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Wang D, Dong X, Zhong MC, Jiang XD, Cui WH, Bendahmane M, Hu JY. Molecular and genetic regulation of petal number variation. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:3233-3247. [PMID: 38546444 DOI: 10.1093/jxb/erae136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 03/26/2024] [Indexed: 06/11/2024]
Abstract
Floral forms with an increased number of petals, also known as double-flower phenotypes, have been selected and conserved in many domesticated plants, particularly in ornamentals, because of their great economic value. The molecular and genetic mechanisms that control this trait are therefore of great interest, not only for scientists, but also for breeders. In this review, we summarize current knowledge of the gene regulatory networks of flower initiation and development and known mutations that lead to variation of petal number in many species. In addition to the well-accepted miR172/AP2-like module, for which many questions remain unanswered, we also discuss other pathways in which mutations also lead to the formation of extra petals, such as those involved in meristem maintenance, hormone signalling, epigenetic regulation, and responses to environmental signals. We discuss how the concept of 'natural mutants' and recent advances in genomics and genome editing make it possible to explore the molecular mechanisms underlying double-flower formation, and how such knowledge could contribute to the future breeding and selection of this trait in more crops.
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Affiliation(s)
- Dan Wang
- Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, 650204 Kunming, Yunnan, China
| | - Xue Dong
- Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 650201 Kunming, Yunnan, China
| | - Mi-Cai Zhong
- Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Xiao-Dong Jiang
- Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Wei-Hua Cui
- Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Mohammed Bendahmane
- Laboratoire Reproduction et Développement des Plantes, INRAE-CNRS-Lyon1-ENS, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Jin-Yong Hu
- Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
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Xing HT, Shi JY, Yin SQ, Wu QH, Lv JL, Li HL. The MYB family and their response to abiotic stress in ginger (Zingiber officinale Roscoe). BMC Genomics 2024; 25:460. [PMID: 38730330 PMCID: PMC11088133 DOI: 10.1186/s12864-024-10392-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 05/08/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Zingiber officinale Roscoe, colloquially known as ginger, is a crop of significant medicinal and culinary value that frequently encounters adversity stemming from inhospitable environmental conditions. The MYB transcription factors have garnered recognition for their pivotal role in orchestrating a multitude of plant biological pathways. Nevertheless, the enumeration and characterization of the MYBs within Z. officinale Roscoe remains unknown. This study embarks on a genome-wide scrutiny of the MYB gene lineage in ginger, with the aim of cataloging all ZoMYB genes implicated in the biosynthesis of gingerols and curcuminoids, and elucidating their potential regulatory mechanisms in counteracting abiotic stress, thereby influencing ginger growth and development. RESULTS In this study, we identified an MYB gene family comprising 231 members in ginger genome. This ensemble comprises 74 singular-repeat MYBs (1R-MYB), 156 double-repeat MYBs (R2R3-MYB), and a solitary triple-repeat MYB (R1R2R3-MYB). Moreover, a comprehensive analysis encompassing the sequence features, conserved protein motifs, phylogenetic relationships, chromosome location, and gene duplication events of the ZoMYBs was conducted. We classified ZoMYBs into 37 groups, congruent with the number of conserved domains and gene structure analysis. Additionally, the expression profiles of ZoMYBs during development and under various stresses, including ABA, cold, drought, heat, and salt, were investigated in ginger utilizing both RNA-seq data and qRT-PCR analysis. CONCLUSION This work provides a comprehensive understanding of the MYB family in ginger and lays the foundation for the future investigation of the potential functions of ZoMYB genes in ginger growth, development and abiotic stress tolerance of ginger.
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Affiliation(s)
- Hai-Tao Xing
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, 402168, China.
- Biological Sciences Research Center, Academy for Advanced Interdisciplinary Studies, Southwest University, Chongqing, 400715, China.
- Chongqing Academy of Chinese Materia Medica, Chongqing, 400065, China.
- Chongqing Key Laboratory for Germplasm Innovation of Special Aromatic Spice Plants, Chongqing University of Arts and Sciences, Chongqing, 402168, China.
| | - Jia-Yu Shi
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, 402168, China
| | - Shi-Qing Yin
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, 402168, China
| | - Qing-Hong Wu
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, 402168, China
| | - Jian-Ling Lv
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, 402168, China
| | - Hong-Lei Li
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, 402168, China.
- Chongqing Key Laboratory for Germplasm Innovation of Special Aromatic Spice Plants, Chongqing University of Arts and Sciences, Chongqing, 402168, China.
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Chen Z, Zhang L, Lv Y, Qu S, Liu W, Wang K, Gao S, Zhu F, Cao B, Xu K. A genome assembly of ginger (Zingiber officinale Roscoe) provides insights into genome evolution and 6-gingerol biosynthesis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:682-695. [PMID: 38251816 DOI: 10.1111/tpj.16625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 12/12/2023] [Accepted: 12/22/2023] [Indexed: 01/23/2024]
Abstract
Ginger is cultivated in tropical and subtropical regions and is one of the most crucial spices worldwide owing to its special taste and scent. Here, we present a high-quality genome assembly for 'Small Laiwu Ginger', a famous cultivated ginger in northern China. The ginger genome was phased into two haplotypes, haplotype A (1.55Gb), and haplotype B (1.44Gb). Analysis of Ty1/Copia and Ty3/Gypsy LTR retrotransposon families revealed that both have undergone multiple retrotransposon bursts about 0-1 million years ago. In addition to a recent whole-genome duplication event, there has been a lineage-specific expansion of genes involved in stilbenoid, diarylheptanoid, and gingerol biosynthesis, thereby enhancing 6-gingerol biosynthesis. Furthermore, we focused on the biosynthesis of 6-gingerol, the most important gingerol, and screened key transcription factors ZoMYB106 and ZobHLH148 that regulate 6-gingerol synthesis by transcriptomic and metabolomic analysis in the ginger rhizome at four growth stages. The results of yeast one-hybrid, electrophoretic mobility shift, and dual-luciferase reporter gene assays showed that both ZoMYB106 and ZobHLH148 bind to the promoters of the key rate-limiting enzyme genes ZoCCOMT1 and ZoCCOMT2 in the 6-gingerol synthesis pathway and promote their transcriptional activities. The reference genome, transcriptome, and metabolome data pave the way for further research on the molecular mechanism underlying the biosynthesis of 6-gingerol. Furthermore, it provides precious new resources for the study on the biology and molecular breeding of ginger.
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Affiliation(s)
- Zijing Chen
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, P. R. China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops in Huanghuai Region, Ministry of Agriculture and Rural Affairs, Taian, P. R. China
| | - Ling Zhang
- Laiwu Municipal Agriculture Bureau in Shandong, Jinan, P. R. China
| | - Yao Lv
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, P. R. China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops in Huanghuai Region, Ministry of Agriculture and Rural Affairs, Taian, P. R. China
| | - Shenyang Qu
- Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences, Shenzhen, P. R. China
| | - Wenjun Liu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, P. R. China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops in Huanghuai Region, Ministry of Agriculture and Rural Affairs, Taian, P. R. China
| | - Kai Wang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, P. R. China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops in Huanghuai Region, Ministry of Agriculture and Rural Affairs, Taian, P. R. China
| | - Song Gao
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, P. R. China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops in Huanghuai Region, Ministry of Agriculture and Rural Affairs, Taian, P. R. China
- College of Horticulture and Landscape Architecture, Yaozhou University, Yangzhou, P. R. China
| | - Feng Zhu
- Laiwu Municipal Agriculture Bureau in Shandong, Jinan, P. R. China
| | - Bili Cao
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, P. R. China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops in Huanghuai Region, Ministry of Agriculture and Rural Affairs, Taian, P. R. China
| | - Kun Xu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, P. R. China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops in Huanghuai Region, Ministry of Agriculture and Rural Affairs, Taian, P. R. China
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Hlavatá K, Záveská E, Leong-Škorničková J, Pouch M, Poulsen AD, Šída O, Khadka B, Mandáková T, Fér T. Ancient hybridization and repetitive element proliferation in the evolutionary history of the monocot genus Amomum (Zingiberaceae). FRONTIERS IN PLANT SCIENCE 2024; 15:1324358. [PMID: 38708400 PMCID: PMC11066291 DOI: 10.3389/fpls.2024.1324358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 03/12/2024] [Indexed: 05/07/2024]
Abstract
Genome size variation is a crucial aspect of plant evolution, influenced by a complex interplay of factors. Repetitive elements, which are fundamental components of genomic architecture, often play a role in genome expansion by selectively amplifying specific repeat motifs. This study focuses on Amomum, a genus in the ginger family (Zingiberaceae), known for its 4.4-fold variation in genome size. Using a robust methodology involving PhyloNet reconstruction, RepeatExplorer clustering, and repeat similarity-based phylogenetic network construction, we investigated the repeatome composition, analyzed repeat dynamics, and identified potential hybridization events within the genus. Our analysis confirmed the presence of four major infrageneric clades (A-D) within Amomum, with clades A-C exclusively comprising diploid species (2n = 48) and clade D encompassing both diploid and tetraploid species (2n = 48 and 96). We observed an increase in the repeat content within the genus, ranging from 84% to 89%, compared to outgroup species with 75% of the repeatome. The SIRE lineage of the Ty1-Copia repeat superfamily was prevalent in most analyzed ingroup genomes. We identified significant difference in repeatome structure between the basal Amomum clades (A, B, C) and the most diverged clade D. Our investigation revealed evidence of ancient hybridization events within Amomum, coinciding with a substantial proliferation of multiple repeat groups. This finding supports the hypothesis that ancient hybridization is a driving force in the genomic evolution of Amomum. Furthermore, we contextualize our findings within the broader context of genome size variations and repeatome dynamics observed across major monocot lineages. This study enhances our understanding of evolutionary processes within monocots by highlighting the crucial roles of repetitive elements in shaping genome size and suggesting the mechanisms that drive these changes.
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Affiliation(s)
- Kristýna Hlavatá
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
| | - Eliška Záveská
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
- Institute of Botany, Czech Academy of Science, Průhonice, Czechia
| | - Jana Leong-Škorničková
- Herbarium, Singapore Botanic Gardens, National Parks Board, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Milan Pouch
- Central European Institute of Technology, Masaryk University, Brno, Czechia
- National Center for Biomolecular Research (NCBR), Masaryk University, Kamenice, Czechia
| | - Axel Dalberg Poulsen
- Tropical Diversity Section, Royal Botanic Garden Edinburgh, Edinburgh, United Kingdom
| | - Otakar Šída
- Department of Botany, National Museum in Prague, Prague, Czechia
| | - Bijay Khadka
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
| | - Terezie Mandáková
- Central European Institute of Technology, Masaryk University, Brno, Czechia
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Tomáš Fér
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
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Lu Y, Chen X, Yu H, Zhang C, Xue Y, Zhang Q, Wang H. Haplotype-resolved genome assembly of Phanera championii reveals molecular mechanisms of flavonoid synthesis and adaptive evolution. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:488-505. [PMID: 38173092 DOI: 10.1111/tpj.16620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 12/15/2023] [Accepted: 12/20/2023] [Indexed: 01/05/2024]
Abstract
Phanera championii is a medicinal liana plant that has successfully adapted to hostile karst habitats. Despite extensive research on its medicinal components and pharmacological effects, the molecular mechanisms underlying the biosynthesis of critical flavonoids and its adaptation to karst habitats remain elusive. In this study, we performed high-coverage PacBio and Hi-C sequencing of P. championii, which revealed its high heterozygosity and phased the genome into two haplotypes: Hap1 (384.60 Mb) and Hap2 (383.70 Mb), encompassing a total of 58 612 annotated genes. Comparative genomes analysis revealed that P. championii experienced two whole-genome duplications (WGDs), with approximately 59.59% of genes originating from WGD events, thereby providing a valuable genetic resource for P. championii. Moreover, we identified a total of 112 genes that were strongly positively selected. Additionally, about 81.60 Mb of structural variations between the two haplotypes. The allele-specific expression patterns suggested that the dominant effect of P. championii was the elimination of deleterious mutations and the promotion of beneficial mutations to enhance fitness. Moreover, our transcriptome and metabolome analysis revealed alleles in different tissues or different haplotypes collectively regulate the synthesis of flavonoid metabolites. In summary, our comprehensive study highlights the significance of genomic and morphological adaptation in the successful adaptation of P. championii to karst habitats. The high-quality phased genomes obtained in this study serve as invaluable genomic resources for various applications, including germplasm conservation, breeding, evolutionary studies, and elucidation of pathways governing key biological traits of P. championii.
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Affiliation(s)
- Yongbin Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and the Chinese Academy of Sciences, Yanshan, Guilin, 541006, China
| | - Xiao Chen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Hang Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China
- Key Laboratory of Crop Cultivation and Physiology, Education Department of Guangxi Zhuang Autonomous Region, Guangxi University, Nanning, 530004, China
| | - Chao Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China
- Key Laboratory of Crop Cultivation and Physiology, Education Department of Guangxi Zhuang Autonomous Region, Guangxi University, Nanning, 530004, China
| | - Yajie Xue
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China
- Key Laboratory of Crop Cultivation and Physiology, Education Department of Guangxi Zhuang Autonomous Region, Guangxi University, Nanning, 530004, China
| | - Qiang Zhang
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and the Chinese Academy of Sciences, Yanshan, Guilin, 541006, China
| | - Haifeng Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China
- Key Laboratory of Crop Cultivation and Physiology, Education Department of Guangxi Zhuang Autonomous Region, Guangxi University, Nanning, 530004, China
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Pei Y, Leng L, Sun W, Liu B, Feng X, Li X, Chen S. Whole-genome sequencing in medicinal plants: current progress and prospect. SCIENCE CHINA. LIFE SCIENCES 2024; 67:258-273. [PMID: 37837531 DOI: 10.1007/s11427-022-2375-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 05/23/2023] [Indexed: 10/16/2023]
Abstract
Advancements in genomics have dramatically accelerated the research on medicinal plants, and the development of herbgenomics has promoted the "Project of 1K Medicinal Plant Genome" to decipher their genetic code. However, it is difficult to obtain their high-quality whole genomes because of the prevalence of polyploidy and/or high genomic heterozygosity. Whole genomes of 123 medicinal plants were published until September 2022. These published genome sequences were investigated in this review, covering their classification, research teams, ploidy, medicinal functions, and sequencing strategies. More than 1,000 institutes or universities around the world and 50 countries are conducting research on medicinal plant genomes. Diploid species account for a majority of sequenced medicinal plants. The whole genomes of plants in the Poaceae family are the most studied. Almost 40% of the published papers studied species with tonifying, replenishing, and heat-cleaning medicinal effects. Medicinal plants are still in the process of domestication as compared with crops, thereby resulting in unclear genetic backgrounds and the lack of pure lines, thus making their genomes more difficult to complete. In addition, there is still no clear routine framework for a medicinal plant to obtain a high-quality whole genome. Herein, a clear and complete strategy has been originally proposed for creating a high-quality whole genome of medicinal plants. Moreover, whole genome-based biological studies of medicinal plants, including breeding and biosynthesis, were reviewed. We also advocate that a research platform of model medicinal plants should be established to promote the genomics research of medicinal plants.
