Liu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Wenlong Gou
- Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Xiong Lei
- Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Yi Xiong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yanli Xiong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Qingqing Yu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yao Ling
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xiao Ma
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
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Pan H, Zagorchev L, Chen L, Tao Y, Cai C, Jiang M, Sun Z, Li J. Complete chloroplast genomes of five Cuscuta species and their evolutionary significance in the Cuscuta genus. BMC Genomics 2023; 24:310. [PMID: 37291497 DOI: 10.1186/s12864-023-09427-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 06/03/2023] [Indexed: 06/10/2023] Open
Abstract
BACKGROUND Cuscuta, a parasitic plant species in the Convolvulaceae family, grows in many countries and regions. However, the relationship between some species is still unclear. Therefore, more studies are needed to assess the variation of the chloroplast (cp) genome in Cuscuta species and their relationship with subgenera or sections, thus, providing important information on the evolution of Cuscuta species. RESULTS In the present study, we identified the whole cp genomes of C. epithymum, C. europaea, C. gronovii, C. chinensis and C. japonica, and then constructed a phylogenetic tree of 23 Cuscuta species based on the complete genome sequences and protein-coding genes. The complete cp genome sequences of C. epithymum and C. europaea were 96,292 and 97,661 bp long, respectively, and lacked an inverted repeat region. Most cp genomes of Cuscuta spp. have tetragonal and circular structures except for C. epithymum, C. europaea, C. pedicellata and C. approximata. Based on the number of genes and the structure of cp genome and the patterns of gene reduction, we found that C. epithymum and C. europaea belonged to subgenus Cuscuta. Most of the cp genomes of the 23 Cuscuta species had single nucleotide repeats of A and T. The inverted repeat region boundaries among species were similar in the same subgenera. Several cp genes were lost. In addition, the numbers and types of the lost genes in the same subgenus were similar. Most of the lost genes were related to photosynthesis (ndh, rpo, psa, psb, pet, and rbcL), which could have gradually caused the plants to lose the ability to photosynthesize. CONCLUSION Our results enrich the data on cp. genomes of genus Cuscuta. This study provides new insights into understanding the phylogenetic relationships and variations in the cp genome of Cuscuta species.
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Affiliation(s)
- Hangkai Pan
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, School of Life Sciences, Taizhou University, Taizhou, 318000, China
- School of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Lyuben Zagorchev
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, School of Life Sciences, Taizhou University, Taizhou, 318000, China
- Department of Biochemistry, Faculty of Biology, Sofia University "St. Kliment Ohridski", 8 Dragan Tsankov Blvd., Sofia, 1164, Bulgaria
| | - Luxi Chen
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, School of Life Sciences, Taizhou University, Taizhou, 318000, China
| | - Yutian Tao
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, School of Life Sciences, Taizhou University, Taizhou, 318000, China
- School of Electronics and Information Engineering, Taizhou University, Taizhou, 318000, China
| | - Chaonan Cai
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, School of Life Sciences, Taizhou University, Taizhou, 318000, China
- School of Advanced Study, Taizhou University, Taizhou, 318000, China
| | - Ming Jiang
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, School of Life Sciences, Taizhou University, Taizhou, 318000, China
| | - Zhongshuai Sun
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, School of Life Sciences, Taizhou University, Taizhou, 318000, China
- School of Advanced Study, Taizhou University, Taizhou, 318000, China
| | - Junmin Li
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, School of Life Sciences, Taizhou University, Taizhou, 318000, China.
- School of Advanced Study, Taizhou University, Taizhou, 318000, China.
