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Lan S, Zhai T, Zhang X, Xu L, Gao J, Lai C, Chen Y, Lai Z, Lin Y. Genome-wide identification and expression analysis of the GAD family reveal their involved in embryogenesis and hormones responses in Dimocarpus longan Lour. Gene 2024; 927:148698. [PMID: 38908456 DOI: 10.1016/j.gene.2024.148698] [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: 02/16/2024] [Revised: 06/06/2024] [Accepted: 06/13/2024] [Indexed: 06/24/2024]
Abstract
Glutamate decarboxylase (GAD) is involved in GABA metabolism and plays an essential regulatory role in plant growth, abiotic stresses, and hormone response. This study investigated the expression mechanism of the GAD family during longan early somatic embryogenesis (SE) and identified 6 GAD genes based on the longan genome. Homology analysis indicated that DlGAD genes had a closer relationship with dicotyledonous plants. The analysis of cis-acting elements in the promoter region suggests that the GAD genes were associated with various stress responses and hormones. RNA sequencing (RNA-Seq) and the qRT-PCR data indicated that most DlGAD genes were highly expressed in the incomplete compact pro-embryogenic cultures (ICpEC) and upregulated in longan embryogenic callus (EC) after treatments with 2,4-D, high temperature (35 °C), IAA, and ABA. Moreover, the RNA-Seq analysis also revealed that DlGADs exhibit different expression patterns in various tissues and organs. The subcellular localization results showed that DlGAD5 was localized in the cytoplasm, suggesting that it played a role in the cytoplasm. Transient overexpression of DlGAD5 enhanced the expression levels of DlGADs and increased the activity of glutamate decarboxylase in longan embryogenic callus (EC), while the content of glutamic acid decreased. Thus, the DlGAD gene can play an important role in the early somatic embryogenesis of longan by responding to hormones such as IAA and ABA. DlGAD5 can affect the growth and development of longan by stimulating the expression of the DlGAD gene family, thereby increasing the GAD activity in the early SE of longan, participating in hormone synthesis and signaling pathways.
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Affiliation(s)
- Shuoxian Lan
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Tingkai Zhai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Xueying Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Luzhen Xu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Jie Gao
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Chunwang Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Yan Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
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Zhang Y, Zhang Y, Yu Z, Wang H, Ping B, Liu Y, Liang J, Ma F, Zou Y, Zhao T. Insights into ACO genes across Rosaceae: evolution, expression, and regulatory networks in fruit development. Genes Genomics 2024; 46:1209-1223. [PMID: 39141243 DOI: 10.1007/s13258-024-01551-5] [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: 02/01/2024] [Accepted: 07/05/2024] [Indexed: 08/15/2024]
Abstract
BACKGROUND ACO (1-aminocyclopropane-1-carboxylic acid) serves as a pivotal enzyme within the plant ethylene synthesis pathway, exerting influence over critical facets of plant biology such as flowering, fruit ripening, and seed development. OBJECTIVE This study aims to identify ACO genes from representative Rosaceae genomes, reconstruct their phylogenetic relationships by integrating synteny information, and investigate their expression patterns and networks during fruit development. METHODS we utilize a specialized Hidden Markov Model (HMM), crafted on the sequence attributes of ACO gene-encoded proteins, to systematically identify and analyze ACO gene family members across 12 representative species within the Rosaceae botanical family. Through transcriptome analysis, we delineate the expression patterns of ACO genes in six distinct Rosaceae fruits. RESULTS Our investigation reveals the presence of 62 ACO genes distributed among the surveyed Rosaceae species, characterized by hydrophilic proteins predominantly expressed within the cytoplasm. Phylogenetic analysis categorizes these ACO genes into three discernible classes, namely Class I, Class II, and Class III. Further scrutiny via collinearity assessment indicates a lack of collinearity relationships among these classes, highlighting variations in conserved motifs and promoter types within each class. Transcriptome analysis unveils significant disparities in both expression levels and trends of ACO genes in fruits exhibiting respiratory bursts compared to those that do not. Employing Weighted Gene Co-Expression Network Analysis (WGCNA), we discern that the co-expression correlation of ACO genes within loquat fruit notably differs from that observed in apples. Our findings, derived from Gene Ontology (GO) enrichment results, signify the involvement of ACO genes and their co-expressed counterparts in biological processes linked to terpenoid metabolism and carbohydrate synthesis in loquat. Moreover, our exploration of gene regulatory networks (GRN) highlights the potential pivotal role of the GNAT transcription factor (Ejapchr1G00010380) in governing the overexpression of the ACO gene (Ejapchr10G00001110) within loquat fruits. CONCLUSION The constructed HMM of ACO proteins offers a precise and systematic method for identifying plant ACO proteins, facilitating phylogenetic reconstruction. ACO genes from representative Rosaceae fruits exhibit diverse expression and regulative patterns, warranting further function characterizations.
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Affiliation(s)
- Yuxin Zhang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Yirong Zhang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Ze Yu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Hanyu Wang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Boya Ping
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Yunxiao Liu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Jiakai Liang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Fengwang Ma
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, PR China.
| | - Yangjun Zou
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, PR China.
| | - Tao Zhao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, PR China.
