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Yao J, Qiao Z, Jiang Z, Zhao X, You Z, Zhang W, Feng J, Gong C, Li J. Infection with Jujube Witches' Broom Phytoplasma Alters the Expression Pattern of the Argonaute Gene Family in Ziziphus jujuba. Microorganisms 2025; 13:658. [PMID: 40142550 PMCID: PMC11944418 DOI: 10.3390/microorganisms13030658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2025] [Revised: 03/01/2025] [Accepted: 03/11/2025] [Indexed: 03/28/2025] Open
Abstract
The cultivation of jujube (Ziziphus jujuba) in China is threatened by jujube witches' broom (JWB) disease, a devastating infectious disease associated with JWB phytoplasma ('Candidatus Phytoplasma ziziphi'). In many plants, proteins in the Argonaute (AGO) family, as main components of the RNA-induced silencing complex (RISC), play important roles in RNA silencing and pathogen resistance. The jujube telomere-to-telomere genome was searched by BLAST using Arabidopsis AGOs as probes. A total of nine jujube AGO gene members were identified, with each containing the conserved N-terminal, PZA, and PIWI domains. Phylogenetic analysis revealed that the nine jujube AGOs scattered into all three Arabidopsis AGO clades. Expression patterns of the ZjAGO genes were analyzed in response to phytoplasma in transcriptome data and by qRT-PCR. The jujube-phytoplasma interaction altered the expression of jujube AGO genes. ZjAGO1 and ZjAGO8 were up-regulated in the majority of the eight sampling periods subjected to qRT-PCR analysis. In the transcriptome data, ZjAGO1 and ZjAGO8 were also up-regulated during the key stages 37 and 39 weeks after grafting (WAG) with phytoplasma-infected material. These two jujube Argonaute genes may play important roles in response to JWB phytoplasma infection.
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Affiliation(s)
- Jia Yao
- College of Forestry, Henan Agricultural University, Zhengzhou 450046, China; (J.Y.); (Z.Q.); (Z.J.); (X.Z.); (Z.Y.); (W.Z.)
| | - Zesen Qiao
- College of Forestry, Henan Agricultural University, Zhengzhou 450046, China; (J.Y.); (Z.Q.); (Z.J.); (X.Z.); (Z.Y.); (W.Z.)
| | - Ziming Jiang
- College of Forestry, Henan Agricultural University, Zhengzhou 450046, China; (J.Y.); (Z.Q.); (Z.J.); (X.Z.); (Z.Y.); (W.Z.)
| | - Xueru Zhao
- College of Forestry, Henan Agricultural University, Zhengzhou 450046, China; (J.Y.); (Z.Q.); (Z.J.); (X.Z.); (Z.Y.); (W.Z.)
| | - Ziyang You
- College of Forestry, Henan Agricultural University, Zhengzhou 450046, China; (J.Y.); (Z.Q.); (Z.J.); (X.Z.); (Z.Y.); (W.Z.)
| | - Wenzhe Zhang
- College of Forestry, Henan Agricultural University, Zhengzhou 450046, China; (J.Y.); (Z.Q.); (Z.J.); (X.Z.); (Z.Y.); (W.Z.)
| | - Jiancan Feng
- College of Horticulture, Henan Agricultural University, Zhengzhou 450046, China;
| | - Chenrui Gong
- College of Forestry, Henan Agricultural University, Zhengzhou 450046, China; (J.Y.); (Z.Q.); (Z.J.); (X.Z.); (Z.Y.); (W.Z.)
| | - Jidong Li
- College of Forestry, Henan Agricultural University, Zhengzhou 450046, China; (J.Y.); (Z.Q.); (Z.J.); (X.Z.); (Z.Y.); (W.Z.)
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Guo M, Lian Q, Mei Y, Yang W, Zhao S, Zhang S, Xing X, Zhang H, Gao K, He W, Wang Z, Wang H, Zhou J, Cheng L, Bao Z, Huang S, Yan J, Zhao X. Analyzes of pan-genome and resequencing atlas unveil the genetic basis of jujube domestication. Nat Commun 2024; 15:9320. [PMID: 39472552 PMCID: PMC11522667 DOI: 10.1038/s41467-024-53718-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 10/21/2024] [Indexed: 11/02/2024] Open
Abstract
Jujube (Ziziphus jujuba Mill.), belonging to the Rhamnaceae family, is gaining increasing prominence as a perennial fruit crop with significant economic and medicinal values. Here, we conduct de novo assembly of four reference-grade genomes, encompassing one wild and three cultivated jujube accessions. We present insights into the population structure, genetic diversity, and genomic variations within a diverse collection of 1059 jujube accessions. Analyzes of the jujube pan-genome, based on our four assemblies and four previously released genomes, reveal extensive genomic variations within domestication-associated regions, potentially leading to the discovery of a candidate gene that regulates flowering and fruit ripening. By leveraging the pan-genome and a large-scale resequencing population, we identify two candidate genes involved in domestication traits, including the seed-setting rate, the bearing-shoot length and the leaf size in jujube. These genomic resources will accelerate evolutionary and functional genomics studies of jujube.
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Affiliation(s)
- Mingxin Guo
- College of Life Sciences, Luoyang Normal University, Luoyang, China.
| | - Qun Lian
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- School of Biology & Environmental Science, University College Dublin, Belfield, Dublin, Ireland
| | - Ye Mei
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Wangwang Yang
- College of Life Sciences, Luoyang Normal University, Luoyang, China
| | - Suna Zhao
- College of Life Sciences, Luoyang Normal University, Luoyang, China
| | - Siyuan Zhang
- College of Life Sciences, Luoyang Normal University, Luoyang, China
| | - Xinfeng Xing
- College of Life Sciences, Luoyang Normal University, Luoyang, China
| | - Haixiang Zhang
- College of Life Sciences, Luoyang Normal University, Luoyang, China
| | - Keying Gao
- College of Life Sciences, Luoyang Normal University, Luoyang, China
| | - Wentong He
- National Foundation for Improved Cultivar of Chinese Jujube, Bureau of Natural Resources and Planning of Cangxian County, Cangzhou, China
| | - Zhitong Wang
- National Foundation for Improved Cultivar of Chinese Jujube, Bureau of Natural Resources and Planning of Cangxian County, Cangzhou, China
| | - Huan Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jun Zhou
- School of Biological Science and Engineering, North Minzu University, Yinchuan, China
| | - Lin Cheng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Plant Genetics and Rhizosphere Processes Laboratory, TERRA Teaching and Research Center, University of Liège, Gembloux Agro-Bio Tech, Gembloux, Belgium
| | - Zhigui Bao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Sanwen Huang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jianbin Yan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
| | - Xusheng Zhao
- College of Life Sciences, Luoyang Normal University, Luoyang, China.