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Affiliation(s)
- Yifei Pei
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Liang Leng
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Wei Sun
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Baocai Liu
- Institute of Agricultural Bioresource, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, China
| | - Xue Feng
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Xiwen Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Shilin Chen
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
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Zhang P, Liu D, Ma J, Sun C, Wang Z, Zhu Y, Zhang X, Liu Y. Genome-wide analysis and expression pattern of the ZoPP2C gene family in Zingiber officinale Roscoe. BMC Genomics 2024; 25:83. [PMID: 38245685 PMCID: PMC10799369 DOI: 10.1186/s12864-024-09966-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 01/03/2024] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND Protein phosphatases type 2C (PP2C) are heavily involved in plant growth and development, hormone-related signaling pathways and the response of various biotic and abiotic stresses. However, a comprehensive report identifying the genome-scale of PP2C gene family in ginger is yet to be published. RESULTS In this study, 97 ZoPP2C genes were identified based on the ginger genome. These genes were classified into 15 branches (A-O) according to the phylogenetic analysis and distributed unevenly on 11 ginger chromosomes. The proteins mainly functioned in the nucleus. Similar motif patterns and exon/intron arrangement structures were identified in the same subfamily of ZoPP2Cs. Collinearity analysis indicated that ZoPP2Cs had 33 pairs of fragment duplicated events uniformly distributed on the corresponding chromosomes. Furthermore, ZoPP2Cs showed greater evolutionary proximity to banana's PP2Cs. The forecast of cis-regulatory elements and transcription factor binding sites demonstrated that ZoPP2Cs participate in ginger growth, development, and responses to hormones and stresses. ZoERFs have plenty of binding sites of ZoPP2Cs, suggesting a potential synergistic contribution between ZoERFs and ZoPP2Cs towards regulating growth/development and adverse conditions. The protein-protein interaction network displayed that five ZoPP2Cs (9/23/26/49/92) proteins have robust interaction relationship and potential function as hub proteins. Furthermore, the RNA-Seq and qRT-PCR analyses have shown that ZoPP2Cs exhibit various expression patterns during ginger maturation and responses to environmental stresses such as chilling, drought, flooding, salt, and Fusarium solani. Notably, exogenous application of melatonin led to notable up-regulation of ZoPP2Cs (17/59/11/72/43) under chilling stress. CONCLUSIONS Taken together, our investigation provides significant insights of the ginger PP2C gene family and establishes the groundwork for its functional validation and genetic engineering applications.
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Affiliation(s)
- Pan Zhang
- College of Horticulture and Gardening, Spice Crops Research Institute, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Deqi Liu
- College of Horticulture and Gardening, Spice Crops Research Institute, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Jiawei Ma
- College of Horticulture and Gardening, Spice Crops Research Institute, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Chong Sun
- Special Plants Institute, College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, 402160, China
| | - Zhaofei Wang
- Special Plants Institute, College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, 402160, China
| | - Yongxing Zhu
- College of Horticulture and Gardening, Spice Crops Research Institute, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Xuemei Zhang
- College of Horticulture and Gardening, Spice Crops Research Institute, Yangtze University, Jingzhou, 434025, Hubei, China.
| | - Yiqing Liu
- College of Horticulture and Gardening, Spice Crops Research Institute, Yangtze University, Jingzhou, 434025, Hubei, China.
- Special Plants Institute, College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, 402160, China.
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Han S, Han X, Qi C, Guo F, Yin J, Liu Y, Zhu Y. Genome-Wide Identification of DUF668 Gene Family and Expression Analysis under F. solani, Chilling, and Waterlogging Stresses in Zingiber officinale. Int J Mol Sci 2024; 25:929. [PMID: 38256002 PMCID: PMC10815606 DOI: 10.3390/ijms25020929] [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: 12/10/2023] [Revised: 01/06/2024] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
The domains of unknown function (DUF) superfamilies contain proteins with conserved amino acid sequences without known functions. Among them, DUF668 was indicated widely involving the stress response of plants. However, understanding ZoDUF668 is still lacking. Here, 12 ZoDUF668 genes were identified in ginger by the bioinformatics method and unevenly distributed on six chromosomes. Conserved domain analysis showed that members of the same subfamily had similar conserved motifs and gene structures. The promoter region of ZoDUF668s contained the light, plant hormone and stress-responsive elements. The prediction of miRNA targeting relationship showed that nine ginger miRNAs targeted four ZoDUF668 genes through cleavage. The expression patterns of 12 ZoDUF668 genes under biotic and abiotic stress were analyzed using RT-qPCR. The results showed that the expression of seven ZoDUF668 genes was significantly downregulated under Fusarium solani infection, six ZoDUF668 genes were upregulated under cold stress, and five ZoDUF668 genes were upregulated under waterlogging stress. These results indicate that the ZoDUF668 gene has different expression patterns under different stress conditions. This study provides excellent candidate genes and provides a reference for stress-resistance research in ginger.
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Affiliation(s)
- Shuo Han
- Industrial Crops Institute of Hubei Academy of Agricultural Sciences, Key Laboratory of Vegetable Ecological Cultivation on Highland, Ministry of Agriculture and Rural Affairs, Wuhan 430064, China; (S.H.); (X.H.); (C.Q.)
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, Co-Construction by Ministry and Province, College of Agriculture, Yangtze University, Jingzhou 434025, China; (Y.L.); (Y.Z.)
| | - Xiaowen Han
- Industrial Crops Institute of Hubei Academy of Agricultural Sciences, Key Laboratory of Vegetable Ecological Cultivation on Highland, Ministry of Agriculture and Rural Affairs, Wuhan 430064, China; (S.H.); (X.H.); (C.Q.)
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, Co-Construction by Ministry and Province, College of Agriculture, Yangtze University, Jingzhou 434025, China; (Y.L.); (Y.Z.)
| | - Chuandong Qi
- Industrial Crops Institute of Hubei Academy of Agricultural Sciences, Key Laboratory of Vegetable Ecological Cultivation on Highland, Ministry of Agriculture and Rural Affairs, Wuhan 430064, China; (S.H.); (X.H.); (C.Q.)
| | - Fengling Guo
- Industrial Crops Institute of Hubei Academy of Agricultural Sciences, Key Laboratory of Vegetable Ecological Cultivation on Highland, Ministry of Agriculture and Rural Affairs, Wuhan 430064, China; (S.H.); (X.H.); (C.Q.)
| | - Junliang Yin
- Industrial Crops Institute of Hubei Academy of Agricultural Sciences, Key Laboratory of Vegetable Ecological Cultivation on Highland, Ministry of Agriculture and Rural Affairs, Wuhan 430064, China; (S.H.); (X.H.); (C.Q.)
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, Co-Construction by Ministry and Province, College of Agriculture, Yangtze University, Jingzhou 434025, China; (Y.L.); (Y.Z.)
| | - Yiqing Liu
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, Co-Construction by Ministry and Province, College of Agriculture, Yangtze University, Jingzhou 434025, China; (Y.L.); (Y.Z.)
| | - Yongxing Zhu
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, Co-Construction by Ministry and Province, College of Agriculture, Yangtze University, Jingzhou 434025, China; (Y.L.); (Y.Z.)
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Huang Y, Guo L, Xie L, Shang N, Wu D, Ye C, Rudell EC, Okada K, Zhu QH, Song BK, Cai D, Junior AM, Bai L, Fan L. A reference genome of Commelinales provides insights into the commelinids evolution and global spread of water hyacinth (Pontederia crassipes). Gigascience 2024; 13:giae006. [PMID: 38486346 PMCID: PMC10938897 DOI: 10.1093/gigascience/giae006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/20/2023] [Accepted: 02/08/2024] [Indexed: 03/18/2024] Open
Abstract
Commelinales belongs to the commelinids clade, which also comprises Poales that includes the most important monocot species, such as rice, wheat, and maize. No reference genome of Commelinales is currently available. Water hyacinth (Pontederia crassipes or Eichhornia crassipes), a member of Commelinales, is one of the devastating aquatic weeds, although it is also grown as an ornamental and medical plant. Here, we present a chromosome-scale reference genome of the tetraploid water hyacinth with a total length of 1.22 Gb (over 95% of the estimated size) across 8 pseudochromosome pairs. With the representative genomes, we reconstructed a phylogeny of the commelinids, which supported Zingiberales and Commelinales being sister lineages of Arecales and shed lights on the controversial relationship of the orders. We also reconstructed ancestral karyotypes of the commelinids clade and confirmed the ancient commelinids genome having 8 chromosomes but not 5 as previously reported. Gene family analysis revealed contraction of disease-resistance genes during polyploidization of water hyacinth, likely a result of fitness requirement for its role as a weed. Genetic diversity analysis using 9 water hyacinth lines from 3 continents (South America, Asia, and Europe) revealed very closely related nuclear genomes and almost identical chloroplast genomes of the materials, as well as provided clues about the global dispersal of water hyacinth. The genomic resources of P. crassipes reported here contribute a crucial missing link of the commelinids species and offer novel insights into their phylogeny.
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Affiliation(s)
- Yujie Huang
- Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Zhongyuan Institute of Zhejiang University, Zhengzhou 450000, China
| | - Longbiao Guo
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Lingjuan Xie
- Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Nianmin Shang
- Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Dongya Wu
- Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Chuyu Ye
- Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Eduardo Carlos Rudell
- Department of Crop Sciences, Agricultural School, Federal University of Rio Grande do Sul, Porto Alegre, RS 68011, Brazil
| | - Kazunori Okada
- Agro-Biotechnology Research Center (AgTECH), University of Tokyo, Tokyo 113-8657, Japan
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, Black Mountain Laboratories, Canberra, ACT 2601, Australia
| | - Beng-Kah Song
- School of Science, Monash University Malaysia, Bandar Sunway, Selangor 46150, Malaysia
| | - Daguang Cai
- Department of Molecular Phytopathology and Biotechnology, Christian Albrechts University of Kiel, Kiel D-24118, Germany
| | - Aldo Merotto Junior
- Department of Crop Sciences, Agricultural School, Federal University of Rio Grande do Sul, Porto Alegre, RS 68011, Brazil
| | - Lianyang Bai
- Hunan Weed Science Key Laboratory, Hunan Academy of Agriculture Science, Changsha 410125, China
| | - Longjiang Fan
- Institute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Zhongyuan Institute of Zhejiang University, Zhengzhou 450000, China
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10
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Deng X, Ye Z, Duan J, Chen F, Zhi Y, Huang M, Huang M, Cheng W, Dou Y, Kuang Z, Huang Y, Bian G, Deng Z, Liu T, Lu L. Complete pathway elucidation and heterologous reconstitution of (+)-nootkatone biosynthesis from Alpinia oxyphylla. THE NEW PHYTOLOGIST 2024; 241:779-792. [PMID: 37933426 DOI: 10.1111/nph.19375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 10/14/2023] [Indexed: 11/08/2023]
Abstract
(+)-Nootkatone is a natural sesquiterpene ketone widely used in food, cosmetics, pharmaceuticals, and agriculture. It is also regarded as one of the most valuable terpenes used commercially. However, plants contain trace amounts of (+)-nootkatone, and extraction from plants is insufficient to meet market demand. Alpinia oxyphylla is a well-known medicinal plant in China, and (+)-nootkatone is one of the main components within the fruits. By transcriptome mining and functional screening using a precursor-providing yeast chassis, the complete (+)-nootkatone biosynthetic pathway in Alpinia oxyphylla was identified. A (+)-valencene synthase (AoVS) was identified as a novel monocot-derived valencene synthase; three (+)-valencene oxidases AoCYP6 (CYP71BB2), AoCYP9 (CYP71CX8), and AoCYP18 (CYP701A170) were identified by constructing a valencene-providing yeast strain. With further characterisation of a cytochrome P450 reductase (AoCPR1) and three dehydrogenases (AoSDR1/2/3), we successfully reconstructed the (+)-nootkatone biosynthetic pathway in Saccharomyces cerevisiae, representing a basis for its biotechnological production. Identifying the biosynthetic pathway of (+)-nootkatone in A. oxyphylla unravelled the molecular mechanism underlying its formation in planta and also supported the bioengineering production of (+)-nootkatone. The highly efficient yeast chassis screening method could be used to elucidate the complete biosynthetic pathway of other valuable plant natural products in future.
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Affiliation(s)
- Xiaomin Deng
- National Key Laboratory for Tropical Crop Breeding/Ministry of Agriculture Key Laboratory of Biology and Genetic Resources of Rubber Tree/State Key Laboratory Breeding Base of Cultivation and Physiology for Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
- Department of Urology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, Hubei, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, Hubei, China
| | - Ziling Ye
- Wuhan Hesheng Technology Co., Ltd, Wuhan, 430074, Hubei, China
| | - Jingyu Duan
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, Hubei, China
| | - Fangfang Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, Hubei, China
| | - Yao Zhi
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, Hubei, China
| | - Man Huang
- Wuhan Hesheng Technology Co., Ltd, Wuhan, 430074, Hubei, China
| | - Minjian Huang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, Hubei, China
| | - Weijia Cheng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, Hubei, China
| | - Yujie Dou
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, Hubei, China
| | - Zhaolin Kuang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, Hubei, China
| | - Yanglei Huang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, Hubei, China
| | - Guangkai Bian
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, Hubei, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, Hubei, China
| | - Tiangang Liu
- Department of Urology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, Hubei, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, Hubei, China
- Wuhan Hesheng Technology Co., Ltd, Wuhan, 430074, Hubei, China
- Wuhan University of Taikang Medical School, Wuhan University, Wuhan, 430071, Hubei, China
| | - Li Lu
- Department of Urology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, Hubei, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, Hubei, China
- Hubei Hongshan Laboratory, Wuhan, 430071, Hubei, China
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11
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Nestor BJ, Bayer PE, Fernandez CGT, Edwards D, Finnegan PM. Approaches to increase the validity of gene family identification using manual homology search tools. Genetica 2023; 151:325-338. [PMID: 37817002 PMCID: PMC10692271 DOI: 10.1007/s10709-023-00196-8] [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: 06/07/2023] [Accepted: 10/01/2023] [Indexed: 10/12/2023]
Abstract
Identifying homologs is an important process in the analysis of genetic patterns underlying traits and evolutionary relationships among species. Analysis of gene families is often used to form and support hypotheses on genetic patterns such as gene presence, absence, or functional divergence which underlie traits examined in functional studies. These analyses often require precise identification of all members in a targeted gene family. Manual pipelines where homology search and orthology assignment tools are used separately are the most common approach for identifying small gene families where accurate identification of all members is important. The ability to curate sequences between steps in manual pipelines allows for simple and precise identification of all possible gene family members. However, the validity of such manual pipeline analyses is often decreased by inappropriate approaches to homology searches including too relaxed or stringent statistical thresholds, inappropriate query sequences, homology classification based on sequence similarity alone, and low-quality proteome or genome sequences. In this article, we propose several approaches to mitigate these issues and allow for precise identification of gene family members and support for hypotheses linking genetic patterns to functional traits.
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Affiliation(s)
- Benjamin J Nestor
- School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia.
