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Weyya G, Belay A, Tadesse E. Passion fruit ( Passiflora edulis Sims) by-products as a source of bioactive compounds for non-communicable disease prevention: extraction methods and mechanisms of action: a systematic review. Front Nutr 2024; 11:1340511. [PMID: 38903622 PMCID: PMC11187344 DOI: 10.3389/fnut.2024.1340511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 05/21/2024] [Indexed: 06/22/2024] Open
Abstract
Introduction The review titled Passion fruit by-products as a source of bioactive compounds for non-communicable disease prevention: extraction methods and mechanisms provide valuable insights into the health benefits and industrial applications of passion fruit waste. Passion fruits are a tropical and subtropical vine species, which produces edible fruits. Many food product types can be made from passion fruits. However, during passion fruit processing, large amounts of waste are released in to the environment. This review focuses on extraction methods of bioactive compounds from passion fruit by-products such as leaves, peels, seeds, and bagasse. Methods This comprehensive review focuses on the bioactive compounds present in passion fruit by-products, emphasis on their mechanisms of action on non-communicable diseases. It also provides a detailed analysis of the extraction methods used to obtain these bioactive compounds, their potential industrial applications, and the factors that affect extraction efficiency. Results This review encourages further research and innovation in utilization of passion fruit waste as a source of bioactive compounds for non- communicable disease prevention and their mechanisms of action. This can advance the circular economy. It also highlights the importance of sustainable and green extraction methods, which have gained attention due to environmental concerns. Discussion Unlike previous reviews, this comprehensive article explores the potential health benefits of multiple passion fruit waste products. It also examines the possible applications of these extracts for industrial goods such as food additives, colorants, nutraceuticals, natural antioxidants, and antimicrobial agents. Overall, it contributes new information emphasizing the potential of passion fruit by-products as a source of bioactive, and the findings have implications for the scientific community and industry, promoting a deeper understanding of the health benefits and sustainable practices associated with passion fruit waste utilization.
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Affiliation(s)
- Getu Weyya
- Department of Food Science and Applied Nutrition, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia
| | - Abera Belay
- Department of Food Science and Applied Nutrition, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia
| | - Eneyew Tadesse
- Department of Food Science and Applied Nutrition, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia
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2
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Yu H, Li Y, Han W, Bao L, Liu F, Ma Y, Pu Z, Zeng Q, Zhang L, Bao Z, Wang S. Pan-evolutionary and regulatory genome architecture delineated by an integrated macro- and microsynteny approach. Nat Protoc 2024; 19:1623-1678. [PMID: 38514839 DOI: 10.1038/s41596-024-00966-4] [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: 04/07/2022] [Accepted: 12/20/2023] [Indexed: 03/23/2024]
Abstract
The forthcoming massive genome data generated by the Earth BioGenome Project will open up a new era of comparative genomics, for which genome synteny analysis provides an important framework. Profiling genome synteny represents an essential step in elucidating genome architecture, regulatory blocks/elements and their evolutionary history. Here we describe PanSyn, ( https://github.com/yhw320/PanSyn ), the most comprehensive and up-to-date genome synteny pipeline, providing step-by-step instructions and application examples to demonstrate its usage. PanSyn inherits both basic and advanced functions from existing popular tools, offering a user-friendly, highly customized approach for genome macrosynteny analysis and integrated pan-evolutionary and regulatory analysis of genome architecture, which are not yet available in public synteny software or tools. The advantages of PanSyn include: (i) advanced microsynteny analysis by functional profiling of microsynteny genes and associated regulatory elements; (ii) comprehensive macrosynteny analysis, including the inference of karyotype evolution from ancestors to extant species; and (iii) functional integration of microsynteny and macrosynteny for pan-evolutionary profiling of genome architecture and regulatory blocks, as well as integration with external functional genomics datasets from three- or four-dimensional genome and ENCODE projects. PanSyn requires basic knowledge of the Linux environment and Perl programming language and the ability to access a computer cluster, especially for large-scale genomic comparisons. Our protocol can be easily implemented by a competent graduate student or postdoc and takes several days to weeks to execute for dozens to hundreds of genomes. PanSyn provides yet the most comprehensive and powerful tool for integrated evolutionary and functional genomics.
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Affiliation(s)
- Hongwei Yu
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yuli Li
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China.
| | - Wentao Han
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Lisui Bao
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Fuyun Liu
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yuanting Ma
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zhongqi Pu
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Qifan Zeng
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Lingling Zhang
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China
| | - Zhenmin Bao
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
- Laboratory for Marine Fisheries and Aquaculture, Laoshan Laboratory, Qingdao, China
| | - Shi Wang
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China.
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China.
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China.
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Zheng YY, Chen LH, Fan BL, Xu Z, Wang Q, Zhao BY, Gao M, Yuan MH, Tahir Ul Qamar M, Jiang Y, Yang L, Wang L, Li W, Cai W, Ma C, Lu L, Song JM, Chen LL. Integrative multiomics profiling of passion fruit reveals the genetic basis for fruit color and aroma. PLANT PHYSIOLOGY 2024; 194:2491-2510. [PMID: 38039148 DOI: 10.1093/plphys/kiad640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/26/2023] [Accepted: 10/29/2023] [Indexed: 12/03/2023]
Abstract
Passion fruit (Passiflora edulis) possesses a complex aroma and is widely grown in tropical and subtropical areas. Here, we conducted the de novo assembly, annotation, and comparison of PPF (P. edulis Sims) and YPF (P. edulis f. flavicarpa) reference genomes using PacBio, Illumina, and Hi-C technologies. Notably, we discovered evidence of recent whole-genome duplication events in P. edulis genomes. Comparative analysis revealed 7.6∼8.1 million single nucleotide polymorphisms, 1 million insertions/deletions, and over 142 Mb presence/absence variations among different P. edulis genomes. During the ripening of yellow passion fruit, metabolites related to flavor, aroma, and color were substantially accumulated or changed. Through joint analysis of genomic variations, differentially expressed genes, and accumulated metabolites, we explored candidate genes associated with flavor, aroma, and color distinctions. Flavonoid biosynthesis pathways, anthocyanin biosynthesis pathways, and related metabolites are pivotal factors affecting the coloration of passion fruit, and terpenoid metabolites accumulated more in PPF. Finally, by heterologous expression in yeast (Saccharomyces cerevisiae), we functionally characterized 12 terpene synthases. Our findings revealed that certain TPS homologs in both YPF and PPF varieties produce identical terpene products, while others yield distinct compounds or even lose their functionality. These discoveries revealed the genetic and metabolic basis of unique characteristics in aroma and flavor between the 2 passion fruit varieties. This study provides resources for better understanding the genome architecture and accelerating genetic improvement of passion fruits.
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Affiliation(s)
- Yu-Yu Zheng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Lin-Hua Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Bing-Liang Fan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Zhenni Xu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Qiuxia Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Bo-Yuan Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Min Gao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Min-Hui Yuan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Muhammad Tahir Ul Qamar
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Yuanyuan Jiang
- Henry Fok School of Biology and Agriculture, Shaoguan University, Shaoguan 512005, China
| | - Liu Yang
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Lingqiang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Weihui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Wenguo Cai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Chongjian Ma
- Henry Fok School of Biology and Agriculture, Shaoguan University, Shaoguan 512005, China
| | - Li Lu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- Hubei Hongshan Laboratory, Wuhan 430071, China
| | - Jia-Ming Song
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Ling-Ling Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
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Garcia E, Koh J, Wu X, Sarkhosh A, Liu T. Tissue-specific proteome profile analysis reveals regulatory and stress responsive networks in passion fruit during storage. Sci Rep 2024; 14:3564. [PMID: 38346991 PMCID: PMC10861471 DOI: 10.1038/s41598-024-52557-8] [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: 07/25/2023] [Accepted: 01/20/2024] [Indexed: 02/15/2024] Open
Abstract
Passiflora edulis, commonly known as passion fruit, is a crop with a fragrant aroma and refreshingly tropical flavor that is a valuable source of antioxidants. It offers a unique opportunity for growers because of its adaptability to tropical and subtropical climates. Passion fruit can be sold in the fresh market or used in value-added products, but its postharvest shelf life has not been well-researched, nor have superior cultivars been well-developed. Understanding the proteins expressed at the tissue level during the postharvest stage can help improve fruit quality and extend shelf life. In this study, we carried out comparative proteomics analysis on four passion fruit tissues, the epicarp, mesocarp, endocarp, and pulp, using multiplexed isobaric tandem mass tag (TMT) labeling quantitation. A total of 3352 proteins were identified, including 295 differentially expressed proteins (DEPs). Of these DEPs, 213 showed a fold increase greater than 1.45 (50 proteins) or a fold decrease less than 0.45 (163 proteins) with different patterns among tissue types. Among the DEPs, there were proteins expressed with functions in oxygen scavenging, lipid peroxidation, response to heat stress, and pathogen resistance. Thirty-six proteins were designated as hypothetical proteins were characterized for potential functions in immunity, cell structure, homeostasis, stress response, protein metabolism and miraculin biosynthesis. This research provides insight into tissue-specific pathways that can be further studied within fruit physiology and postharvest shelf life to aid in implementing effective plant breeding programs. Knowing the tissue-specific function of fruit is essential for improving fruit quality, developing new varieties, identifying health benefits, and optimizing processing techniques.