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Li J, Wang B, Zhang L, Ma Y, Song L, Cao B. Genome-wide study of drought tolerance traits in wild jujube. BMC PLANT BIOLOGY 2024; 24:1000. [PMID: 39448934 PMCID: PMC11520188 DOI: 10.1186/s12870-024-05680-7] [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: 07/14/2024] [Accepted: 10/08/2024] [Indexed: 10/26/2024]
Abstract
BACKGROUND Wild jujube trees in Ningxia, China, demonstrate exceptional drought tolerance. The identification of quantitative trait loci (QTLs) associated with drought resistance and linked genes could significantly enhance molecular breeding efforts for this species. This study involved the measurement of nine drought resistance indicators were measured in 150 wild jujube trees from five regions in Ningxia. Genome-wide association studies (GWAS) were carried out using a range of mixed linear models to pinpoint SNP markers linked to drought resistance. RESULTS The coefficients of variation for the nine leaf traits in wild jujube trees ranged from 14.76 to 62.17%, with broad-sense heritability estimates falling between 0.84 and 0.99. Through GWAS analysis, a total of 12 significant SNPs and 162 potential genes associated with drought resistance were detected. This SNPs explained phenotypic variance ranging from 20.74 to 50.37%. Gene Ontology (GO) functional annotation highlighted five crucial candidate genes‒ZjMYB44, ZjUCLOC, ZjDnaJ50, ZjUCHL22 and ZjHSFB‒linked to drought tolerance in wild jujube. These genes demonstrated a positive correlation with drought tolerance within the wild jujube population. CONCLUSIONS Our findings indicate that these five genes likely play a pivotal role in conferring drought tolerance in wild jujubes. This study offers new insights to support the development of drought-resistant jujube varieties, thereby contributing to sustainable agricultural practices and bolstering food security in arid regions.
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Affiliation(s)
- Jingzu Li
- College of Enology and Horticulture, Ningxia University, Yinchuan, 750021, China
| | - Botao Wang
- College of Enology and Horticulture, Ningxia University, Yinchuan, 750021, China
| | - Lei Zhang
- College of Enology and Horticulture, Ningxia University, Yinchuan, 750021, China
| | - Yaping Ma
- College of Forestry and Prataculture, Ningxia University, Yinchuan, 750021, China
| | - Lihua Song
- College of Forestry and Prataculture, Ningxia University, Yinchuan, 750021, China.
| | - Bing Cao
- College of Forestry and Prataculture, Ningxia University, Yinchuan, 750021, China
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Wei T, Li H, Huang X, Yang P. Chromosome-level genome assembly of two cultivated Jujubes. Sci Data 2024; 11:1144. [PMID: 39420037 PMCID: PMC11486999 DOI: 10.1038/s41597-024-03992-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 10/11/2024] [Indexed: 10/19/2024] Open
Abstract
Jujube (Ziziphus jujuba Mill.) is a valuable tree species with economic, edible, medicinal, and ecological conservation benefits. In this study, we used PacBio HiFi sequencing and Hi-C technology to assemble chromosome-level genomes of two cultivated Jujubes, namely 'Lingwuchangzao' and 'Shiguang'. The genome sizes of 'Lingwuchangzao' and 'Shiguang' were 385.66 Mb and 394.12 Mb, respectively, with contig N50 sizes of 30.62 Mb and 4.30 Mb. These genomes contained 31,082 and 31,015 protein-coding genes, with repeat element contents of 42.11% and 42.33%, respectively. Phylogenetic analysis revealed that 'Lingwuchangzao' was sister to 'Shiguang' and followed by 'Dongzao'. Additionally, comparative analysis of gene families among 'Lingwuchangzao', 'Shiguang', 'Dongzao', 'Junzao', and 'Suanzao' identified 15,988 (57.98%) core gene families, 11,191 (40.59%) disposable gene families, and 394 (1.43%) private gene families. Overall, the assembly of the genomes of these two cultivated Jujube varieties provides valuable genetic information for Jujube evolution, functional genomics research, and molecular breeding.
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Affiliation(s)
- Tianjun Wei
- Institute of Horticulture, NingXia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China.
| | - Hui Li
- Institute of Horticulture, NingXia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China
| | - Xueshuang Huang
- Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese Medicine, School of Pharmaceutical Sciences, Hunan University of Medicine, Huaihua, 418000, China
| | - Peng Yang
- Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese Medicine, School of Pharmaceutical Sciences, Hunan University of Medicine, Huaihua, 418000, China.
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Miao K, Wang Y, Hou L, Liu Y, Liu H, Ji Y. Haplotype-resolved genome assembly of the upas tree (Antiaris toxicaria). Sci Data 2024; 11:1011. [PMID: 39294147 PMCID: PMC11410980 DOI: 10.1038/s41597-024-03860-6] [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: 03/15/2024] [Accepted: 09/04/2024] [Indexed: 09/20/2024] Open
Abstract
The upas tree (Antiaris toxicaria Lesch.) is a medically important plant that contains various specialized metabolites with significant bioactivity. The lack of a reference genome hinders the in-depth study as well as rational exploitation and conservation of this plant. Here, we present the first holotype-resolved chromosome-scale genome of the upas tree. The assembled genome consisted of 26 chromosomes that contain 1.34 Gb of sequencing data with a contig N50 length of 60 Mb. Genome annotation identified 43,500 protein-coding genes in the upas tree genome, of which 98.75% were functionally annotated. This high-quality reference genome will lay the foundation for further studies on the evolution and functional genomics of the upas tree.