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Ahmad W, Asaf S, Al-Rawahi A, Al-Harrasi A, Khan AL. Comparative plastome genomics, taxonomic delimitation and evolutionary divergences of Tetraena hamiensis var. qatarensis and Tetraena simplex (Zygophyllaceae). Sci Rep 2023; 13:7436. [PMID: 37156827 PMCID: PMC10167353 DOI: 10.1038/s41598-023-34477-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 05/02/2023] [Indexed: 05/10/2023] Open
Abstract
The Zygophyllum and Tetraena genera are intriguingly important ecologically and medicinally. Based on morphological characteristics, T. hamiensis var. qatarensis, and T. simplex were transferred from Zygophyllum to Tetraena with the least genomic datasets available. Hence, we sequenced the T. hamiensis and T. simplex and performed in-depth comparative genomics, phylogenetic analysis, and estimated time divergences. The complete plastomes ranged between 106,720 and 106,446 bp-typically smaller than angiosperms plastomes. The plastome circular genomes are divided into large single-copy regions (~ 80,964 bp), small single-copy regions (~ 17,416 bp), and two inverted repeats regions (~ 4170 bp) in both Tetraena species. An unusual shrinkage of IR regions 16-24 kb was identified. This resulted in the loss of 16 genes, including 11 ndh genes which encode the NADH dehydrogenase subunits, and a significant size reduction of Tetraena plastomes compared to other angiosperms. The inter-species variations and similarities were identified using genome-wide comparisons. Phylogenetic trees generated by analyzing the whole plastomes, protein-coding genes, matK, rbcL, and cssA genes exhibited identical topologies, indicating that both species are sisters to the genus Tetraena and may not belong to Zygophyllum. Similarly, based on the entire plastome and proteins coding genes datasets, the time divergence of Zygophyllum and Tetraena was 36.6 Ma and 34.4 Ma, respectively. Tetraena stem ages were 31.7 and 18.2 Ma based on full plastome and protein-coding genes. The current study presents the plastome as a distinguishing and identification feature among the closely related Tetraena and Zygophyllum species. It can be potentially used as a universal super-barcode for identifying plants.
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Affiliation(s)
- Waqar Ahmad
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa, 616, Oman
| | - Sajjad Asaf
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa, 616, Oman
| | - Ahmed Al-Rawahi
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa, 616, Oman
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa, 616, Oman.
| | - Abdul Latif Khan
- Department of Engineering Technology, University of Houston, Sugar Land, TX, 77479, USA.
- Department of Biology and Biochemistry, University of Houston, Houston, USA.
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Alshegaihi RM, Mansour H, Alrobaish SA, Al Shaye NA, Abd El-Moneim D. The First Complete Chloroplast Genome of Cordia monoica: Structure and Comparative Analysis. Genes (Basel) 2023; 14:genes14050976. [PMID: 37239336 DOI: 10.3390/genes14050976] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/10/2023] [Accepted: 04/20/2023] [Indexed: 05/28/2023] Open
Abstract
Cordia monoica is a member of the Boraginaceae family. This plant is widely distributed in tropical regions and has a great deal of medical value as well as economic importance. In the current study, the complete chloroplast (cp) genome of C. monoica was sequenced, assembled, annotated, and reported. This circular chloroplast genome had a size of 148,711 bp, with a quadripartite structure alternating between a pair of repeated inverted regions (26,897-26,901 bp) and a single copy region (77,893 bp). Among the 134 genes encoded by the cp genome, there were 89 protein-coding genes, 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. A total of 1387 tandem repeats were detected, with the hexanucleotides class making up 28 percent of the repeats. Cordia monoica has 26,303 codons in its protein-coding regions, and leucine amino acid was the most frequently encoded amino acid in contrast to cysteine. In addition, 12 of the 89 protein-coding genes were found to be under positive selection. The phyloplastomic taxonomical clustering of the Boraginaceae species provides further evidence that chloroplast genome data are reliable not only at family level but also in deciphering the phylogeny at genus level (e.g., Cordia).
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Affiliation(s)
- Rana M Alshegaihi
- Department of Biology, College of Science, University of Jeddah, Jeddah 21493, Saudi Arabia
| | - Hassan Mansour
- Department of Biological Sciences, Faculty of Science & Arts, King Abdulaziz University, Rabigh 21911, Saudi Arabia
- Department of Botany and Microbiology, Faculty of Science, Suez Canal University, Ismailia 41522, Egypt
| | - Shouaa A Alrobaish
- Department of Biology, College of Science, Qassim University, Buraydah 52377, Saudi Arabia
| | - Najla A Al Shaye
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Diaa Abd El-Moneim
- Department of Plant Production, (Genetic Branch), Faculty of Environmental Agricultural Sciences, Arish University, El-Arish 45511, Egypt
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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] [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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Comprehensive Comparative Analysis and Development of Molecular Markers for Dianthus Species Based on Complete Chloroplast Genome Sequences. Int J Mol Sci 2022; 23:ijms232012567. [PMID: 36293423 PMCID: PMC9604191 DOI: 10.3390/ijms232012567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 11/16/2022] Open
Abstract