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Affiliation(s)
- Ellen Garcia
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Jin Koh
- The Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, 32611, USA
| | - Xingbo Wu
- Department of Environmental Horticulture, Tropical Research and Education Center, University of Florida, Homestead, FL, 33031, USA
| | - Ali Sarkhosh
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA.
| | - Tie Liu
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA.
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Yu C, Wang P, Zhang S, Liu J, Cheng Y, Zhang S, Wu Z. Passionfruit Genomic Database (PGD): a comprehensive resource for passionfruit genomics. BMC Genomics 2024; 25:157. [PMID: 38331722 PMCID: PMC10851451 DOI: 10.1186/s12864-024-10069-9] [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: 08/27/2023] [Accepted: 01/31/2024] [Indexed: 02/10/2024] Open
Abstract
Passionfruit (Passiflora edulis) is a significant fruit crop in the commercial sector, owing to its high nutritional and medicinal value. The advent of high-throughput genomics sequencing technology has led to the publication of a vast amount of passionfruit omics data, encompassing complete genome sequences and transcriptome data under diverse stress conditions. To facilitate the efficient integration, storage, and analysis of these large-scale datasets, and to enable researchers to effectively utilize these omics data, we developed the first passionfruit genome database (PGD). The PGD platform comprises a diverse range of functional modules, including a genome browser, search function, heatmap, gene expression patterns, various tools, sequence alignment, and batch download, thereby providing a user-friendly interface. Additionally, supplementary practical tools have been developed for the PGD, such as gene family analysis tools, gene ontology (GO) terms, a pathway enrichment analysis, and other data analysis and mining tools, which enhance the data's utilization value. By leveraging the database's robust scalability, the intention is to continue to collect and integrate passionfruit omics data in the PGD, providing comprehensive and in-depth support for passionfruit research. The PGD is freely accessible via http://passionfruit.com.cn .
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Affiliation(s)
- Chaowei Yu
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-Construction By Ministry and Province), Yangtze University, Jingzhou, 434025, China
| | - Peng Wang
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-Construction By Ministry and Province), Yangtze University, Jingzhou, 434025, China
| | - Shengjie Zhang
- Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jindian Liu
- Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yingyin Cheng
- Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Songbai Zhang
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-Construction By Ministry and Province), Yangtze University, Jingzhou, 434025, China.
| | - Zujian Wu
- Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Hou Z, Liang J, Cai X, Lin J, Wang X, Liu R, Lu L, Chai G, An C, Chen S, Qin Y, Zheng P. PeHVA22 gene family in passion fruit ( Passiflora edulis): initial characterization and expression profiling diversity. FRONTIERS IN PLANT SCIENCE 2024; 14:1279001. [PMID: 38312363 PMCID: PMC10835403 DOI: 10.3389/fpls.2023.1279001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 12/28/2023] [Indexed: 02/06/2024]
Abstract
Passion fruit, an economically valuable fruit crop, is highly vulnerable to adverse climate conditions. The HVA22 genes, recognized as abscisic acid (ABA) and stress-inducible, play vital roles in stress response and growth regulation in diverse eukaryotic organisms. Here, six HVA22 genes were firstly identified in passion fruit genome and all predicted to be localized within the endoplasmic reticulum. Phylogenetic analyses showed that all PeHVA22s were divided into four subgroups. The gene structural features of PeHVA22 genes clustered in the same subgroup were relatively conserved, while the gene structure characteristics of PeHVA22s from different subgroups varied significantly. PeHVA22A and PeHVA22C closely clustered with barley HVA22 in Group II, were also induced by ABA and drought stress treatment, suggesting conserved roles similar to barley HVA22. Meanwhile, most PeHVA22s exhibited induced expression post-drought treatment but were suppressed under salt, low and high-temperature conditions, indicating a unique role in drought response. Additionally, PeHVA22s displayed tissue-specific expression patterns across diverse tissues, except for PeHVA22B which maybe a pseudogene. Notably, PeHVA22C, PeHVA22E, and PeHVA22F predominantly expressed in fruit, indicating their involvement in fruit development. Almost all PeHVA22s showed variable expression at different developmental stages of stamens or ovules, implying their roles in passion fruit's sexual reproduction. The intricate roles of PeHVA22s may result from diverse regulatory factors including transcription factors and CREs related to plant growth and development, hormone and stress responsiveness. These observations highlighted that PeHVA22s might play conserved roles in ABA response and drought stress tolerance, and also be participated in the regulation of passion fruit growth and floral development.
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Affiliation(s)
- Zhimin Hou
- College of Life Sciences, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jianxiang Liang
- College of Life Sciences, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Xinkai Cai
- College of Life Sciences, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jingting Lin
- College of Life Sciences, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaomei Wang
- Horticulture Research Institute, Guangxi Academy of Agricultural Sciences, Nanning Investigation Station of South Subtropical Fruit Trees, Ministry of Agriculture, Nanning, China
| | - Ruoyu Liu
- Pingtan Science and Technology Research Institute, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lin Lu
- College of Life Sciences, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Gaifeng Chai
- College of Life Sciences, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chang An
- College of Life Sciences, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shengzhen Chen
- College of Life Sciences, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuan Qin
- College of Life Sciences, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
- Pingtan Science and Technology Research Institute, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ping Zheng
- College of Life Sciences, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
- Pingtan Science and Technology Research Institute, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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Ma F, Zhou H, Yang H, Huang D, Xing W, Wu B, Li H, Hu W, Song S, Xu Y. WRKY transcription factors in passion fruit analysis reveals key PeWRKYs involved in abiotic stress and flavonoid biosynthesis. Int J Biol Macromol 2024; 256:128063. [PMID: 37963507 DOI: 10.1016/j.ijbiomac.2023.128063] [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: 08/16/2023] [Revised: 11/09/2023] [Accepted: 11/10/2023] [Indexed: 11/16/2023]
Abstract
WRKY transcription factors (TFs) are a superfamily of regulators involved in plant responses to pathogens and abiotic stress. Passion fruit is famous for its unique flavor and nutrient-rich juice, but its growth is limited by environmental factors and pathogens. In this study, 55 WRKY genes were identified from the Passiflora edulis genome. The structure and evolutionary characteristics of PeWRKYs were analyzed using a bioinformatics approach. PeWRKYs were classified into seven subgroups (I, IIa, IIb, IIc, IId, IIe, III) according to their homologs in Arabidopsis thaliana. Group IIa PeWRKY48 gene was highly up-regulated under cold stress by RNA expression analysis, and transgenic PeWRKY48 in yeast and Arabidopsis showed resistance exposure to cold, salt, and drought stress. Metabolome and transcriptome co-expression analysis of two different disease resistance genotypes of P. edulis identified PeWRKY30 as a key TF co-expressed with flavonoid accumulation in yellow fruit P. edulis, which may contribute to biotic or abiotic resistance. The qRT-PCR verified the expression of key genes in different tissues of P. edulis and in different species of Passiflora. This study provides a set of WRKY candidate genes that will facilitate the genetic improvement of disease and abiotic tolerance in passion fruit.