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Affiliation(s)
- Ke Miao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, China
| | - Ya Wang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Luxiao Hou
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, China
| | - Yan Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, China
| | - Haiyang Liu
- State Key Laboratory of Phytochemistry and Natural Medicine, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
| | - Yunheng Ji
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
- State Key Laboratory of Phytochemistry and Natural Medicine, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Population, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
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Jo J, Park JS, Won H, Jeong JS, Jung TW, Lee KJ, Lee SA. The first Chromosomal-level genome assembly of Sageretia thea using Nanopore long reads and Pore-C technology. Sci Data 2024; 11:959. [PMID: 39242678 PMCID: PMC11379895 DOI: 10.1038/s41597-024-03798-9] [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: 06/13/2024] [Accepted: 08/19/2024] [Indexed: 09/09/2024] Open
Abstract
Sageretia thea, a notable species within the mock buckthorn genus, is recognized for its intriguing biogeographical distribution and diverse medicinal properties. Despite this significance, genomic studies on S. thea are still in the nascent stages. We present the first chromosome-level genome assembly of S. thea that was generated using a combination of Oxford Nanopore long-read and Illumina short-read sequencing technologies complemented by Pore-C chromatin conformation capture. The genome assembly had a size of 197.8 Mb with 12 chromosomal scaffolds and a scaffold N50 length of 15.9 Mb. A total of 25,434 protein-coding genes were identified and functionally annotated, and the gene model indicated 96.5% complete eukaryotic BUSCOs. Additionally, orthologous gene profiling and synteny analysis were performed to elucidate the evolutionary relationships within the Rhamnaceae family and Rosales. This high-quality chromosomal genome is the first genomic view of S. thea, which will serve as the basis for future studies on its biological and medicinal properties, and evolutionary history.
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Affiliation(s)
- Jihoon Jo
- Division of Genetic Resources, Honam National Institute of Biological Resources (HNIBR), Mokpo, Republic of Korea
| | - Jong-Soo Park
- Division of Botany, Honam National Institute of Biological Resources (HNIBR), Mokpo, Republic of Korea
| | - Hari Won
- Division of Genetic Resources, Honam National Institute of Biological Resources (HNIBR), Mokpo, Republic of Korea
| | - Jun Seong Jeong
- Division of Genetic Resources, Honam National Institute of Biological Resources (HNIBR), Mokpo, Republic of Korea
| | - Tae Won Jung
- Division of Exhibition, Honam National Institute of Biological Resources (HNIBR), Mokpo, Republic of Korea
| | - Kyung Jun Lee
- Division of Genetic Resources, Honam National Institute of Biological Resources (HNIBR), Mokpo, Republic of Korea
| | - Shin Ae Lee
- Division of Genetic Resources, Honam National Institute of Biological Resources (HNIBR), Mokpo, Republic of Korea.
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Satterlee JW, Alonso D, Gramazio P, Jenike KM, He J, Arrones A, Villanueva G, Plazas M, Ramakrishnan S, Benoit M, Gentile I, Hendelman A, Shohat H, Fitzgerald B, Robitaille GM, Green Y, Swartwood K, Passalacqua MJ, Gagnon E, Hilgenhof R, Huggins TD, Eizenga GC, Gur A, Rutten T, Stein N, Yao S, Poncet A, Bellot C, Frary A, Knapp S, Bendahmane M, Särkinen T, Gillis J, Van Eck J, Schatz MC, Eshed Y, Prohens J, Vilanova S, Lippman ZB. Convergent evolution of plant prickles by repeated gene co-option over deep time. Science 2024; 385:eado1663. [PMID: 39088611 PMCID: PMC11305333 DOI: 10.1126/science.ado1663] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 06/06/2024] [Indexed: 08/03/2024]
Abstract
An enduring question in evolutionary biology concerns the degree to which episodes of convergent trait evolution depend on the same genetic programs, particularly over long timescales. In this work, we genetically dissected repeated origins and losses of prickles-sharp epidermal projections-that convergently evolved in numerous plant lineages. Mutations in a cytokinin hormone biosynthetic gene caused at least 16 independent losses of prickles in eggplants and wild relatives in the genus Solanum. Homologs underlie prickle formation across angiosperms that collectively diverged more than 150 million years ago, including rice and roses. By developing new Solanum genetic systems, we leveraged this discovery to eliminate prickles in a wild species and an indigenously foraged berry. Our findings implicate a shared hormone activation genetic program underlying evolutionarily widespread and recurrent instances of plant morphological innovation.
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Affiliation(s)
- James W. Satterlee
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - David Alonso
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Pietro Gramazio
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Katharine M. Jenike
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Jia He
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Andrea Arrones
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Gloria Villanueva
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Mariola Plazas
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Srividya Ramakrishnan
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Matthias Benoit
- French National Institute for Agriculture, Food, and Environment, Laboratory of Plant-Microbe Interactions, Toulouse, France
| | - Iacopo Gentile
- School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Anat Hendelman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Hagai Shohat
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Blaine Fitzgerald
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Gina M. Robitaille
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Yumi Green
- Boyce Thompson Institute, Ithaca, New York, USA
| | | | - Michael J. Passalacqua
- School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Edeline Gagnon
- Department of Integrative Biology, University of Guelph, Ontario, Canada
- Royal Botanic Garden Edinburgh, Edinburgh, UK
| | | | - Trevis D. Huggins
- USDA-ARS, Dale Bumpers National Rice Research Center, Stuttgart, AR, USA
| | - Georgia C. Eizenga
- USDA-ARS, Dale Bumpers National Rice Research Center, Stuttgart, AR, USA
| | - Amit Gur
- Cucurbits Section, Department of Vegetable Sciences, Agricultural Research Organization, Newe Ya’ar Research Center, Ramat Yishay, Israel
| | - Twan Rutten
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
- Crop Plant Genetics, Martin Luther University of Halle-Wittenberg, Halle (Saale), Germany
| | - Shengrui Yao
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, USA
- Sustainable Agriculture Sciences Center, New Mexico State University, Alcalde, NM, USA
| | - Adrien Poncet
- Laboratoire Reproduction et Developpement des Plantes, INRAE, CNRS, Universite Lyon, Ecole Normale Superieure de Lyon, Lyon, France
| | - Clement Bellot
- Laboratoire Reproduction et Developpement des Plantes, INRAE, CNRS, Universite Lyon, Ecole Normale Superieure de Lyon, Lyon, France
| | - Amy Frary
- Department of Biological Sciences, Mount Holyoke College, South Hadley, MA, USA
| | | | - Mohammed Bendahmane
- Laboratoire Reproduction et Developpement des Plantes, INRAE, CNRS, Universite Lyon, Ecole Normale Superieure de Lyon, Lyon, France
| | | | - Jesse Gillis
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Physiology Department and Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Joyce Van Eck
- Boyce Thompson Institute, Ithaca, New York, USA
- Plant Breeding and Genetics Section, Cornell University, Ithaca, NY USA
| | - Michael C. Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Yuval Eshed
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Santiago Vilanova
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Zachary B. Lippman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
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8
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Li X, Chen Y, Zhang Z, He Q, Tian T, Jiao Y, Cao L. Genome-wide identification of starch phosphorylase gene family in Rosa chinensis and expression in response to abiotic stress. Sci Rep 2024; 14:13917. [PMID: 38886497 PMCID: PMC11183051 DOI: 10.1038/s41598-024-64937-1] [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: 02/14/2024] [Accepted: 06/14/2024] [Indexed: 06/20/2024] Open
Abstract
Chinese rose (Rosa chinensis) is an important ornamental plant, with economic, cultural, and symbolic significance. During the application of outdoor greening, adverse environments such as high temperature and drought are often encountered, which affect its application scope and ornamental quality. The starch phosphorylase (Pho) gene family participate in the synthesis and decomposition of starch, not only related to plant energy metabolism, but also plays an important role in plant stress resistance. The role of Pho in combating salinity and high temperature stress in R. chinensis remains unknown. In this work, 4 Phos from R. chinensis were detected with Pfam number of Pho (PF00343.23) and predicted by homolog-based prediction (HBP). The Phos are characterized by sequence lengths of 821 to 997 bp, and the proteins are predicted to subcellularly located in the plastid and cytoplasm. The regulatory regions of the Phos contain abundant stress and phytohormone-responsive cis-acting elements. Based on transcriptome analysis, the Phos were found to respond to abiotic stress factors such as drought, salinity, high temperature, and plant phytohormone of jasmonic acid and salicylic acid. The response of Phos to abiotic stress factors such as salinity and high temperature was confirmed by qRT-PCR analysis. To evaluate the genetic characteristics of Phos, a total of 69 Phos from 17 species were analyzed and then classified into 3 groups in phylogenetic tree. The collinearity analysis of Phos in R. chinensis and other species was conducted for the first time. This work provides a view of evolution for the Pho gene family and indicates that Phos play an important role in abiotic stress response of R. chinensis.
