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Wang H, Li XY, Jiang Y, Jin ZT, Ma DK, Liu B, Xu C, Ge BJ, Wang T, Fan Q, Jin SH, Liu GN, Liu BB. Refining the phylogeny and taxonomy of the apple tribe Maleae (Rosaceae): insights from phylogenomic analyses of 563 plastomes and a taxonomic synopsis of Photinia and its allies in the Old World. PHYTOKEYS 2024; 242:161-227. [PMID: 38854497 PMCID: PMC11161682 DOI: 10.3897/phytokeys.242.117481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 04/21/2024] [Indexed: 06/11/2024]
Abstract
This study addresses the longstanding absence of a comprehensive phylogenetic backbone for the apple tribe Maleae, a deficiency attributed to limited taxon and marker sampling. We conducted an extensive taxon sampling, incorporating 563 plastomes from a diverse range of 370 species encompassing 26 presently recognized genera. Employing a range of phylogenetic inference methods, including RAxML and IQ-TREE2 for Maximum Likelihood (ML) analyses, we established a robust phylogenetic framework for the Maleae tribe. Our phylogenomic investigations provided compelling support for three major clades within Maleae. By integrating nuclear phylogenetic data with morphological and chromosomal evidence, we propose an updated infra-tribal taxonomic system, comprising subtribe Malinae Reveal, subtribe Lindleyinae Reveal, and subtribe Vauqueliniinae B.B.Liu (subtr. nov.). Plastid phylogenetic analysis also confirmed the monophyly of most genera, except for Amelanchier, Malus, Sorbus sensu lato, and Stranvaesia. In addition, we present a comprehensive taxonomic synopsis of Photinia and its morphological allies in the Old World, recognizing 27 species and ten varieties within Photinia, three species and two varieties within Stranvaesia, and two species and three varieties within Weniomeles. Furthermore, we also lectotypified 12 names and made two new combinations, Photiniamicrophylla (J.E.Vidal) B.B.Liu and Weniomelesatropurpurea (P.L.Chiu ex Z.H.Chen & X.F.Jin) B.B.Liu.
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Affiliation(s)
- Hui Wang
- College of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou, Zhejiang 311300, ChinaZhejiang Agriculture and Forestry UniversityHangzhouChina
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, ChinaInstitute of Botany, Chinese Academy of SciencesBeijingChina
- China National Botanical Garden, Beijing 100093, ChinaChina National Botanical GardenBeijingChina
| | - Xiao-Ya Li
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, ChinaInstitute of Botany, Chinese Academy of SciencesBeijingChina
- China National Botanical Garden, Beijing 100093, ChinaChina National Botanical GardenBeijingChina
- University of Chinese Academy of Sciences, Beijing 100049, ChinaUniversity of Chinese Academy of SciencesBeijingChina
| | - Yan Jiang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, ChinaInstitute of Botany, Chinese Academy of SciencesBeijingChina
- China National Botanical Garden, Beijing 100093, ChinaChina National Botanical GardenBeijingChina
- University of Chinese Academy of Sciences, Beijing 100049, ChinaUniversity of Chinese Academy of SciencesBeijingChina
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, ChinaSouth China Botanical Garden, Chinese Academy of SciencesGuangzhouChina
| | - Ze-Tao Jin
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, ChinaInstitute of Botany, Chinese Academy of SciencesBeijingChina
- China National Botanical Garden, Beijing 100093, ChinaChina National Botanical GardenBeijingChina
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, Jiangsu 210095, ChinaNanjing Agricultural UniversityNanjingChina
| | - Dai-Kun Ma
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, ChinaInstitute of Botany, Chinese Academy of SciencesBeijingChina
- China National Botanical Garden, Beijing 100093, ChinaChina National Botanical GardenBeijingChina
- University of Chinese Academy of Sciences, Beijing 100049, ChinaUniversity of Chinese Academy of SciencesBeijingChina
| | - Bing Liu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, ChinaInstitute of Botany, Chinese Academy of SciencesBeijingChina
- China National Botanical Garden, Beijing 100093, ChinaChina National Botanical GardenBeijingChina
