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Cristani M, Micale N. Bioactive Compounds from Medicinal Plants as Potential Adjuvants in the Treatment of Mild Acne Vulgaris. Molecules 2024; 29:2394. [PMID: 38792254 PMCID: PMC11124055 DOI: 10.3390/molecules29102394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/15/2024] [Accepted: 05/17/2024] [Indexed: 05/26/2024] Open
Abstract
In recent years, there has been a growing interest in the use of medicinal plants and phytochemicals as potential treatments for acne vulgaris. This condition, characterized by chronic inflammation, predominantly affects adolescents and young adults. Conventional treatment typically targets the key factors contributing to its development: the proliferation of Cutibacterium acnes and the associated inflammation. However, these treatments often involve the use of potent drugs. As a result, the exploration of herbal medicine as a complementary approach has emerged as a promising strategy. By harnessing the therapeutic properties of medicinal plants and phytochemicals, it may be possible to address acne vulgaris while minimizing the reliance on strong drugs. This approach not only offers potential benefits for individuals seeking alternative treatments but also underscores the importance of natural remedies of plant origin in dermatological care. The primary aim of this study was to assess the antimicrobial, antioxidant, and anti-inflammatory properties of plants and their phytochemical constituents in the management of mild acne vulgaris. A comprehensive search of scientific databases was conducted from 2018 to September 2023. The findings of this review suggest that medicinal plants and their phytochemical components hold promise as treatments for mild acne vulgaris. However, it is crucial to note that further research employing high-quality evidence and standardized methodologies is essential to substantiate their efficacy and safety profiles.
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Affiliation(s)
| | - Nicola Micale
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università di Messina, Viale F. Stagno D’Alcontres 31, I-98166 Messina, Italy;
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Han S, Zhang S, Yi R, Bi D, Ding H, Yang J, Ye Y, Xu W, Wu L, Zhuo R, Kan X. Phylogenomics and plastomics offer new evolutionary perspectives on Kalanchoideae (Crassulaceae). ANNALS OF BOTANY 2024; 133:585-604. [PMID: 38359907 PMCID: PMC11037489 DOI: 10.1093/aob/mcae017] [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: 01/05/2024] [Accepted: 02/08/2024] [Indexed: 02/17/2024]
Abstract
BACKGROUND AND AIMS Kalanchoideae is one of three subfamilies within Crassulaceae and contains four genera. Despite previous efforts, the phylogeny of Kalanchoideae remains inadequately resolved with persistent issues including low support, unstructured topologies and polytomies. This study aimed to address two central objectives: (1) resolving the pending phylogenetic questions within Kalanchoideae by using organelle-scale 'barcodes' (plastomes) and nuclear data; and (2) investigating interspecific diversity patterns among Kalanchoideae plastomes. METHODS To explore the plastome evolution in Kalanchoideae, we newly sequenced 38 plastomes representing all four constituent genera (Adromischus, Cotyledon, Kalanchoe and Tylecodon). We performed comparative analyses of plastomic features, including GC and gene contents, gene distributions at the IR (inverted repeat) boundaries, nucleotide divergence, plastomic tRNA (pttRNA) structures and codon aversions. Additionally, phylogenetic inferences were inferred using both the plastomic dataset (79 genes) and nuclear dataset (1054 genes). KEY RESULTS Significant heterogeneities were observed in plastome lengths among Kalanchoideae, strongly correlated with LSC (large single copy) lengths. Informative diversities existed in the gene content at SSC/IRa (small single copy/inverted repeat a), with unique patterns individually identified in Adromischus leucophyllus and one major Kalanchoe clade. The ycf1 gene was assessed as a shared hypervariable region among all four genera, containing nine lineage-specific indels. Three pttRNAs exhibited unique structures specific to Kalanchoideae and the genera Adromischus and Kalanchoe. Moreover, 24 coding sequences revealed a total of 41 lineage-specific unused codons across all four constituent genera. The phyloplastomic inferences clearly depicted internal branching patterns in Kalanchoideae. Most notably, by both plastid- and nuclear-based phylogenies, our research offers the first evidence that Kalanchoe section Eukalanchoe is not monophyletic. CONCLUSIONS This study conducted comprehensive analyses on 38 newly reported Kalanchoideae plastomes. Importantly, our results not only reconstructed well-resolved phylogenies within Kalanchoideae, but also identified highly informative unique markers at the subfamily, genus and species levels. These findings significantly enhance our understanding of the evolutionary history of Kalanchoideae.
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Affiliation(s)
- Shiyun Han
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Sijia Zhang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Ran Yi
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - De Bi
- Suzhou Polytechnic Institute of Agriculture, Suzhou 215000, China
| | - Hengwu Ding
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Jianke Yang
- School of Basic Medical Sciences, Wannan Medical College, Wuhu 241000, China
| | - Yuanxin Ye
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Wenzhong Xu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Longhua Wu
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Renying Zhuo
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Xianzhao Kan
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
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Wong KH, Zheng T, Yue GGL, Li MC, Wu HY, Tong MH, Zhao XL, Chen HB, Lau CBS, Shaw PC, Lau DTW. A systematic approach for authentication of medicinal Patrinia species using an integration of morphological, chemical and molecular methods. Sci Rep 2024; 14:6566. [PMID: 38503940 PMCID: PMC10951358 DOI: 10.1038/s41598-024-57115-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 03/14/2024] [Indexed: 03/21/2024] Open
Abstract
Four common Patrinia species, including P. heterophylla, P. monandra, P. scabiosifolia and P. villosa, have been documented as herbal medicines with various clinical applications, such as anti-cancer, anti-diarrhea and sedative. However, the authentication of medicinal Patrinia species poses a problem, particularly with the processed herbal materials. This study aimed to systematically authenticate the four medicinal Patrinia species in the market using morphological and chemical characterization, as well as DNA markers. We found the species identity authenticated by traditional morphologies were in good agreement with both chemical and molecular results. The four species showed species-specific patterns in chromatographic profiles with distinct chemical markers. We also revealed the power of complete chloroplast genomes in species authentication. The sequences of targeted loci, namely atpB, petA, rpl2-rpl23 and psaI-ycf4, contained informative nucleotides for the species differentiation. Our results also facilitate authentication of medicinal Patrinia species using new DNA barcoding markers. To the best of our knowledge, this is the first report on the application of morphology, chemical fingerprinting, complete chloroplast genomes and species-specific Insertion-Deletions (InDels) in differentiating Patrinia species. This study reported on the power of a systematic, multidisciplinary approach in authenticating medicinal Patrinia species.
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Affiliation(s)
- Kwan-Ho Wong
- Shiu-Ying Hu Herbarium, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Li Dak Sum Yip Yio Chin R&D Centre for Chinese Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Tao Zheng
- Institute of Chinese Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- State Key Laboratory of Research On Bioactivities and Clinical Applications of Medicinal Plants, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Grace Gar-Lee Yue
- Institute of Chinese Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- State Key Laboratory of Research On Bioactivities and Clinical Applications of Medicinal Plants, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Man-Ching Li
- Shiu-Ying Hu Herbarium, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Hoi-Yan Wu
- Li Dak Sum Yip Yio Chin R&D Centre for Chinese Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Man-Ho Tong
- Institute of Chinese Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- State Key Laboratory of Research On Bioactivities and Clinical Applications of Medicinal Plants, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Xin-Lei Zhao
- The Institute of Medicinal Plant Development, The Chinese Academy of Medical Sciences and Peking Union Medical College, Haidian, Beijing, China
| | - Hu-Biao Chen
- School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China
| | - Clara Bik-San Lau
- Li Dak Sum Yip Yio Chin R&D Centre for Chinese Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.
- Institute of Chinese Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.
- State Key Laboratory of Research On Bioactivities and Clinical Applications of Medicinal Plants, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.
- Department of Pharmacology and Pharmacy & School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
| | - Pang-Chui Shaw
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.
- Li Dak Sum Yip Yio Chin R&D Centre for Chinese Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.
- Institute of Chinese Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.
- State Key Laboratory of Research On Bioactivities and Clinical Applications of Medicinal Plants, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.
| | - David Tai-Wai Lau
- Shiu-Ying Hu Herbarium, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.
- Li Dak Sum Yip Yio Chin R&D Centre for Chinese Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.
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Zhang L, Meng Y, Wang D, He GH, Zhang JM, Wen J, Nie ZL. Plastid genome data provide new insights into the dynamic evolution of the tribe Ampelopsideae (Vitaceae). BMC Genomics 2024; 25:247. [PMID: 38443830 PMCID: PMC10916268 DOI: 10.1186/s12864-024-10149-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 02/21/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND Ampelopsideae J. Wen & Z.L. Nie is a small-sized tribe of Vitaceae Juss., including ca. 47 species from four genera showing a disjunct distribution worldwide across all the continents except Antarctica. There are numerous species from the tribe that are commonly used as medicinal plants with immune-modulating, antimicrobial, and anti-hypertensive properties. The tribe is usually recognized into three clades, i.e., Ampelopsis Michx., Nekemias Raf., and the Southern Hemisphere clade. However, the relationships of the three clades differ greatly between the nuclear and the plastid topologies. There has been limited exploration of the chloroplast phylogenetic relationships within Ampelopsideae, and studies on the chloroplast genome structure of this tribe are only available for a few individuals. In this study, we aimed to investigate the evolutionary characteristics of plastid genomes of the tribe, including their genome structure and evolutionary insights. RESULTS We sequenced, assembled, and annotated plastid genomes of 36 species from the tribe and related taxa in the family. Three main clades were recognized within Ampelopsideae, corresponding to Ampelopsis, Nekemias, and the Southern Hemisphere lineage, respectively, and all with 100% bootstrap supports. The genome sequences and content of the tribe are highly conserved. However, comparative analyses suggested that the plastomes of Nekemias demonstrate a contraction in the large single copy region and an expansion in the inverted repeat region, and possess a high number of forward and palindromic repeat sequences distinct from both Ampelopsis and the Southern Hemisphere taxa. CONCLUSIONS Our results highlighted plastome variations in genome length, expansion or contraction of the inverted repeat region, codon usage bias, and repeat sequences, are corresponding to the three lineages of the tribe, which probably faced with different environmental selection pressures and evolutionary history. This study provides valuable insights into understanding the evolutionary patterns of plastid genomes within the Ampelopsideae of Vitaceae.