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Affiliation(s)
- Xu Li
- Hunan Provincial Key Laboratory of Dong Medicine, Ethnic Medicine Research Center, Hunan University of Medicine, Huaihua, 418000, China
| | - Yang Chen
- Hunan Provincial Key Laboratory of Dong Medicine, Ethnic Medicine Research Center, Hunan University of Medicine, Huaihua, 418000, China
| | - Zaiqi Zhang
- Hunan Provincial Key Laboratory of Dong Medicine, Ethnic Medicine Research Center, Hunan University of Medicine, Huaihua, 418000, China.
| | - Qin He
- Hunan Provincial Key Laboratory of Dong Medicine, Ethnic Medicine Research Center, Hunan University of Medicine, Huaihua, 418000, China
| | - Tingting Tian
- Hunan Provincial Key Laboratory of Dong Medicine, Ethnic Medicine Research Center, Hunan University of Medicine, Huaihua, 418000, China
| | - Yangmiao Jiao
- Hunan Provincial Key Laboratory of Dong Medicine, Ethnic Medicine Research Center, Hunan University of Medicine, Huaihua, 418000, China.
| | - Liang Cao
- Hunan Provincial Key Laboratory of Dong Medicine, Ethnic Medicine Research Center, Hunan University of Medicine, Huaihua, 418000, China.
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Li K, Chen R, Abudoukayoumu A, Wei Q, Ma Z, Wang Z, Hao Q, Huang J. Haplotype-resolved T2T reference genomes for wild and domesticated accessions shed new insights into the domestication of jujube. HORTICULTURE RESEARCH 2024; 11:uhae071. [PMID: 38725458 PMCID: PMC11079485 DOI: 10.1093/hr/uhae071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 02/28/2024] [Indexed: 05/12/2024]
Abstract
Chinese jujube (Ziziphus jujuba Mill.) is one of the most important deciduous tree fruits in China, with substantial economic and nutritional value. Jujube was domesticated from its wild progenitor, wild jujube (Z. jujuba var. spinosa), and both have high medicinal value. Here we report the 767.81- and 759.24-Mb haplotype-resolved assemblies of a dry-eating 'Junzao' jujube (JZ) and a wild jujube accession (SZ), using a combination of multiple sequencing strategies. Each assembly yielded two complete haplotype-resolved genomes at the telomere-to-telomere (T2T) level, and ~81.60 and 69.07 Mb of structural variations were found between the two haplotypes within JZ and SZ, respectively. Comparative genomic analysis revealed a large inversion on each of chromosomes 3 and 4 between JZ and SZ, and numerous genes were affected by structural variations, some of which were associated with starch and sucrose metabolism. A large-scale population analysis of 672 accessions revealed that wild jujube originated from the lower reaches of the Yellow River and was initially domesticated at local sites. It spread widely and was then independently domesticated at the Shanxi-Shaanxi Gorge of the middle Yellow River. In addition, we identified some new selection signals regions on genomes, which are involved in the tissue development, pollination, and other aspects of jujube tree morphology and fertilization domestication. In conclusion, our study provides high-quality reference genomes of jujube and wild jujube and new insights into the domestication history of jujube.
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Affiliation(s)
- Kun Li
- Key Laboratory of National Forestry and Grassland Administration on Forest Cultivation on the Loess Plateau, College of Forestry, Northwest A&F University, Yangling 712100, China
| | - Ruihong Chen
- College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Ayimaiti Abudoukayoumu
- Key Laboratory of National Forestry and Grassland Administration on Forest Cultivation on the Loess Plateau, College of Forestry, Northwest A&F University, Yangling 712100, China
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Qian Wei
- Key Laboratory of National Forestry and Grassland Administration on Forest Cultivation on the Loess Plateau, College of Forestry, Northwest A&F University, Yangling 712100, China
| | - Zhibo Ma
- Key Laboratory of National Forestry and Grassland Administration on Forest Cultivation on the Loess Plateau, College of Forestry, Northwest A&F University, Yangling 712100, China
| | - Zhengyang Wang
- Key Laboratory of National Forestry and Grassland Administration on Forest Cultivation on the Loess Plateau, College of Forestry, Northwest A&F University, Yangling 712100, China
| | - Qing Hao
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Jian Huang
- Key Laboratory of National Forestry and Grassland Administration on Forest Cultivation on the Loess Plateau, College of Forestry, Northwest A&F University, Yangling 712100, China
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10
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Shao L, Qiao P, Wang J, Peng Y, Wang Y, Dong W, Li J. Comparative analysis of jujube and sour jujube gave insight into their difference in genetic diversity and suitable habitat. Front Genet 2024; 15:1322285. [PMID: 38380425 PMCID: PMC10878421 DOI: 10.3389/fgene.2024.1322285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 01/16/2024] [Indexed: 02/22/2024] Open
Abstract
Jujube (Ziziphus jujuba var. jujuba Mill.) and sour jujube (Z. jujuba var. spinosa (Bunge) Hu ex H.F.Chow.) are economically, nutritionally, and ecologically significant members of the Rhamnaceae family. Despite their importance, insufficient research on their genetics and habitats has impeded effective conservation and utilization. To address this knowledge gap, we conducted plastome sequencing, integrated distribution data from China, and assessed genetic diversity and suitable habitat. The plastomes of both species exhibited high conservation and low genetic diversity. A new-found 23 bp species-specific Indel in the petL-petG enabled us to develop a rapid Indel-based identification marker for species discrimination. Phylogenetic analysis and dating illuminated their genetic relationship, showing speciation occurred 6.9 million years ago, in a period of dramatic global temperature fluctuations. Substantial variations in suitable climatic conditions were observed, with the mean temperature of the coldest quarter as the primary factor influencing distributions (-3.16°C-12.73°C for jujube and -5.79°C to 4.11°C for sour jujube, suitability exceeding 0.6). Consequently, distinct conservation strategies are warranted due to differences in suitable habitats, with jujube having a broader distribution and sour jujube concentrated in Northern China. In conclusion, disparate habitats and climatic factors necessitate tailored conservation approaches. Comparing genetic diversity and developing rapid species-specific primers will further enhance the sustainable utilization of these valuable species.