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Tian J, Chen Z, Jiang C, Li S, Yun X, He C, Wang D. Chromosome-scale genome assembly of Docynia delavayi provides new insights into the α-farnesene biosynthesis. Int J Biol Macromol 2024; 278:134820. [PMID: 39154695 DOI: 10.1016/j.ijbiomac.2024.134820] [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: 06/20/2024] [Revised: 08/14/2024] [Accepted: 08/15/2024] [Indexed: 08/20/2024]
Abstract
Docynia delavayi is an economically significant fruit species with a high market potential due to the special aroma of its fruit. Here, a 653.34 Mb high-quality genome of D. delavayi was first reported, of which 93.8 % of the sequences (612.98 Mb) could be anchored to 17 chromosomes, containing 48,325 protein-coding genes. Ks analysis proved that two whole genome duplication (WGD) events occurred in D. delavayi, resulting in the expansion of genes associated with terpene biosynthesis, which promoted its fruit-specific aroma production. Combined multi-omics analysis, α-farnesene was detected as the most abundant aroma substance emitted by D. delavayi fruit during storage, meanwhile one α-farnesene synthase gene (AFS) and 15 transcription factors (TFs) were identified as the candidate genes potentially involved in α-farnesene biosynthesis. Further studies for the regulation network of α-farnesene biosynthesis revealed that DdebHLH, DdeERF1 and DdeMYB could activate the transcription of DdeAFS. To our knowledge, it is the first report that MYB TF plays a regulatory role in α-farnesene biosynthesis, which will greatly facilitate future breeding programs for D. delavayi.
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Affiliation(s)
- Jinhong Tian
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming 650224, China; Key Laboratory for Forest Genetics and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming 650224, China
| | - Zhuo Chen
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming 650224, China; Key Laboratory for Forest Genetics and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming 650224, China
| | - Can Jiang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming 650224, China; Key Laboratory for Forest Genetics and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming 650224, China
| | - Siguang Li
- Yunnan Academy of Forestry and Grassland, Kunming 650201, China
| | - Xinhua Yun
- Yunnan Academy of Forestry and Grassland, Kunming 650201, China.
| | - Chengzhong He
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming 650224, China; Key Laboratory for Forest Genetics and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming 650224, China.
| | - Dawei Wang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming 650224, China; Key Laboratory for Forest Genetics and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming 650224, China.
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Huang D, Wu B, Chen G, Xing W, Xu Y, Ma F, Li H, Hu W, Huang H, Yang L, Song S. Genome-wide analysis of the passion fruit invertase gene family reveals involvement of PeCWINV5 in hexose accumulation. BMC PLANT BIOLOGY 2024; 24:836. [PMID: 39243043 PMCID: PMC11378628 DOI: 10.1186/s12870-024-05392-y] [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: 03/08/2024] [Accepted: 07/05/2024] [Indexed: 09/09/2024]
Abstract
BACKGROUND Invertases (INVs) are key enzymes in sugar metabolism, cleaving sucrose into glucose and fructose and playing an important role in plant development and the stress response, however, the INV gene family in passion fruit has not been systematically reported. RESULTS In this study, a total of 16 PeINV genes were identified from the passion fruit genome and named according to their subcellular location and chromosome position. These include six cell wall invertase (CWINV) genes, two vacuolar invertase (VINV) genes, and eight neutral/alkaline invertase (N/AINV) genes. The gene structures, phylogenetic tree, and cis-acting elements of PeINV gene family were predicted using bioinformatics methods. Results showed that the upstream promoter region of the PeINV genes contained various response elements; particularly, PeVINV2, PeN/AINV3, PeN/AINV5, PeN/AINV6, PeN/AINV7, and PeN/AINV8 had more response elements. Additionally, the expression profiles of PeINV genes under different abiotic stresses (drought, salt, cold temperature, and high temperature) indicated that PeCWINV5, PeCWINV6, PeVINV1, PeVINV2, PeN/AINV2, PeN/AINV3, PeN/AINV6, and PeN/AINV7 responded significantly to these abiotic stresses, which was consistent with cis-acting element prediction results. Sucrose, glucose, and fructose are main soluble components in passion fruit pulp. The contents of total soluble sugar, hexoses, and sweetness index increased significantly at early stages during fruit ripening. Transcriptome data showed that with an increase in fruit development and maturity, the expression levels of PeCWINV2, PeCWINV5, and PeN/AINV3 exhibited an up-regulated trend, especially for PeCWINV5 which showed highest abundance, this correlated with the accumulation of soluble sugar and sweetness index. Transient overexpression results demonstrated that the contents of fructose, glucose and sucrose increased in the pulp of PeCWINV5 overexpressing fruit. It is speculated that this cell wall invertase gene, PeCWINV5, may play an important role in sucrose unloading and hexose accumulation. CONCLUSION In this study, we systematically identified INV genes in passion fruit for the first time and further investigated their physicochemical properties, evolution, and expression patterns. Furthermore, we screened out a key candidate gene involved in hexose accumulation. This study lays a foundation for further study on INV genes and will be beneficial on the genetic improvement of passion fruit breeding.
