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Li H, Liu Y, Fan P, Dai Z, Hao J, Duan W, Liang Z, Wang Y. The Genome of Vitis zhejiang-adstricta Strengthens the Protection and Utilization of the Endangered Ancient Grape Endemic to China. PLANT & CELL PHYSIOLOGY 2024; 65:216-227. [PMID: 37930871 PMCID: PMC10873524 DOI: 10.1093/pcp/pcad140] [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: 06/02/2023] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 11/08/2023]
Abstract
Vitis zhejiang-adstricta (V. zhejiang-adstricta) is one of the most important and endangered wild grapes. It is a national key protected wild, rare and endangered ancient grape endemic to China and used as a candidate material for resistance breeding owing to its excellent significant disease resistance. Here, we present a high-quality chromosome-level assembly of V. zhejiang-adstricta (IB-VB-01), comprising 506.66 Mb assembled into 19 pseudo-chromosomes. The contig N50 length is 3.91 Mb with 31,196 annotated protein-coding genes. Comparative genome and evolutionary analyses illustrated that V. zhejiang-adstricta has a specific position in the evolution of East Asian Vitis and shared a common ancestor with Vitis vinifera during the divergence of the two species about 10.42 (between 9.34 and 11.12) Mya. The expanded gene families compared with those in plants were related to disease resistance, and constructed gene families were related to plant growth and primary metabolism. With the analysis of gene family expansion and contraction, the evolution of environmental adaptability and especially the NBS-LRR gene family of V. zhejiang-adstricta was elucidated based on the pathways of resistance genes (R genes), unique genes and structural variations. The near-complete and accurate diploid V. zhejiang-adstricta reference genome obtained herein serves as an important complement to wild grape genomes and will provide valuable genomic resources for investigating the genomic architecture of V. zhejiang-adstricta as well as for improving disease resistance breeding strategies in grape.
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Affiliation(s)
- Huayang Li
- Beijing Key Laboratory of Grape Science and Enology, CAS Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, China
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
- China National Botanical Garden, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
- University of Chinese Academy of Sciences, 19 Yuquan Rd, Beijing 100049, PR China
| | - Yongbo Liu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, 8 Dayangfang, Beijing 100012, PR China
| | - Peige Fan
- Beijing Key Laboratory of Grape Science and Enology, CAS Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, China
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
- China National Botanical Garden, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
| | - Zhanwu Dai
- Beijing Key Laboratory of Grape Science and Enology, CAS Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, China
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
- China National Botanical Garden, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
| | - Jiachen Hao
- China National Botanical Garden, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
| | - Wei Duan
- Beijing Key Laboratory of Grape Science and Enology, CAS Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, China
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
- China National Botanical Garden, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
| | - Zhenchang Liang
- Beijing Key Laboratory of Grape Science and Enology, CAS Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, China
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
- China National Botanical Garden, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
| | - Yi Wang
- Beijing Key Laboratory of Grape Science and Enology, CAS Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, China
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
- China National Botanical Garden, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
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Qin YQ, Zhang MH, Yang CY, Nie ZL, Wen J, Meng Y. Phylogenomics and divergence pattern of Polygonatum (Asparagaceae: Polygonateae) in the north temperate region. Mol Phylogenet Evol 2024; 190:107962. [PMID: 37926394 DOI: 10.1016/j.ympev.2023.107962] [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: 07/18/2023] [Revised: 10/23/2023] [Accepted: 11/01/2023] [Indexed: 11/07/2023]
Abstract
Polygonatum is the largest genus of tribe Polygonateae (Asparagaceae) and is widely distributed in the temperate Northern Hemisphere, especially well diversified in southwestern China to northeastern Asia. Phylogenetic relationships of many species are still controversial. Hence it is necessary to clarify their phylogenetic relationships and infer possible reticulate relationships for the genus. In this study, genome-wide data of 43 species from Polygonatum and its closely related taxa were obtained by Hyb-Seq sequencing. The phylogenetic trees constructed from genome-wide nuclear and chloroplast sequences strongly supported the monophyly of Polygonatum with division into three major clades. A high level of incongruence was detected between nuclear and chloroplast trees as well as among gene trees within the genus, but all occurred within each major clade. However, introgression tests and reticulate evolution analyses revealed low level of gene flow and weak introgression events in the genus, suggesting hybridization and introgression were not dominant during the evolutionary diversification of Polygonatum in the Northern Hemisphere. This study provides important insights into reconstructing evolutionary relationships and speciation pattern of taxa from the north temperate flora.
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Affiliation(s)
- Yu-Qian Qin
- College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan 416000, China
| | - Meng-Hua Zhang
- College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan 416000, China
| | - Chu-Yun Yang
- College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan 416000, China
| | - Ze-Long Nie
- 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
| | - Ying Meng
- College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan 416000, China.
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Duan L, Fu L, Chen HF. Phylogenomic cytonuclear discordance and evolutionary histories of plants and animals. SCIENCE CHINA. LIFE SCIENCES 2023; 66:2946-2948. [PMID: 37930475 DOI: 10.1007/s11427-023-2456-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 09/19/2023] [Indexed: 11/07/2023]
Affiliation(s)
- Lei Duan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
- South China National Botanical Garden, Guangzhou, 510650, China.
| | - Lin Fu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
| | - Hong-Feng Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
- South China National Botanical Garden, Guangzhou, 510650, China.