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Affiliation(s)
- Funing Ma
- Tropical Crops Genetic Resources Institute, CATAS, Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, National Key Laboratory for Tropical Crop Breeding, Germplasm Repository of Passiflora, Haikou 571101, China; Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, CATAS, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Hongwu Zhou
- Yunnan Agricultural University, Yunnan 650201, China
| | - Huiting Yang
- Yunnan Agricultural University, Yunnan 650201, China
| | - Dongmei Huang
- Tropical Crops Genetic Resources Institute, CATAS, Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, National Key Laboratory for Tropical Crop Breeding, Germplasm Repository of Passiflora, Haikou 571101, China; Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, CATAS, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Wenting Xing
- Tropical Crops Genetic Resources Institute, CATAS, Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, National Key Laboratory for Tropical Crop Breeding, Germplasm Repository of Passiflora, Haikou 571101, China; Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, CATAS, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Bin Wu
- Tropical Crops Genetic Resources Institute, CATAS, Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, National Key Laboratory for Tropical Crop Breeding, Germplasm Repository of Passiflora, Haikou 571101, China; Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, CATAS, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Hongli Li
- Tropical Crops Genetic Resources Institute, CATAS, Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, National Key Laboratory for Tropical Crop Breeding, Germplasm Repository of Passiflora, Haikou 571101, China; Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, CATAS, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Wenbin Hu
- Tropical Crops Genetic Resources Institute, CATAS, Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, National Key Laboratory for Tropical Crop Breeding, Germplasm Repository of Passiflora, Haikou 571101, China; Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, CATAS, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Shun Song
- Tropical Crops Genetic Resources Institute, CATAS, Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, National Key Laboratory for Tropical Crop Breeding, Germplasm Repository of Passiflora, Haikou 571101, China; Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, CATAS, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China.
| | - Yi Xu
- Tropical Crops Genetic Resources Institute, CATAS, Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, National Key Laboratory for Tropical Crop Breeding, Germplasm Repository of Passiflora, Haikou 571101, China; Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, CATAS, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China.
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Zou Y, Wang J, Peng D, Zhang X, Tembrock LR, Yang J, Zhao J, Liao H, Wu Z. Multi-integrated genomic data for Passiflora foetida provides insights into genome size evolution and floral development in Passiflora. MOLECULAR HORTICULTURE 2023; 3:27. [PMID: 38105261 PMCID: PMC10726625 DOI: 10.1186/s43897-023-00076-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/03/2023] [Indexed: 12/19/2023]
Abstract
Passiflora is a plant genus known for its extremely distinctive and colorful flowers and a wide range of genome size variation. However, how genome characteristics are related to flower traits among Passiflora species remains poorly understood. Here, we assembled a chromosome-scale genome of P. foetida, which belongs to the same subgenus as the commercial passionfruit P. edulis. The genome of P. foetida is smaller (424.16 Mb) and contains fewer copies of long terminal repeat retrotransposons (LTR-RTs). The disparity in LTR-RTs is one of the main contributors to the differences in genome sizes between these two species and possibly in floral traits. Additionally, we observed variation in insertion times and copy numbers of LTR-RTs across different transposable element (TE) lineages. Then, by integrating transcriptomic data from 33 samples (eight floral organs and flower buds at three developmental stages) with phylogenomic and metabolomic data, we conducted an in-depth analysis of the expression, phylogeny, and copy number of MIKC-type MADS-box genes and identified essential biosynthetic genes responsible for flower color and scent from glandular bracts and other floral organs. Our study pinpoints LRT-RTs as an important player in genome size variation in Passiflora species and provides insights into future genetic improvement.
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Affiliation(s)
- Yi Zou
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, 650504, China
| | - Jie Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Dan Peng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- College of Agriculture, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaoni Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Kunpeng Institute of Modern Agriculture at Foshan, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Luke R Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Jinliang Yang
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Jianli Zhao
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, 650504, China.
| | - Hong Liao
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, 650504, China.
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
- Kunpeng Institute of Modern Agriculture at Foshan, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China.
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9
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Liang J, Lu L, Zhang W, Chi M, Shen M, An C, Chen S, Wang X, Liu R, Qin Y, Zheng P. Comprehensive characterization and expression analysis of enzymatic antioxidant gene families in passion fruit ( Passiflora edulis). iScience 2023; 26:108329. [PMID: 38026217 PMCID: PMC10656276 DOI: 10.1016/j.isci.2023.108329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/15/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023] Open
Abstract
Passion fruit, a valuable tropical fruit, faces climate-related growth challenges. Antioxidant enzymes are vital for both stress protection and growth regulation in plants. We first provided systemic analysis of enzymatic antioxidant gene families in passion fruit, identifying 90 members including 11 PeSODs, 45 PeAPXs, 8 PeCATs, 7 PeGPXs, 6 PeMDHARs, 8 PeDHARs, and 5 PeGRs. Gene members in each gene family with same subcellular localization showed closer phylogenetic relationship. Many antioxidant genes exhibited tissue- or developmental stage-specific expression patterns during floral and fruit development, with some widely expressed. Their co-expressed genes were linked to photosynthesis and energy metabolism, suggesting roles in protecting highly proliferating tissues from oxidative damage. Potential genes for enhancing temperature stress resistance were identified. The involvement of diverse regulatory factors including miRNAs, transcription factors, and CREs might contribute to the complex roles of antioxidant genes. This study informs future research on antioxidant genes and passion fruit breeding.
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Affiliation(s)
- Jianxiang Liang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lin Lu
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wenbin Zhang
- Xinluo Breeding Center for Excellent Germplasms, Longyan 361000, China
| | - Ming Chi
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mengqian Shen
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chang An
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shengzhen Chen
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaomei Wang
- Horticulture Research Institute, Guangxi Academy of Agricultural Sciences, Nanning Investigation Station of South Subtropical Fruit Trees, Ministry of Agriculture, Nanning 530004, China
| | - Ruoyu Liu
- Pingtan Science and Technology Research Institute, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuan Qin
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Pingtan Science and Technology Research Institute, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ping Zheng
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Pingtan Science and Technology Research Institute, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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10
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Qiu Y, Li Y, Wu L, Wei H, Fu J, Chen W, Lin S, Yang S, Zhang R, Shang W, Liao C, Zeng S, Luo Y, Cai W. Analysis of Important Volatile Organic Compounds and Genes Produced by Aroma of Pepper Fruit by HS-SPME-GC/MS and RNA Sequencing. PLANTS (BASEL, SWITZERLAND) 2023; 12:2246. [PMID: 37375872 DOI: 10.3390/plants12122246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/01/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023]
Abstract
Pepper is an important condiment, and its aroma affects its commercial value. In this study, transcriptome sequencing and combined headspace solid-phase microextraction and gas chromatography-mass spectrometry (HS-SPME-GC-MS) were used to analyze the differentially expressed genes and volatile organic compounds in spicy and non-spicy pepper fruits. Compared with non-spicy fruits, there were 27 up-regulated volatile organic compounds (VOCs) and 3353 up-regulated genes (Up-DEGs) in spicy fruits. The results of KEGG enrichment analysis of the Up-DEGs combined with differential VOCs analysis showed that fatty acid biosynthesis and terpenoid biosynthesis may be the main metabolic pathways for aroma differences between non-spicy and spicy pepper fruits. The expression levels of the fatty acid biosynthesis-related genes FAD, LOX1, LOX5, HPL, and ADH and the key terpene synthesis gene TPS in spicy pepper fruits were significantly higher than those in non-spicy pepper fruits. The differential expression of these genes may be the reason for the different aroma. The results can provide reference for the development and utilization of high-aroma pepper germplasm resources and the breeding of new varieties.