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Affiliation(s)
- Dongmei Huang
- Tropical Crops Genetic Resources Institute, National Key Laboratory for Tropical Crop Breeding / Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture and Rual Affairs / Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province / Germplasm Repository of Passiflora, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 571101, P.R. China
| | - Bin Wu
- Tropical Crops Genetic Resources Institute, National Key Laboratory for Tropical Crop Breeding / Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture and Rual Affairs / Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province / Germplasm Repository of Passiflora, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 571101, P.R. China
| | - Ge Chen
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Key Laboratory of Passion fruit Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, 530007, P.R. China
| | - Wenting Xing
- Tropical Crops Genetic Resources Institute, National Key Laboratory for Tropical Crop Breeding / Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture and Rual Affairs / Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province / Germplasm Repository of Passiflora, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 571101, P.R. China
| | - Yi Xu
- Tropical Crops Genetic Resources Institute, National Key Laboratory for Tropical Crop Breeding / Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture and Rual Affairs / Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province / Germplasm Repository of Passiflora, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 571101, P.R. China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Hainan Seed Industry Laboratory, Sanya, Hainan, 572025, P.R. China
| | - Funing Ma
- Tropical Crops Genetic Resources Institute, National Key Laboratory for Tropical Crop Breeding / Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture and Rual Affairs / Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province / Germplasm Repository of Passiflora, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 571101, P.R. China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Hainan Seed Industry Laboratory, Sanya, Hainan, 572025, P.R. China
| | - Hongli Li
- Tropical Crops Genetic Resources Institute, National Key Laboratory for Tropical Crop Breeding / Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture and Rual Affairs / Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province / Germplasm Repository of Passiflora, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 571101, P.R. China
| | - Wenbin Hu
- Tropical Crops Genetic Resources Institute, National Key Laboratory for Tropical Crop Breeding / Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture and Rual Affairs / Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province / Germplasm Repository of Passiflora, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 571101, P.R. China
| | - Haijie Huang
- Tropical Crops Genetic Resources Institute, National Key Laboratory for Tropical Crop Breeding / Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture and Rual Affairs / Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province / Germplasm Repository of Passiflora, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 571101, P.R. China
| | - Liu Yang
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Key Laboratory of Passion fruit Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, 530007, P.R. China.
| | - Shun Song
- Tropical Crops Genetic Resources Institute, National Key Laboratory for Tropical Crop Breeding / Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture and Rual Affairs / Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province / Germplasm Repository of Passiflora, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 571101, P.R. China.
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Hainan Seed Industry Laboratory, Sanya, Hainan, 572025, P.R. China.
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Duan L, Hou Z, Zhang W, Liang S, Huangfu M, Zhang J, Yang T, Dong J, Che D. Genome-wide analysis of the WOX gene family and function exploration of RhWOX331 in rose ( R. 'The Fairy'). FRONTIERS IN PLANT SCIENCE 2024; 15:1461322. [PMID: 39290741 PMCID: PMC11405225 DOI: 10.3389/fpls.2024.1461322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Accepted: 08/13/2024] [Indexed: 09/19/2024]
Abstract
WOXs are a class of plant-specific transcription factors that play key roles in plant growth and stress responses. However, the mechanism by which WOXs influence adventitious root development in Rosa hybrida remains unclear. In this study, RcWOX gene family in rose was identified and phylogenetically analyzed using bioinformatics analysis. A total of 381 RcWOX gene members were localized on seven chromosomes except of nine members. The main cis-acting elements involved in hormonal, light, developmental, and abiotic stress responses were identified in the promoters of RcWOX genes, suggesting their regulation by these signals. Nine RhWOX genes had significant different expression during rooting process of rose. RhWOX331, RhWOX308, RhWOX318 were positive with the formation of rose roots. RhWOX331 was positively involved in the formation of adventitious root primordia, which gene coding a transcription factor localized in the nucleus. The HOX conserved domain in the protein contributed to the self-activating activity of RhWOX331. We obtained genetically modified Arabidopsis to validate the function of RhWOX331. Overexpression of RhWOX331 gene alleviated the inhibition of root length of A. thaliana primary roots by high concentration of IBA and NPA, and significantly increased the number of lateral roots on the primary roots, as well as the height of A. thaliana plants. Additionally, RhWOX331 promoted adventitious root formation in A. thaliana and mitigated hormonal inhibition by exogenous 6-BA, NPA, and GA3. The RhWOX331 promoter contained cis-acting elements such as ABRE, Box 4 and CGTCA-motif et.al. GUS activity analysis showed that the gene acted at the cotyledon attachment site. Taken together, these studies identified a significant expansion of the RcWOX gene family, inferred roles of certain branch members in adventitious root formation, elucidated the function of RhWOX331 in adventitious root initiation, and laid the foundation for further research on the function of WOX gene family in roses.