Dianthus spp. is a genus with high economic and ornamental value in the Caryophyllaceae, which include the famous fresh-cut carnation and the traditional Chinese herbal medicine, D. superbus. Despite the Dianthus species being seen everywhere in our daily lives, its genome information and phylogenetic relationships remain elusive. Thus, we performed the assembly and annotation of chloroplast genomes for 12 individuals from seven Dianthus species. On this basis, we carried out the first comprehensive and systematic analysis of the chloroplast genome sequence characteristics and the phylogenetic evolution of Dianthus. The chloroplast genome of 12 Dianthus individuals ranged from 149,192 bp to 149,800 bp, containing 124 to 126 functional genes. Sequence repetition analysis showed the number of simple sequence repeats (SSRs) ranged from 75 to 80, tandem repeats ranged from 23 to 41, and pair-dispersed repeats ranged from 28 to 43. Next, we calculated the synonymous nucleotide substitution rates (Ks) of all 76 protein coding genes to obtain the evolution rate of these coding genes in Dianthus species; rpl22 showed the highest Ks (0.0471), which suggested that it evolved the swiftest. By reconstructing the phylogenetic relationships within Dianthus and other species of Caryophyllales, 16 Dianthus individuals (12 individuals reported in this study and four individuals downloaded from NCBI) were divided into two strongly supported sister clades (Clade A and Clade B). The Clade A contained five species, namely D. caryophyllus, D. barbatus, D. gratianopolitanus, and two cultivars (‘HY’ and ‘WC’). The Clade B included four species, in which D. superbus was a sister branch with D. chinensis, D. longicalyx, and F1 ‘87M’ (the hybrid offspring F1 from D. chinensis and ‘HY’). Further, based on sequence divergence analysis and hypervariable region analysis, we selected several regions that had more divergent sequences, to develop DNA markers. Additionally, we found that one DNA marker can be used to differentiate Clade A and Clade B in Dianthus. Taken together, our results provide useful information for our understanding of Dianthus classification and chloroplast genome evolution.
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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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Comparative analysis of two Korean irises (Iris ruthenica and I. uniflora, Iridaceae) based on plastome sequencing and micromorphology. Sci Rep 2022; 12:9424. [PMID: 35676304 PMCID: PMC9177672 DOI: 10.1038/s41598-022-13528-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 05/06/2022] [Indexed: 11/12/2022] Open
Abstract
Iris ruthenica Ker Gawl. and I. uniflora Pall. ex Link, which are rare and endangered species in Korea, possess considerable horticultural and medicinal value among Korean irises. However, discrimination of the species is hindered by extensive morphological similarity. Thus, the aim of the present study was to identify discriminating features by comparing the species’ complete plastid genome (i.e., plastome) sequences and micromorphological features, including leaf margins, stomatal complex distribution (hypostomatic vs. amphistomatic leaves), anther stomata density, and tepal epidermal cell patterns. Plastome comparison revealed slightly divergent regions within intergenic spacer regions, and the most variable sequences, which were distributed in non-coding regions, could be used as molecular markers for the discrimination of I. ruthenica and I. uniflora. Phylogenetic analysis of the Iris species revealed that I. ruthenica and I. uniflora formed a well-supported clade. The comparison of plastomes and micromorphological features performed in this study provides useful information for elucidating taxonomic, phylogenetic, and evolutionary relationships in Iridaceae. Further studies, including those based on molecular cytogenetic approaches using species specific markers, will offer insights into species delimitation of the two closely related Iris species.
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Wang X, Dorjee T, Chen Y, Gao F, Zhou Y. The complete chloroplast genome sequencing analysis revealed an unusual IRs reduction in three species of subfamily Zygophylloideae. PLoS One 2022; 17:e0263253. [PMID: 35108324 PMCID: PMC8809528 DOI: 10.1371/journal.pone.0263253] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 01/17/2022] [Indexed: 11/18/2022] Open
Abstract
Tetraena mongolica, Zygophyllum xanthoxylon, and Z. fabago are three typical dryland plants with important ecological values in subfamily Zygophylloideae of Zygophyllaceae. Studies on the chloroplast genomes of them are favorable for understanding the diversity and phylogeny of Zygophyllaceae. Here, we sequenced and assembled the whole chloroplast genomes of T. mongolica, Z. xanthoxylon, and Z. fabago, and performed comparative genomic and phylogenetic analysis. The total size, structure, gene content and orders of these three chloroplast genomes were similar, and the three chloroplast genomes exhibited a typical quadripartite structure with a large single-copy region (LSC; 79,696–80,291 bp), a small single-copy region (SSC; 16,462–17,162 bp), and two inverted repeats (IRs; 4,288–4,413 bp). A total of 107 unique genes were identified from the three chloroplast genomes, including 70 protein-coding genes, 33 tRNAs, and 4 rRNAs. Compared with other angiosperms, the three chloroplast genomes were significantly reduced in overall length due to an unusual 16–24 kb shrinkage of IR regions and loss of the 11 genes which encoded subunits of NADH dehydrogenase. Genome-wide comparisons revealed similarities and variations between the three species and others. Phylogenetic analysis based on the three chloroplast genomes supported the opinion that Zygophyllaceae belonged to Zygophyllales in Fabids, and Z. xanthoxylon and Z. fabago belonged to Zygophyllum. The genome-wide comparisons revealed the similarity and variations between the chloroplast genomes of the three Zygophylloideae species and other plant species. This study provides a valuable molecular biology evidence for further studies of phylogenetic status of Zygophyllaceae.