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Affiliation(s)
- Yinhui Qiu
- Sanming Academy of Agricultural Sciences, Sanming 365509, China
- Fujian Key Laboratory of Crop Genetic Improvement and Innovative Utilization for Mountain Area, Sanming 365509, China
| | - Yongqing Li
- Sanming Academy of Agricultural Sciences, Sanming 365509, China
- Fujian Key Laboratory of Crop Genetic Improvement and Innovative Utilization for Mountain Area, Sanming 365509, China
| | - Lidong Wu
- Sanming Academy of Agricultural Sciences, Sanming 365509, China
- Fujian Key Laboratory of Crop Genetic Improvement and Innovative Utilization for Mountain Area, Sanming 365509, China
| | - Hang Wei
- Institute of Agricultural Quality Standards and Testing Technology, Fujian Academy of Agricultural Sciences, Fuzhou 350002, China
| | - Jianwei Fu
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Weiting Chen
- Sanming Academy of Agricultural Sciences, Sanming 365509, China
- Fujian Key Laboratory of Crop Genetic Improvement and Innovative Utilization for Mountain Area, Sanming 365509, China
| | - Shuting Lin
- Sanming Academy of Agricultural Sciences, Sanming 365509, China
- Fujian Key Laboratory of Crop Genetic Improvement and Innovative Utilization for Mountain Area, Sanming 365509, China
| | - Sheng Yang
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Rui Zhang
- Sanming Academy of Agricultural Sciences, Sanming 365509, China
- Fujian Key Laboratory of Crop Genetic Improvement and Innovative Utilization for Mountain Area, Sanming 365509, China
| | - Wei Shang
- Sanming Academy of Agricultural Sciences, Sanming 365509, China
- Fujian Key Laboratory of Crop Genetic Improvement and Innovative Utilization for Mountain Area, Sanming 365509, China
| | - Chengshu Liao
- Sanming Academy of Agricultural Sciences, Sanming 365509, China
- Fujian Key Laboratory of Crop Genetic Improvement and Innovative Utilization for Mountain Area, Sanming 365509, China
| | - Shaogui Zeng
- Sanming Academy of Agricultural Sciences, Sanming 365509, China
- Fujian Key Laboratory of Crop Genetic Improvement and Innovative Utilization for Mountain Area, Sanming 365509, China
| | - Ying Luo
- Sanming Academy of Agricultural Sciences, Sanming 365509, China
- Fujian Key Laboratory of Crop Genetic Improvement and Innovative Utilization for Mountain Area, Sanming 365509, China
| | - Weiwei Cai
- Sanming Academy of Agricultural Sciences, Sanming 365509, China
- Fujian Key Laboratory of Crop Genetic Improvement and Innovative Utilization for Mountain Area, Sanming 365509, China
- College of Horticultural Sciences, Zhejiang Agriculture and Forestry University, Hangzhou 350002, China
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11
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Wang L, Liu Y, Chai G, Zhang D, Fang Y, Deng K, Aslam M, Niu X, Zhang W, Qin Y, Wang X. Identification of passion fruit HSF gene family and the functional analysis of PeHSF-C1a in response to heat and osmotic stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 200:107800. [PMID: 37253279 DOI: 10.1016/j.plaphy.2023.107800] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/22/2023] [Accepted: 05/25/2023] [Indexed: 06/01/2023]
Abstract
Heat stress transcription factors (HSFs) are the major regulators of plant response to environmental stress, especially heat and drought stress. To gain a deeper understanding of the mechanisms underlying HSFs in the abiotic stress response of passion fruit, we conducted an in silico analysis of the HSF gene family. Through bioinformatics and phylogenetic analyses, we identified 18 PeHSF members and classified them into A, B, and C groups. Collinearity analysis results revealed that the expansion of the PeHSF gene family was due to the presence of segmental duplication. Furthermore, gene structure and protein domain analysis illustrated that PeHSFs in the same subgroup are relatively conserved. Conserved motif and function domain analysis suggested that PeHSF proteins possess typical conserved functional domains of the HSF family. A protein interaction network and 3D structure prediction were used to study the potential regulatory relationship of PeHSFs. Additionally, the subcellular localization results of PeHSF-A6a, PeHSF-B4b, and PeHSF-C1a were consistent with the predictions. RNA-seq and RT-qPCR analysis revealed the expression patterns of PeHSFs in different tissues of passion fruit floral organs. Promoter analysis and the expression patterns of the PeHSFs under different treatments demonstrated their involvement in various abiotic stress processes. Notably, overexpression of PeHSF-C1a consistently enhanced tolerance to drought and heat stress in Arabidopsis. Overall, our findings provide a scientific basis for further functional studies of PeHSFs that could contribute to improvement of passion fruit breeding.
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Affiliation(s)
- Lulu Wang
- Horticulture Research Institute, Guangxi Academy of Agricultural Sciences, Nanning Investigation Station of South Subtropical Fruit Trees, Ministry of Agriculture, Nanning, 530007, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, Guangxi, 530004, China
| | - Yanhui Liu
- College of Life Sciences, Longyan University, Longyan, 364000, China
| | - Gaifeng Chai
- College of Agriculture, College of Life Sciences, Pingtan Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Dan Zhang
- College of Agriculture, College of Life Sciences, Pingtan Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Yunying Fang
- College of Agriculture, College of Life Sciences, Pingtan Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Kao Deng
- College of Agriculture, College of Life Sciences, Pingtan Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Mohammad Aslam
- College of Agriculture, College of Life Sciences, Pingtan Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Xiaoping Niu
- College of Agriculture, College of Life Sciences, Pingtan Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Wenbin Zhang
- Fine Variety Breeding Farm in Xinluo District, Longyan, 364000, China
| | - Yuan Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, Guangxi, 530004, China; College of Agriculture, College of Life Sciences, Pingtan Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.
| | - Xiaomei Wang
- Horticulture Research Institute, Guangxi Academy of Agricultural Sciences, Nanning Investigation Station of South Subtropical Fruit Trees, Ministry of Agriculture, Nanning, 530007, China.
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12
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Xu Y, Li P, Ma F, Huang D, Xing W, Wu B, Sun P, Xu B, Song S. Characterization of the NAC Transcription Factor in Passion Fruit ( Passiflora edulis) and Functional Identification of PeNAC-19 in Cold Stress. PLANTS (BASEL, SWITZERLAND) 2023; 12:1393. [PMID: 36987081 PMCID: PMC10051797 DOI: 10.3390/plants12061393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/07/2023] [Accepted: 03/13/2023] [Indexed: 06/19/2023]
Abstract
The NAC (NAM, ATAF and CUC) gene family plays an important role in plant development and abiotic stress response. However, up to now, the identification and research of the NAC (PeNAC) family members of passion fruit are still lacking. In this study, 25 PeNACs were identified from the passion fruit genome, and their functions under abiotic stress and at different fruit-ripening stages were analyzed. Furthermore, we analyzed the transcriptome sequencing results of PeNACs under four various abiotic stresses (drought, salt, cold and high temperature) and three different fruit-ripening stages, and verified the expression results of some genes by qRT-PCR. Additionally, tissue-specific analysis showed that most PeNACs were mainly expressed in flowers. In particular, PeNAC-19 was induced by four various abiotic stresses. At present, low temperatures have seriously endangered the development of passion fruit cultivation. Therefore, PeNAC-19 was transformed into tobacco, yeast and Arabidopsis to study their function of resisting low temperature. The results show that PeNAC-19 responded to cold stress significantly in tobacco and Arabidopsis, and could improve the low temperature tolerance of yeast. This study not only improved the understanding of the PeNAC gene family characteristics and evolution, but also provided new insights into the regulation of the PeNAC gene at different stages of fruit maturation and abiotic stresses.
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Affiliation(s)
- Yi Xu
- State Key Laboratory of Biological Breeding for Tropical Crops, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Germplasm Repository of Passiflora, Hainan Province, Hainan 571101, China
- Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya 571101, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 571101, China
| | - Pengfei Li
- College of Tropical Crops, Yunnan Agricultural University, Kunming 650201, China
| | - Funing Ma
- State Key Laboratory of Biological Breeding for Tropical Crops, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Germplasm Repository of Passiflora, Hainan Province, Hainan 571101, China
- Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya 571101, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 571101, China
| | - Dongmei Huang
- State Key Laboratory of Biological Breeding for Tropical Crops, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Germplasm Repository of Passiflora, Hainan Province, Hainan 571101, China
| | - Wenting Xing
- State Key Laboratory of Biological Breeding for Tropical Crops, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Germplasm Repository of Passiflora, Hainan Province, Hainan 571101, China
| | - Bin Wu
- State Key Laboratory of Biological Breeding for Tropical Crops, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Germplasm Repository of Passiflora, Hainan Province, Hainan 571101, China
| | - Peiguang Sun
- State Key Laboratory of Biological Breeding for Tropical Crops, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Germplasm Repository of Passiflora, Hainan Province, Hainan 571101, China
| | - Binqiang Xu
- State Key Laboratory of Biological Breeding for Tropical Crops, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Germplasm Repository of Passiflora, Hainan Province, Hainan 571101, China
| | - Shun Song
- State Key Laboratory of Biological Breeding for Tropical Crops, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Germplasm Repository of Passiflora, Hainan Province, Hainan 571101, China
- Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya 571101, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 571101, China
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13
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Li A, Yang Q, Li R, Dai X, Cai K, Lei Y, Jia K, Jiang Y, Zan L. Chromosome-level genome assembly for takin (Budorcas taxicolor) provides insights into its taxonomic status and genetic diversity. Mol Ecol 2023; 32:1323-1334. [PMID: 35467052 DOI: 10.1111/mec.16483] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 03/29/2022] [Accepted: 04/17/2022] [Indexed: 11/29/2022]
Abstract
The takin (Budorcas taxicolor) is one of the largest bovid herbivores in the subfamily Caprinae. The takin is at high risk of extinction, but its taxonomic status and genetic diversity remain unclear. In this study, we constructed the first reference genome of Bu. taxicolor using PacBio long High-Fidelity reads and Hi-C technology. The assembled genome is ~2.95 Gb with a contig N50 of 68.05 Mb, which were anchored onto 25+XY chromosomes. We found that the takin was more closely related to muskox than to other Caprinae species. Compared to the common ancestral karyotype of bovidae (2n = 60), we found the takin (2n = 52) experienced four chromosome fusions and one large translocation. Furthermore, we resequenced nine golden takins from the main distribution area, the Qinling Mountains, and identified 3.3 million single nucleotide polymorphisms. The genetic diversity of takin was very low (θπ = 0.00028 and heterozygosity =0.00038), among the lowest detected in domestic and wild mammals. Takin genomes showed a high inbreeding coefficient (FROH =0.217), suggesting severe inbreeding depression. The demographic history showed that the effective population size of takins declined significantly from ~100,000 years ago. Our results provide valuable information for protection of takins and insights into their evolution.