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Affiliation(s)
- Lian Duan
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Cold Region Landscape Plants and Applications, Harbin, China
| | - Zhihui Hou
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Cold Region Landscape Plants and Applications, Harbin, China
| | - Wuhua Zhang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Cold Region Landscape Plants and Applications, Harbin, China
| | - Shuang Liang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Cold Region Landscape Plants and Applications, Harbin, China
| | - Minge Huangfu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Cold Region Landscape Plants and Applications, Harbin, China
| | - Jinzhu Zhang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Cold Region Landscape Plants and Applications, Harbin, China
| | - Tao Yang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Cold Region Landscape Plants and Applications, Harbin, China
| | - Jie Dong
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Cold Region Landscape Plants and Applications, Harbin, China
| | - Daidi Che
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Cold Region Landscape Plants and Applications, Harbin, China
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Wang L, Yang H, Xu G, Liu Z, Meng F, Shi L, Liu X, Zheng Y, Zhang G, Yang X, Chen W, Song C, Zhang B. Asteraceae genome database: a comprehensive platform for Asteraceae genomics. FRONTIERS IN PLANT SCIENCE 2024; 15:1445365. [PMID: 39224843 PMCID: PMC11366637 DOI: 10.3389/fpls.2024.1445365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Accepted: 07/30/2024] [Indexed: 09/04/2024]
Abstract
Asteraceae, the largest family of angiosperms, has attracted widespread attention for its exceptional medicinal, horticultural, and ornamental value. However, researches on Asteraceae plants face challenges due to their intricate genetic background. With the continuous advancement of sequencing technology, a vast number of genomes and genetic resources from Asteraceae species have been accumulated. This has spurred a demand for comprehensive genomic analysis within this diverse plant group. To meet this need, we developed the Asteraceae Genomics Database (AGD; http://cbcb.cdutcm.edu.cn/AGD/). The AGD serves as a centralized and systematic resource, empowering researchers in various fields such as gene annotation, gene family analysis, evolutionary biology, and genetic breeding. AGD not only encompasses high-quality genomic sequences, and organelle genome data, but also provides a wide range of analytical tools, including BLAST, JBrowse, SSR Finder, HmmSearch, Heatmap, Primer3, PlantiSMASH, and CRISPRCasFinder. These tools enable users to conveniently query, analyze, and compare genomic information across various Asteraceae species. The establishment of AGD holds great significance in advancing Asteraceae genomics, promoting genetic breeding, and safeguarding biodiversity by providing researchers with a comprehensive and user-friendly genomics resource platform.
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Affiliation(s)
- Liang Wang
- State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- China Resources Sanjiu Medical & Pharmaceutical Co., Ltd, Shenzhen, China
| | - Hanting Yang
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Guoqing Xu
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Zhaoyu Liu
- State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Fanbo Meng
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - LiangRui Shi
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xiongfeng Liu
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yixuan Zheng
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Guichun Zhang
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xinyu Yang
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Wei Chen
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Chi Song
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Boli Zhang
- State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
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Wang B, Xiao Y, Yan M, Fan W, Zhu Y, Li W, Li T. Gene Duplication and Functional Diversification of MADS-Box Genes in Malus × domestica following WGD: Implications for Fruit Type and Floral Organ Evolution. Int J Mol Sci 2024; 25:8962. [PMID: 39201650 PMCID: PMC11354807 DOI: 10.3390/ijms25168962] [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: 08/01/2024] [Revised: 08/12/2024] [Accepted: 08/14/2024] [Indexed: 09/02/2024] Open
Abstract
The evolution of the MADS-box gene family is essential for the rapid differentiation of floral organs and fruit types in angiosperms. Two key processes drive the evolution of gene families: gene duplication and functional differentiation. Duplicated copies provide the material for variation, while advantageous mutations can confer new functions on gene copies. In this study, we selected the Rosaceae family, which includes a variety of fruit types and flower organs, as well as species that existed before and after whole-genome duplication (WGD). The results indicate that different fruit types are associated with different copies of MADS-box gene family duplications and WGD events. While most gene copies derived from WGD have been lost, MADS-box genes not only retain copies derived from WGD but also undergo further gene duplication. The sequences, protein structures, and expression patterns of these gene copies have undergone significant differentiation. This work provides a clear example of MADS-box genes in the context of gene duplication and functional differentiation, offering new insights into the evolution of fruit types and floral organs.
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Affiliation(s)
| | | | | | | | | | | | - Tianzhong Li
- College of Horticulture, China Agricultural University, Beijing 100193, China; (B.W.); (Y.X.); (M.Y.); (W.F.); (Y.Z.); (W.L.)
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Wang Z, Liu J, Qi X, Su D, Yang J, Cui X. Study of Endogenous Viruses in the Strawberry Plants. Viruses 2024; 16:1306. [PMID: 39205280 PMCID: PMC11359110 DOI: 10.3390/v16081306] [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: 07/24/2024] [Revised: 08/12/2024] [Accepted: 08/15/2024] [Indexed: 09/04/2024] Open
Abstract
Endogenous viral elements (EVEs) have been reported to exist widely in the genomes of eukaryotic organisms, and they are closely associated with the growth, development, genetics, adaptation, and evolution of their hosts. In this study, two methods-homologous sequence search and genome alignment-were used to explore the endogenous viral sequences in the genomes of Fragaria species. Results revealed abundant endogenous pararetroviruses (EPRVs) in the genomes of Fragaria species, including 786 sequences belonging to five known taxa such as Caulimovirus and other unclassified taxa. Differences were observed in the detected EPRVs between the two methods, with the homologous sequence search having a greater number of EPRVs. On the contrary, genome alignment identified various types and sources of virus-like sequences. Furthermore, through genome alignment, a 267-bp sequence with 95% similarity to the gene encoding the aphid-transmitted protein of Strawberry vein banding virus (Caulimovirus venafragariae) was discovered in the F. chiloensis genome, which was likely a recent insertion. In addition, the statistical analysis of the genome alignment results indicated a remarkably higher abundance of virus-like sequences in the genomes of polyploid strawberries compared with diploid ones. Moreover, the differences in virus-like sequences were observed between the genomes of Fragaria species and those of their close relatives. This study enriched the diversity of viruses that infect strawberries, and laid a theoretical foundation for further research on the origin of endogenous viruses in the strawberry genome, host-virus interactions, adaptation, evolution, and their functions.