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Affiliation(s)
- Lei Zhang
- Hunan Provincial key Laboratory of Ecological Conservation and Sustainable Utilization of Wulingshan Resources, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, 416000, China
| | - Ying Meng
- Hunan Provincial key Laboratory of Ecological Conservation and Sustainable Utilization of Wulingshan Resources, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, 416000, China
| | - Da Wang
- Hunan Provincial key Laboratory of Ecological Conservation and Sustainable Utilization of Wulingshan Resources, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, 416000, China
| | - Guan-Hao He
- Hunan Provincial key Laboratory of Ecological Conservation and Sustainable Utilization of Wulingshan Resources, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, 416000, China
| | - Jun-Ming Zhang
- Hunan Provincial key Laboratory of Ecological Conservation and Sustainable Utilization of Wulingshan Resources, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, 416000, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013-7012, USA
| | - Ze-Long Nie
- Hunan Provincial key Laboratory of Ecological Conservation and Sustainable Utilization of Wulingshan Resources, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, 416000, China.
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Fu QL, Mo ZQ, Xiang XG, Milne RI, Jacquemyn H, Burgess KS, Sun YN, Yan H, Qiu L, Yang BY, Tan SL. Plastome phylogenomics and morphological traits analyses provide new insights into the phylogenetic position, species delimitation and speciation of Triplostegia (Caprifoliaceae). BMC PLANT BIOLOGY 2023; 23:645. [PMID: 38097946 PMCID: PMC10722739 DOI: 10.1186/s12870-023-04663-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 12/05/2023] [Indexed: 12/17/2023]
Abstract
BACKGROUND The genus Triplostegia contains two recognized species, T. glandulifera and T. grandiflora, but its phylogenetic position and species delimitation remain controversial. In this study, we assembled plastid genomes and nuclear ribosomal DNA (nrDNA) cistrons sampled from 22 wild Triplostegia individuals, each from a separate population, and examined these with 11 recently published Triplostegia plastomes. Morphological traits were measured from herbarium specimens and wild material, and ecological niche models were constructed. RESULTS Triplostegia is a monophyletic genus within the subfamily Dipsacoideae comprising three monophyletic species, T. glandulifera, T. grandiflora, and an unrecognized species Triplostegia sp. A, which occupies much higher altitude than the other two. The new species had previously been misidentified as T. glandulifera, but differs in taproot, leaf, and other characters. Triplotegia is an old genus, with stem age 39.96 Ma, and within it T. glandulifera diverged 7.94 Ma. Triplostegia grandiflora and sp. A diverged 1.05 Ma, perhaps in response to Quaternary climate fluctuations. Niche overlap between Triplostegia species was positively correlated with their phylogenetic relatedness. CONCLUSIONS Our results provide new insights into the species delimitation of Triplostegia, and indicate that a taxonomic revision of Triplostegia is needed. We also identified that either rpoB-trnC or ycf1 could serve as a DNA barcode for Triplostegia.
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Affiliation(s)
- Qing-Li Fu
- Jiangxi Province Key Laboratory of Plant Resources, School of Life Sciences, Nanchang University, Nanchang, Jiangxi, 330031, China
| | - Zhi-Qiong Mo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Xiao-Guo Xiang
- Jiangxi Province Key Laboratory of Plant Resources, School of Life Sciences, Nanchang University, Nanchang, Jiangxi, 330031, China
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Institute of Life Science, Nanchang University, Nanchang, Jiangxi, 330031, China
| | - Richard I Milne
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JH, UK
| | - Hans Jacquemyn
- KU Leuven, Department of Biology, Plant Conservation and Population Biology, B-3001, Leuven, Belgium
| | - Kevin S Burgess
- College of Letters and Sciences, Columbus State University, University System of Georgia, Columbus, GA, 31907-5645, USA
| | - Ya-Nan Sun
- Jiangxi Province Key Laboratory of Plant Resources, School of Life Sciences, Nanchang University, Nanchang, Jiangxi, 330031, China
| | - Hua Yan
- Jiangxi Province Key Laboratory of Plant Resources, School of Life Sciences, Nanchang University, Nanchang, Jiangxi, 330031, China
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Institute of Life Science, Nanchang University, Nanchang, Jiangxi, 330031, China
| | - Li Qiu
- Jiangxi Province Key Laboratory of Plant Resources, School of Life Sciences, Nanchang University, Nanchang, Jiangxi, 330031, China
| | - Bo-Yun Yang
- Jiangxi Province Key Laboratory of Plant Resources, School of Life Sciences, Nanchang University, Nanchang, Jiangxi, 330031, China
| | - Shao-Lin Tan
- Jiangxi Province Key Laboratory of Plant Resources, School of Life Sciences, Nanchang University, Nanchang, Jiangxi, 330031, China.
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Sun X, Zhan Y, Li S, Liu Y, Fu Q, Quan X, Xiong J, Gang H, Zhang L, Qi H, Wang A, Huo J, Qin D, Zhu C. Complete chloroplast genome assembly and phylogenetic analysis of blackcurrant ( Ribes nigrum), red and white currant ( Ribes rubrum), and gooseberry ( Ribes uva-crispa) provide new insights into the phylogeny of Grossulariaceae. PeerJ 2023; 11:e16272. [PMID: 37842068 PMCID: PMC10573389 DOI: 10.7717/peerj.16272] [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: 06/15/2023] [Accepted: 09/19/2023] [Indexed: 10/17/2023] Open
Abstract
Background Blackcurrant (Ribes nigrum), red currant (R. rubrum), white currant (R. rubrum), and gooseberry (R. uva-crispa) belong to Grossulariaceae and are popular small-berry crops worldwide. The lack of genomic data has severely limited their systematic classification and molecular breeding. Methods The complete chloroplast (cp) genomes of these four taxa were assembled for the first time using MGI-DNBSEQ reads, and their genome structures, repeat elements and protein-coding genes were annotated. By genomic comparison of the present four and previous released five Ribes cp genomes, the genomic variations were identified. By phylogenetic analysis based on maximum-likelihood and Bayesian methods, the phylogeny of Grossulariaceae and the infrageneric relationships of the Ribes were revealed. Results The four cp genomes have lengths ranging from 157,450 to 157,802 bp and 131 shared genes. A total of 3,322 SNPs and 485 Indels were identified from the nine released Ribes cp genomes. Red currant and white currant have 100% identical cp genomes partially supporting the hypothesis that white currant (R. rubrum) is a fruit color variant of red currant (R. rubrum). The most polymorphic genic and intergenic region is ycf1 and trnT-psbD, respectively. The phylogenetic analysis demonstrated the monophyly of Grossulariaceae in Saxifragales and the paraphyletic relationship between Saxifragaceae and Grossulariaceae. Notably, the Grossularia subgenus is well nested within the Ribes subgenus and shows a paraphyletic relationship with the co-ancestor of Calobotrya and Coreosma sections, which challenges the dichotomous subclassification of the Ribes genus based on morphology (subgenus Ribes and subgenus Grossularia). These data, results, and insights lay a foundation for the phylogenetic research and breeding of Ribes species.
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Affiliation(s)
- Xinyu Sun
- College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Ying Zhan
- College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Songlin Li
- College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Yu Liu
- College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Qiang Fu
- College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Xin Quan
- College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Jinyu Xiong
- College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Huixin Gang
- College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, China
- National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions, National Development and Reform Commission, Harbin, Heilongjiang, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, Harbin, Heilongjiang, China
| | - Lijun Zhang
- National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions, National Development and Reform Commission, Harbin, Heilongjiang, China
- Heilongjiang Institute of Green Food Science, Harbin, Heilongjiang, China
| | - Huijuan Qi
- National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions, National Development and Reform Commission, Harbin, Heilongjiang, China
- Heilongjiang Institute of Green Food Science, Harbin, Heilongjiang, China
| | - Aoxue Wang
- College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, Harbin, Heilongjiang, China
| | - Junwei Huo
- College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, China
- National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions, National Development and Reform Commission, Harbin, Heilongjiang, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, Harbin, Heilongjiang, China
| | - Dong Qin
- College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, China
- National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions, National Development and Reform Commission, Harbin, Heilongjiang, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, Harbin, Heilongjiang, China
| | - Chenqiao Zhu
- College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, China
- National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions, National Development and Reform Commission, Harbin, Heilongjiang, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, Harbin, Heilongjiang, China
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Liu LL, Li JH, Sun ZS. Complete chloroplast genome of Lonicera ligustrina Wall. (Caprifoliaceae) and its phylogenetic implications. Mitochondrial DNA B Resour 2023; 8:903-907. [PMID: 37645476 PMCID: PMC10461517 DOI: 10.1080/23802359.2023.2239386] [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: 11/16/2022] [Accepted: 07/17/2023] [Indexed: 08/31/2023] Open
Abstract
Lonicera ligustrina is a folk medicinal herb in China and India with highly potential medicinal value. Here, we reported the complete chloroplast (cp) genome of L. ligustrina (GenBank accession number: ON968694). The cp genome was 155,330 bp long, with a large single-copy region (LSC) of 88,855 bp and a small single-copy region (SSC) of 18,647 bp separated by a pair of inverted repeats (IRs) of 23,914 bp. We also reconstructed the phylogeny of Lonicera using maximum likelihood (ML) method, including our data and previously reported cp genomes of related taxa. The current study indicated that L. ligustrina is sister with the Nintooa clade of subgen. Lonicera.
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Affiliation(s)
- Li-Li Liu
- College of Chemistry and Materials Engineering, Quzhou University, Quzhou, China
- Quzhou Academy of Agricultural and Forestry Sciences, Quzhou, China
| | - Jian-Hui Li
- College of Chemistry and Materials Engineering, Quzhou University, Quzhou, China
| | - Zhong-Shuai Sun
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
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Sun QH, Morales-Briones DF, Wang HX, Landis JB, Wen J, Wang HF. Target sequence capture data shed light on the deeper evolutionary relationships of subgenus Chamaecerasus in Lonicera (Caprifoliaceae). Mol Phylogenet Evol 2023; 184:107808. [PMID: 37156329 DOI: 10.1016/j.ympev.2023.107808] [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: 08/11/2022] [Revised: 04/29/2023] [Accepted: 05/01/2023] [Indexed: 05/10/2023]
Abstract
The genus Lonicera L. is widely distributed in the north temperate zone and is well-known for its high species richness and morphological diversity. Previous studies have suggested that many sections of Lonicera are not monophyletic and phylogenetic relationships within the genus are still poorly resolved. In this study, we sampled 37 accessions of Lonicera, covering four sections of subgenus Chamaecerasus plus six outgroup taxa, to recover the main clades of Lonicera based on sequences of nuclear loci generated by target enrichment and cpDNA from genome skimming. We found extensive cytonuclear discordance across the subgenus. Both nuclear and plastid phylogenetic analyses supported subgenus Chamaecerasus sister to subgenus Lonicera. Within subgenus Chamaecerasus, sections Isika and Nintooa were each polyphyletic. Based on the nuclear and chloroplast phylogenies, we propose to merge Lonicera korolkowii into section Coeloxylosteum and Lonicera caerulea into section Nintooa. In addition, Lonicera is estimated to have originated in the mid Oligocene (26.45 Ma). The stem age of section Nintooa was estimated to be 17.09 Ma (95% HPD: 13.30-24.45). The stem age of subgenus Lonicera was estimated to be 16.35 Ma (95% HPD: 14.12-23.66). Ancestral area reconstruction analyses indicate that subgenus Chamaecerasus originated in East Asia and Central Asia. In addition, sections Coeloxylosteum and Nintooa originated in East Asia, with subsequent dispersals into other areas. The aridification of the Asian interior likely promoted the rapid radiation of sections Coeloxylosteum and Nintooa within this region. Moreover, our biogeographic analysis fully supports the Bering and the North Atlantic Land Bridge hypotheses for the intercontinental migrations in the Northern Hemisphere. Overall, this study provides new insights into the taxonomically complex lineages of subgenus Chamaecerasus and the process of speciation.