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Affiliation(s)
- Anning Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Qimeng Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.,Center for Ruminant Genetic and Evolution, Northwest A&F University, Yangling, Shaanxi, China
| | - Ran Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.,Center for Ruminant Genetic and Evolution, Northwest A&F University, Yangling, Shaanxi, China
| | - Xuelei Dai
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.,Center for Ruminant Genetic and Evolution, Northwest A&F University, Yangling, Shaanxi, China
| | - Keli Cai
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yinghu Lei
- Research Center for the Qinling Giant Panda (Shaanxi Rare Wildlife Rescue Base), Shaanxi Academy of Forestry Sciences, Zhouzhi, Shaanxi, China
| | - Kangsheng Jia
- Research Center for the Qinling Giant Panda (Shaanxi Rare Wildlife Rescue Base), Shaanxi Academy of Forestry Sciences, Zhouzhi, Shaanxi, China
| | - Yu Jiang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.,Center for Ruminant Genetic and Evolution, Northwest A&F University, Yangling, Shaanxi, China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.,Research Center for the Qinling Giant Panda (Shaanxi Rare Wildlife Rescue Base), Shaanxi Academy of Forestry Sciences, Zhouzhi, Shaanxi, China
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14
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Liang J, Fang Y, An C, Yao Y, Wang X, Zhang W, Liu R, Wang L, Aslam M, Cheng Y, Qin Y, Zheng P. Genome-wide identification and expression analysis of the bHLH gene family in passion fruit (Passiflora edulis) and its response to abiotic stress. Int J Biol Macromol 2023; 225:389-403. [PMID: 36400210 DOI: 10.1016/j.ijbiomac.2022.11.076] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/23/2022] [Accepted: 11/01/2022] [Indexed: 11/17/2022]
Abstract
Passion fruit is a tropical fruit crop with significant agricultural, economic and ornamental values. The growth and development of passion fruit are greatly affected by climatic conditions. In plants, the basic helix-loop-helix (bHLH) gene family plays essential roles in the floral organ and fruit development, as well as stress response. However, the characteristics and functions of the bHLH genes of passion fruit remain unclear. Here, 138 passion fruit bHLH members were identified and classified into 20 subfamilies. The structural analysis illustrated that PebHLH proteins of the specific subfamily are relatively conserved. Collinearity analysis indicated that the expansion of the PebHLH gene family mainly took place by segmental duplication, and the structural diversity of duplicated genes might contribute to their functional diversity. PebHLHs, which potentially regulate different floral organ and fruit development, were further screened out, and many of these genes were differentially expressed under various stress treatments. The co-presence of different cis-regulatory elements involved in developmental regulation, hormone and stress responses in the promoter regions of PebHLHs might be closely related to their diverse regulatory roles. Overall, this study will be helpful for further functional investigation of PebHLHs and provides clues for improvement of the passion fruit breeding.
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Affiliation(s)
- Jianxiang Liang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yunying Fang
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chang An
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Yuanbin Yao
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaomei Wang
- Horticulture Research Institute, Guangxi Academy of Agricultural Sciences, Nanning Investigation Station of South Subtropical Fruit Trees, Ministry of Agriculture, Nanning 530004, China
| | - Wenbin Zhang
- Xinluo Breeding Center for Excellent Germplasms, Longyan 361000, China
| | - Ruoyu Liu
- Pingtan Science and Technology Research Institute, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lulu Wang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Mohammad Aslam
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yan Cheng
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuan Qin
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning 530004, China; Pingtan Science and Technology Research Institute, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Ping Zheng
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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15
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Genome-Wide Identification and Characterization of the SBP Gene Family in Passion Fruit ( Passiflora edulis Sims). Int J Mol Sci 2022; 23:ijms232214153. [PMID: 36430627 PMCID: PMC9695787 DOI: 10.3390/ijms232214153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/13/2022] [Accepted: 11/14/2022] [Indexed: 11/19/2022] Open
Abstract
The SQUAMOSA promoter binding proteins (SBPs) gene family plays important roles in plant growth and development. The SBP gene family has been identified and reported in many species, but it has not been well studied in passion fruit. In this study, a total of 14 SBP genes were identified in passion fruit and named from PeSBP1 to PeSBP14 based on their chromosomal distribution. The phylogenetic tree, gene structure, conserved motifs, collinearity analysis, and expression patterns of the identified SBP members were analyzed. We classified the PeSBP genes into eight groups (I to VIII) according to the phylogenetic tree, gene structure, and conserved motifs. Synteny analysis found that 5 homologous gene pairs existed in PeSBP genes and 11 orthologous gene pairs existed between passion fruit and Arabidopsis. Synonymous nucleotide substitution analysis showed that the PeSBP genes were under strong negative selection. The expression pattern of PeSBP genes in seed, root, leaf, and flower showed that nine of the PeSBP genes displayed high expression in the leaf and the flower. The expression patterns of PeSBP3/6/8/9/10 were further detected by qRT-PCR. In addition, differences in the expression levels occurred for each gene in the different flower organs and at the different developmental stages. There were large differences among SBPs based on transcriptional levels under cold, heat, salt, and osmotic stress conditions. Altogether, this study provides an overview of SBP genes in passion fruit and lays the foundation for further functional analysis.
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16
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Zhou T, Bai G, Hu Y, Ruhsam M, Yang Y, Zhao Y. De novo genome assembly of the medicinal plant Gentiana macrophylla provides insights into the genomic evolution and biosynthesis of iridoids. DNA Res 2022; 29:6748869. [PMID: 36197098 PMCID: PMC9724787 DOI: 10.1093/dnares/dsac034] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 08/24/2022] [Accepted: 09/12/2022] [Indexed: 12/13/2022] Open
Abstract
Gentiana macrophylla is a perennial herb in the Gentianaceae family, whose dried roots are used in traditional Chinese medicine. Here, we assembled a chromosome-level genome of G. macrophylla using a combination of Nanopore, Illumina, and Hi-C scaffolding approaches. The final genome size was ~1.79 Gb (contig N50 = 720.804 kb), and 98.89% of the genome sequences were anchored on 13 pseudochromosomes (scaffold N50 = 122.73 Mb). The genome contained 55,337 protein-coding genes, and 73.47% of the assemblies were repetitive sequences. Genome evolution analysis indicated that G. macrophylla underwent two rounds of whole-genome duplication after the core eudicot γ genome triplication event. We further identified candidate genes related to the biosynthesis of iridoids, and the corresponding gene families mostly expanded in G. macrophylla. In addition, we found that root-specific genes are enriched in pathways involved in defense responses, which may greatly improve the biological adaptability of G. macrophylla. Phylogenomic analyses showed a sister relationship of asterids and rosids, and all Gentianales species formed a monophyletic group. Our study contributes to the understanding of genome evolution and active component biosynthesis in G. macrophylla and provides important genomic resource for the genetic improvement and breeding of G. macrophylla.
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Affiliation(s)
- Tao Zhou
- Corresponding author: Tel. +86 29 8265 5424. (T.Z.); (Y.Z.)
| | | | | | - Markus Ruhsam
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK
| | - Yanci Yang
- School of Biological Science and Technology, Baotou Teachers’ College, Baotou, China
| | - Yuemei Zhao
- Corresponding author: Tel. +86 29 8265 5424. (T.Z.); (Y.Z.)