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Affiliation(s)
- Lingzhi Shao
- School of Biology and Food Science, Hebei Normal University for Nationalities, Chengde, China
| | - Ping Qiao
- Dexing Research and Training Center of Chinese Medical Sciences, China Academy of Chinese Medical Sciences, Dexing, China
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jingyi Wang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yanfang Peng
- School of Biology and Food Science, Hebei Normal University for Nationalities, Chengde, China
| | - Yiheng Wang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Wenpan Dong
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Jie Li
- School of Biology and Food Science, Hebei Normal University for Nationalities, Chengde, China
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11
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Yang M, Han L, Zhang S, Dai L, Li B, Han S, Zhao J, Liu P, Zhao Z, Liu M. Insights into the evolution and spatial chromosome architecture of jujube from an updated gapless genome assembly. PLANT COMMUNICATIONS 2023; 4:100662. [PMID: 37482683 PMCID: PMC10777365 DOI: 10.1016/j.xplc.2023.100662] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 07/17/2023] [Accepted: 07/20/2023] [Indexed: 07/25/2023]
Affiliation(s)
- Meng Yang
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China.
| | - Lu Han
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Shufeng Zhang
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Li Dai
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China; Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Bin Li
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Shoukun Han
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Jin Zhao
- College of Life Sciences, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Ping Liu
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China; Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Zhihui Zhao
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China; Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Mengjun Liu
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China; Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, Hebei 071001, China.
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12
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Li B, Muhammad N, Zhang S, Lan Y, Yang Y, Han S, Liu M, Yang M. Multiple-Genome-Based Simple Sequence Repeat Is an Efficient and Successful Method in Genotyping and Classifying Different Jujube Germplasm Resources. PLANTS (BASEL, SWITZERLAND) 2023; 12:2885. [PMID: 37571038 PMCID: PMC10421302 DOI: 10.3390/plants12152885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/23/2023] [Accepted: 08/03/2023] [Indexed: 08/13/2023]
Abstract
Jujube (Ziziphus jujuba Mill.) is a commercially important tree native to China, known for its high nutritional value and widespread distribution, as well as its diverse germplasm resources. Being resilient to harsh climatic conditions, the cultivation of jujube could provide a solution to food insecurity and income for people of arid and semi-arid regions in and outside of China. The evaluation of germplasm resources and genetic diversity in jujube necessitates the use of Simple Sequence Repeat (SSR) markers. SSR markers are highly polymorphic and can be used to evaluate the genetic diversity within and between cultivars of Chinese jujube, and are important for conservation biology, breeding programs, and the discovery of important traits for Chinese jujube improvement in China and abroad. However, traditional methods of SSR development are time-consuming and inadequate to meet the growing research demands. To address this issue, we developed a novel approach called Multiple-Genome-Based SSR identification (MGB-SSR), which utilizes the genomes of three jujube cultivars to rapidly screen for polymorphic SSRs in the jujube genome. Through the screening process, we identified 12 pairs of SSR primers, which were then used to successfully classify 249 jujube genotypes. Based on the genotyping results, a digital ID card was established, enabling the complete identification of all 249 jujube plants. The MGB-SSR approach proved efficient in rapidly detecting polymorphic SSRs within the jujube genome. Notably, this study represents the first successful differentiation of jujube germplasm resources using 12 SSR markers, with 4 markers successfully identifying triploid jujube genotypes. These findings offer valuable information for the classification of Chinese jujube germplasm, thereby providing significant assistance to jujube researchers and breeders in identifying unknown jujube germplasm.
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Affiliation(s)
- Bin Li
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (B.L.)
| | - Noor Muhammad
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (B.L.)
| | - Shufeng Zhang
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (B.L.)
| | - Yunxin Lan
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (B.L.)
| | - Yihan Yang
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (B.L.)
| | - Shoukun Han
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (B.L.)
| | - Mengjun Liu
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (B.L.)
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding 071000, China
| | - Meng Yang
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (B.L.)
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13
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Zhang Y, Niu N, Li S, Liu Y, Xue C, Wang H, Liu M, Zhao J. Virus-Induced Gene Silencing (VIGS) in Chinese Jujube. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12112115. [PMID: 37299093 DOI: 10.3390/plants12112115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 05/23/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023]
Abstract
Virus-induced gene silencing (VIGS) is a fast and efficient method for assaying gene function in plants. At present, the VIGS system mediated by Tobacco rattle virus (TRV) has been successfully practiced in some species such as cotton and tomato. However, little research of VIGS systems has been reported in woody plants, nor in Chinese jujube. In this study, the TRV-VIGS system of jujube was firstly investigated. The jujube seedlings were grown in a greenhouse with a 16 h light/8 h dark cycle at 23 °C. After the cotyledon was fully unfolded, Agrobacterium mixture containing pTRV1 and pTRV2-ZjCLA with OD600 = 1.5 was injected into cotyledon. After 15 days, the new leaves of jujube seedlings showed obvious photo-bleaching symptoms and significantly decreased expression of ZjCLA, indicating that the TRV-VIGS system had successfully functioned on jujube. Moreover, it found that two injections on jujube cotyledon could induce higher silencing efficiency than once injection. A similar silencing effect was then also verified in another gene, ZjPDS. These results indicate that the TRV-VIGS system in Chinese jujube has been successfully established and can be applied to evaluate gene function, providing a breakthrough in gene function verification methods.