- Centre for Applied Bioinformatics, University of Western Australia, Perth, WA, 6009, Australia.
| | - Philipp E Bayer
- School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia
- Centre for Applied Bioinformatics, University of Western Australia, Perth, WA, 6009, Australia
| | - Cassandria G Tay Fernandez
- School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia
- Centre for Applied Bioinformatics, University of Western Australia, Perth, WA, 6009, Australia
| | - David Edwards
- School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia
- Centre for Applied Bioinformatics, University of Western Australia, Perth, WA, 6009, Australia
| | - Patrick M Finnegan
- School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia
- Centre for Applied Bioinformatics, University of Western Australia, Perth, WA, 6009, Australia
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12
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Liu M, Li C, Jiang T, Wang R, Wang Y, Zhang W, Pan X. Chromosome-scale genome assembly provides insights into flower coloration mechanisms of Canna indica. Int J Biol Macromol 2023; 251:126148. [PMID: 37591424 DOI: 10.1016/j.ijbiomac.2023.126148] [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: 05/17/2023] [Revised: 07/28/2023] [Accepted: 08/03/2023] [Indexed: 08/19/2023]
Abstract
Canna indica, which produce conspicuous and colorful flowers, are widely appreciated as ornamental plants. We used Pacific Biosciences sequencing (PacBio) and chromosome conformation capture (Hi-C) genome scaffolding to build a high-quality chromosome-scale genome assembly of C. indica and the genome assembly was 821Mb with a contig N50 of 48Mb assembled into nine chromosomes. The genome of C. indica was predicted to contain 31,130 genes and 30,816 genes were functionally annotated. Genome annotation identified 522 Mb (63.59 %) as repetitive sequences. Genome evolution analysis showed that whole-genome duplication occurred 53.4 million years ago. Transcriptome analysis revealed that petal coloration was linked with the expression of genes encoding enzymes involved in anthocyanin biosynthesis, carotenoid biosynthesis, and the methylerythritol phosphate (MEP) pathway. Furthermore, modules of co-expressed genes and hub genes were identified via weighted gene co-expression network analysis. These results suggested that, in Canna indica, deep red petal coloration was regulated by CHS2 and yellow petal coloration was associated with expression of ARF6 and NAC14. Considered together, the current study revealed a high-quality reference genome which may provide new insights into the molecular basis of flower coloration in Canna indica and help enhance the conservation and breeding of ornamental plants in general.
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Affiliation(s)
- Mengmeng Liu
- College of Agriculture, Guizhou University, Guiyang 550025, People's Republic of China.
| | - Cheng Li
- College of Agriculture, Guizhou University, Guiyang 550025, People's Republic of China.
| | - Tang Jiang
- College of Agriculture, Guizhou University, Guiyang 550025, People's Republic of China.
| | - Ruipu Wang
- College of Agriculture, Guizhou University, Guiyang 550025, People's Republic of China.
| | - Yong Wang
- College of Agriculture, Guizhou University, Guiyang 550025, People's Republic of China.
| | - Wen'e Zhang
- College of Agriculture, Guizhou University, Guiyang 550025, People's Republic of China.
| | - Xuejun Pan
- College of Agriculture, Guizhou University, Guiyang 550025, People's Republic of China.
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13
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Shelake RM, Jadhav AM, Bhosale PB, Kim JY. Unlocking secrets of nature's chemists: Potential of CRISPR/Cas-based tools in plant metabolic engineering for customized nutraceutical and medicinal profiles. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108070. [PMID: 37816270 DOI: 10.1016/j.plaphy.2023.108070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/12/2023]
Abstract
Plant species have evolved diverse metabolic pathways to effectively respond to internal and external signals throughout their life cycle, allowing adaptation to their sessile and phototropic nature. These pathways selectively activate specific metabolic processes, producing plant secondary metabolites (PSMs) governed by genetic and environmental factors. Humans have utilized PSM-enriched plant sources for millennia in medicine and nutraceuticals. Recent technological advances have significantly contributed to discovering metabolic pathways and related genes involved in the biosynthesis of specific PSM in different food crops and medicinal plants. Consequently, there is a growing demand for plant materials rich in nutrients and bioactive compounds, marketed as "superfoods". To meet the industrial demand for superfoods and therapeutic PSMs, modern methods such as system biology, omics, synthetic biology, and genome editing (GE) play a crucial role in identifying the molecular players, limiting steps, and regulatory circuitry involved in PSM production. Among these methods, clustered regularly interspaced short palindromic repeats-CRISPR associated protein (CRISPR/Cas) is the most widely used system for plant GE due to its simple design, flexibility, precision, and multiplexing capabilities. Utilizing the CRISPR-based toolbox for metabolic engineering (ME) offers an ideal solution for developing plants with tailored preventive (nutraceuticals) and curative (therapeutic) metabolic profiles in an ecofriendly way. This review discusses recent advances in understanding the multifactorial regulation of metabolic pathways, the application of CRISPR-based tools for plant ME, and the potential research areas for enhancing plant metabolic profiles.
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Affiliation(s)
- Rahul Mahadev Shelake
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Republic of Korea.
| | - Amol Maruti Jadhav
- Research Institute of Green Energy Convergence Technology (RIGET), Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Pritam Bhagwan Bhosale
- Department of Veterinary Medicine, Research Institute of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Republic of Korea; Division of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea; Nulla Bio Inc, 501 Jinju-daero, Jinju, 52828, Republic of Korea.
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14
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Jiang Y, Jiang D, Xia M, Gong M, Li H, Xing H, Zhu X, Li HL. Genome-Wide Identification and Expression Analysis of the TCP Gene Family Related to Developmental and Abiotic Stress in Ginger. PLANTS (BASEL, SWITZERLAND) 2023; 12:3389. [PMID: 37836129 PMCID: PMC10574737 DOI: 10.3390/plants12193389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 09/16/2023] [Accepted: 09/19/2023] [Indexed: 10/15/2023]
Abstract
Ginger (Zingiber officinale Roscoe), a widely consumed edible and medicinal plant, possesses significant nutritional and economic value. Abiotic stresses such as drought and low temperatures can impact the growth and development of ginger. The plant-specific transcription factor Teosinte branched1/cycloidea/proliferating cell factor (TCP) has progressively been identified in various plants for its role in regulating plant growth and development as well as conferring resistance to abiotic stresses. However, limited information on the TCP family is available in ginger. In this study, we identified 20 TCP members in the ginger genome, which were randomly distributed across 9 chromosomes. Based on phylogenetic analysis, these ginger TCP were classified into two subfamilies: Class I (PCF) and Class II (CIN, CYC/TB). The classification of the identified ginger TCPs was supported by a multi-species phylogenetic tree and motif structure analysis, suggesting that the amplification of the ginger TCP gene family occurred prior to the differentiation of angiosperms. The promoter region of ginger TCP genes was found to contain numerous cis-acting elements associated with plant growth, development, and abiotic stress response. Among these elements, the stress response element, anaerobic induction, and MYB binding site play a dominant role in drought responsiveness. Additionally, expression pattern analysis revealed variations in the expression of ginger TCP gene among different tissues and in response to diverse abiotic stresses (drought, low temperature, heat, and salt). Our research offers a thorough examination of TCP members within the ginger plant. This analysis greatly contributes to the understanding of how TCP genes regulate tissue development and response to stress, opening up new avenues for further exploration in this field.
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Affiliation(s)
- Yajun Jiang
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; (Y.J.); (D.J.); (M.X.); (M.G.); (H.L.)
| | - Dongzhu Jiang
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; (Y.J.); (D.J.); (M.X.); (M.G.); (H.L.)
| | - Maoqin Xia
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; (Y.J.); (D.J.); (M.X.); (M.G.); (H.L.)
| | - Min Gong
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; (Y.J.); (D.J.); (M.X.); (M.G.); (H.L.)
| | - Hui Li
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; (Y.J.); (D.J.); (M.X.); (M.G.); (H.L.)
| | - Haitao Xing
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; (Y.J.); (D.J.); (M.X.); (M.G.); (H.L.)
| | - Xuedong Zhu
- Yudongnan Academy of Agricultural Sciences, Chongqing 408000, China
| | - Hong-Lei Li
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; (Y.J.); (D.J.); (M.X.); (M.G.); (H.L.)
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15
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Yang P, Ling XY, Zhou XF, Chen YX, Wang TT, Lin XJ, Zhao YY, Ye YS, Huang LX, Sun YW, Qi YX, Ma DM, Zhan RT, Huang XS, Yang JF. Comparing genomes of Fructus Amomi-producing species reveals genetic basis of volatile terpenoid divergence. PLANT PHYSIOLOGY 2023; 193:1244-1262. [PMID: 37427874 DOI: 10.1093/plphys/kiad400] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/25/2023] [Accepted: 06/13/2023] [Indexed: 07/11/2023]
Abstract
Wurfbainia longiligularis and Wurfbainia villosa are both rich in volatile terpenoids and are 2 primary plant sources of Fructus Amomi used for curing gastrointestinal diseases. Metabolomic profiling has demonstrated that bornyl diphosphate (BPP)-related terpenoids are more abundant in the W. villosa seeds and have a wider tissue distribution in W. longiligularis. To explore the genetic mechanisms underlying the volatile terpenoid divergence, a high-quality chromosome-level genome of W. longiligularis (2.29 Gb, contig N50 of 80.39 Mb) was assembled. Functional characterization of 17 terpene synthases (WlTPSs) revealed that WlBPPS, along with WlTPS 24/26/28 with bornyl diphosphate synthase (BPPS) activity, contributes to the wider tissue distribution of BPP-related terpenoids in W. longiligularis compared to W. villosa. Furthermore, transgenic Nicotiana tabacum showed that the GCN4-motif element positively regulates seed expression of WvBPPS and thus promotes the enrichment of BPP-related terpenoids in W. villosa seeds. Systematic identification and analysis of candidate TPS in 29 monocot plants from 16 families indicated that substantial expansion of TPS-a and TPS-b subfamily genes in Zingiberaceae may have driven increased diversity and production of volatile terpenoids. Evolutionary analysis and functional identification of BPPS genes showed that BPP-related terpenoids may be distributed only in the Zingiberaceae of monocot plants. This research provides valuable genomic resources for breeding and improving Fructus Amomi with medicinal and edible value and sheds light on the evolution of terpenoid biosynthesis in Zingiberaceae.
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Affiliation(s)
- Peng Yang
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
- Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese Medicine, School of Pharmaceutical Sciences, Hunan University of Medicine, Huaihua 418000, China
| | - Xu-Yi Ling
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Xiao-Fan Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Yuan-Xia Chen
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Tian-Tian Wang
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Xiao-Jing Lin
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Yuan-Yuan Zhao
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Yu-Shi Ye
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Lin-Xuan Huang
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Ye-Wen Sun
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Yu-Xin Qi
- Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese Medicine, School of Pharmaceutical Sciences, Hunan University of Medicine, Huaihua 418000, China
| | - Dong-Ming Ma
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Ruo-Ting Zhan
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Xue-Shuang Huang
- Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese Medicine, School of Pharmaceutical Sciences, Hunan University of Medicine, Huaihua 418000, China
| | - Jin-Fen Yang
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
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16
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Zhang W, Yang Y, Zhu X, Yang S, Liao X, Li H, Li Z, Liao Q, Tang J, Zhao G, Wu L. Integrated analyses of metabolomics and transcriptomics reveal the potential regulatory roles of long non-coding RNAs in gingerol biosynthesis. BMC Genomics 2023; 24:490. [PMID: 37633894 PMCID: PMC10464350 DOI: 10.1186/s12864-023-09553-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 08/03/2023] [Indexed: 08/28/2023] Open
Abstract
BACKGROUND As the characteristic functional component in ginger, gingerols possess several health-promoting properties. Long non-coding RNAs (lncRNAs) act as crucial regulators of diverse biological processes. However, lncRNAs in ginger are not yet identified so far, and their potential roles in gingerol biosynthesis are still unknown. In this study, metabolomic and transcriptomic analyses were performed in three main ginger cultivars (leshanhuangjiang, tonglingbaijiang, and yujiang 1 hao) in China to understand the potential roles of the specific lncRNAs in gingerol accumulation. RESULTS A total of 744 metabolites were monitored by metabolomics analysis, which were divided into eleven categories. Among them, the largest group phenolic acid category contained 143 metabolites, including 21 gingerol derivatives. Of which, three gingerol analogs, [8]-shogaol, [10]-gingerol, and [12]-shogaol, accumulated significantly. Moreover, 16,346 lncRNAs, including 2,513, 1,225, and 2,884 differentially expressed (DE) lncRNA genes (DELs), were identified in all three comparisons by transcriptomic analysis. Gene ontology enrichment (GO) analysis showed that the DELs mainly enriched in the secondary metabolite biosynthetic process, response to plant hormones, and phenol-containing compound metabolic process. Correlation analysis revealed that the expression levels of 11 DE gingerol biosynthesis enzyme genes (GBEGs) and 190 transcription factor genes (TF genes), such as MYB1, ERF100, WRKY40, etc. were strongly correlation coefficient with the contents of the three gingerol analogs. Furthermore, 7 and 111 upstream cis-acting lncRNAs, 1,200 and 2,225 upstream trans-acting lncRNAs corresponding to the GBEGs and TF genes were identified, respectively. Interestingly, 1,184 DELs might function as common upstream regulators to these GBEGs and TFs genes, such as LNC_008452, LNC_006109, LNC_004340, etc. Furthermore, protein-protein interaction networks (PPI) analysis indicated that three TF proteins, MYB4, MYB43, and WRKY70 might interact with four GBEG proteins (PAL1, PAL2, PAL3, and 4CL-4). CONCLUSION Based on these findings, we for the first time worldwide proposed a putative regulatory cascade of lncRNAs, TFs genes, and GBEGs involved in controlling of gingerol biosynthesis. These results not only provide novel insights into the lncRNAs involved in gingerol metabolism, but also lay a foundation for future in-depth studies of the related molecular mechanism.
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Affiliation(s)
- Wenlin Zhang
- Chongqing Key Laboratory of Economic Plant Biotechnology, College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, 402160, China
- College of Food Science, Southwest University, Beibei, 400715, China
| | - Yang Yang
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, College of Agronomy and Biotechnology, Southwest University, Beibei, 400715, China
| | - Xuedong Zhu
- Southeast Chongqing Academy of Agricultural Sciences, Fuling, 408000, China
| | - Suyu Yang
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, College of Agronomy and Biotechnology, Southwest University, Beibei, 400715, China
| | - Ximei Liao
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, College of Agronomy and Biotechnology, Southwest University, Beibei, 400715, China
| | - Honglei Li
- Chongqing Key Laboratory of Economic Plant Biotechnology, College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, 402160, China
| | - Zhexin Li
- Chongqing Key Laboratory of Economic Plant Biotechnology, College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, 402160, China
| | - Qinhong Liao
- Chongqing Key Laboratory of Economic Plant Biotechnology, College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, 402160, China
| | - Jianmin Tang
- Chongqing Key Laboratory of Economic Plant Biotechnology, College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, 402160, China.
| | - Guohua Zhao
- College of Food Science, Southwest University, Beibei, 400715, China.
| | - Lin Wu
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, College of Agronomy and Biotechnology, Southwest University, Beibei, 400715, China.