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17
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Drought Stress Stimulates the Terpenoid Backbone and Triterpenoid Biosynthesis Pathway to Promote the Synthesis of Saikosaponin in Bupleurum chinense DC. Roots. Molecules 2022; 27:molecules27175470. [PMID: 36080237 PMCID: PMC9457724 DOI: 10.3390/molecules27175470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 11/17/2022] Open
Abstract
Bupleurum chinense is an important medicinal plant in China; however, little is known regarding how this plant transcribes and synthesizes saikosaponins under drought stress. Herein, we investigated how drought stress stimulates the transcriptional changes of B. chinense to synthesize saikosaponins. Short-term drought stress induced the accumulation of saikosaponins, especially from the first re-watering stage (RD_1 stage) to the second re-watering stage (RD_2 stage). Saikosaponin-a and saikosaponin-d increased by 84.60% and 75.13%, respectively, from the RD_1 stage to the RD_2 stage. Drought stress also stimulated a rapid increase in the levels of the hormones abscisic acid, salicylic acid, and jasmonic acid. We screened 49 Unigenes regarding the terpenoid backbone and triterpenoid biosynthesis, of which 33 differential genes were significantly up-regulated during drought stress. Moreover, one P450 and two UGTs are possibly involved in the synthesis of saikosaponins, while some transcription factors may be involved in regulating the expression of key enzyme genes. Our study provides a reference for the cultivation of B. chinense and a practical means to ensure the quality (safety and effectiveness) of B. chinense for medicinal use, as well as insights into the modernization of the China Agriculture Research System.
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18
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Yang Q, Li B, Rizwan HM, Sun K, Zeng J, Shi M, Guo T, Chen F. Genome-wide identification and comprehensive analyses of NAC transcription factor gene family and expression analysis under Fusarium kyushuense and drought stress conditions in Passiflora edulis. FRONTIERS IN PLANT SCIENCE 2022; 13:972734. [PMID: 36092439 PMCID: PMC9453495 DOI: 10.3389/fpls.2022.972734] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 07/27/2022] [Indexed: 05/07/2023]
Abstract
The NAC gene family is one of the largest plant transcription factors (TFs) families and plays important roles in plant growth, development, metabolism, and biotic and abiotic stresses. However, NAC gene family has not been reported in passion fruit (Passiflora edulis). In this study, a total of 105 NAC genes were identified in the passion fruit genome and were unevenly distributed across all nine-passion fruit chromomere, with a maximum of 48 PeNAC genes on chromosome one. The physicochemical features of all 105 PeNAC genes varied including 120 to 3,052 amino acids, 3 to 8 conserved motifs, and 1 to 3 introns. The PeNAC genes were named (PeNAC001-PeNAC105) according to their chromosomal locations and phylogenetically grouped into 15 clades (NAC-a to NAC-o). Most PeNAC proteins were predicted to be localized in the nucleus. The cis-element analysis indicated the possible roles of PeNAC genes in plant growth, development, light, hormones, and stress responsiveness. Moreover, the PeNAC gene duplications including tandem (11 gene pairs) and segmental (12 gene pairs) were identified and subjected to purifying selection. All PeNAC proteins exhibited similar 3D structures, and a protein-protein interaction network analysis with known Arabidopsis proteins was predicted. Furthermore, 17 putative ped-miRNAs were identified to target 25 PeNAC genes. Potential TFs including ERF, BBR-BPC, Dof, and bZIP were identified in promoter region of all 105 PeNAC genes and visualized in a TF regulatory network. GO and KEGG annotation analysis exposed that PeNAC genes were related to different biological, molecular, and cellular terms. The qRT-PCR expression analysis discovered that most of the PeNAC genes including PeNAC001, PeNAC003, PeNAC008, PeNAC028, PeNAC033, PeNAC058, PeNAC063, and PeNAC077 were significantly upregulated under Fusarium kyushuense and drought stress conditions compared to controls. In conclusion, these findings lay the foundation for further functional studies of PeNAC genes to facilitate the genetic improvement of plants to stress resistance.
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Affiliation(s)
| | | | | | | | | | | | | | - Faxing Chen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
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19
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Rizwan HM, Waheed A, Ma S, Li J, Arshad MB, Irshad M, Li B, Yang X, Ali A, Ahmed MAA, Shaheen N, Scholz SS, Oelmüller R, Lin Z, Chen F. Comprehensive Genome-Wide Identification and Expression Profiling of Eceriferum ( CER) Gene Family in Passion Fruit ( Passiflora edulis) Under Fusarium kyushuense and Drought Stress Conditions. FRONTIERS IN PLANT SCIENCE 2022; 13:898307. [PMID: 35832215 PMCID: PMC9272567 DOI: 10.3389/fpls.2022.898307] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
Plant surfaces are covered with cuticle wax and are the first barrier between a plant and environmental stresses. Eceriferum (CER) is an important gene family involved in wax biosynthesis and stress resistance. In this study, for the first time, 34 CER genes were identified in the passion fruit (Passiflora edulis) genome, and PeCER proteins varied in physicochemical properties. A phylogenetic tree was constructed and divided into seven clades to identify the evolutionary relationship with other plant species. Gene structure analyses revealed that conserved motifs ranged from 1 to 24, and that exons ranged from 1 to 29. The cis-element analysis provides insight into possible roles of PeCER genes in plant growth, development and stress responses. The syntenic analysis revealed that segmental (six gene pairs) and tandem (six gene pairs) gene duplication played an important role in the expansion of PeCER genes and underwent a strong purifying selection. In addition, 12 putative ped-miRNAs were identified to be targeting 16 PeCER genes, and PeCER6 was the most targeted by four miRNAs including ped-miR157a-5p, ped-miR164b-5p, ped-miR319b, and ped-miR319l. Potential transcription factors (TFs) such as ERF, AP2, MYB, and bZIP were predicted and visualized in a TF regulatory network interacting with PeCER genes. GO and KEGG annotation analysis revealed that PeCER genes were highly related to fatty acid, cutin, and wax biosynthesis, plant-pathogen interactions, and stress response pathways. The hypothesis that most PeCER proteins were predicted to localize to the plasma membrane was validated by transient expression assays of PeCER32 protein in onion epidermal cells. qRT-PCR expression results showed that most of the PeCER genes including PeCER1, PeCER11, PeCER15, PeCER17, and PeCER32 were upregulated under drought and Fusarium kyushuense stress conditions compared to controls. These findings provide a foundation for further studies on functions of PeCER genes to further facilitate the genetic modification of passion fruit wax biosynthesis and stress resistance.