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Affiliation(s)
- Yao Zhang
- College of Life Science, Hebei Agricultural University, Baoding 071000, China
| | - Nazi Niu
- College of Life Science, Hebei Agricultural University, Baoding 071000, China
| | - Shijia Li
- College of Life Science, Hebei Agricultural University, Baoding 071000, China
| | - Yin Liu
- College of Life Science, Hebei Agricultural University, Baoding 071000, China
| | - Chaoling Xue
- College of Life Science, Hebei Agricultural University, Baoding 071000, China
| | - Huibin Wang
- College of Life Science, Hebei Agricultural University, Baoding 071000, China
| | - Mengjun Liu
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding 071000, China
| | - Jin Zhao
- College of Life Science, Hebei Agricultural University, Baoding 071000, China
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14
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Yang M, Ma Y, Si X, Liu X, Geng X, Wen X, Li G, Zhang L, Yang C, Zhang Z. Analysis of the Glycoside Hydrolase Family 1 from Wild Jujube Reveals Genes Involved in the Degradation of Jujuboside A. Genes (Basel) 2023; 14:1135. [PMID: 37372316 DOI: 10.3390/genes14061135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/17/2023] [Accepted: 05/19/2023] [Indexed: 06/29/2023] Open
Abstract
Jujubosides are the major medicinal ingredients of Ziziphi Spinosae Semen (the seed of wild jujube). To date, a complete understanding of jujuboside's metabolic pathways has not been attained. This study has systematically identified 35 β-glucosidase genes belonging to the glycoside hydrolase family 1 (GH1) using bioinformatic methods based on the wild jujube genome. The conserved domains and motifs of the 35 putative β-glucosidases, along with the genome locations and exon-intron structures of 35 β-glucosidase genes were revealed. The potential functions of the putative proteins encoded by the 35 β-glucosidase genes are suggested based on their phylogenetic relationships with Arabidopsis homologs. Two wild jujube β-glucosidase genes were heterologously expressed in Escherichia coli, and the recombinant proteins were able to convert jujuboside A (JuA) into jujuboside B (JuB). Since it has been previously reported that JuA catabolites, including JuB and other rare jujubosides, may play crucial roles in the jujuboside's pharmacological activity, it is suggested that these two proteins can be used to enhance the utilization potential of jujubosides. This study provides new insight into the metabolism of jujubosides in wild jujube. Furthermore, the characterization of β-glucosidase genes is expected to facilitate investigations involving the cultivation and breeding of wild jujube.
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Affiliation(s)
- Mingjun Yang
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou 730050, China
| | - Yimian Ma
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Xupeng Si
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou 730050, China
| | - Xiaofeng Liu
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou 730050, China
| | - Xin Geng
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Xin Wen
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Guoqiong Li
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Liping Zhang
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Chengmin Yang
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Zheng Zhang
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
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15
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Jiao Y, Li X, Huang X, Liu F, Zhang Z, Cao L. The Identification of SQS/ SQE/ OSC Gene Families in Regulating the Biosynthesis of Triterpenes in Potentilla anserina. Molecules 2023; 28:2782. [PMID: 36985754 PMCID: PMC10051230 DOI: 10.3390/molecules28062782] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 03/30/2023] Open
Abstract
The tuberous roots of Potentilla anserina (Pan) are an edible and medicinal resource in Qinghai-Tibetan Plateau, China. The triterpenoids from tuberous roots have shown promising anti-cancer, hepatoprotective, and anti-inflammatory properties. In this study, we carried out phylogenetic analysis of squalene synthases (SQSs), squalene epoxidases (SQEs), and oxidosqualene cyclases (OSCs) in the pathway of triterpenes. In total, 6, 26, and 20 genes of SQSs, SQEs, and OSCs were retrieved from the genome of Pan, respectively. Moreover, 6 SQSs and 25 SQEs genes expressed in two sub-genomes (A and B) of Pan. SQSs were not expanded after whole-genome duplication (WGD), and the duplicated genes were detected in SQEs. Twenty OSCs were divided into two clades of cycloartenol synthases (CASs) and β-amyrin synthases (β-ASs) by a phylogenetic tree, characterized with gene duplication and evolutionary divergence. We speculated that β-ASs and CASs may participate in triterpenes synthesis. The data presented act as valuable references for future studies on the triterpene synthetic pathway of Pan.
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Affiliation(s)
- Yangmiao Jiao
- Hunan Provincial Key Laboratory of Dong Medicine, Ethnic Medicine Research Center, Hunan University of Medicine, Huaihua 418000, China; (Y.J.); (X.L.); (X.H.); (F.L.)
- Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese Medicine, School of Pharmacy, Hunan University of Medicine, Huaihua 418000, China
| | - Xu Li
- Hunan Provincial Key Laboratory of Dong Medicine, Ethnic Medicine Research Center, Hunan University of Medicine, Huaihua 418000, China; (Y.J.); (X.L.); (X.H.); (F.L.)
| | - Xueshuang Huang
- Hunan Provincial Key Laboratory of Dong Medicine, Ethnic Medicine Research Center, Hunan University of Medicine, Huaihua 418000, China; (Y.J.); (X.L.); (X.H.); (F.L.)
- Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese Medicine, School of Pharmacy, Hunan University of Medicine, Huaihua 418000, China
| | - Fan Liu
- Hunan Provincial Key Laboratory of Dong Medicine, Ethnic Medicine Research Center, Hunan University of Medicine, Huaihua 418000, China; (Y.J.); (X.L.); (X.H.); (F.L.)
| | - Zaiqi Zhang
- Hunan Provincial Key Laboratory of Dong Medicine, Ethnic Medicine Research Center, Hunan University of Medicine, Huaihua 418000, China; (Y.J.); (X.L.); (X.H.); (F.L.)
| | - Liang Cao
- Hunan Provincial Key Laboratory of Dong Medicine, Ethnic Medicine Research Center, Hunan University of Medicine, Huaihua 418000, China; (Y.J.); (X.L.); (X.H.); (F.L.)