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Jiang D, Xia M, Xing H, Gong M, Jiang Y, Liu H, Li HL. Exploring the Heat Shock Transcription Factor ( HSF) Gene Family in Ginger: A Genome-Wide Investigation on Evolution, Expression Profiling, and Response to Developmental and Abiotic Stresses. PLANTS (BASEL, SWITZERLAND) 2023; 12:2999. [PMID: 37631210 PMCID: PMC10459109 DOI: 10.3390/plants12162999] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/11/2023] [Accepted: 08/18/2023] [Indexed: 08/27/2023]
Abstract
Ginger is a valuable crop known for its nutritional, seasoning, and health benefits. However, abiotic stresses, such as high temperature and drought, can adversely affect its growth and development. Heat shock transcription factors (HSFs) have been recognized as crucial elements for enhancing heat and drought resistance in plants. Nevertheless, no previous study has investigated the HSF gene family in ginger. In this research, a total of 25 ZoHSF members were identified in the ginger genome, which were unevenly distributed across ten chromosomes. The ZoHSF members were divided into three groups (HSFA, HSFB, and HSFC) based on their gene structure, protein motifs, and phylogenetic relationships with Arabidopsis. Interestingly, we found more collinear gene pairs between ZoHSF and HSF genes from monocots, such as rice, wheat, and banana, than dicots like Arabidopsis thaliana. Additionally, we identified 12 ZoHSF genes that likely arose from duplication events. Promoter analysis revealed that the hormone response elements (MEJA-responsiveness and abscisic acid responsiveness) were dominant among the various cis-elements related to the abiotic stress response in ZoHSF promoters. Expression pattern analysis confirmed differential expression of ZoHSF members across different tissues, with most showing responsiveness to heat and drought stress. This study lays the foundation for further investigations into the functional role of ZoHSFs in regulating abiotic stress responses in ginger.
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Affiliation(s)
- Dongzhu Jiang
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; (D.J.); (M.X.); (H.X.); (Y.J.)
- College of Horticulture and Gardening, Yangtze University, Jingzhou 433200, China
| | - Maoqin Xia
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; (D.J.); (M.X.); (H.X.); (Y.J.)
| | - Haitao Xing
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; (D.J.); (M.X.); (H.X.); (Y.J.)
| | - Min Gong
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing 404100, China;
| | - Yajun Jiang
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; (D.J.); (M.X.); (H.X.); (Y.J.)
| | - Huanfang Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China;
| | - Hong-Lei Li
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; (D.J.); (M.X.); (H.X.); (Y.J.)
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18
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Chen X, Sun S, Han X, Li C, Wang F, Nie B, Hou Z, Yang S, Ji J, Li G, Wang Y, Han X, Yue J, Li C, Li W, Zhang L, Yang D, Wang L. Multiomics comparison among populations of three plant sources of Amomi Fructus. HORTICULTURE RESEARCH 2023; 10:uhad128. [PMID: 37560015 PMCID: PMC10407604 DOI: 10.1093/hr/uhad128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 06/11/2023] [Indexed: 08/11/2023]
Abstract
Amomi Fructus (Sharen, AF) is a traditional Chinese medicine (TCM) from three source species (or varieties), including Wurfbainia villosa var. villosa (WVV), W. villosa var. xanthioides (WVX), or W. longiligularis (WL). Among them, WVV has been transplanted from its top-geoherb region, Guangdong, to its current main production area, Yunnan, for >50 years in China. However, the genetic and transcriptomic differentiation among multiple AF source species (or varieties) and between the origin and transplanted populations of WVV is unknown. In our study, the observed overall higher expression of terpenoid biosynthesis genes in WVV than in WVX provided possible evidence for the better pharmacological effect of WVV. We also screened six candidate borneol dehydrogenases (BDHs) that potentially catalyzed borneol into camphor in WVV and functionally verified them. Highly expressed genes at the P2 stage of WVV, Wv05G1424 and Wv05G1438, were capable of catalyzing the formation of camphor from (+)-borneol, (-)-borneol and DL-isoborneol. Moreover, the BDH genes may experience independent evolution after acquiring the ancestral copies, and the following tandem duplications might account for the abundant camphor content in WVV. Furthermore, four populations of WVV, WVX, and WL are genetically differentiated, and the gene flow from WVX to WVV in Yunnan contributed to the greater genetic diversity in the introduced population (WVV-JH) than in its top-geoherb region (WVV-YC), which showed the lowest genetic diversity and might undergo genetic degradation. In addition, terpene synthesis (TPS) and BDH genes were selected among populations of multiple AF source species (or varieties) and between the top- and non-top-geoherb regions, which might explain the difference in metabolites between these populations. Our findings provide important guidance for the conservation, genetic improvement, and industrial development of the three source species (or varieties) and for identifying top-geoherbalism with molecular markers, and proper clinical application of AF.
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Affiliation(s)
- Xinlian Chen
- School of Pharmaceutical Sciences, Sun Yat-Sen University, 510006 Guangzhou, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120 Shenzhen, China
| | - Shichao Sun
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120 Shenzhen, China
| | - Xiaoxu Han
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120 Shenzhen, China
| | - Cheng Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120 Shenzhen, China
| | - Fengjiao Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120 Shenzhen, China
| | - Bao Nie
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120 Shenzhen, China
| | - Zhuangwei Hou
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120 Shenzhen, China
| | - Song Yang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120 Shenzhen, China
| | - Jiaojiao Ji
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120 Shenzhen, China
| | - Ge Li
- Yunnan Key Laboratory of Southern Medicine Utilization, Yunnan Branch Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, 666100 Jinghong, China
| | - Yanqian Wang
- Yunnan Key Laboratory of Southern Medicine Utilization, Yunnan Branch Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, 666100 Jinghong, China
| | - Xiaoyu Han
- School of Pharmaceutical Sciences, Sun Yat-Sen University, 510006 Guangzhou, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120 Shenzhen, China
| | - Jianjun Yue
- School of Pharmaceutical Sciences, Sun Yat-Sen University, 510006 Guangzhou, China
- School of Traditional Dai-Thai Medicine, West Yunnan University of Applied Sciences, 666100 Jinghong, China
| | - Cui Li
- National Center for TCM Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, 530023 Nanning, China
| | - Wei Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120 Shenzhen, China
| | - Lixia Zhang
- Yunnan Key Laboratory of Southern Medicine Utilization, Yunnan Branch Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, 666100 Jinghong, China
| | - Depo Yang
- School of Pharmaceutical Sciences, Sun Yat-Sen University, 510006 Guangzhou, China
| | - Li Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120 Shenzhen, China
- Kunpeng Institute of Modern Agriculture at Foshan, Chinese Academy of Agricultural Sciences, 528200 Foshan, China
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Zhang P, Wang Y, Wang J, Li G, Li S, Ma J, Peng X, Yin J, Liu Y, Zhu Y. Transcriptomic and physiological analyses reveal changes in secondary metabolite and endogenous hormone in ginger (Zingiber officinale Rosc.) in response to postharvest chilling stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107799. [PMID: 37271022 DOI: 10.1016/j.plaphy.2023.107799] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/08/2023] [Accepted: 05/24/2023] [Indexed: 06/06/2023]
Abstract
Storing postharvest ginger at low temperatures can extend its shelf life, but can also lead to chilling injury, loss of flavor, and excessive water loss. To investigate the effects of chilling stress on ginger quality, morphological, physiological, and transcriptomic changes were examined after storage at 26 °C, 10 °C, and 2 °C for 24 h. Compared to 26 °C and 10 °C, storage at 2 °C significantly increased the concentrations of lignin, soluble sugar, flavonoids, and phenolics, as well as the accumulation of H2O2, O2-, and thiobarbituric acid reactive substances (TBARS). Additionally, chilling stress inhibited the levels of indoleacetic acid, while enhancing gibberellin, abscisic acid, and jasmonic acid, which may have increased postharvest ginger's adaptation to chilling. Storage at 10 °C decreased lignin concentration and oxidative damage, and induced less fluctuant changes in enzymes and hormones than storage at 2 °C. RNA-seq revealed that the number of differentially expressed genes (DEGs) increased with decreasing temperature. Functional enrichment analysis of the 523 DEGs that exhibited similar expression patterns between all treatments indicated that they were primarily enriched in phytohormone signaling, biosynthesis of secondary metabolites, and cold-associated MAPK signaling pathways. Key enzymes related to 6-gingerol and curcumin biosynthesis were downregulated at 2 °C, suggesting that cold storage may negatively impact ginger quality. Additionally, 2 °C activated the MKK4/5-MPK3/6-related protein kinase pathway, indicating that chilling may increase the risk of ginger pathogenesis.
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Affiliation(s)
- Pan Zhang
- Spice Crops Research Institute, College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Yanhong Wang
- Spice Crops Research Institute, College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Jie Wang
- Spice Crops Research Institute, College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Gang Li
- Spice Crops Research Institute, College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Siyun Li
- Spice Crops Research Institute, College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Jiawei Ma
- Jingzhou Jiazhiyuan Biotechnology Co. Ltd., Jingzhou, 434025, Hubei, China
| | - Xiangyan Peng
- Spice Crops Research Institute, College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Junliang Yin
- College of Agriculture, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Yiqing Liu
- Spice Crops Research Institute, College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China.
| | - Yongxing Zhu
- Spice Crops Research Institute, College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China.
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20
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Ren Y, Li WB, Li ZX, Zhang WL, Jue DW, Xing HT, Li HL, Li Q. Dynamic transcriptome profiling provides insights into rhizome enlargement in ginger (Zingiber officinale Rosc.). PLoS One 2023; 18:e0287969. [PMID: 37450442 PMCID: PMC10348538 DOI: 10.1371/journal.pone.0287969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 06/17/2023] [Indexed: 07/18/2023] Open
Abstract
The rhizome is an economically important part of ginger (Zingiber officinale Rosc.). However, the mechanism of ginger rhizome enlargement remains unclear. In this study, we performed an integrated analysis of the hormone content and transcriptome of ginger at three rhizome enlargement stages: initial enlargement (S1), middle enlargement (S2), and peak enlargement (S3). With rhizome enlargement, the levels of the hormones zeatin (ZT), gibberellic acid (GA), indole acetic acid (IAA), and jasmonic acid (JA) were significantly increased, and this increase was positively correlated with rhizome diameter. Transcriptomic analysis identified a large number of differentially expressed genes (DEGs); the number of DEGs were 2,206 in the transition from S1 to S2, and 1,151 in the transition from S2 to S3. The expression of several genes related to hormone biosynthesis and signalling and cell division or expansion, and transcription factors was significantly altered, which suggests that these genes play essential roles in rhizome enlargement. The results of correlation analysis suggested that the process of ginger rhizome enlargement may be primarily related to the regulation of endogenous cytokinin, GA3, auxin, and JA biosynthesis pathways and signal transduction; GRAS, HB, MYB, MYB122, bZIP60, ARF1, ARF2, E2FB1, and E2FB2, which may regulate the expression of rhizome formation-related genes; and CYC2, CDKB1, CDKB2, EXPA1, and XTH7, which may mediate cell division and expansion. These results provide gene resources and information that will be useful for the molecular breeding in ginger.
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Affiliation(s)
- Yun Ren
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Wen Bo Li
- School of Advanced Agriculture and Bioengineering, Yangtze Normal University, Fuling, Chongqing, China
| | - Zhe Xin Li
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Wen Lin Zhang
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Deng Wei Jue
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Hai Tao Xing
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Hong Lei Li
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Qiang Li
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
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21
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Wang X, Tian S, Wang H, Yang L, Zou X, Baskaran XR, Li Q, Xing H, Li HL. The complete chloroplast genome sequence of Zingiber teres S. Q. Tong & Y. M. Xia (Zingiberaceae). Mitochondrial DNA B Resour 2023; 8:699-703. [PMID: 37383606 PMCID: PMC10294729 DOI: 10.1080/23802359.2023.2226256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 06/12/2023] [Indexed: 06/30/2023] Open
Abstract
Here, the complete chloroplast genome sequence of Zingiber teres is described using MGI paired-end sequencing. The genome is 163,428 bp in length and contains a small single-copy region (SSC) of 15,782 bp, a large single-copy region (LSC) of 88,142 bp, and two inverted repeat (IR) regions of 29,752 bp. The overall GC content is 36.1%, and the GC content of the IR regions is 41.1%, which is higher than that of both the LSC region (33.8%) and SSC region (29.5%). The genome of Z. teres contains 133 complete genes, including 88 protein-coding genes (79 protein-coding gene species), 38 tRNA genes (28 tRNA species), and 8 rRNA genes (four rRNA species). Maximum likelihood phylogenetic analysis yielded a well-resolved tree of the genus Zingiber, and Z. teres and Zingiber mioga were sister species in this tree. The development of DNA barcodes could aid the identification of Zingiber species.
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Affiliation(s)
- Xiao Wang
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, China
| | - Shuming Tian
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, China
| | - Hao Wang
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, China
| | - Lin Yang
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, China
| | - Xiaoling Zou
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, China
| | | | - Qiang Li
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, China
| | - Haitao Xing
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, China
| | - Hong-Lei Li
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, China
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22
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Tang M, Huang J, Ma X, Du J, Bi Y, Guo P, Lu H, Wang L. A near-complete genome assembly of Thalia dealbata Fraser (Marantaceae). FRONTIERS IN PLANT SCIENCE 2023; 14:1183361. [PMID: 37384358 PMCID: PMC10298163 DOI: 10.3389/fpls.2023.1183361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/26/2023] [Indexed: 06/30/2023]
Abstract
This study presents a chromosome-level, near-complete genome assembly of Thalia dealbata (Marantaceae), a typical emergent wetland plant with high ornamental and environmental value. Based on 36.99 Gb PacBio HiFi reads and 39.44 Gb Hi-C reads, we obtained a 255.05 Mb assembly, of which 251.92 Mb (98.77%) were anchored into eight pseudo-chromosomes. Five pseudo-chromosomes were completely assembled, and the other three had one to two gaps. The final assembly had a high contig N50 value (29.80 Mb) and benchmarking universal single-copy orthologs (BUSCO) recovery score (97.52%). The T. dealbata genome had 100.35 Mb repeat sequences, 24,780 protein-coding genes, and 13,679 non-coding RNAs. Phylogenetic analysis revealed that T. dealbata was closest to Zingiber officinale, whose divergence time was approximately 55.41 million years ago. In addition, 48 and 52 significantly expanded and contracted gene families were identified within the T. dealbata genome. Moreover, 309 gene families were specific to T. dealbata, and 1,017 genes were positively selected. The T. dealbata genome reported in this study provides a valuable genomic resource for further research on wetland plant adaptation and the genome evolution dynamics. This genome is also beneficial for the comparative genomics of Zingiberales species and flowering plants.