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Affiliation(s)
| | - Abdul Waheed
- Key Laboratory for Bio Pesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Songfeng Ma
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiankun Li
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Muhammad Bilal Arshad
- Department of Plant Breeding and Genetics, College of Agriculture, University of Sargodha, Sargodha, Pakistan
| | - Muhammad Irshad
- College of Horticulture, The University of Agriculture, Peshawar, Pakistan
| | - Binqi Li
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xuelian Yang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ahmad Ali
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mohamed A. A. Ahmed
- Plant Production Department (Horticulture-Medicinal and Aromatic Plants), Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria, Egypt
| | - Nusrat Shaheen
- Department of Chemistry, Abbottabad University of Science and Technology, Abbottabad, Pakistan
| | - Sandra S. Scholz
- Matthias Schleiden Institute, Plant Physiology, Friedrich-Schiller-University Jena, Jena, Germany
| | - Ralf Oelmüller
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- Matthias Schleiden Institute, Plant Physiology, Friedrich-Schiller-University Jena, Jena, Germany
| | - Zhimin Lin
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Faxing Chen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
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20
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Bai G, Chen C, Zhao C, Zhou T, Li D, Zhou T, Li W, Lu Y, Cong X, Jia Y, Li S. The chromosome-level genome for Toxicodendron vernicifluum provides crucial insights into Anacardiaceae evolution and urushiol biosynthesis. iScience 2022; 25:104512. [PMID: 35733792 PMCID: PMC9207680 DOI: 10.1016/j.isci.2022.104512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 04/21/2022] [Accepted: 05/27/2022] [Indexed: 12/04/2022] Open
Abstract
The lacquer tree (Toxicodendron vernicifluum (Stokes) F.A. Barkley) is an important tree with economic, industrial, and medicinal values. Here, we generated the reference genome of T. vernicifluum at the chromosome level with 491.93 Mb in size, in which 98.26% of the assembled contigs were anchored onto 15 pseudochromosomes with the scaffold N50 of 32.97 Mb. Comparative genomic analysis revealed the gene families related to urushiol biosynthesis were expanded, contributing to the ecological fitness and biological adaptability of the lacquer tree. We combined multi-omics data to identify genes that encode key enzymes in the T. vernicifluum urushiol and lignin biosynthetic pathways. Furthermore, the unique active metabolites, such as butin and fisetin, in cultivar lacquers were identified by metabolism profiling. Our work would provide crucial insights into metabolite synthesis such as urushiol and lignin, meanwhile offer a basis for further exploration of the cultivation and breeding of T. vernicifluum and other Anacardiaceae members. We provide the first chromosome-level genome for Toxicodendron vernicifluum We explore the phylogenetic position of lacquer tree We identify genes involved in the urushiol and lignin biosynthetic pathways Analysis of the unique active metabolites in cultivar lacquers by LC-MS/MS is reported
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Affiliation(s)
- Guoqing Bai
- Xi’an Botanical Garden of Shaanxi Province, Shaanxi Province Qinling-Bashan Mountains Engineering Research Centre of Conservation and Utilization of Biological Resources, Xi’an 710061, China
| | - Chen Chen
- Xi’an Botanical Garden of Shaanxi Province, Shaanxi Province Qinling-Bashan Mountains Engineering Research Centre of Conservation and Utilization of Biological Resources, Xi’an 710061, China
| | - Chenxi Zhao
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tao Zhou
- School of Pharmacy, Xi’an Jiaotong University, Xi’an 710061, China
| | - Dan Li
- SDIC Biotech Investment Co., Ltd., Shanghai 200082, China
| | - Tianhua Zhou
- College of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, China
| | - Weimin Li
- Xi’an Botanical Garden of Shaanxi Province, Shaanxi Province Qinling-Bashan Mountains Engineering Research Centre of Conservation and Utilization of Biological Resources, Xi’an 710061, China
| | - Yuan Lu
- Xi’an Botanical Garden of Shaanxi Province, Shaanxi Province Qinling-Bashan Mountains Engineering Research Centre of Conservation and Utilization of Biological Resources, Xi’an 710061, China
| | - Xiaofeng Cong
- Xi’an Botanical Garden of Shaanxi Province, Shaanxi Province Qinling-Bashan Mountains Engineering Research Centre of Conservation and Utilization of Biological Resources, Xi’an 710061, China
| | - Yun Jia
- Xi’an Botanical Garden of Shaanxi Province, Shaanxi Province Qinling-Bashan Mountains Engineering Research Centre of Conservation and Utilization of Biological Resources, Xi’an 710061, China
| | - Sifeng Li
- Xi’an Botanical Garden of Shaanxi Province, Shaanxi Province Qinling-Bashan Mountains Engineering Research Centre of Conservation and Utilization of Biological Resources, Xi’an 710061, China
- Corresponding author
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21
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Sun Y, Shang L, Zhu QH, Fan L, Guo L. Twenty years of plant genome sequencing: achievements and challenges. TRENDS IN PLANT SCIENCE 2022; 27:391-401. [PMID: 34782248 DOI: 10.1016/j.tplants.2021.10.006] [Citation(s) in RCA: 94] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 09/15/2021] [Accepted: 10/18/2021] [Indexed: 05/27/2023]
Abstract
Publication of the complete genome sequence of Arabidopsis thaliana, the first plant reference genome, in December 2000 heralded the beginning of the plant genome era. Over the past 20 years reference genomes have been generated for hundreds of plant species, spanning non-vascular to flowering plants. Releasing these plant genomes has dramatically advanced studies in all disciplines of plant biology. Importantly, multiple reference-level genomes have been generated for the major crops and their progenitors, enabling the creation of pan-genomes and exploration of domestication history and natural variations that can be adopted by modern crop breeding. We summarize the progress of plant genome sequencing and the challenges of sequencing more complex plant genomes and generating pan-genomes.
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Affiliation(s)
- Yanqing Sun
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou, China
| | - Lianguang Shang
- 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, China
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, Black Mountain Laboratories, Canberra, Australia
| | - Longjiang Fan
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou, China; Zhejiang University City College School of Medicine, Hangzhou, China.
| | - Longbiao Guo
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China.
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22
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Rizwan HM, Shaozhong F, Li X, Bilal Arshad M, Yousef AF, Chenglong Y, Shi M, Jaber MYM, Anwar M, Hu SY, Yang Q, Sun K, Ahmed MAA, Min Z, Oelmüller R, Zhimin L, Chen F. Genome-Wide Identification and Expression Profiling of KCS Gene Family in Passion Fruit ( Passiflora edulis) Under Fusarium kyushuense and Drought Stress Conditions. FRONTIERS IN PLANT SCIENCE 2022; 13:872263. [PMID: 35548275 PMCID: PMC9081883 DOI: 10.3389/fpls.2022.872263] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/03/2022] [Indexed: 05/02/2023]
Abstract
Plant and fruit surfaces are covered with cuticle wax and provide a protective barrier against biotic and abiotic stresses. Cuticle wax consists of very-long-chain fatty acids (VLCFAs) and their derivatives. β-Ketoacyl-CoA synthase (KCS) is a key enzyme in the synthesis of VLCFAs and provides a precursor for the synthesis of cuticle wax, but the KCS gene family was yet to be reported in the passion fruit (Passiflora edulis). In this study, thirty-two KCS genes were identified in the passion fruit genome and phylogenetically grouped as KCS1-like, FAE1-like, FDH-like, and CER6-like. Furthermore, thirty-one PeKCS genes were positioned on seven chromosomes, while one PeKCS was localized to the unassembled genomic scaffold. The cis-element analysis provides insight into the possible role of PeKCS genes in phytohormones and stress responses. Syntenic analysis revealed that gene duplication played a crucial role in the expansion of the PeKCS gene family and underwent a strong purifying selection. All PeKCS proteins shared similar 3D structures, and a protein-protein interaction network was predicted with known Arabidopsis proteins. There were twenty putative ped-miRNAs which were also predicted that belong to nine families targeting thirteen PeKCS genes. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation results were highly associated with fatty acid synthase and elongase activity, lipid metabolism, stress responses, and plant-pathogen interaction. The highly enriched transcription factors (TFs) including ERF, MYB, Dof, C2H2, TCP, LBD, NAC, and bHLH were predicted in PeKCS genes. qRT-PCR expression analysis revealed that most PeKCS genes were highly upregulated in leaves including PeKCS2, PeKCS4, PeKCS8, PeKCS13, and PeKCS9 but not in stem and roots tissues under drought stress conditions compared with controls. Notably, most PeKCS genes were upregulated at 9th dpi under Fusarium kyushuense biotic stress condition compared to controls. This study provides a basis for further understanding the functions of KCS genes, improving wax and VLCFA biosynthesis, and improvement of passion fruit resistance.
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Affiliation(s)
| | - Fang Shaozhong
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Xiaoting Li
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Muhammad Bilal Arshad
- Department of Plant Breeding and Genetics, College of Agriculture, University of Sargodha, Sargodha, Pakistan
| | - Ahmed Fathy Yousef
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- Department of Horticulture, College of Agriculture, University of Al-Azhar, Assiut, Egypt
| | - Yang Chenglong
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Meng Shi
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mohammed Y. M. Jaber
- Department of Plant Production and Protection, Faculty of Agriculture and Veterinary Medicine, An-Najah National University, Nablus, Palestine
| | - Muhammad Anwar
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Shuai-Ya Hu
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agriculture University, Nanjing, China
| | - Qiang Yang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kaiwei Sun
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mohamed A. A. Ahmed
- Plant Production Department (Horticulture-Medicinal and Aromatic Plants), Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria, Egypt
| | - Zheng Min
- Department of Horticulture, Fujian Agricultural Vocational College, Fuzhou, China
| | - Ralf Oelmüller
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- Matthias Schleiden Institute, Plant Physiology, Friedrich-Schiller-University Jena, Jena, Germany
| | - Lin Zhimin
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences, Fuzhou, China
- *Correspondence: Lin Zhimin,
| | - Faxing Chen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- Faxing Chen,
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23
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Sader M, Vaio M, Cauz-Santos LA, Dornelas MC, Vieira MLC, Melo N, Pedrosa-Harand A. Large vs small genomes in Passiflora: the influence of the mobilome and the satellitome. PLANTA 2021; 253:86. [PMID: 33792791 DOI: 10.1007/s00425-021-03598-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 03/18/2021] [Indexed: 05/22/2023]
Abstract
While two lineages of retrotransposons were more abundant in larger Passiflora genomes, the satellitome was more diverse and abundant in the smallest genome analysed. Repetitive sequences are ubiquitous and fast-evolving elements responsible for size variation and large-scale organization of plant genomes. Within Passiflora genus, a tenfold variation in genome size, not attributed to polyploidy, is known. Here, we applied a combined in silico and cytological approach to study the organization and diversification of repetitive elements in three species of this genus representing its known range in genome size variation. Sequences were classified in terms of type and repetitiveness and the most abundant were mapped to chromosomes. We identified long terminal repeat (LTR) retrotransposons as the most abundant elements in the three genomes, showing a considerable variation among species. Satellite DNAs (satDNAs) were less representative, but highly diverse between subgenera. Our results clearly confirm that the largest genome species (Passiflora quadrangularis) presents a higher accumulation of repetitive DNA sequences, specially Angela and Tekay elements, making up most of its genome. Passiflora cincinnata, with intermediate genome and from the same subgenus, showed similarity with P. quadrangularis regarding the families of repetitive DNA sequences, but in different proportions. On the other hand, Passiflora organensis, the smallest genome, from a different subgenus, presented greater diversity and the highest proportion of satDNA. Altogether, our data indicates that while large genomes evolved by an accumulation of retrotransposons, the smallest genome known for the genus has evolved by diversification of different repeat types, particularly satDNAs.