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Affiliation(s)
- Qing-Hui Sun
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, 571199, China
| | - Diego F Morales-Briones
- Department of Plant and Microbial Biology, College of Biological Sciences, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, Saint Paul, MN 55108, USA; Systematics, Biodiversity and Evolution of Plants, Department of Biology I, Ludwig-Maximilians-Universität München, Menzinger Str. 67, 80638, Munich, Germany
| | - Hong-Xin Wang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; Zhai Mingguo Academician Work Station, Sanya University, Sanya 572022, China
| | - Jacob B Landis
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY 14850, USA; BTI Computational Biology Center, Boyce Thompson Institute, Ithaca, NY 14853, USA
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC-166, Smithsonian Institution, PO Box 37012, Washington, DC 20013-7012, USA
| | - Hua-Feng Wang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; Key Laboratory of Tropical Biological Resources of Ministry of Education, College of Tropical Crops, Hainan University, Haikou 570228, China.
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9
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Srivastav M, Clement WL, Landrein S, Zhang J, Howarth DG, Donoghue MJ. A phylogenomic analysis of Lonicera and its bearing on the evolution of organ fusion. AMERICAN JOURNAL OF BOTANY 2023; 110:e16143. [PMID: 36807121 DOI: 10.1002/ajb2.16143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 01/26/2023] [Accepted: 01/26/2023] [Indexed: 05/11/2023]
Abstract
PREMISE The ~140 species of Lonicera are characterized by variously fused leaves, bracteoles, and ovaries, making it a model system for studying the evolution and development of organ fusion. However, previous phylogenetic analyses, based mainly on chloroplast DNA markers, have yielded uncertain and conflicting results. A well-supported phylogeny of Lonicera will allow us to trace the evolutionary history of organ fusion. METHODS We inferred the phylogeny of Lonicera using restriction site-associated DNA sequencing (RADSeq), sampling all major clades and 18 of the 23 subsections. This provided the basis for inferring the evolution of five fusion-related traits. RESULTS RADSeq data yielded a well-resolved and well-supported phylogeny. The two traditionally recognized subgenera (Periclymenum and Chamaecerasus), three of the four sections (Isoxylosteum, Coeloxylosteum, and Nintooa), and half of the subsections sampled were recovered as monophyletic. However, the large and heterogeneous section Isika was strongly supported as paraphyletic. Nintooa, a clade of ~22 mostly vine-forming species, including L. japonica, was recovered in a novel position, raising the possibility of cytonuclear discordance. We document the parallel evolution of fused leaves, bracteoles, and ovaries, with rare reversals. Most strikingly, complete cupules, in which four fused bracteoles completely enclose two unfused ovaries, arose at least three times. Surprisingly, these appear to have evolved directly from ancestors with free bracteoles instead of partial cupules. CONCLUSIONS We provide the most comprehensive and well-supported phylogeny of Lonicera to date. Our inference of multiple evolutionary shifts in organ fusion provides a solid foundation for in depth developmental and functional analyses.
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Affiliation(s)
- Mansa Srivastav
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, 06520, USA
| | - Wendy L Clement
- Department of Biology, The College of New Jersey, Ewing, New Jersey, 08628, USA
| | - Sven Landrein
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China
| | - Jingbo Zhang
- Department of Biological Sciences, St. John's University, Queens, New York, 11439, USA
| | - Dianella G Howarth
- Department of Biological Sciences, St. John's University, Queens, New York, 11439, USA
| | - Michael J Donoghue
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, 06520, USA
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10
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Zhu C, Sun X, Fu Q, Zhan Y, Li S, Liu Y, Yu M, Qin D, Zhang L, Huo J. Complete chloroplast genome and phylogenetic analysis of Lonicera caerulea var. edulis (Caprifoliaceae). Mitochondrial DNA B Resour 2023; 8:314-318. [PMID: 36860479 PMCID: PMC9970238 DOI: 10.1080/23802359.2023.2180309] [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: 02/27/2023] Open
Abstract
Lonicera caerulea var. edulis, known as "blue honeysuckle" or "Haskap," is a deciduous shrub that belongs to the Caprifoliaceae family. Characterized by the high cold hardiness and high quality of fruit, it has become a novel cash crop in cold regions worldwide. The lack of available chloroplast (cp) genome information limits studies of its molecular breeding and phylogeny. Here, the complete cp genome of Lonicera caerulea var. edulis was assembled and characterized for the first time. It was 155,142 bp in length with 38.43% of GC content, including 23,841 bp inverted repeat regions (IRs), an 88,737 bp large single-copy region (LSC), and an 18,723 bp small single-copy region (SSC). A total of 132 genes, including 85 protein-coding genes, 8 rRNA genes, and 39 tRNA genes were annotated. Phylogenetic analysis indicated that L. caerulea var. edulis was closely related to L. tangutica. These data and results provide a valuable resource for the development of breeding tools and genetic diversity studies for L. caerulea.
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Affiliation(s)
- Chenqiao Zhu
- College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin, China,National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions, National Development and Reform Commission, Harbin, China,Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China,CONTACT Chenqiao Zhu College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin, China600 Changjiang Street, Xiangfang District, Harbin, 150030, China; National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions, National Development and Reform Commission, Harbin, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Xinyu Sun
- College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Qiang Fu
- College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Ying Zhan
- College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Songlin Li
- College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Yu Liu
- College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Min Yu
- National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions, National Development and Reform Commission, Harbin, China,College of Life Science, Northeast Agricultural University, Harbin, China
| | - Dong Qin
- College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin, China,National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions, National Development and Reform Commission, Harbin, China,Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Lijun Zhang
- National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions, National Development and Reform Commission, Harbin, China,Heilongjiang Institute of Green Food Science, Harbin, China
| | - Junwei Huo
- College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin, China,National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions, National Development and Reform Commission, Harbin, China,Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
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11
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Song S, Cameron KM, Wang Y, Wang S, Jin X, Hina F, Yang Z, Li P. Phylogenomics and phylogeography of Menispermum (Menispermaceae). FRONTIERS IN PLANT SCIENCE 2023; 14:1116300. [PMID: 36909420 PMCID: PMC9992823 DOI: 10.3389/fpls.2023.1116300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Phylogenomics have been widely used to resolve ambiguous and controversial evolutionary relationships among plant species and genera, and the identification of unique indels in plastomes may even help to understand the evolution of some plant families. Menispermum L. (Menispermaceae) consists of three species, M. dauricum DC., M. canadense L., and M. mexicanum Rose, which are disjuncly distributed among East Asia, Eastern North America and Mexico. Taxonomists continue to debate whether M. mexicanum is a distinct species, a variety of M. dauricum, or simply a synonym of M. canadense. To date, no molecular systematics studies have included this doubtful species in phylogenetic analyses. METHODS In this study, we examined phylogenomics and phylogeography of Menispermum across its entire range using 29 whole plastomes of Menispermaceae and 18 ITS1&ITS2 sequences of Menispermeae. We reconstructed interspecific relationships of Menispermum and explored plastome evolution in Menispermaceae, revealing several genomic hotspot regions for the family. RESULTS AND DISCUSSION Phylogenetic and network analyses based on whole plastome and ITS1&ITS2 sequences show that Menispermum clusters into two clades with high support values, Clade A (M. dauricum) and Clade B (M. canadense + M. mexicanum). However, M. mexicanum is nested within M. canadense and, as a result, we support that M. mexicanum is a synonym of M. canadense. We also identified important molecular variations in the plastomes of Menispermaceae. Several indels and consequently premature terminations of genes occur in Menispermaceae. A total of 54 regions were identified as the most highly variable plastome regions, with nucleotide diversity (Pi) values > 0.05, including two coding genes (matK, ycf1), four introns (trnK intron, rpl16 intron, rps16 intron, ndhA intron), and 48 intergenic spacer (IGS) regions. Of these, four informative hotspot regions (trnH-psbA, ndhF-rpl32, trnK-rps16, and trnP-psaJ) should be especially useful for future studies of phylogeny, phylogeography and conservation genetics of Menispermaceae.
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Affiliation(s)
- Shiqiang Song
- College of Life Sciences and Technologies, Tarim University, Alar, China
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Kenneth M. Cameron
- Department of Botany, University of Wisconsin, Madison, WI, United States
| | - Yuguo Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai, China
| | - Shenyi Wang
- Department of Botany, University of Wisconsin, Madison, WI, United States
| | - Xinjie Jin
- College of Life and Environmental Science, Wenzhou University, Wenzhou, China
| | - Faiza Hina
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Zhaoping Yang
- College of Life Sciences and Technologies, Tarim University, Alar, China
| | - Pan Li
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
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12
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Kang H, An SM, Park YJ, Lee YB, Lee JH, Cheon KS, Kim KA. Population Genomics Study and Implications for the Conservation of Zabelia tyaihyonii Based on Genotyping-By-Sequencing. PLANTS (BASEL, SWITZERLAND) 2022; 12:171. [PMID: 36616299 PMCID: PMC9823854 DOI: 10.3390/plants12010171] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/26/2022] [Accepted: 12/26/2022] [Indexed: 06/17/2023]
Abstract
Zabelia tyaihyonii (Nakai) Hisauti and H. Hara is a perennial shrub endemic to Republic of Korea that grows naturally in only a very limited region of the dolomite areas of Gangwon-do and Chungcheongbuk-do Provinces in the Republic of Korea. Given its geographical characteristics, it is more vulnerable than more widely distributed species. Despite the need for comprehensive information to support conservation, population genetic information for this species is very scarce. In this study, we analyzed the genetic diversity and population structure of 94 individuals from six populations of Z. tyaihyonii using a genotyping-by-sequencing (GBS) approach to provide important information for proper conservation and management. Our results, based on 3088 single nucleotide polymorphisms (SNPs), showed a mean expected heterozygosity (He) of 0.233, no sign of within-population inbreeding (GIS that was close to or even below zero in all populations), and a high level of genetic differentiation (FST = 0.170). Analysis of molecular variance (AMOVA) indicated that the principal molecular variance existed within populations (84.5%) rather than among populations (17.0%). We suggested that six management units were proposed for conservation considering Bayesian structure analysis and phylogenetic analysis, and given the various current situations faced by Z. tyaihyonii, it is believed that not only the in situ conservation but also the ex situ conservation should be considered.