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Affiliation(s)
- Min Tang
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, China
| | - Jialin Huang
- School of Chemical Biology and Environment, Yuxi Normal University, Yuxi, China
| | - Xiangli Ma
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Juan Du
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, China
| | - Yufen Bi
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Peiwen Guo
- School of Mathematical Sciences, Xiamen University, Xiamen, China
| | - Hao Lu
- Scientific Research Department, Kunming Novo Medical Laboratory Co., Ltd., Kunming, China
| | - Lei Wang
- Scientific Research Department, Kunming Novo Medical Laboratory Co., Ltd., Kunming, China
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Pan K, Dai S, Tian J, Zhang J, Liu J, Li M, Li S, Zhang S, Gao B. Chromosome-level genome and multi-omics analyses provide insights into the geo-herbalism properties of Alpinia oxyphylla. FRONTIERS IN PLANT SCIENCE 2023; 14:1161257. [PMID: 37360712 PMCID: PMC10285302 DOI: 10.3389/fpls.2023.1161257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 05/17/2023] [Indexed: 06/28/2023]
Abstract
Introduction Alpinia oxyphylla Miquel (A. oxyphylla), one of the "Four Famous South Medicines" in China, is an essential understory cash crop that is planted widely in the Hainan, Guangdong, Guangxi, and Fujian provinces. Particularly, A. oxyphylla from Hainan province is highly valued as the best national product for geo-herbalism and is an important indicator of traditional Chinese medicine efficacy. However, the molecular mechanism underlying the formation of its quality remains unspecified. Methods To this end, we employed a multi-omics approach to investigate the authentic quality formation of A. oxyphylla. Results In this study, we present a high-quality chromosome-level genome assembly of A. oxyphylla, with contig N50 of 76.96 Mb and a size of approximately 2.08Gb. A total of 38,178 genes were annotated, and the long terminal repeats were found to have a high frequency of 61.70%. Phylogenetic analysis demonstrated a recent whole-genome duplication event (WGD), which occurred before A. oxyphylla's divergence from W. villosa (~14 Mya) and is shared by other species from the Zingiberaceae family (Ks, ~0.3; 4DTv, ~0.125). Further, 17 regions from four provinces were comprehensively assessed for their metabolite content, and the quality of these four regions varied significantly. Finally, genomic, metabolic, and transcriptomic analyses undertaken on these regions revealed that the content of nootkatone in Hainan was significantly different from that in other provinces. Discussion Overall, our findings provide novel insights into germplasm conservation, geo-herbalism evaluation, and functional genomic research for the medicinal plant A. oxyphylla.
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Affiliation(s)
- Kun Pan
- Hainan Provincial Key Laboratory for Research and Development of Tropical Herbs, Haikou Key Laboratory of Li Nationality Medicine, Hainan Ouality Monitoring and Technology Service Center for Chinese Materia MedicaRaw Materials, School of Pharmacy, Hainan Medical University, Haikou, Hainan, China
| | - Shuiping Dai
- Hainan Provincial Key Laboratory for Research and Development of Tropical Herbs, Haikou Key Laboratory of Li Nationality Medicine, Hainan Ouality Monitoring and Technology Service Center for Chinese Materia MedicaRaw Materials, School of Pharmacy, Hainan Medical University, Haikou, Hainan, China
| | - Jianping Tian
- Hainan Provincial Key Laboratory for Research and Development of Tropical Herbs, Haikou Key Laboratory of Li Nationality Medicine, Hainan Ouality Monitoring and Technology Service Center for Chinese Materia MedicaRaw Materials, School of Pharmacy, Hainan Medical University, Haikou, Hainan, China
| | - Junqing Zhang
- Hainan Provincial Key Laboratory for Research and Development of Tropical Herbs, Haikou Key Laboratory of Li Nationality Medicine, Hainan Ouality Monitoring and Technology Service Center for Chinese Materia MedicaRaw Materials, School of Pharmacy, Hainan Medical University, Haikou, Hainan, China
- Academician Workstation of Hainan Province and The Specific Research Fund of The Innovation Platform for Academicians of Hainan Province, Haikou, Hainan, China
| | - Jiaqi Liu
- Hainan Provincial Key Laboratory for Research and Development of Tropical Herbs, Haikou Key Laboratory of Li Nationality Medicine, Hainan Ouality Monitoring and Technology Service Center for Chinese Materia MedicaRaw Materials, School of Pharmacy, Hainan Medical University, Haikou, Hainan, China
| | - Ming Li
- Hainan Provincial Key Laboratory for Research and Development of Tropical Herbs, Haikou Key Laboratory of Li Nationality Medicine, Hainan Ouality Monitoring and Technology Service Center for Chinese Materia MedicaRaw Materials, School of Pharmacy, Hainan Medical University, Haikou, Hainan, China
| | - Shanshan Li
- Hainan Provincial Key Laboratory for Research and Development of Tropical Herbs, Haikou Key Laboratory of Li Nationality Medicine, Hainan Ouality Monitoring and Technology Service Center for Chinese Materia MedicaRaw Materials, School of Pharmacy, Hainan Medical University, Haikou, Hainan, China
| | - Shengkui Zhang
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, China
| | - Bingmiao Gao
- Hainan Provincial Key Laboratory for Research and Development of Tropical Herbs, Haikou Key Laboratory of Li Nationality Medicine, Hainan Ouality Monitoring and Technology Service Center for Chinese Materia MedicaRaw Materials, School of Pharmacy, Hainan Medical University, Haikou, Hainan, China
- Academician Workstation of Hainan Province and The Specific Research Fund of The Innovation Platform for Academicians of Hainan Province, Haikou, Hainan, China
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Kong W, Wang Y, Zhang S, Yu J, Zhang X. Recent Advances in Assembly of Complex Plant Genomes. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:427-439. [PMID: 37100237 PMCID: PMC10787022 DOI: 10.1016/j.gpb.2023.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 03/18/2023] [Accepted: 04/07/2023] [Indexed: 04/28/2023]
Abstract
Over the past 20 years, tremendous advances in sequencing technologies and computational algorithms have spurred plant genomic research into a thriving era with hundreds of genomes decoded already, ranging from those of nonvascular plants to those of flowering plants. However, complex plant genome assembly is still challenging and remains difficult to fully resolve with conventional sequencing and assembly methods due to high heterozygosity, highly repetitive sequences, or high ploidy characteristics of complex genomes. Herein, we summarize the challenges of and advances in complex plant genome assembly, including feasible experimental strategies, upgrades to sequencing technology, existing assembly methods, and different phasing algorithms. Moreover, we list actual cases of complex genome projects for readers to refer to and draw upon to solve future problems related to complex genomes. Finally, we expect that the accurate, gapless, telomere-to-telomere, and fully phased assembly of complex plant genomes could soon become routine.
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Affiliation(s)
- Weilong Kong
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Yibin Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Shengcheng Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Jiaxin Yu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xingtan Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
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Mao J, Wang Y, Wang B, Li J, Zhang C, Zhang W, Li X, Li J, Zhang J, Li H, Zhang Z. High-quality haplotype-resolved genome assembly of cultivated octoploid strawberry. HORTICULTURE RESEARCH 2023; 10:uhad002. [PMID: 37077373 PMCID: PMC10108017 DOI: 10.1093/hr/uhad002] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 01/03/2023] [Indexed: 05/03/2023]
Abstract
Cultivated strawberry (Fragaria × ananassa), a perennial herb belonging to the family Rosaceae, is a complex octoploid with high heterozygosity at most loci. However, there is no research on the haplotype of the octoploid strawberry genome. Here we aimed to obtain a high-quality genome of the cultivated strawberry cultivar, "Yanli", using single molecule real-time sequencing and high-throughput chromosome conformation capture technology. The "Yanli" genome was 823 Mb in size, with a long terminal repeat assembly index of 14.99. The genome was phased into two haplotypes, Hap1 (825 Mb with contig N50 of 26.70 Mb) and Hap2 (808 Mb with contig N50 of 27.51 Mb). Using the combination of Hap1 and Hap2, we obtained for the first time a haplotype-resolved genome with 56 chromosomes for the cultivated octoploid strawberry. We identified a ~ 10 Mb inversion and translocation on chromosome 2-1. 104 957 and 102 356 protein-coding genes were annotated in Hap1 and Hap2, respectively. Analysis of the genes related to the anthocyanin biosynthesis pathway revealed the structural diversity and complexity in the expression of the alleles in the octoploid F. × ananassa genome. In summary, we obtained a high-quality haplotype-resolved genome assembly of F. × ananassa, which will provide the foundation for investigating gene function and evolution of the genome of cultivated octoploid strawberry.
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Affiliation(s)
| | | | - Baotian Wang
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
| | - Jiqi Li
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
| | - Chao Zhang
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
| | - Wenshuo Zhang
- School of Information Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Xue Li
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
| | - Jie Li
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
| | - Junxiang Zhang
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
- Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, Shenyang 110866, China
| | - He Li
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
- Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, Shenyang 110866, China
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Tian S, Wan Y, Jiang D, Gong M, Lin J, Xia M, Shi C, Xing H, Li HL. Genome-Wide Identification, Characterization, and Expression Analysis of GRAS Gene Family in Ginger ( Zingiber officinale Roscoe). Genes (Basel) 2022; 14:96. [PMID: 36672837 PMCID: PMC9859583 DOI: 10.3390/genes14010096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 12/30/2022] Open
Abstract
GRAS family proteins are one of the most abundant transcription factors in plants; they play crucial roles in plant development, metabolism, and biotic- and abiotic-stress responses. The GRAS family has been identified and functionally characterized in some plant species. However, this family in ginger (Zingiber officinale Roscoe), a medicinal crop and non-prescription drug, remains unknown to date. In the present study, 66 GRAS genes were identified by searching the complete genome sequence of ginger. The GRAS family is divided into nine subfamilies based on the phylogenetic analyses. The GRAS genes are distributed unevenly across 11 chromosomes. By analyzing the gene structure and motif distribution of GRAS members in ginger, we found that the GRAS genes have more than one cis-acting element. Chromosomal location and duplication analysis indicated that whole-genome duplication, tandem duplication, and segmental duplication may be responsible for the expansion of the GRAS family in ginger. The expression levels of GRAS family genes are different in ginger roots and stems, indicating that these genes may have an impact on ginger development. In addition, the GRAS genes in ginger showed extensive expression patterns under different abiotic stresses, suggesting that they may play important roles in the stress response. Our study provides a comprehensive analysis of GRAS members in ginger for the first time, which will help to better explore the function of GRAS genes in the regulation of tissue development and response to stress in ginger.
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Affiliation(s)
- Shuming Tian
- College of Landscape Architecture and life Science/Institute of special Plants, Chongqing University of Arts and Sciences, Chongqing 402168, China
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing 404020, China
| | - Yuepeng Wan
- College of Landscape Architecture and life Science/Institute of special Plants, Chongqing University of Arts and Sciences, Chongqing 402168, China
| | - Dongzhu Jiang
- College of Landscape Architecture and life Science/Institute of special Plants, Chongqing University of Arts and Sciences, Chongqing 402168, China
| | - Min Gong
- College of Landscape Architecture and life Science/Institute of special Plants, Chongqing University of Arts and Sciences, Chongqing 402168, China
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing 404020, China
| | - Junyao Lin
- College of Landscape Architecture and life Science/Institute of special Plants, Chongqing University of Arts and Sciences, Chongqing 402168, China
| | - Maoqin Xia
- College of Landscape Architecture and life Science/Institute of special Plants, Chongqing University of Arts and Sciences, Chongqing 402168, China
| | - Cuiping Shi
- College of Landscape Architecture and life Science/Institute of special Plants, Chongqing University of Arts and Sciences, Chongqing 402168, China
| | - Haitao Xing
- Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing University of Arts and Sciences, Chongqing 402160, China
| | - Hong-Lei Li
- College of Landscape Architecture and life Science/Institute of special Plants, Chongqing University of Arts and Sciences, Chongqing 402168, China
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Timilsena PR, Wafula EK, Barrett CF, Ayyampalayam S, McNeal JR, Rentsch JD, McKain MR, Heyduk K, Harkess A, Villegente M, Conran JG, Illing N, Fogliani B, Ané C, Pires JC, Davis JI, Zomlefer WB, Stevenson DW, Graham SW, Givnish TJ, Leebens-Mack J, dePamphilis CW. Phylogenomic resolution of order- and family-level monocot relationships using 602 single-copy nuclear genes and 1375 BUSCO genes. FRONTIERS IN PLANT SCIENCE 2022; 13:876779. [PMID: 36483967 PMCID: PMC9723157 DOI: 10.3389/fpls.2022.876779] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 09/29/2022] [Indexed: 05/26/2023]
Abstract
We assess relationships among 192 species in all 12 monocot orders and 72 of 77 families, using 602 conserved single-copy (CSC) genes and 1375 benchmarking single-copy ortholog (BUSCO) genes extracted from genomic and transcriptomic datasets. Phylogenomic inferences based on these data, using both coalescent-based and supermatrix analyses, are largely congruent with the most comprehensive plastome-based analysis, and nuclear-gene phylogenomic analyses with less comprehensive taxon sampling. The strongest discordance between the plastome and nuclear gene analyses is the monophyly of a clade comprising Asparagales and Liliales in our nuclear gene analyses, versus the placement of Asparagales and Liliales as successive sister clades to the commelinids in the plastome tree. Within orders, around six of 72 families shifted positions relative to the recent plastome analysis, but four of these involve poorly supported inferred relationships in the plastome-based tree. In Poales, the nuclear data place a clade comprising Ecdeiocoleaceae+Joinvilleaceae as sister to the grasses (Poaceae); Typhaceae, (rather than Bromeliaceae) are resolved as sister to all other Poales. In Commelinales, nuclear data place Philydraceae sister to all other families rather than to a clade comprising Haemodoraceae+Pontederiaceae as seen in the plastome tree. In Liliales, nuclear data place Liliaceae sister to Smilacaceae, and Melanthiaceae are placed sister to all other Liliales except Campynemataceae. Finally, in Alismatales, nuclear data strongly place Tofieldiaceae, rather than Araceae, as sister to all the other families, providing an alternative resolution of what has been the most problematic node to resolve using plastid data, outside of those involving achlorophyllous mycoheterotrophs. As seen in numerous prior studies, the placement of orders Acorales and Alismatales as successive sister lineages to all other extant monocots. Only 21.2% of BUSCO genes were demonstrably single-copy, yet phylogenomic inferences based on BUSCO and CSC genes did not differ, and overall functional annotations of the two sets were very similar. Our analyses also reveal significant gene tree-species tree discordance despite high support values, as expected given incomplete lineage sorting (ILS) related to rapid diversification. Our study advances understanding of monocot relationships and the robustness of phylogenetic inferences based on large numbers of nuclear single-copy genes that can be obtained from transcriptomes and genomes.