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16
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Du S, Hu X, Guo Y, Wang S, Yang X, Wu Z, Huang Y. A comparative plastomic analysis of Ziziphus jujuba var. spinosa (Bunge) Hu ex H. F. Chow and implication of the origin of Chinese jujube. AOB PLANTS 2023; 15:plad006. [PMID: 37025103 PMCID: PMC10071050 DOI: 10.1093/aobpla/plad006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 02/17/2023] [Indexed: 06/19/2023]
Abstract
Comparative plastomics can be used to explicitly dissect various types of plastome variation. In the present study, the plastome variation pattern of Ziziphus jujuba var. spinosa (also called sour jujube) and its phylogenomic relationship with Chinese jujube were investigated. Plastomes of 21 sour jujube individuals were sequenced and assembled. The length of the sour jujube plastomes ranged between 159399 and 161279 bp. The plastomes exhibited collinearity of structure, gene order and content. The most divergent regions were located in the intergenic spacers, such as trnR-UCU-atpA and psbZ-trnG-UCC. Sliding window analysis demonstrated that the sequence variation among the sour jujube plastomes was relatively low. Sixty-two to 76 SSRs with 4 motif types were identified in the sour jujube plastomes with a predominant motif type of A/T. Three protein-coding genes exhibited higher nonsynonymous/synonymous substitution ratios, indicating that these genes may undergo positive selection. A total of 80 SNPs were detected and 1266 potential RNA editing sites of 23 protein-coding genes were predicted. In the phylogenomic tree constructed, sour jujube has a sister relationship to Chinese jujube, which indicates that Chinese jujube may have originated or been domesticated from sour jujube. The present study explicitly investigated the individual-level plastome variation of sour jujube and provides potential valuable molecular markers for future genetic-related study of this lineage.
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Affiliation(s)
- Shuhui Du
- College of Forestry, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Xiaoyan Hu
- College of Food Science and Technology, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Yuanting Guo
- College of Forestry, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Shengji Wang
- College of Forestry, Shanxi Agricultural University, Taigu, Shanxi, China
| | | | - Zhenzhen Wu
- Taian Dushihuaxiang Agricultural Technology Co., Ltd, Taian, Shandong, China
| | - Yuyin Huang
- Shandong Huinongtianxia Science and Technology Information Consulting Co., Ltd, Taian, Shandong, China
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17
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Zhang C, Geng Y, Liu H, Wu M, Bi J, Wang Z, Dong X, Li X. Low-acidity ALUMINUM-DEPENDENT MALATE TRANSPORTER4 genotype determines malate content in cultivated jujube. PLANT PHYSIOLOGY 2023; 191:414-427. [PMID: 36271866 PMCID: PMC9806563 DOI: 10.1093/plphys/kiac491] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
Jujube (Ziziphus jujuba Mill.), the most economically important fruit tree in Rhamnaceae, was domesticated from sour jujube (Z. jujuba Mill. var. spinosa (Bunge) Hu ex H.F.Chow.). During domestication, fruit sweetness increased and acidity decreased. Reduction in organic acid content is crucial for the increase in sweetness of jujube fruit. In this study, the determination of malate content among 46 sour jujube and 35 cultivated jujube accessions revealed that malate content varied widely in sour jujube (0.90-13.31 mg g-1) but to a lesser extent in cultivated jujube (0.33-2.81 mg g-1). Transcriptome sequencing analysis showed that the expression level of Aluminum-Dependent Malate Transporter 4 (ZjALMT4) was substantially higher in sour jujube than in jujube. Correlation analysis of mRNA abundance and fruit malate content and transient gene overexpression showed that ZjALMT4 participates in malate accumulation. Further sequencing analyses revealed that three genotypes of the W-box in the promoter of ZjALMT4 in sour jujube associated with malate content were detected, and the genotype associated with low malate content was fixed in jujube. Yeast one-hybrid screening showed that ZjWRKY7 binds to the W-box region of the high-acidity genotype in sour jujube, whereas the binding ability was weakened in jujube. Transient dual-luciferase and overexpression analyses showed that ZjWRKY7 directly binds to the promoter of ZjALMT4, activating its transcription, and thereby promoting malate accumulation. These findings provide insights into the mechanism by which ZjALMT4 modulates malate accumulation in sour jujube and jujube. The results are of theoretical and practical importance for the exploitation and domestication of germplasm resources.
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Affiliation(s)
- Chunmei Zhang
- State Forestry and Grassland Administration Key Laboratory of Silviculture in downstream areas of the Yellow River, College of Forestry, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Yanqiu Geng
- State Forestry and Grassland Administration Key Laboratory of Silviculture in downstream areas of the Yellow River, College of Forestry, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Hanxiao Liu
- State Forestry and Grassland Administration Key Laboratory of Silviculture in downstream areas of the Yellow River, College of Forestry, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Mengjia Wu
- State Forestry and Grassland Administration Key Laboratory of Silviculture in downstream areas of the Yellow River, College of Forestry, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Jingxin Bi
- State Forestry and Grassland Administration Key Laboratory of Silviculture in downstream areas of the Yellow River, College of Forestry, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | | | | | - Xingang Li
- College of Forestry, Northwest A&F University, Yangling, China
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18
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Wang W, Zhang Z, Li X. Identification and expression analysis of BURP domain-containing genes in jujube and their involvement in low temperature and drought response. BMC Genomics 2022; 23:692. [PMID: 36203136 PMCID: PMC9541082 DOI: 10.1186/s12864-022-08907-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/26/2022] [Indexed: 11/17/2022] Open
Abstract
Background Plant-specific BURP domain-containing genes are involved in plant development and stress responses. However, the role of BURP family in jujube (Ziziphus jujuba Mill.) has not been investigated. Results In this study, 17 BURP genes belonging to four subfamilies were identified in jujube based on homology analysis, gene structures, and conserved motif confirmation. Gene duplication analysis indicated both tandem duplication and segmental duplication had contributed to ZjBURP expansion. The ZjBURPs were extensively expressed in flowers, young fruits, and jujube leaves. Transcriptomic data and qRT-PCR analysis further revealed that ZjBURPs also significantly influence fruit development, and most genes could be induced by low temperature, salinity, and drought stresses. Notably, several BURP genes significantly altered expression in response to low temperature (ZjPG1) and drought stresses (ZjBNM7, ZjBNM8, and ZjBNM9). Conclusions These results provided insights into the possible roles of ZjBURPs in jujube development and stress response. These findings would help selecting candidate ZjBURP genes for cold- and drought-tolerant jujube breeding. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08907-9.