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Affiliation(s)
- Mariela Sader
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Pernambuco, Brazil.
| | - Magdalena Vaio
- Laboratory of Plant Genome Evolution and Domestication, Department of Plant Biology, Faculty of Agronomy, University of the Republic, Montevideo, Uruguay
| | - Luiz Augusto Cauz-Santos
- Genetics Department, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | | | - Maria Lucia Carneiro Vieira
- Genetics Department, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Natoniel Melo
- Laboratory of Biotechnology, Embrapa Semiarid, Petrolina, Pernambuco, Brazil
| | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Pernambuco, Brazil
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24
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Cheng QQ, Ouyang Y, Tang ZY, Lao CC, Zhang YY, Cheng CS, Zhou H. Review on the Development and Applications of Medicinal Plant Genomes. FRONTIERS IN PLANT SCIENCE 2021; 12:791219. [PMID: 35003182 PMCID: PMC8732986 DOI: 10.3389/fpls.2021.791219] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/23/2021] [Indexed: 05/04/2023]
Abstract
With the development of sequencing technology, the research on medicinal plants is no longer limited to the aspects of chemistry, pharmacology, and pharmacodynamics, but reveals them from the genetic level. As the price of next-generation sequencing technology becomes affordable, and the long-read sequencing technology is established, the medicinal plant genomes with large sizes have been sequenced and assembled more easily. Although the review of plant genomes has been reported several times, there is no review giving a systematic and comprehensive introduction about the development and application of medicinal plant genomes that have been reported until now. Here, we provide a historical perspective on the current situation of genomes in medicinal plant biology, highlight the use of the rapidly developing sequencing technologies, and conduct a comprehensive summary on how the genomes apply to solve the practical problems in medicinal plants, like genomics-assisted herb breeding, evolution history revelation, herbal synthetic biology study, and geoherbal research, which are important for effective utilization, rational use and sustainable protection of medicinal plants.
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Affiliation(s)
- Qi-Qing Cheng
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Yue Ouyang
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Zi-Yu Tang
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Chi-Chou Lao
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Yan-Yu Zhang
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Chun-Song Cheng
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
| | - Hua Zhou
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
- Joint Laboratory for Translational Cancer Research of Chinese Medicine, The Ministry of Education of the People’s Republic of China, Macau University of Science and Technology, Taipa, Macao SAR, China
- *Correspondence: Hua Zhou,
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25
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Gui F, Lan T, Zhao Y, Guo W, Dong Y, Fang D, Liu H, Li H, Wang H, Hao R, Cheng X, Li Y, Yang P, Sahu SK, Chen Y, Cheng L, He S, Liu P, Fan G, Lu H, Hu G, Dong W, Chen B, Jiang Y, Zhang Y, Xu H, Lin F, Slippers B, Postma A, Jackson M, Abate BA, Tesfaye K, Demie AL, Bayeleygne MD, Degefu DT, Chen F, Kuria PK, Kinyua ZM, Liu TX, Yang H, Huang F, Liu X, Sheng J, Kang L. Genomic and transcriptomic analysis unveils population evolution and development of pesticide resistance in fall armyworm Spodoptera frugiperda. Protein Cell 2020; 13:513-531. [PMID: 33108584 PMCID: PMC9226219 DOI: 10.1007/s13238-020-00795-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 09/15/2020] [Indexed: 11/24/2022] Open
Abstract
The fall armyworm (FAW), Spodoptera frugiperda, is a destructive pest native to America and has recently become an invasive insect pest in China. Because of its rapid spread and great risks in China, understanding of FAW genetic background and pesticide resistance is urgent and essential to develop effective management strategies. Here, we assembled a chromosome-level genome of a male FAW (SFynMstLFR) and compared re-sequencing results of the populations from America, Africa, and China. Strain identification of 163 individuals collected from America, Africa and China showed that both C and R strains were found in the American populations, while only C strain was found in the Chinese and African populations. Moreover, population genomics analysis showed that populations from Africa and China have close relationship with significantly genetic differentiation from American populations. Taken together, FAWs invaded into China were most likely originated from Africa. Comparative genomics analysis displayed that the cytochrome p450 gene family is extremely expanded to 425 members in FAW, of which 283 genes are specific to FAW. Treatments of Chinese populations with twenty-three pesticides showed the variant patterns of transcriptome profiles, and several detoxification genes such as AOX, UGT and GST specially responded to the pesticides. These findings will be useful in developing effective strategies for management of FAW in China and other invaded areas.
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Affiliation(s)
- Furong Gui
- State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China.,Yunnan Plateau Characteristic Agriculture Industry Research Institute, Kunming, 650201, China
| | - Tianming Lan
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Yue Zhao
- State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
| | - Wei Guo
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Yang Dong
- State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China.,Yunnan Plateau Characteristic Agriculture Industry Research Institute, Kunming, 650201, China
| | - Dongming Fang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Haimeng Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Hongli Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Ruoshi Hao
- Yunnan Plateau Characteristic Agriculture Industry Research Institute, Kunming, 650201, China
| | | | - Yahong Li
- Yunnan Plant Protection and Quarantine Station, Kunming, 650034, China
| | - Pengcheng Yang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Yaping Chen
- State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
| | - Le Cheng
- BGI-Yunnan, No. 389 Haiyuan Road, High-tech Development Zone, Kunming, 650106, China
| | - Shuqi He
- State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
| | - Ping Liu
- MGI, BGI-Shenzhen, Shenzhen, 518083, China
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Haorong Lu
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen, 518120, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, 518120, China
| | - Guohai Hu
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen, 518120, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, 518120, China
| | - Wei Dong
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Bin Chen
- State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
| | - Yuan Jiang
- BGI-Americas, One Broadway, 14th Floor, Cambridge, MA, 02142, USA
| | - Yongwei Zhang
- BGI-Americas, One Broadway, 14th Floor, Cambridge, MA, 02142, USA
| | - Hanhong Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Fei Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Bernard Slippers
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Alisa Postma
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Matthew Jackson
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | | | - Kassahun Tesfaye
- Ethiopian Biotechnology Institute, Addis Ababa, Ethiopia.,College of Natural Science, Addis Ababa University, Addis Ababa, Ethiopia
| | | | | | - Dawit Tesfaye Degefu
- Melkassa Agricultural Research Center, Ethiopian Institute of Agricultural Research, Melkassa, Addis Ababa, Ethiopia
| | - Feng Chen
- MGI, BGI-Shenzhen, Shenzhen, 518083, China
| | - Paul K Kuria
- Kenya Agricultural and Livestock Research Organization, P.O. Box 57811, Nairobi, 00800, Kenya
| | - Zachary M Kinyua
- Kenya Agricultural and Livestock Research Organization, P.O. Box 57811, Nairobi, 00800, Kenya
| | - Tong-Xian Liu
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, 266109, China
| | - Huanming Yang
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, 518120, China.,Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Shenzhen, 518120, China
| | - Fangneng Huang
- Department of Entomology, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA.
| | - Xin Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China. .,Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, 518120, China.
| | - Jun Sheng
- State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China. .,Yunnan Plateau Characteristic Agriculture Industry Research Institute, Kunming, 650201, China.
| | - Le Kang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China. .,Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China. .,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100101, China.
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