| | - Chao Xu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, ChinaInstitute of Botany, Chinese Academy of SciencesBeijingChina
- China National Botanical Garden, Beijing 100093, ChinaChina National Botanical GardenBeijingChina
| | - Bin-Jie Ge
- Eastern China Conservation Center for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, No.3888 Chenhua Road, Songjiang District, Shanghai 201602, ChinaShanghai Chenshan Botanical GardenShanghaiChina
| | - Ting Wang
- Hangzhou Botanical Garden (Hangzhou West Lake Academy of Landscape Science), Hangzhou, Zhejiang 310000, ChinaHangzhou Botanical GardenHangzhouChina
| | - Qiang Fan
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, ChinaSun Yat-sen UniversityGuangzhouChina
| | - Shui-Hu Jin
- College of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou, Zhejiang 311300, ChinaZhejiang Agriculture and Forestry UniversityHangzhouChina
| | - Guang-Ning Liu
- Key Laboratory of National Forestry and Grassland Administration on Plant Ex situ Conservation, Xiangshan-Wofosi Road, Beijing 100093, ChinaKey Laboratory of National Forestry and Grassland Administration on Plant Ex situ ConservationBeijingChina
- Beijing Botanical Garden, Beijing 100093, ChinaBeijing Botanical GardenBeijingChina
| | - Bin-Bin Liu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, ChinaInstitute of Botany, Chinese Academy of SciencesBeijingChina
- China National Botanical Garden, Beijing 100093, ChinaChina National Botanical GardenBeijingChina
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Busnena BA, Beerhues L, Liu B. Biphenyls and dibenzofurans of the rosaceous subtribe Malinae and their role as phytoalexins. PLANTA 2023; 258:78. [PMID: 37689618 PMCID: PMC10492887 DOI: 10.1007/s00425-023-04228-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 08/23/2023] [Indexed: 09/11/2023]
Abstract
MAIN CONCLUSION Biphenyl and dibenzofuran phytoalexins are differentially distributed among species of the rosaceous subtribe Malinae, which includes apple and pear, and exhibit varying inhibitory activity against phytopathogenic microorganisms. Biphenyls and dibenzofurans are specialized metabolites, which are formed in species of the rosaceous subtribe Malinae upon elicitation by biotic and abiotic inducers. The subtribe Malinae (previously Pyrinae) comprises approximately 1000 species, which include economically important fruit trees such as apple and pear. The present review summarizes the current status of knowledge of biphenyls and dibenzofurans in the Malinae, mainly focusing on their role as phytoalexins. To date, 46 biphenyls and 41 dibenzofurans have been detected in 44 Malinae species. Structurally, 54 simple molecules, 23 glycosidic compounds and 10 miscellaneous structures were identified. Functionally, 21 biphenyls and 21 dibenzofurans were demonstrated to be phytoalexins. Furthermore, their distribution in species of the Malinae, inhibitory activities against phytopathogens, and structure-activity relationships were studied. The most widely distributed phytoalexins of the Malinae are the three biphenyls aucuparin (3), 2'-methoxyaucuparin (7), and 4'-methoxyaucuparin (9) and the three dibenzofurans α-cotonefuran (47), γ-cotonefuran (49), and eriobofuran (53). The formation of biphenyl and dibenzofuran phytoalexins appears to be an essential defense weapon of the Malinae against various stresses. Manipulating phytoalexin formation may enhance the disease resistance in economically important fruit trees. However, this approach requires an extensive understanding of how the compounds are formed. Although the biosynthesis of biphenyls was partially elucidated, formation of dibenzofurans remains largely unclear. Thus, further efforts have to be made to gain deeper insight into the distribution, function, and metabolism of biphenyls and dibenzofurans in the Malinae.
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Affiliation(s)
- Belnaser A Busnena
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Mendelssohnstraße 1, 38106, Braunschweig, Germany
| | - Ludger Beerhues
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Mendelssohnstraße 1, 38106, Braunschweig, Germany
| | - Benye Liu
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Mendelssohnstraße 1, 38106, Braunschweig, Germany.