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Affiliation(s)
- Prakash Raj Timilsena
- Department of Biology and Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States
| | - Eric K. Wafula
- Department of Biology and Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States
| | - Craig F. Barrett
- Department of Biology, West Virginia University, Morgantown, WV, United States
| | - Saravanaraj Ayyampalayam
- Georgia Advanced Computing Resource Center, University of Georgia, Athens, GA, United States
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | - Joel R. McNeal
- Department of Ecology, Evolution, and Organismal Biology, Biology Kennesaw State University, Kennesaw, GA, United States
| | - Jeremy D. Rentsch
- Department of Biology, Francis Marion University, Florence, SC, United States
| | - Michael R. McKain
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, United States
| | - Karolina Heyduk
- School of Life Sciences, University of Hawai’i at Mānoa, Honolulu, HI, United States
| | - Alex Harkess
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Matthieu Villegente
- Institut des Sciences Exactes et Appliquees (ISEA), University of New Caledonia, Noumea, New Caledonia
| | - John G. Conran
- Australian Centre for Evolutionary Biology and Biodiversity & Sprigg Geobiology Centre, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Nicola Illing
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Bruno Fogliani
- Institut des Sciences Exactes et Appliquees (ISEA), University of New Caledonia, Noumea, New Caledonia
| | - Cécile Ané
- Department of Botany, University of Wisconsin-Madison, Madison, WI, United States
- Department of Statistics, University of Wisconsin–Madison, Madison, WI, United States
| | - J. Chris Pires
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Jerrold I. Davis
- School of Integrative Plant Sciences and L.H. Bailey Hortorium, Cornell University, Ithaca, NY, United States
| | - Wendy B. Zomlefer
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | | | | | - Thomas J. Givnish
- Department of Botany, University of Wisconsin-Madison, Madison, WI, United States
| | - James Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | - Claude W. dePamphilis
- Department of Biology and Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States
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Yang P, Zhao HY, Wei JS, Zhao YY, Lin XJ, Su J, Li FP, Li M, Ma DM, Tan XK, Liang HL, Sun YW, Zhan RT, He GZ, Zhou XF, Yang JF. Chromosome-level genome assembly and functional characterization of terpene synthases provide insights into the volatile terpenoid biosynthesis of Wurfbainia villosa. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:630-645. [PMID: 36071028 DOI: 10.1111/tpj.15968] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 09/04/2022] [Indexed: 06/15/2023]
Abstract
Wurfbainia villosa is a well-known medicinal and edible plant that is widely cultivated in the Lingnan region of China. Its dried fruits (called Fructus Amomi) are broadly used in traditional Chinese medicine for curing gastrointestinal diseases and are rich in volatile terpenoids. Here, we report a high-quality chromosome-level genome assembly of W. villosa with a total size of approximately 2.80 Gb, 42 588 protein-coding genes, and a very high percentage of repetitive sequences (87.23%). Genome analysis showed that W. villosa likely experienced a recent whole-genome duplication event prior to the W. villosa-Zingiber officinale divergence (approximately 11 million years ago), and a recent burst of long terminal repeat insertions afterward. The W. villosa genome enabled the identification of 17 genes involved in the terpenoid skeleton biosynthesis pathway and 66 terpene synthase (TPS) genes. We found that tandem duplication events have an important contribution to the expansion of WvTPSs, which likely drove the production of volatile terpenoids. In addition, functional characterization of 18 WvTPSs, focusing on the TPS-a and TPS-b subfamilies, showed that most of these WvTPSs are multi-product TPS and are predominantly expressed in seeds. The present study provides insights into the genome evolution and the molecular basis of the volatile terpenoids diversity in W. villosa. The genome sequence also represents valuable resources for the functional gene research and molecular breeding of W. villosa.
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Affiliation(s)
- Peng Yang
- School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese Medicine, School of Pharmaceutical Sciences, Hunan University of Medicine, Huaihua, 418000, China
| | - Hai-Ying Zhao
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- The Second Clinical Medical College of Guangxi University of Science and Technology, Louzhou, 5450000, China
| | - Jie-Shu Wei
- School of Pharmacy, Guangzhou Xinhua University, Guangzhou, 510520, China
| | - Yuan-Yuan Zhao
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Xiao-Jing Lin
- School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Jing Su
- Agricultural Experimental Station of Yangchun City (Amomum villosum Testing farm of Yangchun City), Yangchun, 529600, China
| | - Fang-Ping Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China
| | - Meng Li
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Dong-Ming Ma
- School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Xu-Kai Tan
- Grandomics Biosciences, Beijing, 102200, China
| | - Hui-Lin Liang
- School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Ye-Wen Sun
- School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Ruo-Ting Zhan
- School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Guo-Zhen He
- School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Xiao-Fan Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China
| | - Jin-Fen Yang
- School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
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Wang CW, Michelle Wong JW, Yeh SS, Eric Hsieh Y, Tseng CH, Yang SH, Tang SL. Soil Bacterial Community May Offer Solutions for Ginger Cultivation. Microbiol Spectr 2022; 10:e0180322. [PMID: 36098526 PMCID: PMC9603371 DOI: 10.1128/spectrum.01803-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/26/2022] [Indexed: 12/31/2022] Open
Abstract
The Taitung region is one of Taiwan's main sites for ginger agriculture. Due to issues with disease and nutrients, farmers cannot use continuous cropping techniques on ginger, meaning that the ginger industry is constantly searching for new land. Continuous cropping increases the risk of infection by Pythium myriotylum and Ralstonia solanacearum, which cause soft rot disease and bacterial wilt, respectively. In addition, fertilizer additives, which are commonly used to increase trace elements in the soil, cannot restore the soil when it is undergoing continuous cropping on ginger, even when there has been no observable decrease in trace elements in the soil. Recent studies about soil microbiome manipulation and the application of microorganisms have shown that plant-associated microbes have the ability to improve plant growth and facilitate sustainable agriculture, but studies of this kind still need to be carried out on ginger cultivation. Therefore, in this study, we used the bacterial 16S V3-V4 hypervariable region of the 16S rRNA region to investigate microbe compositions in ginger soil to identify the difference between ginger soil with and without disease. Later, to investigate the influence of the well-known biocontrol agent B. velezensis and the fungicide Etridiazole on soil microbes and ginger productivity, we designed an experiment that collected the soil samples according to the different periods of ginger cultivation to examine the microbial community dynamics in the rhizome and bulk soil. We demonstrated that B. velezensis is beneficial to ginger reproduction. In accordance with our results, we suggest that B. velezensis may influence the plant's growth by adjusting its soil microbial composition. Etridiazole, on the other hand, may have some side effects on the ginger or beneficial bacteria in the soils that inhibit ginger reproduction. IMPORTANCE Pythium myriotylum and Ralstonia solanacearum cause soft rot disease and bacterial wilt, respectively. In this study, we used the bacterial 16S V3-V4 hypervariable region of the 16S rRNA region to investigate microbe compositions in healthy and diseased ginger soil and find out the influence of the well-known biocontrol agent B. velezensis and the fungicide Etridiazole on soil microbes and ginger productivity. These results demonstrated that B. velezensis benefits ginger reproduction and may influence the soil bacterial composition, while Etridiazole may have some side effects on the ginger or beneficial bacteria in the soils. The interactions among ginger, biocontrol agents, and fungicides need to be further investigated.
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Affiliation(s)
- Chih-Wei Wang
- Taitung District Agricultural Research and Extension Station, Council of Agriculture, Executive Yuan, Taitung, Taiwan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Molecular and Biological Agricultural Sciences, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | | | - Shu-Shuo Yeh
- Institute of Fisheries Science, National Taiwan University, Taipei, Taiwan
| | - Yunli Eric Hsieh
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Systems Biology and Mathematical Modelling, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | | | - Shan-Hua Yang
- Institute of Fisheries Science, National Taiwan University, Taipei, Taiwan
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Molecular and Biological Agricultural Sciences, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
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30
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Guo L, Yao H, Chen W, Wang X, Ye P, Xu Z, Zhang S, Wu H. Natural products of medicinal plants: biosynthesis and bioengineering in post-genomic era. HORTICULTURE RESEARCH 2022; 9:uhac223. [PMID: 36479585 PMCID: PMC9720450 DOI: 10.1093/hr/uhac223] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 09/22/2022] [Indexed: 06/01/2023]
Abstract
Globally, medicinal plant natural products (PNPs) are a major source of substances used in traditional and modern medicine. As we human race face the tremendous public health challenge posed by emerging infectious diseases, antibiotic resistance and surging drug prices etc., harnessing the healing power of medicinal plants gifted from mother nature is more urgent than ever in helping us survive future challenge in a sustainable way. PNP research efforts in the pre-genomic era focus on discovering bioactive molecules with pharmaceutical activities, and identifying individual genes responsible for biosynthesis. Critically, systemic biological, multi- and inter-disciplinary approaches integrating and interrogating all accessible data from genomics, metabolomics, structural biology, and chemical informatics are necessary to accelerate the full characterization of biosynthetic and regulatory circuitry for producing PNPs in medicinal plants. In this review, we attempt to provide a brief update on the current research of PNPs in medicinal plants by focusing on how different state-of-the-art biotechnologies facilitate their discovery, the molecular basis of their biosynthesis, as well as synthetic biology. Finally, we humbly provide a foresight of the research trend for understanding the biology of medicinal plants in the coming decades.
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Affiliation(s)
- Li Guo
- Corresponding authors. E-mails: ;
| | | | | | - Xumei Wang
- School of Pharmacy, Xi’an Jiaotong University, Xi’an 710061, China
| | - Peng Ye
- State Key laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory For Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Zhichao Xu
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Sisheng Zhang
- State Key laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory For Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Hong Wu
- Corresponding authors. E-mails: ;
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31
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Yin Y, Xie X, Zhou L, Yin X, Guo S, Zhou X, Li Q, Shi X, Peng C, Gao J. A chromosome-scale genome assembly of turmeric provides insights into curcumin biosynthesis and tuber formation mechanism. FRONTIERS IN PLANT SCIENCE 2022; 13:1003835. [PMID: 36226278 PMCID: PMC9549246 DOI: 10.3389/fpls.2022.1003835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 09/06/2022] [Indexed: 06/01/2023]
Abstract
Curcuma longa, known as the 'golden spice' and 'life spice', is one of the most commonly utilized spices in the world and also has medicinal, cosmetic, dye and flavoring values. Herein, we present the chromosomal-level genome for turmeric to explore the differences between tubers and rhizomes in the regulation of curcumin biosynthesis and the mechanism of tuber formation. We assembled the turmeric genome into 21 pseudochromosomes using Pacbio long reads complemented with Hi-C technologies, which has a total length of 1.11 Gb with scaffold N50 of 50.12 Mb and contains 49,612 protein-coding genes. Genomic evolutionary analysis indicated that turmeric and ginger have shared a recent WGD event. Contraction analysis of gene families showed possible roles for transcription factors, phytohormone signaling, and plant-pathogen interactions associated genes in adaptation to harsh environments. Transcriptomic data from tubers at different developmental stages indicated that candidate genes related to phytohormone signaling and carbohydrate metabolic responses may be associated with the induction of tuber formation. The difference in curcumin content between rhizomes and tubers reflected the remodeling of secondary metabolites under environmental stress, which was associated with plant defense in response to abiotic stresses. Overall, the availability of the C. longa genome provides insight into tuber formation and curcumin biosynthesis in turmeric as well as facilitating the understanding of other Curcuma species.
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Affiliation(s)
- Yanpeng Yin
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xiaofang Xie
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Luojing Zhou
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xianmei Yin
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Shuai Guo
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xianjian Zhou
- Sichuan Provincial Key Laboratory of Quality and Innovation Research of Chinese Materia Medica, Sichuan Academy of Traditional Chinese Medicine Sciences, Chengdu, China
| | - Qingmiao Li
- Sichuan Provincial Key Laboratory of Quality and Innovation Research of Chinese Materia Medica, Sichuan Academy of Traditional Chinese Medicine Sciences, Chengdu, China
| | - Xiaodong Shi
- School of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Cheng Peng
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Jihai Gao
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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Gao Y, Lu Y, Zhang N, Udenigwe CC, Zhang Y, Fu Y. Preparation, pungency and bioactivity of gingerols from ginger ( Zingiber officinale Roscoe): a review. Crit Rev Food Sci Nutr 2022; 64:2708-2733. [PMID: 36135317 DOI: 10.1080/10408398.2022.2124951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Ginger has been widely used for different purposes, such as condiment, functional food, drugs, and cosmetics. Gingerols, the main pungent component in ginger, possess a variety of bioactivities. To fully understand the significance of gingerols in the food and pharmaceutical industry, this paper first recaps the composition and physiochemical properties of gingerols, and the major extraction and synthesis methods. Furthermore, the pungency and bioactivity of gingerols are reviewed. In addition, the food application of gingerols and future perspectives are discussed. Gingerols, characterized by a 3-methoxy-4-hydroxyphenyl moiety, are divided into gingerols, shogaols, paradols, zingerone, gingerdiones and gingerdiols. At present, gingerols are extracted by conventional, innovative, and integrated extraction methods, and synthesized by chemical, biological and in vitro cell synthesis methods. Gingerols can activate transient receptor potential vanilloid type 1 (TRPV1) and induce signal transduction, thereby exhibiting its pungent properties and bioactivity. By targeted mediation of various cell signaling pathways, gingerols display potential anticancer, antibacterial, blood glucose regulatory, hepato- and renal-protective, gastrointestinal regulatory, nerve regulatory, and cardiovascular protective effects. This review contributes to the application of gingerols as functional ingredients in the food and pharmaceutical industry.
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Affiliation(s)
- Yuge Gao
- College of Food Science, Southwest University, Chongqing, China
- Westa College, Southwest University, Chongqing, China
| | - Yujia Lu
- Department of Epidemiology, Harvard University T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Na Zhang
- Key Laboratory of Food Science and Engineering of Heilongjiang Province, College of Food Engineering, Harbin University of Commerce, Harbin, China
| | - Chibuike C Udenigwe
- School of Nutrition Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, Ontario, Canada
| | - Yuhao Zhang
- College of Food Science, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Chongqing, China
| | - Yu Fu
- College of Food Science, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Chongqing, China
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Yu T, Ma X, Liu Z, Feng X, Wang Z, Ren J, Cao R, Zhang Y, Nie F, Song X. TVIR: a comprehensive vegetable information resource database for comparative and functional genomic studies. HORTICULTURE RESEARCH 2022; 9:uhac213. [PMID: 36483087 PMCID: PMC9719039 DOI: 10.1093/hr/uhac213] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 09/14/2022] [Indexed: 06/17/2023]
Abstract
Vegetables are an indispensable part of the daily diet of humans. Therefore, it is vital to systematically study the genomic data of vegetables and build a platform for data sharing and analysis. In this study, a comprehensive platform for vegetables with a user-friendly Web interface-The Vegetable Information Resource (TVIR, http://tvir.bio2db.com)-was built based on the genomes of 59 vegetables. TVIR database contains numerous important functional genes, including 5215 auxin genes, 2437 anthocyanin genes, 15 002 flowering genes, 79 830 resistance genes, and 2639 glucosinolate genes of 59 vegetables. In addition, 2597 N6-methyladenosine (m6A) genes were identified, including 513 writers, 1058 erasers, and 1026 readers. A total of 2 101 501 specific clustered regularly interspaced short palindromic repeat (CRISPR) guide sequences and 17 377 miRNAs were detected and deposited in TVIR database. Information on gene synteny, duplication, and orthologs is also provided for 59 vegetable species. TVIR database contains 2 346 850 gene annotations by the Swiss-Prot, TrEMBL, Gene Ontology (GO), Pfam, and Non-redundant (Nr) databases. Synteny, Primer Design, Blast, and JBrowse tools are provided to facilitate users in conducting comparative genomic analyses. This is the first large-scale collection of vegetable genomic data and bioinformatic analysis. All genome and gene sequences, annotations, and bioinformatic results can be easily downloaded from TVIR. Furthermore, transcriptome data of 98 vegetables have been collected and collated, and can be searched by species, tissues, or different growth stages. TVIR is expected to become a key hub for vegetable research globally. The database will be updated with newly assembled vegetable genomes and comparative genomic studies in the future.