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Affiliation(s)
- Wenzhu Wang
- College of Forestry, Research Center for Jujube Engineering and Technology of State Forestry Administration, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zhong Zhang
- College of Forestry, Research Center for Jujube Engineering and Technology of State Forestry Administration, Northwest A&F University, Yangling, 712100, Shaanxi, China.,Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518116, Guangdong, China
| | - Xingang Li
- College of Forestry, Research Center for Jujube Engineering and Technology of State Forestry Administration, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Ma Z, Zhao X, He A, Cao Y, Han Q, Lu Y, Yong JWH, Huang J. Mycorrhizal symbiosis reprograms ion fluxes and fatty acid metabolism in wild jujube during salt stress. PLANT PHYSIOLOGY 2022; 189:2481-2499. [PMID: 35604107 PMCID: PMC9342988 DOI: 10.1093/plphys/kiac239] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 04/30/2022] [Indexed: 05/25/2023]
Abstract
Chinese jujube (Ziziphus jujuba) is an important fruit tree in China, and soil salinity is the main constraint affecting jujube production. It is unclear how arbuscular mycorrhizal (AM) symbiosis supports jujube adaptation to salt stress. Herein, we performed comparative physiological, ion flux, fatty acid (FA) metabolomic, and transcriptomic analyses to examine the mechanism of AM jujube responding to salt stress. AM seedlings showed better performance during salt stress. AM symbiosis altered phytohormonal levels: indole-3-acetic acid and abscisic acid contents were significantly increased in AM roots and reduced by salt stress. Mycorrhizal colonization enhanced root H+ efflux and K+ influx, while inducing expression of plasma membrane-type ATPase 7 (ZjAHA7) and high-affinity K+ transporter 2 (ZjHAK2) in roots. High K+/Na+ homeostasis was maintained throughout salt exposure. FA content was elevated in AM leaves as well as roots, especially for palmitic acid, oleic acid, trans oleic acid, and linoleic acid, and similar effects were also observed in AM poplar (Populus. alba × Populus. glandulosa cv. 84K) and Medicago truncatula, indicating AM symbiosis elevating FA levels could be a conserved physiological effect. Gene co-expression network analyses uncovered a core gene set including 267 genes in roots associated with AM symbiosis and conserved transcriptional responses, for example, FA metabolism, phytohormone signal transduction, SNARE interaction in vesicular transport, and biotin metabolism. In contrast to widely up-regulated genes related to FA metabolism in AM roots, limited genes were affected in leaves. We propose a model of AM symbiosis-linked reprogramming of FA metabolism and provide a comprehensive insight into AM symbiosis with a woody species adaptation to salt stress.
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Affiliation(s)
- Zhibo Ma
- Key Laboratory of National Forestry and Grassland Administration on Silviculture in Loess Plateau, College of Forestry, Northwest A&F University, Yangling 712100, China
| | - Xinchi Zhao
- Key Laboratory of National Forestry and Grassland Administration on Silviculture in Loess Plateau, College of Forestry, Northwest A&F University, Yangling 712100, China
| | - Aobing He
- Key Laboratory of National Forestry and Grassland Administration on Silviculture in Loess Plateau, College of Forestry, Northwest A&F University, Yangling 712100, China
| | - Yan Cao
- Key Laboratory of National Forestry and Grassland Administration on Silviculture in Loess Plateau, College of Forestry, Northwest A&F University, Yangling 712100, China
| | - Qisheng Han
- Farmland Irrigation Research Institute, Chinese Academy of Agricultural Sciences, Xinxiang 453002, China
| | - Yanjun Lu
- Key Laboratory of National Forestry and Grassland Administration on Silviculture in Loess Plateau, College of Forestry, Northwest A&F University, Yangling 712100, China
| | - Jean Wan Hong Yong
- Department of Biosystems and Technology, Swedish University of Agricultural Sciences, Alnarp 75007, Sweden
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Du S, Hu X, Yang X, Yu W, Wang Z. Genetic diversity and population dynamic of Ziziphus jujuba var. spinosa (Bunge) Hu ex H. F. Chow in Central China. Ecol Evol 2022; 12:e9101. [PMID: 35898427 PMCID: PMC9309028 DOI: 10.1002/ece3.9101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 06/04/2022] [Accepted: 06/23/2022] [Indexed: 11/09/2022] Open
Abstract
Phylogeographic research concerning Central China has been rarely conducted. Population genetic and phylogeography of Ziziphus jujuba var. spinosa (also called sour jujube) were investigated to improve our understanding of plant phylogeographic patterns in Central China. Single-copy nuclear gene markers and complete chloroplast genome data were applied to 328 individuals collected from 21 natural populations of sour jujube in China. Nucleotide variation of sour jujube was relatively high (π = 0.00720, θ w = 0.00925), which resulted from the mating system and complex population dynamics. Analysis of molecular variation analysis revealed that most of the total variation was attributed to variation within populations, and a high level of genetic differentiation among populations was detected (F st = 0.197). Relatively low long-distance dispersal capability and vitality of pollen contributed to high genetic differentiation among populations. Differences in the environmental conditions and long distance among populations further restricted gene flow. Structure clustering analysis uncovered intraspecific divergence between central and marginal populations. Migrate analysis found a high level of gene flow between these two intraspecific groups. Bayesian skyline plot detected population expansion of these two intraspecific groups. Network and phylogeny analysis of chloroplast haplotypes also found intraspecific divergence, and the divergence time was estimated to occur at about 55.86 Ma. Haplotype native to the Loess Plateau was more ancient, and multiple glacial refugia of sour jujube were found to locate at the Loess Plateau, areas adjacent to the Qinling Mountains and Tianmu Mountains. Species distribution model analysis found a typical contraction-expansion model corresponding to the Quaternary climatic oscillations. In the future, the distribution of sour jujube may shift to high-latitude areas. This study provides new insights for phylogeographic research of temperate plant species distributed in Central China and sets a solid foundation for the application of the scientific management strategy of Z. jujuba var. spinosa.
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Affiliation(s)
- Shuhui Du
- College of Forestry, Shanxi Key Laboratory of Cultivation and Development on Functional Oil Trees in the Northern ChinaShanxi Agricultural University TaiguJinzhongChina
| | - Xiaoyan Hu
- College of Forestry, Shanxi Key Laboratory of Cultivation and Development on Functional Oil Trees in the Northern ChinaShanxi Agricultural University TaiguJinzhongChina
| | - Xiuyun Yang
- College of Forestry, Shanxi Key Laboratory of Cultivation and Development on Functional Oil Trees in the Northern ChinaShanxi Agricultural University TaiguJinzhongChina
| | - Wendong Yu
- College of Horticulture and Plant ProtectionYangzhou UniversityYangzhouChina
| | - Zhaoshan Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of ForestryChinese Academy of ForestryBeijingChina
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