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Tang C, Chen X, Deng Y, Geng L, Ma J, Wei X. Complete chloroplast genomes of Sorbus sensu stricto (Rosaceae): comparative analyses and phylogenetic relationships. BMC PLANT BIOLOGY 2022; 22:495. [PMID: 36273120 PMCID: PMC9587547 DOI: 10.1186/s12870-022-03858-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Sorbus sensu stricto (Sorbus s.s.) is a genus with important economical values because of its beautiful leaves, and flowers and especially the colorful fruits. It belongs to the tribe Maleae of the family Rosaceae, and comprises about 90 species mainly distributed in China. There is on-going dispute about its infrageneric classification and species delimitation as the species are morphologically similar. With the aim of shedding light on the circumscription of taxa within the genus, phylogenetic analyses were performed using 29 Sorbus s.s. chloroplast (cp) genomes (16 newly sequenced) representing two subgenera and eight sections. RESULTS The 16 cp genomes newly sequenced range between 159,646 bp and 160,178 bp in length. All the samples examined and 22 taxa re-annotated in Sorbus sensu lato (Sorbus s.l.) contain 113 unique genes with 19 of these duplicated in the inverted repeat (IR). Six hypervariable regions including trnR-atpA, petN-psbM, rpl32-trnL, trnH-psbA, trnT-trnL and ndhC-trnV were screened and 44-53 SSRs and 14-31 dispersed repeats were identified as potential molecular markers. Phylogenetic analyses under ML/BI indicated that Sorbus s.l. is polyphyletic, but Sorbus s.s. and the other five segregate genera, Aria, Chamaemespilus, Cormus, Micromeles and Torminalis are monophyletic. Two major clades and four sub-clades resolved with full-support within Sorbus s.s. are not consistent with the existing infrageneric classification. Two subgenera, subg. Sorbus and subg. Albocarmesinae are supported as monophyletic when S. tianschanica is transferred to subg. Albocarmesinae from subg. Sorbus and S. hupehensis var. paucijuga transferred to subg. Sorbus from subg. Albocarmesinae, respectively. The current classification at sectional level is not supported by analysis of cp genome phylogeny. CONCLUSION Phylogenomic analyses of the cp genomes are useful for inferring phylogenetic relationships in Sorbus s.s. Though genome structure is highly conserved in the genus, hypervariable regions and repeat sequences used are the most promising molecule makers for population genetics, species delimitation and phylogenetic studies.
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Affiliation(s)
- Chenqian Tang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Xin Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China.
| | - Yunfei Deng
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Liyang Geng
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Jianhui Ma
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Xueyan Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
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Chen X, Ma J, Geng L. Taxonomic notes on Sorbusmegalocarpa (Rosaceae) and related taxa. PHYTOKEYS 2022; 201:131-138. [PMID: 36762314 PMCID: PMC9848915 DOI: 10.3897/phytokeys.201.84027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 06/02/2022] [Indexed: 06/18/2023]
Abstract
Four Sorbus taxa endemic to China, S.arguta, S.guanxianensis, S.megalocarpavar.megalocarpa and S.megalocarpavar.cuneata, are morphologically similar to one another in having large brown fruits with persistent calyx and dense lenticels. In literature, either all of the four taxa were accepted, or two of them, S.arguta and S.megalocarpavar.cuneata, were treated as synonyms of S.megalocarpavar.megalocarpa, or S.guanxianensis alone was dubious. In this study, based on morphological comparison, S.arguta is reinstated for its relatively small inflorescence, small fruit and timing of flowering after leaves are unfolded. S.megalocarpavar.cuneata is confirmed as a synonym and S.guanxianensis is proposed as a new heterotypic synonym of S.megalocarpa.
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Affiliation(s)
- Xin Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, ChinaNanjing Forestry UniversityNanjingChina
| | - JianHui Ma
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, ChinaNanjing Forestry UniversityNanjingChina
| | - LiYang Geng
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, ChinaNanjing Forestry UniversityNanjingChina
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