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Affiliation(s)
- Xiaoyang Wang
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Tashi Dorjee
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Yiru Chen
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Fei Gao
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
- * E-mail: (FG); (YZ)
| | - Yijun Zhou
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
- * E-mail: (FG); (YZ)
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The comparative studies of complete chloroplast genomes in Actinidia (Actinidiaceae): novel insights into heterogenous variation, clpP gene annotation and phylogenetic relationships. Mol Genet Genomics 2022; 297:535-551. [PMID: 35175427 DOI: 10.1007/s00438-022-01868-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 01/30/2022] [Indexed: 10/19/2022]
Abstract
The genus Actinidia, also called kiwifruit, is characterized with abundant balanced nutritional metabolites, including exceptionally high vitamin C content. However, the traditional classification could not fully reflect the actual Actinidia species' relationships, which need further revision through more accurate approaches. Compared to the nuclear genome, the chloroplast genome has simple heredity characteristics, conserved genome structure and small size, suitable for deciphering complicated species' phylogenetic relationships. Here, the genome-wide comprehensive comparative analyses were performed over 29 independent chloroplast genomes' sequences derived from 25 Actinidia taxa. The average genome size is 156,673.38 bp, with an average 37.20% GC content. The long repeat sequences rather than SSRs (simple sequence repeats) in Actinidia were revealed to be the causal agent leading to the chloroplast genome size expansion. The clpP gene sequences with exon merge and intron deletion were annotated in all the 29 chloroplast genomes tested, which has been previously reported to be lost in Actinidia species. Comprehensive sequence analyses indicated the distinct variation at the clpP gene locus was Actinidiaceae-specific, emerging after the Actinidiaceae-other Ericales species divergence. Four highly divergent sequences (i.e., rps16 ~ trnQ-UUG, rps4 ~ trnT-UGU, petA ~ psbJ, and rps12 ~ psbB) evolved in the LSC (large single-copy) and SSC (small single-copy) regions embodying rps12 ~ psbB (including clpP gene and its up/downstream noncoding sequence) were identified as variation hot spots in Actinidia species. Based on either LSC region alone, combined sequences of LSC and SSC or the whole chloroplast genome sequences, three identical phylogenetic trees of the 25 Actinidia taxa with relatively improved resolution were reconstructed, consistently supporting the reticulate evolutionary lineage in Actinidia. Our findings could help to better understand the evolution characteristics of chloroplast genomes and phylogenetic relationships among Actinidia species.
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Park I, Song JH, Yang S, Chae S, Moon BC. Plastid Phylogenomic Data Offers Novel Insights Into the Taxonomic Status of the Trichosanthes kirilowii Complex (Cucurbitaceae) in South Korea. FRONTIERS IN PLANT SCIENCE 2021; 12:559511. [PMID: 34386020 PMCID: PMC8353159 DOI: 10.3389/fpls.2021.559511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 07/08/2021] [Indexed: 06/13/2023]
Abstract
Trichosanthes is a genus in Cucurbitaceae comprising 90-100 species. Trichosanthes species are valuable as herbaceous medicinal ingredients. The fruits, seeds, and roots of species such as T. kirilowii and T. rosthornii are used in Korean traditional herbal medicines. T. rosthornii is only found in China, whereas in South Korea two varieties, T. kirilowii var. kirilowii and T. kirilowii var. japonica, are distributed. T. kirilowii var. kirilowii and T. kirilowii var. japonica have different fruit and leaf shapes but are recognized as belonging to the same species. Furthermore, although its members have herbal medicine applications, genomic information of the genus is still limited. The broad goals of this study were (i) to evaluate the taxonomy of Trichosanthes using plastid phylogenomic data and (ii) provide molecular markers specific for T. kirilowii var. kirilowii and T. kirilowii var. japonica, as these have differences in their pharmacological effectiveness and thus should not be confused and adulterated. Comparison of five Trichosanthes plastid genomes revealed locally divergent regions, mainly within intergenic spacer regions (trnT-UGU-trnL-UAA: marker name Tri, rrn4.5-rrn5: TRr, trnE-UUC-trnT-GGU: TRtt). Using these three markers as DNA-barcodes for important herbal medicine species in Trichosanthes, the identity of Trichosanthes material in commercial medicinal products in South Korea could be successfully determined. Phylogenetic analysis of the five Trichosanthes species revealed that the species are clustered within tribe Sicyoeae. T. kirilowii var. kirilowii and T. rosthornii formed a clade with T. kirilowii var. japonica as their sister group. As T. kirilowii in its current circumscription is paraphyletic and as the two varieties can be readily distinguished morphologically (e.g., in leaf shape), T. kirilowii var. japonica should be treated (again) as an independent species, T. japonica.