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Affiliation(s)
| | | | | | | | - Zhiyuan Wang
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Jun Ren
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Rui Cao
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Yingchao Zhang
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Fulei Nie
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei 063210, China
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Valderrama E, Landis JB, Skinner D, Maas PJM, Maas-van de Kramer H, André T, Grunder N, Sass C, Pinilla-Vargas M, Guan CJ, Phillips HR, de Almeida AMR, Specht CD. The genetic mechanisms underlying the convergent evolution of pollination syndromes in the Neotropical radiation of Costus L. FRONTIERS IN PLANT SCIENCE 2022; 13:874322. [PMID: 36161003 PMCID: PMC9493542 DOI: 10.3389/fpls.2022.874322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 06/27/2022] [Indexed: 06/16/2023]
Abstract
Selection together with variation in floral traits can act to mold floral form, often driven by a plant's predominant or most effective pollinators. To investigate the evolution of traits associated with pollination, we developed a phylogenetic framework for evaluating tempo and mode of pollination shifts across the genus Costus L., known for its evolutionary toggle between traits related to bee and bird pollination. Using a target enrichment approach, we obtained 957 loci for 171 accessions to expand the phylogenetic sampling of Neotropical Costus. In addition, we performed whole genome resequencing for a subset of 20 closely related species with contrasting pollination syndromes. For each of these 20 genomes, a high-quality assembled transcriptome was used as reference for consensus calling of candidate loci hypothesized to be associated with pollination-related traits of interest. To test for the role these candidate genes may play in evolutionary shifts in pollinators, signatures of selection were estimated as dN/dS across the identified candidate loci. We obtained a well-resolved phylogeny for Neotropical Costus despite conflict among gene trees that provide evidence of incomplete lineage sorting and/or reticulation. The overall topology and the network of genome-wide single nucleotide polymorphisms (SNPs) indicate that multiple shifts in pollination strategy have occurred across Costus, while also suggesting the presence of previously undetected signatures of hybridization between distantly related taxa. Traits related to pollination syndromes are strongly correlated and have been gained and lost in concert several times throughout the evolution of the genus. The presence of bract appendages is correlated with two traits associated with defenses against herbivory. Although labellum shape is strongly correlated with overall pollination syndrome, we found no significant impact of labellum shape on diversification rates. Evidence suggests an interplay of pollination success with other selective pressures shaping the evolution of the Costus inflorescence. Although most of the loci used for phylogenetic inference appear to be under purifying selection, many candidate genes associated with functional traits show evidence of being under positive selection. Together these results indicate an interplay of phylogenetic history with adaptive evolution leading to the diversification of pollination-associated traits in Neotropical Costus.
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Affiliation(s)
- Eugenio Valderrama
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, United States
| | - Jacob B. Landis
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, United States
- BTI Computational Biology Center, Boyce Thompson Institute, Ithaca, NY, United States
| | - Dave Skinner
- Le Jardin Ombragé, Tallahassee, FL, United States
| | - Paul J. M. Maas
- Section Botany, Naturalis Biodiversity Center, Leiden, Netherlands
| | | | - Thiago André
- Departamento de Botânica, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil
| | - Nikolaus Grunder
- Department of Biological Sciences, California State University, East Bay, Hayward, CA, United States
| | - Chodon Sass
- University and Jepson Herbaria, University of California, Berkeley, Berkeley, CA, United States
| | - Maria Pinilla-Vargas
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, United States
| | - Clarice J. Guan
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, United States
| | - Heather R. Phillips
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, United States
| | | | - Chelsea D. Specht
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, United States
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Liao X, Ye Y, Zhang X, Peng D, Hou M, Fu G, Tan J, Zhao J, Jiang R, Xu Y, Liu J, Yang J, Liu W, Tembrock LR, Zhu G, Wu Z. The genomic and bulked segregant analysis of Curcuma alismatifolia revealed its diverse bract pigmentation. ABIOTECH 2022; 3:178-196. [PMID: 36304840 PMCID: PMC9590460 DOI: 10.1007/s42994-022-00081-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/05/2022] [Indexed: 11/15/2022]
Abstract
Compared with most flowers where the showy part comprises specialized leaves (petals) directly subtending the reproductive structures, most Zingiberaceae species produce showy "flowers" through modifications of leaves (bracts) subtending the true flowers throughout an inflorescence. Curcuma alismatifolia, belonging to the Zingiberaceae family, a plant species originating from Southeast Asia, has become increasingly popular in the flower market worldwide because of its varied and esthetically pleasing bracts produced in different cultivars. Here, we present the chromosome-scale genome assembly of C. alismatifolia "Chiang Mai Pink" and explore the underlying mechanisms of bract pigmentation. Comparative genomic analysis revealed C. alismatifolia contains a residual signal of whole-genome duplication. Duplicated genes, including pigment-related genes, exhibit functional and structural differentiation resulting in diverse bract colors among C. alismatifolia cultivars. In addition, we identified the key genes that produce different colored bracts in C. alismatifolia, such as F3'5'H, DFR, ANS and several transcription factors for anthocyanin synthesis, as well as chlH and CAO in the chlorophyll synthesis pathway by conducting transcriptomic analysis, bulked segregant analysis using both DNA and RNA data, and population genomic analysis. This work provides data for understanding the mechanism of bract pigmentation and will accelerate breeding in developing novel cultivars with richly colored bracts in C. alismatifolia and related species. It is also important to understand the variation in the evolution of the Zingiberaceae family. Supplementary Information The online version contains supplementary material available at 10.1007/s42994-022-00081-6.
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Affiliation(s)
- Xuezhu Liao
- 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, 518120 China
| | - Yuanjun Ye
- Guangdong Provincial Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Xiaoni Zhang
- 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, 518120 China
| | - Dan Peng
- 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, 518120 China
| | - Mengmeng Hou
- 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, 518120 China
| | - Gaofei Fu
- 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, 518120 China
| | - Jianjun Tan
- Guangdong Provincial Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Jianli Zhao
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming, 650504 China
| | - Rihong Jiang
- Guangxi Engineering and Technology Research Center for Woody Spices, Guangxi Key Laboratory for Cultivation and Utilization of Special Non-Timber Forest Crops, Guangxi Forestry Research Institute, Nanning, 530002 China
| | - Yechun Xu
- Guangdong Provincial Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Jinmei Liu
- Guangdong Provincial Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Jinliang Yang
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583 USA
| | - Wusheng Liu
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607 USA
| | - Luke R Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523 USA
| | - Genfa Zhu
- Guangdong Provincial Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Zhiqiang Wu
- 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, 518120 China.,Kunpeng Institute of Modern Agriculture at Foshan, Foshan, 528200 China
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Taheri S, Teo CH, Heslop-Harrison JS, Schwarzacher T, Tan YS, Wee WY, Khalid N, Biswas MK, Mutha NVR, Mohd-Yusuf Y, Gan HM, Harikrishna JA. Genome Assembly and Analysis of the Flavonoid and Phenylpropanoid Biosynthetic Pathways in Fingerroot Ginger ( Boesenbergia rotunda). Int J Mol Sci 2022; 23:7269. [PMID: 35806276 PMCID: PMC9266397 DOI: 10.3390/ijms23137269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/20/2022] [Accepted: 06/27/2022] [Indexed: 01/27/2023] Open
Abstract
Boesenbergia rotunda (Zingiberaceae), is a high-value culinary and ethno-medicinal plant of Southeast Asia. The rhizomes of this herb have a high flavanone and chalcone content. Here we report the genome analysis of B. rotunda together with a complete genome sequence as a hybrid assembly. B. rotunda has an estimated genome size of 2.4 Gb which is assembled as 27,491 contigs with an N50 size of 12.386 Mb. The highly heterozygous genome encodes 71,072 protein-coding genes and has a 72% repeat content, with class I TEs occupying ~67% of the assembled genome. Fluorescence in situ hybridization of the 18 chromosome pairs at the metaphase showed six sites of 45S rDNA and two sites of 5S rDNA. An SSR analysis identified 238,441 gSSRs and 4604 EST-SSRs with 49 SSR markers common among related species. Genome-wide methylation percentages ranged from 73% CpG, 36% CHG and 34% CHH in the leaf to 53% CpG, 18% CHG and 25% CHH in the embryogenic callus. Panduratin A biosynthetic unigenes were most highly expressed in the watery callus. B rotunda has a relatively large genome with a high heterozygosity and TE content. This assembly and data (PRJNA71294) comprise a source for further research on the functional genomics of B. rotunda, the evolution of the ginger plant family and the potential genetic selection or improvement of gingers.
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Affiliation(s)
- Sima Taheri
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Kuala Lumpur 50603, Malaysia; (S.T.); (C.H.T.); (Y.M.-Y.)
| | - Chee How Teo
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Kuala Lumpur 50603, Malaysia; (S.T.); (C.H.T.); (Y.M.-Y.)
| | - John S. Heslop-Harrison
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK; (T.S.); (M.K.B.)
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Trude Schwarzacher
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK; (T.S.); (M.K.B.)
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Yew Seong Tan
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia;
| | - Wei Yee Wee
- School of Science, Monash University Malaysia, Subang Jaya 47500, Malaysia;
| | - Norzulaani Khalid
- Department of Biology, International University of Malaya-Wales, Kuala Lumpur 50603, Malaysia;
| | - Manosh Kumar Biswas
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK; (T.S.); (M.K.B.)
| | - Naresh V. R. Mutha
- Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN 37203, USA;
| | - Yusmin Mohd-Yusuf
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Kuala Lumpur 50603, Malaysia; (S.T.); (C.H.T.); (Y.M.-Y.)
- Biology Division, Centre for Foundation Studies in Science, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Han Ming Gan
- Department of Biological Sciences, Sunway University, Bandar Sunway, Petaling Jaya 47500, Malaysia;
| | - Jennifer Ann Harikrishna
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Kuala Lumpur 50603, Malaysia; (S.T.); (C.H.T.); (Y.M.-Y.)
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia;
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Li G, Ma J, Yin J, Guo F, Xi K, Yang P, Cai X, Jia Q, Li L, Liu Y, Zhu Y. Identification of Reference Genes for Reverse Transcription-Quantitative PCR Analysis of Ginger Under Abiotic Stress and for Postharvest Biology Studies. FRONTIERS IN PLANT SCIENCE 2022; 13:893495. [PMID: 35734245 PMCID: PMC9207462 DOI: 10.3389/fpls.2022.893495] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
Gene expression analysis largely improves our understanding of the molecular basis underpinning various plant biological processes. Stable reference genes play a foundational role during the normalization of gene expression levels. However, until now, there have been few reference genes suitable for ginger reverse transcription-quantitative PCR (RT-qPCR) research. In this study, 29 candidate reference genes with stable expression patterns across multiple ginger tissues and 13 commonly used reference genes were selected to design RT-qPCR primers. After amplification specificity validation, 32 candidates were selected and further evaluated by RT-qPCR using samples from various organs subjected to NaCl, drought, heat, waterlogging, and chilling stress. Four strategies, including delta-CT, BestKeeper, geNorm, and NormFinder, were used to rank the stability of reference genes, and the ranks produced by these four strategies were comprehensively evaluated by RefFinder to determine the final rank. Overall, the top three stability reference genes indicated by RefFinder were RBP > ATPase > 40S_S3. Their expression pattern correlation analysis showed that the coefficients among each pair of RBP, ATPase, and 40S_S3 were larger than 0.96, revealing consistent and stable expression patterns under various treatments. Then, the expression of three pathogenesis-related (PR) genes and seven MYB genes in rhizomes during postharvest storage and subjected to pathogen infection was normalized by RBP, ATPase, 40S_S3, RBP and ATPase, ATPase and 40S-S3, and RBP and 40S-S3. The results showed that PR and MYB genes were induced by postharvest deterioration and pathogen infection. The correlation coefficients of RBP/ATPase, RBP/40S_S3, ATPase/40S_S3, RBP and ATPase/ATPase and 40S-S3, RBP and ATPase/RBP and 40S-S3, and ATPase and 40S-S3/RBP and 40S-S3 were 0.99, 0.96, 0.99, 0.99, 1.00, and 1.00, respectively, which confirmed the stability of these three reference genes in postharvest biology studies of ginger. In summary, this study identified appropriate reference genes for RT-qPCR in ginger and facilitated gene expression studies under biotic and abiotic stress conditions.
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Affiliation(s)
- Gang Li
- College of Horticulture and Gardening, Spice Crops Research Institute, Yangtze University, Jingzhou, China
| | - Jiawei Ma
- College of Horticulture and Gardening, Spice Crops Research Institute, Yangtze University, Jingzhou, China
| | - Junliang Yin
- College of Horticulture and Gardening, Spice Crops Research Institute, Yangtze University, Jingzhou, China
| | - Fengling Guo
- Institute of Economic Crops, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Keyong Xi
- College of Horticulture and Gardening, Spice Crops Research Institute, Yangtze University, Jingzhou, China
| | - Peihua Yang
- College of Horticulture and Gardening, Spice Crops Research Institute, Yangtze University, Jingzhou, China
| | - Xiaodong Cai
- College of Horticulture and Gardening, Spice Crops Research Institute, Yangtze University, Jingzhou, China
| | - Qie Jia
- College of Horticulture and Gardening, Spice Crops Research Institute, Yangtze University, Jingzhou, China
| | - Lu Li
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, China
| | - Yiqing Liu
- College of Horticulture and Gardening, Spice Crops Research Institute, Yangtze University, Jingzhou, China
| | - Yongxing Zhu
- College of Horticulture and Gardening, Spice Crops Research Institute, Yangtze University, Jingzhou, China
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Sun F, Yan C, Lv Y, Pu Z, Liao Z, Guo W, Dai M. Genome Sequencing of Amomum tsao-ko Provides Novel Insight Into Its Volatile Component Biosynthesis. FRONTIERS IN PLANT SCIENCE 2022; 13:904178. [PMID: 35720564 PMCID: PMC9198571 DOI: 10.3389/fpls.2022.904178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
As an important economic and medicinal crop, Amomum tsao-ko is rich in volatile oils and widely used in food additives, essential oils, and traditional Chinese medicine. However, the lack of the genome remains a limiting factor for understanding its medicinal properties at the molecular level. Here, based on 288.72 Gb of PacBio long reads and 105.45 Gb of Illumina paired-end short reads, we assembled a draft genome for A. tsao-ko (2.70 Gb in size, contig N50 of 2.45 Mb). Approximately 90.07% of the predicted genes were annotated in public databases. Based on comparative genomic analysis, genes involved in secondary metabolite biosynthesis, flavonoid metabolism, and terpenoid biosynthesis showed significant expansion. Notably, the DXS, GGPPS, and CYP450 genes, which participate in rate-limiting steps for terpenoid backbone biosynthesis and modification, may form the genetic basis for essential oil formation in A. tsao-ko. The assembled A. tsao-ko draft genome provides a valuable genetic resource for understanding the unique features of this plant and for further evolutionary and agronomic studies of Zingiberaceae species.