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Affiliation(s)
- Halam Kang
- Department of Biological Science, Sangji University, Wonju 26339, Republic of Korea
| | - Sung-Mo An
- Department of Biological Science, Sangji University, Wonju 26339, Republic of Korea
| | - Yoo-Jung Park
- Department of Biological Science, Sangji University, Wonju 26339, Republic of Korea
| | - Yoo-Bin Lee
- Department of Biological Science, Sangji University, Wonju 26339, Republic of Korea
| | - Jung-Hyun Lee
- Department of Biology Education, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Kyeong-Sik Cheon
- Department of Biological Science, Sangji University, Wonju 26339, Republic of Korea
| | - Kyung-Ah Kim
- Environmental Research Institute, Kangwon National University, Chuncheon 24341, Republic of Korea
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13
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Yang Z, Ma W, Yang X, Wang L, Zhao T, Liang L, Wang G, Ma Q. Plastome phylogenomics provide new perspective into the phylogeny and evolution of Betulaceae (Fagales). BMC PLANT BIOLOGY 2022; 22:611. [PMID: 36566190 PMCID: PMC9789603 DOI: 10.1186/s12870-022-03991-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Betulaceae is a relatively small but morphologically diverse family, with many species having important economic and ecological values. Although plastome structure of Betulaceae has been reported sporadically, a comprehensive exploration for plastome evolution is still lacking. Besides, previous phylogenies had been constructed based on limited gene fragments, generating unrobust phylogenetic framework and hindering further studies on divergence ages, biogeography and character evolution. Here, 109 plastomes (sixteen newly assembled and 93 previously published) were subject to comparative genomic and phylogenomic analyses to reconstruct a robust phylogeny and trace the diversification history of Betulaceae. RESULTS All Betulaceae plastomes were highly conserved in genome size, gene order, and structure, although specific variations such as gene loss and IR boundary shifts were revealed. Ten divergent hotspots, including five coding regions (Pi > 0.02) and five noncoding regions (Pi > 0.035), were identified as candidate DNA barcodes for phylogenetic analysis and species delimitation. Phylogenomic analyses yielded high-resolution topology that supported reciprocal monophyly between Betula and Alnus within Betuloideae, and successive divergence of Corylus, Ostryopsis, and Carpinus-Ostrya within Coryloideae. Incomplete lineage sorting and hybridization may be responsible for the mutual paraphyly between Ostrya and Carpinus. Betulaceae ancestors originated from East Asia during the upper Cretaceous; dispersals and subsequent vicariance accompanied by historical environment changes contributed to its diversification and intercontinental disjunction. Ancestral state reconstruction indicated the acquisition of many taxonomic characters was actually the results of parallel or reversal evolution. CONCLUSIONS Our research represents the most comprehensive taxon-sampled and plastome-level phylogenetic inference for Betulaceae to date. The results clearly document global patterns of plastome structural evolution, and established a well-supported phylogeny of Betulaceae. The robust phylogenetic framework not only provides new insights into the intergeneric relationships, but also contributes to a perspective on the diversification history and evolution of the family.
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Affiliation(s)
- Zhen Yang
- State Key Laboratory of Tree Genetics and Breeding, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- National Innovation Alliance of Hazelnut Industry, Beijing, 100091, China
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing, 100091, China
| | - Wenxu Ma
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Forest Botany and Tree Physiology, University of Goettingen, 37077, Goettingen, Germany
| | | | - Lujun Wang
- Anhui Academy of Forestry, Hefei, 230031, China
| | - Tiantian Zhao
- State Key Laboratory of Tree Genetics and Breeding, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- National Innovation Alliance of Hazelnut Industry, Beijing, 100091, China
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing, 100091, China
| | - Lisong Liang
- State Key Laboratory of Tree Genetics and Breeding, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- National Innovation Alliance of Hazelnut Industry, Beijing, 100091, China
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing, 100091, China
| | - Guixi Wang
- State Key Laboratory of Tree Genetics and Breeding, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- National Innovation Alliance of Hazelnut Industry, Beijing, 100091, China
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing, 100091, China
| | - Qinghua Ma
- State Key Laboratory of Tree Genetics and Breeding, Beijing, 100091, China.
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
- National Innovation Alliance of Hazelnut Industry, Beijing, 100091, China.
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing, 100091, China.
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14
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Wang J, Zhao R, Zhang Z. Complete chloroplast genome sequences of Acanthocalyx alba and Acanthocalyx nepalensis subsp. delavayi (Caprifoliaceae). Mitochondrial DNA B Resour 2022; 7:1716-1718. [PMID: 36188667 PMCID: PMC9518610 DOI: 10.1080/23802359.2022.2124824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
In this study, the chloroplast genomes of Acanthocalyx alba (Hand.-Mazz., 1925) and Acanthocalyx nepalensis subsp. delavayi (Franchet, 1885) were sequenced, and their total lengths were 148,720 bp and 149,253 bp, respectively. The A. alba genome contained two inverted repeat regions (IRs) of 21,849 bp, a large single-copy region (LSC) of 89,084 bp, and a small single-copy region (SSC) of 15,938 bp, whereas A. nepalensis subsp. delavayi contained two IRs of 21,736 bp, one LSC of 89,034 bp, and one SSC of 16,747 bp. The chloroplast genomes of both A. alba and A. nepalensis subsp. delavayi contained 109 genes, including 72 mRNA, 33 tRNA, and four rRNA genes. Phylogenetic analysis suggested that A. alba is in a clade with A. nepalensis subsp. delavayi. This study provides useful data for further phylogenetic studies of A. alba and A. nepalensis subsp. delavayi.
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Affiliation(s)
- Junjun Wang
- School of Pharmacy, Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
- Sichuan Provincial Qiang-Yi Medicinal Resources Protection and Utilization Technology Engineering Laboratory, Chengdu, China
| | - Riza Zhao
- School of Pharmacy, Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
- Sichuan Provincial Qiang-Yi Medicinal Resources Protection and Utilization Technology Engineering Laboratory, Chengdu, China
| | - Zhifeng Zhang
- School of Pharmacy, Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
- Sichuan Provincial Qiang-Yi Medicinal Resources Protection and Utilization Technology Engineering Laboratory, Chengdu, China
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15
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Mo RJ, Wang HX, Chen DJ, Zhu ZX, Qiao W, Wang HF. Complete plastome sequence of Lonicera gynochlamydea Hemsl. (Caprifoliaceae). Mitochondrial DNA B Resour 2022; 7:1380-1381. [PMID: 35911467 PMCID: PMC9336488 DOI: 10.1080/23802359.2022.2101396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
We report and characterize the complete plastome of Lonicera gynochlamydea Hemsl. L. gynochlamydea is a shrub, belonging to the family Caprifoliaceae. Our results show that the length of the complete plastome is 154,643 bp, including 131 genes consisting of 84 protein-coding genes, 39 tRNA genes, and eight rRNA genes. The plastome exhibits the typical quadripartite structure and gene content of angiosperms, composed of two inverted repeats (IRs) regions of 23,846 bp, a large single-copy (LSC) region of 88,298 bp, and a small single-copy (SSC) region of 18,653 bp. The total G/C content in L. gynochlamydea plastome is 38.4%. The complete plastome sequence of L. gynochlamydea will make contributions to the conservation genetics of this species as well as to phylogenetic studies in Caprifoliaceae.
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Affiliation(s)
- Rong-Jia Mo
- Sanya Nanfan Research Institute of Hainan University, Sanya, China
| | - Hong-Xin Wang
- Sanya Nanfan Research Institute of Hainan University, Sanya, China
- Zhai Mingguo Academician Work Station, Sanya University, Sanya, China
| | - Da-Juan Chen
- Sanya Nanfan Research Institute of Hainan University, Sanya, China
| | - Zhi-Xin Zhu
- Sanya Nanfan Research Institute of Hainan University, Sanya, China
| | - Wang Qiao
- Hainan Grand Modern Agriculture Development Co. Ltd., Qionghai, China
| | - Hua-Feng Wang
- Sanya Nanfan Research Institute of Hainan University, Sanya, China
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16
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Song S, Zubov D, Comes HP, Li H, Liu X, Zhong X, Lee J, Yang Z, Li P. Plastid Phylogenomics and Plastome Evolution of Nandinoideae (Berberidaceae). FRONTIERS IN PLANT SCIENCE 2022; 13:913011. [PMID: 35873997 PMCID: PMC9302238 DOI: 10.3389/fpls.2022.913011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
Subfamily Nandinoideae Heintze (Berberidaceae), comprising four genera and ca. 19 species, is disjunctively distributed in eastern North America vs. Eurasia (eastern Asia, Central Asia, Middle East, and southeastern Europe), and represents an ideal taxon to explore plastid phylogenomics and plastome evolution in Berberidaceae. Many species of this subfamily have been listed as national or international rare and endangered plants. In this study, we sequenced and assembled 20 complete plastomes, representing three genera and 13 species of Nandinoideae. Together with six plastomes from GenBank, a total of 26 plastomes, representing all four genera and 16 species of Nandinoideae, were used for comparative genomic and phylogenomic analyses. These plastomes showed significant differences in overall size (156,626-161,406 bp), which is mainly due to the expansion in inverted repeat (IR) regions and/or insertion/deletion (indel) events in intergenic spacer (IGS) regions. A 75-bp deletion in the ndhF gene occurred in Leontice and Gymnospermium when compared with Nandina and Caulophyllum. We found a severe truncation at the 5' end of ycf1 in three G. altaicum plastomes, and a premature termination of ropC1 in G. microrrhynchum. Our phylogenomic results support the topology of {Nandina, [Caulophyllum, (Leontice, Gymnospermium)]}. Within the core genus Gymnospermium, we identified G. microrrhynchum from northeastern Asia (Clade A) as the earliest diverging species, followed by G. kiangnanense from eastern China (Clade B), while the rest species clustered into the two sister clades (C and D). Clade C included three species from West Tianshan (G. albertii, G. darwasicum, G. vitellinum). Clade D consisted of G. altaicum from northern Central Asia, plus one species from the Caucasus Mountains (G. smirnovii) and three from southeastern Europe (G. odessanum, G. peloponnesiacum, G. scipetarum). Overall, we identified 21 highly variable plastome regions, including two coding genes (rpl22, ycf1) and 19 intergenic spacer (IGS) regions, all with nucleotide diversity (Pi) values > 0.02. These molecular markers should serve as powerful tools (including DNA barcodes) for future phylogenetic, phylogeographic and conservation genetic studies.