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Affiliation(s)
- Inkyu Park
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju, South Korea
| | - Jun-Ho Song
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju, South Korea
| | - Sungyu Yang
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju, South Korea
| | - Sungwook Chae
- Herbal Medicine Research Division, Korea Institute of Oriental Medicine, Daejeon, South Korea
| | - Byeong Cheol Moon
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju, South Korea
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Park I, Yang S, Choi G, Moon BC, Song JH. An Integrated Approach for Efficient and Accurate Medicinal Cuscutae Semen Identification. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1410. [PMID: 33105814 PMCID: PMC7690581 DOI: 10.3390/plants9111410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/11/2020] [Accepted: 10/20/2020] [Indexed: 11/16/2022]
Abstract
To guarantee the safety and efficacy of herbal medicines, accurate identification and quality evaluation are crucial. The ripe dried seeds of Cuscuta australis R.Br. and C. chinensis Lam. are known as Cuscutae Semen (CS) and are widely consumed in Northeast Asia; however, the seeds of other species can be misidentified as CS owing to morphological similarities, leading to misuse. In this report, we propose a multilateral strategy combining microscopic techniques with statistical analysis and DNA barcoding using a genus-specific primer to facilitate the identification and authentication of CS. Morphology-based identification using microscopy revealed that the useful diagnostic characteristics included general shape, embryo exudation, hairiness, and testa ornamentation, which were used to develop an effective identification key. In addition, we conducted DNA barcoding-based identification to ensure accurate authentication. A novel DNA barcode primer was produced from the chloroplast rbcL gene by comparative analysis using Cuscuta chloroplast genome sequences, which allowed four Cuscuta species and adulterants to be discriminated completely. Therefore, this investigation overcame the limitations of universal DNA barcodes for Cuscuta species with high variability. We believe that this integrated approach will enable CS to be differentiated from other species, thereby improving its quality control and product safety in medicinal markets.
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Affiliation(s)
| | | | | | - Byeong Cheol Moon
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju 58245, Korea; (I.P.); (S.Y.); (G.C.)
| | - Jun-Ho Song
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju 58245, Korea; (I.P.); (S.Y.); (G.C.)
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Song JH, Yang S, Choi G. Taxonomic Implications of Leaf Micromorphology Using Microscopic Analysis: A Tool for Identification and Authentication of Korean Piperales. PLANTS 2020; 9:plants9050566. [PMID: 32365585 PMCID: PMC7285214 DOI: 10.3390/plants9050566] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/22/2020] [Accepted: 04/26/2020] [Indexed: 01/15/2023]
Abstract
A comparative study of the leaf micromorphology of Korean Piperales, including medicinal materials, was performed through light microscopy and scanning electron microscopy, to evaluate their taxonomic significance. Piperales possessed both amphistomatic and hypostomatic leaves. The epidermal area ranged from 38 to 5077 μm2, and the stomatal area ranged from 201 to 2129 μm2. The stomatal index on the abaxial surface was higher than that on the abaxial surface. Anomocytic stomata occurred most commonly, but actinocytic, anisocytic, tetracytic, and staurocytic stomata were also found in certain taxa. Secretory idioblasts were found on all taxa studied except Aristolochia. Three main types of trichomes were defined—(1) glandular trichome; (2) simple multicellular trichome; and (3) two-armed multicellular Y-shaped trichome. Although the quantitative data on its own had somewhat limited taxonomic value, the various qualitative characteristics (e.g., epidermal surfaces, stomata types and positions, trichome types and density, and secretory idioblast types) had great taxonomic value. These characteristics might be taxonomically relevant and useful for developing an identification key. Additionally, we evaluated and supported the previous taxonomic system of Korean Asarum, using leaf micromorphological characteristics. Finally, through the application for authentication of herbal medicine, we revealed that leaf micromorphological characteristics can be used for accurate authentication.
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Affiliation(s)
| | | | - Goya Choi
- Correspondence: ; Tel.: +82-61-338-7118
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