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Affiliation(s)
- Zongneng Wang
- School of Life Sciences, Yunnan University, Kunming 650500, China; (Z.W.); (J.L.); (X.Q.); (D.S.)
| | - Jian Liu
- School of Life Sciences, Yunnan University, Kunming 650500, China; (Z.W.); (J.L.); (X.Q.); (D.S.)
| | - Xingyang Qi
- School of Life Sciences, Yunnan University, Kunming 650500, China; (Z.W.); (J.L.); (X.Q.); (D.S.)
| | - Daifa Su
- School of Life Sciences, Yunnan University, Kunming 650500, China; (Z.W.); (J.L.); (X.Q.); (D.S.)
| | - Junyu Yang
- School of Life Sciences, Yunnan University, Kunming 650500, China; (Z.W.); (J.L.); (X.Q.); (D.S.)
- Yunnan International Joint Laboratory of Virology and Immunology, Kunming 650500, China
| | - Xiaolong Cui
- School of Life Sciences, Yunnan University, Kunming 650500, China; (Z.W.); (J.L.); (X.Q.); (D.S.)
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9
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Skytte Af Sätra J, Garkava-Gustavsson L, Ingvarsson PK. Why we thrive beneath a northern sky - genomic signals of selection in apple for adaptation to northern Sweden. Heredity (Edinb) 2024; 133:67-77. [PMID: 38834867 PMCID: PMC11286948 DOI: 10.1038/s41437-024-00693-2] [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: 01/26/2024] [Revised: 05/16/2024] [Accepted: 05/16/2024] [Indexed: 06/06/2024] Open
Abstract
Good understanding of the genomic regions underlying adaptation of apple to boreal climates is needed to facilitate efficient breeding of locally adapted apple cultivars. Proper infrastructure for phenotyping and evaluation is essential for identification of traits responsible for adaptation, and dissection of their genetic composition. However, such infrastructure is costly and currently not available for the boreal zone of northern Sweden. Therefore, we used historical pomological data on climate adaptation of 59 apple cultivars and whole genome sequencing to identify genomic regions that have undergone historical selection among apple cultivars recommended for cultivation in northern Sweden. We found the apple collection to be composed of two ancestral groups that are largely concordant with the grouping into 'hardy' and 'not hardy' cultivars based on the pomological literature. Using a number of genome-wide scans for signals of selection, we obtained strong evidence of positive selection at a genomic region around 29 MbHFTH1 of chromosome 1 among apple cultivars in the 'hardy' group. Using phased genotypic data from the 20 K apple Infinium® SNP array, we identified haplotypes associated with the two cultivar groups and traced transmission of these haplotypes through the pedigrees of some apple cultivars. This demonstrates that historical data from pomological literature can be analyzed by population genomic approaches as a step towards revealing the genomic control of a key property for a horticultural niche market. Such knowledge is needed to facilitate efficient breeding strategies for development of locally adapted apple cultivars in the future. The current study illustrates the response to a very strong selective pressure imposed on tree crops by climatic factors, and the importance of genetic research on this topic and feasibility of breeding efforts in the light of the ongoing climate change.
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Affiliation(s)
- J Skytte Af Sätra
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden.
| | - L Garkava-Gustavsson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - P K Ingvarsson
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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10
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Jara-Cornejo K, Zúñiga PE, Rivera-Mora C, Bustos E, Garrido-Bigotes A, Ruiz-Lara S, Figueroa CR. YABBY transcription factor family in the octoploid Fragaria × ananassa and five diploid Fragaria species. PLANT BIOLOGY (STUTTGART, GERMANY) 2024; 26:735-748. [PMID: 38924267 DOI: 10.1111/plb.13656] [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: 09/12/2023] [Accepted: 04/02/2024] [Indexed: 06/28/2024]
Abstract
YABBY genes encode specific TFs of seed plants involved in development and formation of leaves, flowers, and fruit. In the present work, genome-wide and expression analyses of the YABBY gene family were performed in six species of the Fragaria genus: Fragaria × ananassa, F. daltoniana, F. nilgerrensis, F. pentaphylla, F. viridis, and F. vesca. The chromosomal location, synteny pattern, gene structure, and phylogenetic analyses were carried out. By combining RNA-seq data and RT-qPCR analysis we explored specific expression of YABBYs in F. × ananassa and F. vesca. We also analysed the promoter regions of FaYABBYs and performed MeJA application to F. × ananassa fruit to observe effects on gene expression. We identified and characterized 25 YABBY genes in F. × ananassa and six in each of the other five species, which belong to FIL/YAB3 (YABBY1), YAB2 (YABBY2), YAB5 (YABBY5), CRC, and INO clades previously described. Division of the YABBY1 clade into YABBY1.1 and YABBY1.2 subclades is reported. We observed differential expression according to tissue, where some FaYABBYs are expressed mainly in leaves and flowers and to a minor extent during fruit development of F. × ananassa. Specifically, the FaINO genes contain jasmonate-responsive cis-acting elements in their promoters which may be functional since FaINOs are upregulated in F. × ananassa fruit under MeJA treatment. This study suggests that YABBY TFs play an important role in the development- and environment-associated responses of the Fragaria genus.