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Affiliation(s)
- Shiqiang Song
- College of Life Sciences and Technologies, Tarim University, Alar, China
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Dmitriy Zubov
- National Academy of Medical Sciences of Ukraine, Kyiv, Ukraine
| | - Hans Peter Comes
- Department of Environment & Biodiversity, University of Salzburg, Salzburg, Austria
| | - Haiwen Li
- College of Life Sciences and Technologies, Tarim University, Alar, China
| | - Xuelian Liu
- College of Life Science, Tonghua Normal University, Tonghua, China
| | - Xin Zhong
- Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Joongku Lee
- Department of Environment and Forest Resources, Chungnam National University, Daejeon, South Korea
| | - Zhaoping Yang
- College of Life Sciences and Technologies, Tarim University, Alar, China
| | - Pan Li
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Biosystem Homeostasis and Protection, Ministry of Education, Zhejiang University, Hangzhou, China
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17
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Liu H, Liu W, Ahmad I, Xiao Q, Li X, Zhang D, Fang J, Zhang G, Xu B, Gao Q, Chen S. Complete Chloroplast Genome Sequence of Triosteum sinuatum, Insights into Comparative Chloroplast Genomics, Divergence Time Estimation and Phylogenetic Relationships among Dipsacales. Genes (Basel) 2022; 13:genes13050933. [PMID: 35627318 PMCID: PMC9141360 DOI: 10.3390/genes13050933] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/06/2022] [Accepted: 05/17/2022] [Indexed: 12/10/2022] Open
Abstract
Triosteum himalayanum, Triosteum pinnatifidum (Triosteum L., Caprifoliaceae, Dipsacales) are widely distributed in China while Triosteum sinuatum mainly occurrs in northeast China. Few reports have been determined on the genus Triosteum. In the present research, we sequenced 2 chloroplast genomes of Triosteum and analyzed 18 chloroplast genomes, trying to explore the sequence variations and phylogeny of genus Triosteum in the order Dipsacales. The chloroplast genomes of the genus Triosteum ranged from 154,579 bp to 157,178 bp, consisting of 132 genes (86 protein-coding genes, 38 transfer RNA genes, and 8 ribosomal RNA genes). Comparative analyses and phylogenetic analysis supported the division of Dipsacales into two clades, Adoxaceae and six other families. Among the six families, a clade of Valerianaceae+Dipsacaceae was recovered as a sister to a clade of Morinaceae+Linnaeaceae. A closer relationship of T. himalayanum and T. pinnatifidum among three species was revealed. Our research supported that Loniceraferdinandi and Triosteum was closely related. Zabelia had a closer relationship with Linnaea borealis and Dipelta than Morinaceae. The divergence between T. sinuatum and two other species in Triosteum was dated to 13.4 mya.
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Affiliation(s)
- HaiRui Liu
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810008, China; (H.L.); (D.Z.)
- College of Eco-Environmental Engineering, Qinghai University, Xining 810008, China; (Q.X.); (X.L.); (J.F.); (G.Z.); (B.X.)
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810001, China;
| | - WenHui Liu
- Department of Geological Engineering, Qinghai University, Xining 810016, China;
| | - Israr Ahmad
- Department of Botany, Women University of AJK, Bagh 12500, Pakistan;
| | - QingMeng Xiao
- College of Eco-Environmental Engineering, Qinghai University, Xining 810008, China; (Q.X.); (X.L.); (J.F.); (G.Z.); (B.X.)
| | - XuMin Li
- College of Eco-Environmental Engineering, Qinghai University, Xining 810008, China; (Q.X.); (X.L.); (J.F.); (G.Z.); (B.X.)
| | - DeJun Zhang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810008, China; (H.L.); (D.Z.)
- College of Eco-Environmental Engineering, Qinghai University, Xining 810008, China; (Q.X.); (X.L.); (J.F.); (G.Z.); (B.X.)
| | - Jie Fang
- College of Eco-Environmental Engineering, Qinghai University, Xining 810008, China; (Q.X.); (X.L.); (J.F.); (G.Z.); (B.X.)
| | - GuoFan Zhang
- College of Eco-Environmental Engineering, Qinghai University, Xining 810008, China; (Q.X.); (X.L.); (J.F.); (G.Z.); (B.X.)
| | - Bin Xu
- College of Eco-Environmental Engineering, Qinghai University, Xining 810008, China; (Q.X.); (X.L.); (J.F.); (G.Z.); (B.X.)
| | - QingBo Gao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810001, China;
- Correspondence:
| | - ShiLong Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810001, China;
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18
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Wan J, Jiang CX, Tang Y, Ma GL, Tong YP, Jin ZX, Zang Y, E.A. Osman E, Li J, Xiong J, Hu JF. Structurally diverse glycosides of secoiridoid, bisiridoid, and triterpene-bisiridoid conjugates from the flower buds of two Caprifoliaceae plants and their ATP-citrate lyase inhibitory activities. Bioorg Chem 2022; 120:105630. [DOI: 10.1016/j.bioorg.2022.105630] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/12/2022] [Accepted: 01/15/2022] [Indexed: 01/18/2023]
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Moghaddam M, Ohta A, Shimizu M, Terauchi R, Kazempour-Osaloo S. The complete chloroplast genome of Onobrychis gaubae (Fabaceae-Papilionoideae): comparative analysis with related IR-lacking clade species. BMC PLANT BIOLOGY 2022; 22:75. [PMID: 35183127 PMCID: PMC8858513 DOI: 10.1186/s12870-022-03465-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 02/14/2022] [Indexed: 05/24/2023]
Abstract
BACKGROUND Plastome (Plastid genome) sequences provide valuable markers for surveying evolutionary relationships and population genetics of plant species. Papilionoideae (papilionoids) has different nucleotide and structural variations in plastomes, which makes it an ideal model for genome evolution studies. Therefore, by sequencing the complete chloroplast genome of Onobrychis gaubae in this study, the characteristics and evolutionary patterns of plastome variations in IR-loss clade were compared. RESULTS In the present study, the complete plastid genome of O. gaubae, endemic to Iran, was sequenced using Illumina paired-end sequencing and was compared with previously known genomes of the IRLC species of legumes. The O. gaubae plastid genome was 122,688 bp in length and included a large single-copy (LSC) region of 81,486 bp, a small single-copy (SSC) region of 13,805 bp and one copy of the inverted repeat (IRb) of 29,100 bp. The genome encoded 110 genes, including 76 protein-coding genes, 30 transfer RNA (tRNA) genes and four ribosome RNA (rRNA) genes and possessed 83 simple sequence repeats (SSRs) and 50 repeated structures with the highest proportion in the LSC. Comparative analysis of the chloroplast genomes across IRLC revealed three hotspot genes (ycf1, ycf2, clpP) which could be used as DNA barcode regions. Moreover, seven hypervariable regions [trnL(UAA)-trnT(UGU), trnT(GGU)-trnE(UUC), ycf1, ycf2, ycf4, accD and clpP] were identified within Onobrychis, which could be used to distinguish the Onobrychis species. Phylogenetic analyses revealed that O. gaubae is closely related to Hedysarum. The complete O. gaubae genome is a valuable resource for investigating evolution of Onobrychis species and can be used to identify related species. CONCLUSIONS Our results reveal that the plastomes of the IRLC are dynamic molecules and show multiple gene losses and inversions. The identified hypervariable regions could be used as molecular markers for resolving phylogenetic relationships and species identification and also provide new insights into plastome evolution across IRLC.
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Affiliation(s)
- Mahtab Moghaddam
- Department of Plant Biology, Faculty of Biological Sciences, Tarbiat Modares University, 14115-154, Tehran, Iran.
| | - Atsushi Ohta
- Graduate School of Agriculture, Kyoto University, Kyoto, 617-0001, Japan
| | - Motoki Shimizu
- Iwate Biotechnology Research Center, Kitakami, Iwate, 024-0003, Japan
| | - Ryohei Terauchi
- Graduate School of Agriculture, Kyoto University, Kyoto, 617-0001, Japan
- Iwate Biotechnology Research Center, Kitakami, Iwate, 024-0003, Japan
| | - Shahrokh Kazempour-Osaloo
- Department of Plant Biology, Faculty of Biological Sciences, Tarbiat Modares University, 14115-154, Tehran, Iran.
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20
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Villarroel AE, Menegoz K, Quesne CL, Moreno-Gonzalez R. Valerianapraecipitis (Caprifoliaceae), a species new to science and endemic to Central Chile. PHYTOKEYS 2022; 189:81-98. [PMID: 35169385 PMCID: PMC8837557 DOI: 10.3897/phytokeys.189.73959] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 10/13/2021] [Indexed: 06/14/2023]
Abstract
The species Valerianapraecipitis (Caprifoliaceae), new to science and endemic to the Ñuble Region, Central Chile, is formally described. Morphological data support its placement in a new species, clearly different from V.philippiana. A detailed description, insights about its habitat and ecology, distribution map and illustration are provided. A table of comparison is also given with the morphological characters discriminating V.praecipitis from V.philippiana. The species is assessed as Endangered (EN) under the IUCN categories.