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Wei M, Liu J, Wang S, Wang X, Liu H, Ma Q, Wang J, Shi W. Genetic Diversity and Phylogenetic Analysis of Zygophyllum loczyi in Northwest China's Deserts Based on the Resequencing of the Genome. Genes (Basel) 2023; 14:2152. [PMID: 38136974 PMCID: PMC10742952 DOI: 10.3390/genes14122152] [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: 10/01/2023] [Revised: 11/19/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
In order to study the genetics of local adaptation in all main deserts of northwest China, whole genomes of 169 individuals were resequenced, which covers 20 populations of Zygophyllum loczyi (Zygophyllales: Zygophylaceae). We describe more than 15 million single nucleotide polymorphisms and numerous InDels. The expected heterozygosity and PIC values associated with local adaptation varied significantly across biogeographic regions. Variation in environmental factors contributes largely to the population genetic structure of Z. loczyi. Bayesian analysis performed with STRUCTURE defined four genetic clusters, while the results of principle component analysis were similar. Our results shows that the Qaidam Desert group appears to be diverging into two branches characterized by significant geographic separation and gene flow with two neighboring deserts. Geological data assume that it is possible that the Taklamakan Desert was the original distribution site, and Z. loczyi could have migrated later on and expanded within other desert areas. The above findings provide insights into the processes involved in biogeography, phylogeny, and differentiation within the northwest deserts of China.
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Affiliation(s)
- Mengmeng Wei
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable, Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Urumqi 830011, China; (M.W.); (J.L.); (X.W.); (J.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingdian Liu
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable, Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Urumqi 830011, China; (M.W.); (J.L.); (X.W.); (J.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- College of Forestry and Landscape Architecture, Xinjiang Agricultural University, Urumqi 830052, China
| | - Suoming Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China; (S.W.); (H.L.); (Q.M.)
| | - Xiyong Wang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable, Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Urumqi 830011, China; (M.W.); (J.L.); (X.W.); (J.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Turpan Eremophytes Botanic Garden, The Chinese Academy of Sciences, Turpan 838008, China
| | - Haisuang Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China; (S.W.); (H.L.); (Q.M.)
| | - Qing Ma
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China; (S.W.); (H.L.); (Q.M.)
| | - Jiancheng Wang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable, Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Urumqi 830011, China; (M.W.); (J.L.); (X.W.); (J.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Turpan Eremophytes Botanic Garden, The Chinese Academy of Sciences, Turpan 838008, China
| | - Wei Shi
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable, Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Urumqi 830011, China; (M.W.); (J.L.); (X.W.); (J.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Turpan Eremophytes Botanic Garden, The Chinese Academy of Sciences, Turpan 838008, China
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Talavera A, Nie ZL, Ma ZY, Johnson G, Ickert-Bond SM, Zimmer EA, Wen J. Phylogenomic analyses using a new 1013-gene Vitaceae bait-set support major groups of North American Vitis. Mol Phylogenet Evol 2023:107866. [PMID: 37354923 DOI: 10.1016/j.ympev.2023.107866] [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: 02/10/2023] [Revised: 06/16/2023] [Accepted: 06/17/2023] [Indexed: 06/26/2023]
Abstract
A set of newly designed Vitaceae baits targeting 1013 genes was employed to explore phylogenetic relationships among North American Vitis. Eurasian Vitis taxa including Vitis vinifera were found to be nested within North American Vitis subgenus Vitis. North American Vitis subgenus Vitis can be placed into nine main groups: the Monticola group, the Occidentales group, the Californica group, the Vinifera group (introduced from Eurasia), the Mustangensis group, the Palmata group, the Aestivalis group, the Labrusca group, and the Cinerea group. Strong cytonuclear discordances were detected in North American Vitis, with many species non-monophyletic in the plastid phylogeny, while monophyletic in the nuclear phylogeny. The phylogenomic analyses support recognizing four distinct species in the Vitis cinerea complex in North America: V. cinerea, V. baileyana, V. berlandieri, and V. simpsonii. Such treatment will better serve the conservation of wild Vitis diversity in North America. Yet the evolutionary history of Vitis is highly complex, with the concordance analyses indicating conflicting signals across the phylogeny. Cytonuclear discordances and Analyses using the Species Networks applying Quartets (SNaQ) method support extensive hybridizations in North American Vitis. The results further indicate that plastid genomes alone are insufficient for resolving the evolutionary history of plant groups that have undergone rampant hybridization, like the case in North American Vitis. Nuclear gene data are essential for species delimitation, identification and reconstructing evolutionary relationships; therefore, they are imperative for plant phylogenomic studies.
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Affiliation(s)
- Alicia Talavera
- Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, DC 20013-7012, USA; Departamento de Botánica y Fisiología Vegetal, Universidad de Málaga, 29071, Málaga, Spain.
| | - Ze-Long Nie
- Key Laboratory of Plant Resources Conservation and Utilization, College of Biology and Environmental Sciences, Jishou University, Jishou 416000, China
| | - Zhi-Yao Ma
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, 518000 China
| | - Gabriel Johnson
- Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, DC 20013-7012, USA
| | - Stefanie M Ickert-Bond
- UA Museum of the North Herbarium and Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, AK 99775-6960, USA
| | - Elizabeth A Zimmer
- Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, DC 20013-7012, USA
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, DC 20013-7012, USA.
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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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