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Affiliation(s)
- K Jara-Cornejo
- Laboratory of Plant Molecular Physiology, Institute of Biological Sciences, Campus Talca, Universidad de Talca, Talca, Chile
- Doctoral Program in Sciences mention in Plant Biology and Biotechnology, Institute of Biological Sciences, Campus Talca, Universidad de Talca, Talca, Chile
- Functional Genomics Laboratory, Institute of Biological Sciences, Campus Talca, Universidad de Talca, Talca, Chile
- Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, Chile
| | - P E Zúñiga
- Laboratory of Plant Molecular Physiology, Institute of Biological Sciences, Campus Talca, Universidad de Talca, Talca, Chile
- Doctoral Program in Sciences mention in Plant Biology and Biotechnology, Institute of Biological Sciences, Campus Talca, Universidad de Talca, Talca, Chile
- Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, Chile
| | - C Rivera-Mora
- Laboratory of Plant Molecular Physiology, Institute of Biological Sciences, Campus Talca, Universidad de Talca, Talca, Chile
- Doctoral Program in Sciences mention in Plant Biology and Biotechnology, Institute of Biological Sciences, Campus Talca, Universidad de Talca, Talca, Chile
- Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, Chile
| | - E Bustos
- Laboratory of Plant Molecular Physiology, Institute of Biological Sciences, Campus Talca, Universidad de Talca, Talca, Chile
- Doctoral Program in Sciences mention in Plant Biology and Biotechnology, Institute of Biological Sciences, Campus Talca, Universidad de Talca, Talca, Chile
- Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, Chile
| | - A Garrido-Bigotes
- Laboratorio de Epigenética Vegetal, Departamento de Silvicultura, Facultad de Ciencias Forestales, Universidad de Concepción, Concepción, Chile
| | - S Ruiz-Lara
- Functional Genomics Laboratory, Institute of Biological Sciences, Campus Talca, Universidad de Talca, Talca, Chile
- Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, Chile
| | - C R Figueroa
- Laboratory of Plant Molecular Physiology, Institute of Biological Sciences, Campus Talca, Universidad de Talca, Talca, Chile
- Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, Chile
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11
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Li X, Bai Y, Xu C, Liu S, Yu H, Kong L, Du S, Li Q. OysterDB: A Genome Database for Ostreidae. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024; 26:827-834. [PMID: 38822152 DOI: 10.1007/s10126-024-10327-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 05/23/2024] [Indexed: 06/02/2024]
Abstract
The molluscan family Ostreidae, commonly known as oysters, is an important molluscan group due to its economic and ecological importance. In recent years, an abundance of genomic data of Ostreidae species has been generated and available in public domain. However, there is still a lack of a high-efficiency database platform to store and distribute these data with comprehensive tools. In this study, we developed an oyster genome database (OysterDB) to consolidate oyster genomic data. This database includes eight oyster genomes and 208,923 protein-coding gene annotations. Bioinformatic tools, such as BLAST and JBrowse, are integrated into the database to provide a user-friendly platform for homologous sequence searching, visualization of genomes, and screen for candidate gene information. Moreover, OysterDB will be continuously updated with ever-growing oyster genomic resources and facilitate future studies for comparative and functional genomic analysis of oysters ( http://oysterdb.com.cn/ ).
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Affiliation(s)
- Xinchun Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Yitian Bai
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Chengxun Xu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Shikai Liu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Hong Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Shaojun Du
- Institute of Marine and Environmental Technology, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
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12
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Minamikawa MF, Kunihisa M, Moriya S, Shimizu T, Inamori M, Iwata H. Genomic prediction and genome-wide association study using combined genotypic data from different genotyping systems: application to apple fruit quality traits. HORTICULTURE RESEARCH 2024; 11:uhae131. [PMID: 38979105 PMCID: PMC11228094 DOI: 10.1093/hr/uhae131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 04/25/2024] [Indexed: 07/10/2024]
Abstract
With advances in next-generation sequencing technologies, various marker genotyping systems have been developed for genomics-based approaches such as genomic selection (GS) and genome-wide association study (GWAS). As new genotyping platforms are developed, data from different genotyping platforms must be combined. However, the potential use of combined data for GS and GWAS has not yet been clarified. In this study, the accuracy of genomic prediction (GP) and the detection power of GWAS increased for most fruit quality traits of apples when using combined data from different genotyping systems, Illumina Infinium single-nucleotide polymorphism array and genotyping by random amplicon sequencing-direct (GRAS-Di) systems. In addition, the GP model, which considered the inbreeding effect, further improved the accuracy of the seven fruit traits. Runs of homozygosity (ROH) islands overlapped with the significantly associated regions detected by the GWAS for several fruit traits. Breeders may have exploited these regions to select promising apples by breeders, increasing homozygosity. These results suggest that combining genotypic data from different genotyping platforms benefits the GS and GWAS of fruit quality traits in apples. Information on inbreeding could be beneficial for improving the accuracy of GS for fruit traits of apples; however, further analysis is required to elucidate the relationship between the fruit traits and inbreeding depression (e.g. decreased vigor).