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Affiliation(s)
- Alejandro E. Villarroel
- Departamento de Biología, Facultad de Ciencias, Universidad de La Serena, Av. Raúl Bitrán Nachary 1305, La Serena, Chile
- Instituto de Conservación, Biodiversidad y Territorio, Facultad de Ciencias Forestales y Recursos Naturales, Universidad Austral de Chile, Independencia 641, Valdivia, Chile
| | - Kora Menegoz
- Independent researcher. Macal alto S/N, San Fabián de Alico, Chile
| | - Carlos Le Quesne
- Laboratorio de Dendrocronología y Cambio Global, Instituto de Conservación, Biodiversidad y Territorio, Universidad Austral de Chile, Valdivia 5110566, Chile
| | - Ricardo Moreno-Gonzalez
- Department of Palynology and Climate Dynamics, University of Göttingen, Wilhelm-Weber-Str. 2a, 37073 Göttingen, Germany
- Laboratorio de Biodiversidad y Ecología del Dosel, Instituto de Conservación, Biodiversidad y Territorio, Universidad Austral de Chile, Independencia 641, Valdivia, Chile
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21
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Sun QH, Morales-Briones DF, Wang HX, Landis JB, Wen J, Wang HF. Phylogenomic analyses of the East Asian endemic Abelia (Caprifoliaceae) shed insights into the temporal and spatial diversification history with widespread hybridization. ANNALS OF BOTANY 2022; 129:201-216. [PMID: 34950959 PMCID: PMC8796676 DOI: 10.1093/aob/mcab139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 11/15/2021] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS Abelia (Caprifoliaceae) is a small genus with five species, including one artificial hybrid and several natural hybrids. The genus has a discontinuous distribution in Mainland China, Taiwan Island and the Ryukyu Islands, providing a model system to explore the mechanisms of species dispersal in the East Asian flora. However, the current phylogenetic relationships within Abelia remain uncertain. METHODS We reconstructed the phylogenetic relationships within Abelia using nuclear loci generated by target enrichment and plastomes from genome skimming. Divergence time estimation, ancestral area reconstruction and ecological niche modelling (ENM) were used to examine the diversification history of Abelia. KEY RESULTS We found extensive cytonuclear discordance across the genus. By integrating lines of evidence from molecular phylogenies, divergence times and morphology, we propose to merge Abelia macrotera var. zabelioides into A. uniflora. Network analyses suggested that there have been multiple widespread hybridization events among Abelia species. These hybridization events may have contributed to the speciation mechanism and resulted in the high observed morphological diversity. The diversification of Abelia began in the early Eocene, followed by A. chinensis var. ionandra colonizing Taiwan Island during the Middle Miocene. The ENM results suggested an expansion of climatically suitable areas during the Last Glacial Maximum and range contraction during the Last Interglacial. Disjunction between the Himalayan-Hengduan Mountain region and Taiwan Island is probably the consequence of topographical isolation and postglacial contraction. CONCLUSIONS We used genomic data to reconstruct the phylogeny of Abelia and found a clear pattern of reticulate evolution in the group. In addition, our results suggest that shrinkage of postglacial range and the heterogeneity of the terrain have led to the disjunction between Mainland China and Taiwan Island. This study provides important new insights into the speciation process and taxonomy of Abelia.
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Affiliation(s)
- Qing-Hui Sun
- Key Laboratory of Tropical Biological Resources of Ministry of Education, College of Tropical Crops, Hainan University, Haikou, China
| | - Diego F Morales-Briones
- Department of Plant and Microbial Biology, College of Biological Sciences, University of Minnesota, 140 Gortner Laboratory, Saint Paul, MN, USA
- Systematics, Biodiversity and Evolution of Plants, Department of Biology I, Ludwig-Maximilians-Universität München, Menzinger Str. 67, 80638, Munich, Germany
| | - Hong-Xin Wang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, College of Tropical Crops, Hainan University, Haikou, China
- Zhai Mingguo Academician Work Station, Sanya University, Sanya, China
| | - Jacob B Landis
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, USA
- BTI Computational Biology Center, Boyce Thompson Institute, Ithaca, NY, USA
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC-166, Smithsonian Institution, Washington, DC, USA
| | - Hua-Feng Wang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, College of Tropical Crops, Hainan University, Haikou, China
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22
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Gu L, Hou Y, Wang G, Liu Q, Ding W, Weng Q. Characterization of the chloroplast genome of Lonicera ruprechtiana Regel and comparison with other selected species of Caprifoliaceae. PLoS One 2022; 17:e0262813. [PMID: 35077482 PMCID: PMC8789150 DOI: 10.1371/journal.pone.0262813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 01/05/2022] [Indexed: 11/19/2022] Open
Abstract
Lonicera ruprechtiana Regel is widely used as a greening tree in China and also displays excellent pharmacological activities. The phylogenetic relationship between L. ruprechtiana and other members of Caprifoliaceae remains unclear. In this study, the complete cp genome of L. ruprechtiana was identified using high-throughput Illumina pair-end sequencing data. The circular cp genome was 154,611 bp long and has a large single-copy region of 88,182 bp and a small single-copy region of 18,713 bp, with the two parts separated by two inverted repeat (IR) regions (23,858 bp each). A total of 131 genes were annotated, including 8 ribosomal RNAs, 39 transfer RNAs, and 84 protein-coding genes (PCGs). In addition, 49 repeat sequences and 55 simple sequence repeat loci of 18 types were also detected. Codon usage analysis demonstrated that the Leu codon is preferential for the A/U ending. Maximum-likelihood phylogenetic analysis using 22 Caprifoliaceae species revealed that L. ruprechtiana was closely related to Lonicera insularis. Comparison of IR regions revealed that the cp genome of L. ruprechtiana was largely conserved with that of congeneric species. Moreover, synonymous (Ks) and non-synonymous (Ka) substitution rate analysis showed that most genes were under purifying selection pressure; ycf3, and some genes associated with subunits of NADH dehydrogenase, subunits of the cytochrome b/f complex, and subunits of the photosystem had been subjected to strong purifying selection pressure (Ka/Ks < 0.1). This study provides useful genetic information for future study of L. ruprechtiana evolution.
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Affiliation(s)
- Lei Gu
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Yunyan Hou
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Guangyi Wang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Qiuping Liu
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Wei Ding
- Colleage of plant protection, Southwest University, Chongqing, China
| | - Qingbei Weng
- School of Life Sciences, Guizhou Normal University, Guiyang, China
- Qiannan Normal University for Nationalities, Duyun, China
- * E-mail:
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Ogoma CA, Liu J, Stull GW, Wambulwa MC, Oyebanji O, Milne RI, Monro AK, Zhao Y, Li DZ, Wu ZY. Deep Insights Into the Plastome Evolution and Phylogenetic Relationships of the Tribe Urticeae (Family Urticaceae). FRONTIERS IN PLANT SCIENCE 2022; 13:870949. [PMID: 35668809 PMCID: PMC9164014 DOI: 10.3389/fpls.2022.870949] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/15/2022] [Indexed: 05/09/2023]
Abstract
Urticeae s.l., a tribe of Urticaceae well-known for their stinging trichomes, consists of more than 10 genera and approximately 220 species. Relationships within this tribe remain poorly known due to the limited molecular and taxonomic sampling in previous studies, and chloroplast genome (CP genome/plastome) evolution is still largely unaddressed. To address these concerns, we used genome skimming data-CP genome and nuclear ribosomal DNA (18S-ITS1-5.8S-ITS2-26S); 106 accessions-for the very first time to attempt resolving the recalcitrant relationships and to explore chloroplast structural evolution across the group. Furthermore, we assembled a taxon rich two-locus dataset of trnL-F spacer and ITS sequences across 291 accessions to complement our genome skimming dataset. We found that Urticeae plastomes exhibit the tetrad structure typical of angiosperms, with sizes ranging from 145 to 161 kb and encoding a set of 110-112 unique genes. The studied plastomes have also undergone several structural variations, including inverted repeat (IR) expansions and contractions, inversion of the trnN-GUU gene, losses of the rps19 gene, and the rpl2 intron, and the proliferation of multiple repeat types; 11 hypervariable regions were also identified. Our phylogenomic analyses largely resolved major relationships across tribe Urticeae, supporting the monophyly of the tribe and most of its genera except for Laportea, Urera, and Urtica, which were recovered as polyphyletic with strong support. Our analyses also resolved with strong support several previously contentious branches: (1) Girardinia as a sister to the Dendrocnide-Discocnide-Laportea-Nanocnide-Zhengyia-Urtica-Hesperocnide clade and (2) Poikilospermum as sister to the recently transcribed Urera sensu stricto. Analyses of the taxon-rich, two-locus dataset showed lower support but was largely congruent with results from the CP genome and nuclear ribosomal DNA dataset. Collectively, our study highlights the power of genome skimming data to ameliorate phylogenetic resolution and provides new insights into phylogenetic relationships and chloroplast structural evolution in Urticeae.
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Affiliation(s)
- Catherine A. Ogoma
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jie Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Gregory W. Stull
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Moses C. Wambulwa
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Department of Life Sciences, School of Science and Computing, South Eastern Kenya University, Kitui, Kenya
| | - Oyetola Oyebanji
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Richard I. Milne
- School of Biological Sciences, Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Ying Zhao
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- *Correspondence: De-Zhu Li,
| | - Zeng-Yuan Wu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Zeng-Yuan Wu,
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Pascual-Díaz JP, Garcia S, Vitales D. Plastome Diversity and Phylogenomic Relationships in Asteraceae. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10122699. [PMID: 34961169 PMCID: PMC8705268 DOI: 10.3390/plants10122699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/01/2021] [Accepted: 12/04/2021] [Indexed: 06/14/2023]
Abstract
Plastid genomes are in general highly conserved given their slow evolutionary rate, and thus large changes in their structure are unusual. However, when specific rearrangements are present, they are often phylogenetically informative. Asteraceae is a highly diverse family whose evolution is long driven by polyploidy (up to 48x) and hybridization, both processes usually complicating systematic inferences. In this study, we generated one of the most comprehensive plastome-based phylogenies of family Asteraceae, providing information about the structure, genetic diversity and repeat composition of these sequences. By comparing the whole-plastome sequences obtained, we confirmed the double inversion located in the long single-copy region, for most of the species analyzed (with the exception of basal tribes), a well-known feature for Asteraceae plastomes. We also showed that genome size, gene order and gene content are highly conserved along the family. However, species representative of the basal subfamily Barnadesioideae-as well as in the sister family Calyceraceae-lack the pseudogene rps19 located in one inverted repeat. The phylogenomic analysis conducted here, based on 63 protein-coding genes, 30 transfer RNA genes and 21 ribosomal RNA genes from 36 species of Asteraceae, were overall consistent with the general consensus for the family's phylogeny while resolving the position of tribe Senecioneae and revealing some incongruences at tribe level between reconstructions based on nuclear and plastid DNA data.
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Affiliation(s)
- Joan Pere Pascual-Díaz
- Institut Botànic de Barcelona (IBB-CSIC), Passeig del Migdia s/n, 08038 Barcelona, Spain;
| | - Sònia Garcia
- Institut Botànic de Barcelona (IBB-CSIC), Passeig del Migdia s/n, 08038 Barcelona, Spain;
| | - Daniel Vitales
- Institut Botànic de Barcelona (IBB-CSIC), Passeig del Migdia s/n, 08038 Barcelona, Spain;
- Laboratori de Botànica–Unitat Associada CSIC, Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona, Av. Joan XXIII 27-31, 08028 Barcelona, Spain
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Park S, Jun M, Park S, Park S. Lineage-Specific Variation in IR Boundary Shift Events, Inversions, and Substitution Rates among Caprifoliaceae s.l. (Dipsacales) Plastomes. Int J Mol Sci 2021; 22:ijms221910485. [PMID: 34638831 PMCID: PMC8508905 DOI: 10.3390/ijms221910485] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/23/2021] [Accepted: 09/25/2021] [Indexed: 11/18/2022] Open
Abstract
Caprifoliaceae s.l. plastid genomes (plastomes) show that one inversion and two inverted repeat boundary shifts occurred in the common ancestor of this family, after which the plastomes are generally conserved. This study reports plastome sequences of five additional species, Fedia cornucopiae, Valeriana fauriei, and Valerianella locusta from the subfamily Valerianoideae, as well as Dipsacus japonicus and Scabiosa comosa from the subfamily Dipsacoideae. Combined with the published plastomes, these plastomes provide new insights into the structural evolution of plastomes within the family. Moreover, the three plastomes from the subfamily Valerianoideae exhibited accelerated nucleotide substitution rates, particularly at synonymous sites, across the family. The patterns of accD sequence divergence in the family are dynamic with structural changes, including interruption of the conserved domain and increases in nonsynonymous substitution rates. In particular, the Valeriana accD gene harbors a large insertion of amino acid repeat (AAR) motifs, and intraspecific polymorphism with a variable number of AARs in the Valeriana accD gene was detected. We found a correlation between intron losses and increased ratios of nonsynonymous to synonymous substitution rates in the clpP gene with intensified positive selection. In addition, two Dipsacoideae plastomes revealed the loss of the plastid-encoded rps15, and a potential functional gene transfer to the nucleus was confirmed.