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Affiliation(s)
- Fenghui Sun
- School of Laboratory Medicine, Chengdu Medical College, Chengdu, China
| | - Chaochao Yan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Yunyun Lv
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- College of Life Science, Neijiang Normal University, Neijiang, China
| | - Zhonghui Pu
- School of Laboratory Medicine, Chengdu Medical College, Chengdu, China
- Sichuan Provincial Engineering Laboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-Origin Food, Chengdu Medical College, Chengdu, China
| | - Zedong Liao
- School of Laboratory Medicine, Chengdu Medical College, Chengdu, China
| | - Wei Guo
- School of Laboratory Medicine, Chengdu Medical College, Chengdu, China
- Sichuan Provincial Engineering Laboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-Origin Food, Chengdu Medical College, Chengdu, China
| | - Min Dai
- School of Laboratory Medicine, Chengdu Medical College, Chengdu, China
- Sichuan Provincial Engineering Laboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-Origin Food, Chengdu Medical College, Chengdu, China
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Stander EA, Dugé de Bernonville T, Papon N, Courdavault V. Chromosome-scale genomes throw light on plant drug biosynthesis. Trends Pharmacol Sci 2022; 43:542-545. [DOI: 10.1016/j.tips.2022.01.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/14/2022] [Accepted: 01/20/2022] [Indexed: 01/18/2023]
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40
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Xing H, Li Y, Ren Y, Zhao Y, Wu X, Li HL. Genome-wide investigation of microRNAs and expression profiles during rhizome development in ginger (Zingiber officinale Roscoe). BMC Genomics 2022; 23:49. [PMID: 35021996 PMCID: PMC8756691 DOI: 10.1186/s12864-021-08273-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 12/20/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are endogenous, non-coding small functional RNAs that govern the post-transcriptional regulatory system of gene expression and control the growth and development of plants. Ginger is an herb that is well-known for its flavor and medicinal properties. The genes involved in ginger rhizome development and secondary metabolism have been discovered, but the genome-wide identification of miRNAs and their overall expression profiles and targets during ginger rhizome development are largely unknown. In this study, we used BGISEQ-500 technology to perform genome-wide identification of miRNAs from the leaf, stem, root, flower, and rhizome of ginger during three development stages. RESULTS In total, 104 novel miRNAs and 160 conserved miRNAs in 28 miRNA families were identified. A total of 181 putative target genes for novel miRNAs and 2772 putative target genes for conserved miRNAs were predicted. Transcriptional factors were the most abundant target genes of miRNAs, and 17, 9, 8, 4, 13, 8, 3 conserved miRNAs and 5, 7, 4, 5, 5, 15, 9 novel miRNAs showed significant tissue-specific expression patterns in leaf, stem, root, flower, and rhizome. Additionally, 53 miRNAs were regarded as rhizome development-associated miRNAs, which mostly participate in metabolism, signal transduction, transport, and catabolism, suggesting that these miRNAs and their target genes play important roles in the rhizome development of ginger. Twelve candidate miRNA target genes were selected, and then, their credibility was confirmed using qRT-PCR. As the result of qRT-PCR analysis, the expression of 12 candidate target genes showed an opposite pattern after comparison with their miRNAs. The rhizome development system of ginger was observed to be governed by miR156, miR319, miR171a_2, miR164, and miR529, which modulated the expression of the SPL, MYB, GRF, SCL, and NAC genes, respectively. CONCLUSION This is a deep genome-wide investigation of miRNA and identification of miRNAs involved in rhizome development in ginger. We identified 52 rhizome-related miRNAs and 392 target genes, and this provides an important basis for understanding the molecular mechanisms of the miRNA target genes that mediate rhizome development in ginger.
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Affiliation(s)
- Haitao Xing
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, 402168, China
- Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing University of Arts and Sciences, Chongqing, 402168, China
| | - Yuan Li
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, 402168, China.
| | - Yun Ren
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, 402168, China
- Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing University of Arts and Sciences, Chongqing, 402168, China
| | - Ying Zhao
- Research Center for Terrestrial Biodiversity of the South China Sea, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, Hainan, China
| | - Xiaoli Wu
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, 402168, China
| | - Hong-Lei Li
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, 402168, China.
- Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing University of Arts and Sciences, Chongqing, 402168, China.
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Liu X, Gong X, Liu Y, Liu J, Zhang H, Qiao S, Li G, Tang M. Application of High-Throughput Sequencing on the Chinese Herbal Medicine for the Data-Mining of the Bioactive Compounds. FRONTIERS IN PLANT SCIENCE 2022; 13:900035. [PMID: 35909744 PMCID: PMC9331165 DOI: 10.3389/fpls.2022.900035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/10/2022] [Indexed: 05/11/2023]
Abstract
The Chinese Herbal Medicine (CHM) has been used worldwide in clinic to treat the vast majority of human diseases, and the healing effect is remarkable. However, the functional components and the corresponding pharmacological mechanism of the herbs are unclear. As one of the main means, the high-throughput sequencing (HTS) technologies have been employed to discover and parse the active ingredients of CHM. Moreover, a tremendous amount of effort is made to uncover the pharmacodynamic genes associated with the synthesis of active substances. Here, based on the genome-assembly and the downstream bioinformatics analysis, we present a comprehensive summary of the application of HTS on CHM for the synthesis pathways of active ingredients from two aspects: active ingredient properties and disease classification, which are important for pharmacological, herb molecular breeding, and synthetic biology studies.
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Affiliation(s)
- Xiaoyan Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Xun Gong
- Department of Rheumatology and Immunology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Yi Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, China
- Institute of Animal Husbandry, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Junlin Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Hantao Zhang
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Sen Qiao
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Gang Li
- Department of Vascular Surgery, The Second Affiliated Hospital of Shandong First Medical University, Taian, China
- Gang Li,
| | - Min Tang
- School of Life Sciences, Jiangsu University, Zhenjiang, China
- *Correspondence: Min Tang,
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Li P, Bai G, He J, Liu B, Long J, Morcol T, Peng W, Quan F, Luan X, Wang Z, Zhao Y, Cha Y, Liu Y, He J, Wu L, Yang Y, Kennelly EJ, Yang Q, Sun L, Chen Z, Qian W, Hu J, Yan J. Chromosome-level genome assembly of Amomum tsao-ko provides insights into the biosynthesis of flavor compounds. HORTICULTURE RESEARCH 2022; 9:uhac211. [PMID: 36479578 PMCID: PMC9719038 DOI: 10.1093/hr/uhac211] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 09/14/2022] [Indexed: 05/19/2023]
Abstract
Amomum tsao-ko is an economically important spice plant in the ginger family (Zingiberaceae). The dried ripe fruit has been widely used as spice and medicine in Southeast Asia due to its distinct flavor metabolites. However, there is little genomic information available to understand the biosynthesis of its characteristic flavor compounds. Here, we present a high-quality chromosome-level genome of A. tsao-ko with a total length of 2.08 Gb assembled into 24 chromosomes. Potential relationships between genetic variation and chemical constituents were analyzed by a genome-wide association study of 119 representative A. tsao-ko specimens in China. Metabolome and transcriptome correlation analysis of different plant organs and fruit developmental stages revealed the proposed biosynthesis of the characteristic bicyclononane aldehydes and aromatic metabolites in A. tsao-ko fruit. Transcription factors of 20 families may be involved in the regulatory network of terpenoids. This study provides genomic and chemical insights into the biosynthesis of characteristic aroma and flavor constituents, which can be used to improve the quality of A. tsao-ko as food and medicine.
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Affiliation(s)
| | | | | | | | | | - Taylan Morcol
- Department of Biological Sciences, Lehman College and The Graduate Center, City University of New York, Bronx, New York, 10468, USA
| | - Weiyao Peng
- Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Eco-Circular Agriculture, Guangdong Engineering Research Centre for Modern Eco-Agriculture, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Fan Quan
- Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Eco-Circular Agriculture, Guangdong Engineering Research Centre for Modern Eco-Agriculture, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Xinbo Luan
- Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Eco-Circular Agriculture, Guangdong Engineering Research Centre for Modern Eco-Agriculture, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Zhenzhen Wang
- Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Eco-Circular Agriculture, Guangdong Engineering Research Centre for Modern Eco-Agriculture, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Yi Zhao
- Department of Biological Sciences, Lehman College and The Graduate Center, City University of New York, Bronx, New York, 10468, USA
| | - Yunsheng Cha
- Nujiang Green Spice Industry Research Institute, Lushui, Yunnan, 673100, China
| | - Yuanyuan Liu
- Key lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture and Rural Affairs ,Yunnan Provincial Key Lab of Agricultural Biotechnology, Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, 650205, China
| | - Juncai He
- Nujiang Green Spice Industry Research Institute, Lushui, Yunnan, 673100, China
| | - Lianzhang Wu
- Nujiang Green Spice Industry Research Institute, Lushui, Yunnan, 673100, China
| | - Yi Yang
- Nujiang Green Spice Industry Research Institute, Lushui, Yunnan, 673100, China
| | - Edward J Kennelly
- Department of Biological Sciences, Lehman College and The Graduate Center, City University of New York, Bronx, New York, 10468, USA
| | - Quan Yang
- Corresponding authors. E-mail: , , , ,
| | | | - Zepeng Chen
- Guangdong Provincial Tobacco Shaoguan Co. Ltd, Shaoguan, Guangdong, 512000, China
| | | | - Jian Hu
- Corresponding authors. E-mail: , , , ,
| | - Jian Yan
- Corresponding authors. E-mail: , , , ,
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Xing H, Jiang Y, Zou Y, Long X, Wu X, Ren Y, Li Y, Li HL. Genome-wide investigation of the AP2/ERF gene family in ginger: evolution and expression profiling during development and abiotic stresses. BMC PLANT BIOLOGY 2021; 21:561. [PMID: 34823471 PMCID: PMC8620233 DOI: 10.1186/s12870-021-03329-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 11/08/2021] [Indexed: 05/02/2023]
Abstract
BACKGROUND AP2/ERF transcription factors (TFs) constitute one of the largest TF families in plants, which play crucial roles in plant metabolism, growth, and development as well as biotic and abiotic stresses responses. Although the AP2/ERF family has been thoroughly identified in many plant species and several AP2/ERF TFs have been functionally characterized, little is known about this family in ginger (Zingiber officinale Roscoe), an important affinal drug and diet vegetable. Recent completion of the ginger genome sequencing provides an opportunity to investigate the expression profiles of AP2/ERF genes in ginger on a genome-wide basis. RESULTS A total of 163 AP2/ERF genes were obtained in the Z.officinale genome and renamed according to the chromosomal distribution of the ZoAP2/ERF genes. Phylogenetic analysis divided them into three subfamilies, of which 35 belonged to the AP2 subfamily, 120 to ERF, three to RAV, and five to Sololist, respectively, which is in accordance with the number of conserved domains and gene structure analysis. A total of 10 motifs were detected in ZoAP2/ERF genes, and some of the unique motifs were found to be important for the function of ZoAP2/ERF genes. The chromosomal localization, gene structure, and conserved protein motif analyses, as well as the characterization of gene duplication events provided deep insight into the evolutionary features of these ZoAP2/ERF genes. The expression profiles derived from the RNA-seq data and quantitative reserve transcription (qRT-PCR) analysis of ZoAP2/ERFs during development and responses to abiotic stresses were investigated in ginger. CONCLUSION A comprehensive analysis of the AP2/ERF gene expression patterns in various tissues by RNA-seq and qRT-PCR showed that they played an important role in the growth and development of ginger, and genes that might regulate rhizome and flower development were preliminary identified. In additionally, the ZoAP2/ERF family genes that responded to abiotic stresses were also identified. This study is the first time to identify the ZoAP2/ERF family, which contributes to research on evolutionary characteristics and better understanding the molecular basis for development and abiotic stress response, as well as further functional characterization of ZoAP2/ERF genes with an aim of ginger crop improvement.
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Affiliation(s)
- Haitao Xing
- College of Landscape Architecture and life Science/Institute of special Plants, Chongqing University of Arts and Sciences, Chongqing, 402168, China
- Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing University of Arts and Sciences, Chongqing, 402168, China
| | - Yusong Jiang
- College of Landscape Architecture and life Science/Institute of special Plants, Chongqing University of Arts and Sciences, Chongqing, 402168, China
| | - Yong Zou
- College of Landscape Architecture and life Science/Institute of special Plants, Chongqing University of Arts and Sciences, Chongqing, 402168, China
| | - Xiaoling Long
- College of Landscape Architecture and life Science/Institute of special Plants, Chongqing University of Arts and Sciences, Chongqing, 402168, China
| | - Xiaoli Wu
- College of Landscape Architecture and life Science/Institute of special Plants, Chongqing University of Arts and Sciences, Chongqing, 402168, China
| | - Yun Ren
- College of Landscape Architecture and life Science/Institute of special Plants, Chongqing University of Arts and Sciences, Chongqing, 402168, China
- Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing University of Arts and Sciences, Chongqing, 402168, China
| | - Yuan Li
- College of Landscape Architecture and life Science/Institute of special Plants, Chongqing University of Arts and Sciences, Chongqing, 402168, China.
| | - Hong-Lei Li
- College of Landscape Architecture and life Science/Institute of special Plants, Chongqing University of Arts and Sciences, Chongqing, 402168, China.
- Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing University of Arts and Sciences, Chongqing, 402168, China.
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44
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Li HL, Wu L, Dong Z, Jiang Y, Jiang S, Xing H, Li Q, Liu G, Tian S, Wu Z, Li Z, Zhao P, Zhang Y, Tang J, Xu J, Huang K, Liu X, Zhang W, Liao Q, Ren Y, Huang X, Li Q, Li C, Wang Y, Xavier-Ravi B, Li H, Liu Y, Wan T, Liu Q, Zou Y, Jian J, Xia Q, Liu Y. Correction: Haplotype-resolved genome of diploid ginger (Zingiber officinale) and its unique gingerol biosynthetic pathway. HORTICULTURE RESEARCH 2021; 8:242. [PMID: 34711798 PMCID: PMC8553826 DOI: 10.1038/s41438-021-00700-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Affiliation(s)
- Hong-Lei Li
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
- Engineering Research Center for Special Plant Seedlings of Chongqing, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Lin Wu
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
- Engineering Research Center for Special Plant Seedlings of Chongqing, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Zhaoming Dong
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Beibei, Chongqing, China
| | - Yusong Jiang
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
- Engineering Research Center for Special Plant Seedlings of Chongqing, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Sanjie Jiang
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Haitao Xing
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
- Engineering Research Center for Special Plant Seedlings of Chongqing, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Qiang Li
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
- Engineering Research Center for Special Plant Seedlings of Chongqing, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Guocheng Liu
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Shuming Tian
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
- College of Biology and Food Engineering, Chongqign Three Gorges University, Wanzhou, Chongqing, China
| | - Zhangyan Wu
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Zhexin Li
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
- Engineering Research Center for Special Plant Seedlings of Chongqing, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Ping Zhao
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Beibei, Chongqing, China
| | - Yan Zhang
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Beibei, Chongqing, China
| | - Jianmin Tang
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
- Engineering Research Center for Special Plant Seedlings of Chongqing, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Jiabao Xu
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Ke Huang
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
- Engineering Research Center for Special Plant Seedlings of Chongqing, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Xia Liu
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
- Engineering Research Center for Special Plant Seedlings of Chongqing, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Wenlin Zhang
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
- Engineering Research Center for Special Plant Seedlings of Chongqing, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Qinhong Liao
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
- Engineering Research Center for Special Plant Seedlings of Chongqing, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Yun Ren
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
- Engineering Research Center for Special Plant Seedlings of Chongqing, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Xinzheng Huang
- Department of Entomology and MOAKey Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Haidian, Beijing, China
| | - Qingzhi Li
- Jinan Second Agricultural Science Research Institute, Jinan, Shandong, China
| | - Chengyong Li
- Jinan Second Agricultural Science Research Institute, Jinan, Shandong, China
| | - Yi Wang
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Beibei, Chongqing, China
| | | | - Honghai Li
- Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, China
| | - Yang Liu
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, China
- Fairy Lake Botanical Garden and Chinese Academy of Sciences, Shenzhen, Guangdong, China
| | - Tao Wan
- Fairy Lake Botanical Garden and Chinese Academy of Sciences, Shenzhen, Guangdong, China
| | - Qinhu Liu
- Ningyang Science and Technology Bureau, Taian, Shandong, China
| | - Yong Zou
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China.
- Engineering Research Center for Special Plant Seedlings of Chongqing, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China.
| | - Jianbo Jian
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, China.
| | - Qingyou Xia
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Beibei, Chongqing, China.
| | - Yiqing Liu
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China.
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