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Affiliation(s)
- Mai F Minamikawa
- Institute for Advanced Academic Research (IAAR), Chiba University, 1-33 Yayoi, Inage, Chiba, Chiba 263-8522, Japan
- Laboratory of Biometry and Bioinformatics, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Miyuki Kunihisa
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605, Japan
| | - Shigeki Moriya
- Institute of Fruit Tree and Tea Science, NARO, 92-24 Shimokuriyagawa Nabeyashiki, Morioka, Iwate 020-0123, Japan
| | - Tokurou Shimizu
- Institute of Fruit Tree and Tea Science, NARO, Okitsu Nakacho, Shimizu, Shizuoka 424-0292, Japan
| | - Minoru Inamori
- Laboratory of Biometry and Bioinformatics, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Hiroyoshi Iwata
- Laboratory of Biometry and Bioinformatics, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
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13
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Straube J, Hurtado G, Zeisler-Diehl V, Schreiber L, Knoche M. Cuticle deposition ceases during strawberry fruit development. BMC PLANT BIOLOGY 2024; 24:623. [PMID: 38951751 PMCID: PMC11218262 DOI: 10.1186/s12870-024-05327-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 06/24/2024] [Indexed: 07/03/2024]
Abstract
BACKGROUND Ideally, the barrier properties of a fruit's cuticle persist throughout its development. This presents a challenge for strawberry fruit, with their rapid development and thin cuticles. The objective was to establish the developmental time course of cuticle deposition in strawberry fruit. RESULTS Fruit mass and surface area increase rapidly, with peak growth rate coinciding with the onset of ripening. On a whole-fruit basis, the masses of cutin and wax increase but on a unit surface-area basis, they decrease. The decrease is associated with marked increases in elastic strain. The expressions of cuticle-associated genes involved in transcriptional regulation (FaSHN1, FaSHN2, FaSHN3), synthesis of cutin (FaLACS2, FaGPAT3) and wax (FaCER1, FaKCS10, FaKCR1), and those involved in transport of cutin monomers and wax constituents (FaABCG11, FaABCG32) decreased until maturity. The only exceptions were FaLACS6 and FaGPAT6 that are presumably involved in cutin synthesis, and FaCER1 involved in wax synthesis. This result was consistent across five strawberry cultivars. Strawberry cutin consists mainly of C16 and C18 monomers, plus minor amounts of C19, C20, C22 and C24 monomers, ω-hydroxy acids, dihydroxy acids, epoxy acids, primary alcohols, carboxylic acids and dicarboxylic acids. The most abundant monomer is 10,16-dihydroxyhexadecanoic acid. Waxes comprise mainly long-chain fatty acids C29 to C46, with smaller amounts of C16 to C28. Wax constituents are carboxylic acids, primary alcohols, alkanes, aldehydes, sterols and esters. CONCLUSION The downregulation of cuticle deposition during development accounts for the marked cuticular strain, for the associated microcracking, and for their high susceptibility to the disorders of water soaking and cracking.
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Affiliation(s)
- Jannis Straube
- Institute of Horticultural Production Systems, Fruit Science Section, Leibniz University Hannover, Herrenhäuser Straße 2, Hannover, 30419, Germany
| | - Grecia Hurtado
- Institute of Horticultural Production Systems, Fruit Science Section, Leibniz University Hannover, Herrenhäuser Straße 2, Hannover, 30419, Germany
| | - Viktoria Zeisler-Diehl
- Department of Ecophysiology, Institute of Cellular and Molecular Botany (IZMB), University of Bonn, Kirschallee 1, Bonn, 53115, Germany
| | - Lukas Schreiber
- Department of Ecophysiology, Institute of Cellular and Molecular Botany (IZMB), University of Bonn, Kirschallee 1, Bonn, 53115, Germany
| | - Moritz Knoche
- Institute of Horticultural Production Systems, Fruit Science Section, Leibniz University Hannover, Herrenhäuser Straße 2, Hannover, 30419, Germany.