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Affiliation(s)
- Seongjun Park
- Institute of Natural Science, Yeungnam University, Gyeongsan 38541, Gyeongbuk, Korea;
| | - Minji Jun
- Department of Life Sciences, Yeungnam University, Gyeongsan 38541, Gyeongbuk, Korea; (M.J.); (S.P.)
| | - Sunmi Park
- Department of Life Sciences, Yeungnam University, Gyeongsan 38541, Gyeongbuk, Korea; (M.J.); (S.P.)
| | - SeonJoo Park
- Department of Life Sciences, Yeungnam University, Gyeongsan 38541, Gyeongbuk, Korea; (M.J.); (S.P.)
- Correspondence: ; Tel.: +82-53-810-2377
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An updated phylogenetic and biogeographic analysis based on genome skimming data reveals convergent evolution of shrubby habit in Clematis in the Pliocene and Pleistocene. Mol Phylogenet Evol 2021; 164:107259. [PMID: 34303792 DOI: 10.1016/j.ympev.2021.107259] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 03/17/2021] [Accepted: 07/08/2021] [Indexed: 02/08/2023]
Abstract
Convergent evolution, often viewed as the inevitable outcome of natural selection, has received special attention since the time of Darwin. Clematis is well known for its climbing habit, but it has some shrubby species, known as sect. Fruticella s.l. The shrubby Clematis species are distributed in the dry habitats of Central Asia and adjacent areas showing possible convergent evolution. In this study, we assembled the complete plastome and nuclear ribosomal DNA (nrDNA) sequences of 56 Clematis species, representing most sections and covering most of the shrubby species, to reconstruct their evolutionary histories. Using both maximum likelihood and Bayesian methods, the plastome and nrDNA datasets generated similar, but not identical, phylogenetic relationships, which are better resolved than in previous studies. Then, molecular dating, historical range reconstruction, and character optimization analyses were conducted based on this updated phylogenetic framework. All the morphological characters widely used for taxonomy were shown to have evolved multiple times. Molecular dating inferred that Clematis diverged from its sister in the mid Miocene, and all six major clades of Clematis originated during the late Miocene, with a species radiation during the Pliocene to Pleistocene. The results clearly showed that the shrubby habit evolved independently in four lineages of Clematis in Asia. We also revealed that the shrubby lineages have emerged since the very beginning of Pliocene. Asian monsoon variation in the Pliocene and glacial period fluctuation in the Pleistocene may be the driving forces for the origin and diversification of the shrubby Clematis in Central Asia and adjacent dry areas.
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Lee AK, Gilman IS, Srivastav M, Lerner AD, Donoghue MJ, Clement WL. Reconstructing Dipsacales phylogeny using Angiosperms353: issues and insights. AMERICAN JOURNAL OF BOTANY 2021; 108:1122-1142. [PMID: 34254290 PMCID: PMC8362060 DOI: 10.1002/ajb2.1695] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 05/12/2021] [Indexed: 05/04/2023]
Abstract
PREMISE Phylogenetic relationships within major angiosperm clades are increasingly well resolved, but largely informed by plastid data. Areas of poor resolution persist within the Dipsacales, including placement of Heptacodium and Zabelia, and relationships within the Caprifolieae and Linnaeeae, hindering our interpretation of morphological evolution. Here, we sampled a significant number of nuclear loci using a Hyb-Seq approach and used these data to infer the Dipsacales phylogeny and estimate divergence times. METHODS Sampling all major clades within the Dipsacales, we applied the Angiosperms353 probe set to 96 species. Data were filtered based on locus completeness and taxon recovery per locus, and trees were inferred using RAxML and ASTRAL. Plastid loci were assembled from off-target reads, and 10 fossils were used to calibrate dated trees. RESULTS Varying numbers of targeted loci and off-target plastomes were recovered from most taxa. Nuclear and plastid data confidently place Heptacodium with Caprifolieae, implying homoplasy in calyx morphology, ovary development, and fruit type. Placement of Zabelia, and relationships within the Caprifolieae and Linnaeeae, remain uncertain. Dipsacales diversification began earlier than suggested by previous angiosperm-wide dating analyses, but many major splitting events date to the Eocene. CONCLUSIONS The Angiosperms353 probe set facilitated the assembly of a large, single-copy nuclear dataset for the Dipsacales. Nevertheless, many relationships remain unresolved, and resolution was poor for woody clades with low rates of molecular evolution. We favor expanding the Angiosperms353 probe set to include more variable loci and loci of special interest, such as developmental genes, within particular clades.
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Affiliation(s)
- Aaron K. Lee
- Department of BiologyThe College of New JerseyEwingNJ08628USA
- Department of Plant and Microbial BiologyUniversity of Minnesota ‐ Twin CitiesSaint PaulMN55108USA
| | - Ian S. Gilman
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCT06520USA
| | - Mansa Srivastav
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCT06520USA
| | - Ariel D. Lerner
- Department of BiologyThe College of New JerseyEwingNJ08628USA
| | - Michael J. Donoghue
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCT06520USA
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Kim H, Kim J. Structural Mutations in the Organellar Genomes of Valeriana sambucifolia f. dageletiana (Nakai. ex Maekawa) Hara Show Dynamic Gene Transfer. Int J Mol Sci 2021; 22:ijms22073770. [PMID: 33916499 PMCID: PMC8038606 DOI: 10.3390/ijms22073770] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/04/2021] [Accepted: 04/01/2021] [Indexed: 12/18/2022] Open
Abstract
Valeriana sambucifolia f. dageletiana (Nakai. ex Maekawa) Hara is a broad-leaved valerian endemic to Ulleung Island, a noted hot spot of endemism in Korea. However, despite its widespread pharmacological use, this plant remains comparatively understudied. Plant cells generally contain two types of organellar genomes (the plastome and the mitogenome) that have undergone independent evolution, which accordingly can provide valuable information for elucidating the phylogenetic relationships and evolutionary histories of terrestrial plants. Moreover, the extensive mega-data available for plant genomes, particularly those of plastomes, can enable researchers to gain an in-depth understanding of the transfer of genes between different types of genomes. In this study, we analyzed two organellar genomes (the 155,179 bp plastome and the 1,187,459 bp mitogenome) of V. sambucifolia f. dageletiana and detected extensive changes throughout the plastome sequence, including rapid structural mutations associated with inverted repeat (IR) contraction and genetic variation. We also described features characterizing the first reported mitogenome sequence obtained for a plant in the order Dipsacales and confirmed frequent gene transfer in this mitogenome. We identified eight non-plastome-originated regions (NPRs) distributed within the plastome of this endemic plant, for six of which there were no corresponding sequences in the current nucleotide sequence databases. Indeed, one of these unidentified NPRs unexpectedly showed certain similarities to sequences from bony fish. Although this is ostensibly difficult to explain, we suggest that this surprising association may conceivably reflect the occurrence of gene transfer from a bony fish to the plastome of an ancestor of V. sambucifolia f. dageletiana mediated by either fungi or bacteria.
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Affiliation(s)
- Hyoungtae Kim
- Institute of Agriculture Science and Technology, Chungbuk National University, Cheongju, Chungbuk 28644, Korea;
| | - Jungsung Kim
- Department of Forest Science, Chungbuk National University, Cheongju, Chungbuk 28644, Korea
- Correspondence: ; Tel.: +82-43-261-2535
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Chen P, Zhang XF, Landis JB, Zhu ZX, Wang HF. Complete plastome sequence of Xylosma longifolia Clos. (Salicaceae). Mitochondrial DNA B Resour 2021; 6:1085-1086. [PMID: 33796748 PMCID: PMC7995910 DOI: 10.1080/23802359.2021.1899870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Xylosma longifolia is a tree species within Salicaceae and is distributed in Guizhou, Yunnan, Fujian, Guangxi, Guangdong, and Hainan provinces of China as well as in Vietnam, Laos, and India. There are no studies utilizing the complete plastome of Xylosma longifolia in the current literature. Therefore, this report provides a reference for the plastid gene sequence of Xylosma longifolia, and it contributes to the phylogenetic placement and species identification. In this report, we described the complete plastome sequence of Xylosma longifolia. The complete plastome length of Xylosma longifolia is 156,938 bp and has the typical quadripartite structure and gene content of angiosperms, including two inverted repeat (IR) regions of 27,514 bp, a large single-copy (LSC) region of 85,221 bp and a small single-copy (SSC) region of 16,689 bp. The plastome contains 130 genes, including 86 protein coding genes, 36 tRNA genes, eight rRNA genes (5S rRNA, 4.5S rRNA, 16S rRNA, and 23S rRNA). The GC content of the plastome is 36.8%. The complete plastome sequence will be a valuable resource for studies involving the phylogenetic inference of Salicaceae.
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Affiliation(s)
- Peng Chen
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Xiao-Feng Zhang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Jacob B. Landis
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, USA
| | - Zhi-Xin Zhu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Hua-Feng Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
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Wang M, Wang X, Sun J, Wang Y, Ge Y, Dong W, Yuan Q, Huang L. Phylogenomic and evolutionary dynamics of inverted repeats across Angelica plastomes. BMC PLANT BIOLOGY 2021; 21:26. [PMID: 33413122 PMCID: PMC7792290 DOI: 10.1186/s12870-020-02801-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 12/16/2020] [Indexed: 05/27/2023]
Abstract
BACKGROUND Angelica L. (family Apiaceae) is an economically important genus comprising ca. One hundred ten species. Angelica species are found on all continents of the Northern Hemisphere, and East Asia hosts the highest number of species. Morphological characters such as fruit anatomy, leaf morphology and subterranean structures of Angelica species show extreme diversity. Consequently, the taxonomic classification of Angelica species is complex and remains controversial, as the classifications proposed by previous studies based on morphological data and molecular data are highly discordant. In addition, the phylogenetic relationships of major clades in the Angelica group, particularly in the Angelica s. s. clade, remain unclear. Chloroplast (cp) genome sequences have been widely used in phylogenetic studies and for evaluating genetic diversity. RESULTS In this study, we sequenced and assembled 28 complete cp genomes from 22 species, two varieties and two cultivars of Angelica. Combined with 36 available cp genomes in GenBank from representative clades of the subfamily Apioideae, the characteristics and evolutionary patterns of Angelica cp genomes were studied, and the phylogenetic relationships of Angelica species were resolved. The Angelica cp genomes had the typical quadripartite structure including a pair of inverted repeats (IRs: 5836-34,706 bp) separated by a large single-copy region (LSC: 76,657-103,161 bp) and a small single-copy region (SSC: 17,433-21,794 bp). Extensive expansion and contraction of the IR region were observed among cp genomes of Angelica species, and the pattern of the diversification of cp genomes showed high consistency with the phylogenetic placement of Angelica species. Species of Angelica were grouped into two major clades, with most species grouped in the Angelica group and A. omeiensis and A. sinensis grouped in the Sinodielsia with Ligusticum tenuissimum. CONCLUSIONS Our results further demonstrate the power of plastid phylogenomics in enhancing the phylogenetic reconstructions of complex genera and provide new insights into plastome evolution across Angelica L.
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Affiliation(s)
- Mengli Wang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Xin Wang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
- Shenyang Medical College, Shenyang, 110034, China
| | - Jiahui Sun
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Yiheng Wang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Yang Ge
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Wenpan Dong
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China.
| | - Qingjun Yuan
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Luqi Huang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
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Tian X, Guo J, Zhou X, Ma K, Ma Y, Shi T, Shi Y. Comparative and Evolutionary Analyses on the Complete Plastomes of Five Kalanchoe Horticultural Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:705874. [PMID: 34512691 PMCID: PMC8429837 DOI: 10.3389/fpls.2021.705874] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 08/02/2021] [Indexed: 05/11/2023]
Abstract
Many species of the genus Kalanchoe are important horticultural plants. They have evolved the Crassulacean acid metabolism (CAM) photosynthetic pathway to allow them to be better adapted to dry environments. Despite their importance, it is still debating whether Kalanchoe is monophyletic, and understanding the past diversification of this genus requires a tremendous amount of effort and work being devoted to the studies of morphological and molecular characters of this genus. However, molecular information, plastic sequence data, in particular, reported on Kalanchoe species is scarce, and this has posed a great challenge in trying to interpret the evolutionary history of this genus. In this study, plastomes of the five Kalanchoe species, including Kalanchoe daigremontiana, Kalanchoe delagoensis, Kalanchoe fedtschenkoi, Kalanchoe longiflora, and Kalanchoe pinnata, were sequenced and analyzed. The results indicate that the five plastomes are comparable in size, guanine-cytosine (GC) contents and the number of genes, which also demonstrate an insignificant difference in comparison with other species from the family Crassulaceae. About 224 simple sequence repeats (SSRs) and 144 long repeats were identified in the five plastomes, and most of these are distributed in the inverted repeat regions. In addition, highly divergent regions containing either single nucleotide polymorphism (SNP) or insertion or deletion (InDel) mutations are discovered, which could be potentially used for establishing phylogenetic relationships among members of the Kalanchoe genus in future studies. Furthermore, phylogenetic analyses suggest that Bryophyllum should be placed into one single genus as Kalanchoe. Further genomic analyses also reveal that several genes are undergone positive selection. Among them, 11 genes are involved in important cellular processes, such as cell survival, electron transfer, and may have played indispensable roles in the adaptive evolution of Kalanchoe to dry environments.
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Affiliation(s)
- Xiangyu Tian
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Jia Guo
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Xiaojiao Zhou
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Ke Ma
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Yonggui Ma
- Key Laboratory of Medicinal Animal and Plant Resources of Qinghai-Tibetan Plateau, Qinghai Normal University, Xining, China
| | - Tuansheng Shi
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Yuhua Shi
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
- *Correspondence: Yuhua Shi
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32
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Peng F, Zhao Z, Xu B, Han J, Yang Q, Lei Y, Tian B, Liu ZL. Characteristics of Organellar Genomes and Nuclear Internal Transcribed Spacers in the Tertiary Relict Genus Dipelta and Their Phylogenomic Implications. Front Genet 2020; 11:573226. [PMID: 33101393 PMCID: PMC7545908 DOI: 10.3389/fgene.2020.573226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 08/26/2020] [Indexed: 11/13/2022] Open
Affiliation(s)
- Fangfang Peng
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
| | - Zhe Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
| | - Bei Xu
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
| | - Jie Han
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
| | - Qian Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
| | - Yunjing Lei
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
| | - Bin Tian
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, China
| | - Zhan-Lin Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
- *Correspondence: Zhan-Lin Liu,
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Ran H, Liu Y, Wu C, Cao Y. Phylogenetic and Comparative Analyses of Complete Chloroplast Genomes of Chinese Viburnum and Sambucus (Adoxaceae). PLANTS (BASEL, SWITZERLAND) 2020; 9:E1143. [PMID: 32899372 PMCID: PMC7570041 DOI: 10.3390/plants9091143] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/23/2020] [Accepted: 09/01/2020] [Indexed: 12/23/2022]
Abstract
Phylogenetic analyses of complete chloroplast genome sequences have yielded significant improvements in our understanding of relationships in the woody flowering genus Viburnum (Adoxaceae, Dipsacales); however, these relationships were evaluated focusing only on Viburnum species within Central and South America and Southeast Asia. By contrast, despite being a hotspot of Viburnum diversity, phylogenetic relationships of Viburnum species in China are less well known. Here, we characterized the complete chloroplast (cp) genomes of 21 Viburnum species endemic to China, as well as three Sambucus species. These 24 plastomes were highly conserved in genomic structure, gene order and content, also when compared with other Adoxaceae. The identified repeat sequences, simple sequence repeats (SSRs) and highly variable plastid regions will provide potentially valuable genetic resources for further population genetics and phylogeographic studies on Viburnum and Sambucus. Consistent with previous combined phylogenetic analyses of 113 Viburnum species, our phylogenomic analyses based on the complete cp genome sequence dataset confirmed the sister relationship between Viburnum and the Sambucus-Adoxa-Tetradoxa-Sinadoxa group, the monophyly of four recognized sections in Flora of China (i.e., Viburnum sect. Tinus, Viburnum sect. Solenotinus, Viburnum sect. Viburnum and Viburnum sect. Pseudotinus) and the nonmonophyly of Viburnum sect. Odontotinus and Viburnum sect. Megalotinus. Additionally, our study confirmed the sister relationships between the clade Valvatotinus and Viburnum sect. Pseudotinus, as well as between Viburnum sect. Opulus and the Odontotinus-Megalotinus group. Overall, our results clearly document the power of the complete cp genomes in improving phylogenetic resolution, and will contribute to a better understanding of plastome evolution in Chinese Adoxaceae.
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Affiliation(s)
| | | | | | - Yanan Cao
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China; (H.R.); (Y.L.); (C.W.)
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Zhang Y, Zhang QY, Ran H, Cao Y. Characteristic of the complete chloroplast genome of Symphoricarpos sinensis, an important ornamental plant endemic to China. Mitochondrial DNA B Resour 2020; 5:3170-3171. [PMID: 33458099 PMCID: PMC7782690 DOI: 10.1080/23802359.2020.1807423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Symphoricarpos sinensis is an important ornamental plant in China. Due to the lack of efficient molecular markers, although recent studies supported that Symphoricarpos was phylogenetically closely related to Lonicera, Triosteum, Heptacodium, and Leycesteria, relationships among these taxa remained uncertain. To examine the phylogenetic position of Symphoricarpos within Caprifoliaceae, we characterized the complete chloroplast (cp) genome of S. sinensis. The results showed that S. sinensis shared a typical quadripartite structure as with most angiosperms. It was 155,738 bp in length, including two inverted repeat (IR) regions (24,010 bp), a small single-copy (SSC) region (18,942 bp) and a large single-copy (LSC) region (88,776 bp). Phylogenetic analysis demonstrated that Caprifoliaceae and Adoxaceae formed two distinct monophyletic clades, and S. sinensis was closely related to lonicera and Triosteum, albeit with low support. The whole cp genome of S. sinensis will be useful resources for future studies on phylogeny and conservation in Symphoricarpos.
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Affiliation(s)
- Yi Zhang
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Qing Yuan Zhang
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Hang Ran
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Yanan Cao
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
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Li H, Guo Q, Li Q, Yang L. Long-reads reveal that Rhododendron delavayi plastid genome contains extensive repeat sequences, and recombination exists among plastid genomes of photosynthetic Ericaceae. PeerJ 2020; 8:e9048. [PMID: 32351791 PMCID: PMC7183307 DOI: 10.7717/peerj.9048] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 04/02/2020] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Rhododendron delavayi Franch. var. delavayi is a wild ornamental plant species in Guizhou Province, China. The lack of its plastid genome information seriously hinders the further application and conservation of the valuable resource. METHODS The complete plastid genome of R. delavayi was assembled from long sequence reads. The genome was then characterized, and compared with those of other photosynthetic Ericaceae species. RESULTS The plastid genome of R. delavayi has a typical quadripartite structure, and a length of 202,169 bp. It contains a large number of repeat sequences and shows preference for codon usage. The comparative analysis revealed the irregular recombination of gene sets, including rearrangement and inversion, in the large single copy region. The extreme expansion of the inverted repeat region shortened the small single copy, and expanded the full length of the genome. In addition, consistent with traditional taxonomy, R. delavayi with nine other species of the same family were clustered into Ericaceae based on the homologous protein-coding sequences of the plastid genomes. Thus, the long-read assembly of the plastid genome of R. delavayi would provide basic information for the further study of the evolution, genetic diversity, and conservation of R. delavayi and its relatives.
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Affiliation(s)
- Huie Li
- College of Agriculture, Guizhou University, Guiyang, Guizhou, China
| | - Qiqiang Guo
- Institute for Forest Resources & Environment of Guizhou, Guizhou University, Guiyang, Guizhou, China
| | - Qian Li
- College of Agriculture, Guizhou University, Guiyang, Guizhou, China
| | - Lan Yang
- College of Agriculture, Guizhou University, Guiyang, Guizhou, China
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Ran H, Zhang Q, Zhang Y, Miao L, Cao Y. Characteristic of the complete chloroplast genome of L. Korolkowii Stapf, important horticultural plant in China. Mitochondrial DNA B Resour 2020. [DOI: 10.1080/23802359.2020.1749535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
- Hang Ran
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Qingyuan Zhang
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Yi Zhang
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Linlin Miao
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Yanan Cao
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
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