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14
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Méndez-Yáñez A, Sáez D, Rodríguez-Arriaza F, Letelier-Naritelli C, Valenzuela-Riffo F, Morales-Quintana L. Involvement of the GH38 Family Exoglycosidase α-Mannosidase in Strawberry Fruit Ripening. Int J Mol Sci 2024; 25:6581. [PMID: 38928287 PMCID: PMC11203768 DOI: 10.3390/ijms25126581] [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: 05/04/2024] [Revised: 05/31/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
Exoglycosidase enzymes hydrolyze the N-glycosylations of cell wall enzymes, releasing N-glycans that act as signal molecules and promote fruit ripening. Vesicular exoglycosidase α-mannosidase enzymes of the GH38 family (EC 3.2.1.24; α-man) hydrolyze N-glycans in non-reduced termini. Strawberry fruit (Fragaria × ananassa) is characterized by rapid softening as a result of cell wall modifications during the fruit ripening process. Enzymes acting on cell wall polysaccharides explain the changes in fruit firmness, but α-man has not yet been described in F. × ananassa, meaning that the indirect effects of N-glycan removal on its fruit ripening process are unknown. The present study identified 10 GH38 α-man sequences in the F. × ananassa genome with characteristic conserved domains and key residues. A phylogenetic tree built with the neighbor-joining method and three groups of α-man established, of which group I was classified into three subgroups and group III contained only Poaceae spp. sequences. The real-time qPCR results demonstrated that FaMAN genes decreased during fruit ripening, a trend mirrored by the total enzyme activity from the white to ripe stages. The analysis of the promoter regions of these FaMAN genes was enriched with ripening and phytohormone response elements, and contained cis-regulatory elements related to stress responses to low temperature, drought, defense, and salt stress. This study discusses the relevance of α-man in fruit ripening and how it can be a useful target to prolong fruit shelf life.
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Affiliation(s)
- Angela Méndez-Yáñez
- Multidisciplinary Agroindustry Research Laboratory, Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Cinco Poniente #1670, Talca 3467987, Chile
| | - Darwin Sáez
- Multidisciplinary Agroindustry Research Laboratory, Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Cinco Poniente #1670, Talca 3467987, Chile
- Programa de Doctorado en Ciencias Biomédicas, Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Cinco Poniente #1670, Talca 3467987, Chile
| | - Francisca Rodríguez-Arriaza
- Multidisciplinary Agroindustry Research Laboratory, Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Cinco Poniente #1670, Talca 3467987, Chile
| | - Claudio Letelier-Naritelli
- Multidisciplinary Agroindustry Research Laboratory, Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Cinco Poniente #1670, Talca 3467987, Chile
| | - Felipe Valenzuela-Riffo
- Instituto de Ciencias Biológicas, Universidad de Talca, Campus Talca, Avenida Lircay s/n, Talca 3460000, Chile
| | - Luis Morales-Quintana
- Multidisciplinary Agroindustry Research Laboratory, Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Cinco Poniente #1670, Talca 3467987, Chile
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15
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Wang S, Wei S, Deng Y, Wu S, Peng H, Qing Y, Zhai X, Zhou S, Li J, Li H, Feng Y, Yi Y, Li R, Zhang H, Wang Y, Zhang R, Ning L, Yao Y, Fei Z, Zheng Y. HortGenome Search Engine, a universal genomic search engine for horticultural crops. HORTICULTURE RESEARCH 2024; 11:uhae100. [PMID: 38863996 PMCID: PMC11165154 DOI: 10.1093/hr/uhae100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 03/27/2024] [Indexed: 06/13/2024]
Abstract
Horticultural crops comprising fruit, vegetable, ornamental, beverage, medicinal and aromatic plants play essential roles in food security and human health, as well as landscaping. With the advances of sequencing technologies, genomes for hundreds of horticultural crops have been deciphered in recent years, providing a basis for understanding gene functions and regulatory networks and for the improvement of horticultural crops. However, these valuable genomic data are scattered in warehouses with various complex searching and displaying strategies, which increases learning and usage costs and makes comparative and functional genomic analyses across different horticultural crops very challenging. To this end, we have developed a lightweight universal search engine, HortGenome Search Engine (HSE; http://hort.moilab.net), which allows for the querying of genes, functional annotations, protein domains, homologs, and other gene-related functional information of more than 500 horticultural crops. In addition, four commonly used tools, including 'BLAST', 'Batch Query', 'Enrichment analysis', and 'Synteny Viewer' have been developed for efficient mining and analysis of these genomic data.
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Affiliation(s)
- Sen Wang
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Shangxiao Wei
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Yuling Deng
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Shaoyuan Wu
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Haixu Peng
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - You Qing
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Xuyang Zhai
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Shijie Zhou
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Jinrong Li
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Hua Li
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Yijian Feng
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Yating Yi
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Rui Li
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Hui Zhang
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Yiding Wang
- College of Intelligent Science and Engineering, Beijing University of Agriculture, Beijing 102206, China
| | - Renlong Zhang
- College of Intelligent Science and Engineering, Beijing University of Agriculture, Beijing 102206, China
| | - Lu Ning
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
- Library, Beijing University of Agriculture, Beijing 102206, China
| | - Yuncong Yao
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
- USDA-ARS, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
| | - Yi Zheng
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
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16
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Castanera R, de Tomás C, Ruggieri V, Vicient C, Eduardo I, Aranzana MJ, Arús P, Casacuberta JM. A phased genome of the highly heterozygous 'Texas' almond uncovers patterns of allele-specific expression linked to heterozygous structural variants. HORTICULTURE RESEARCH 2024; 11:uhae106. [PMID: 38883330 PMCID: PMC11179849 DOI: 10.1093/hr/uhae106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 04/01/2024] [Indexed: 06/18/2024]
Abstract
The vast majority of traditional almond varieties are self-incompatible, and the level of variability of the species is very high, resulting in a high-heterozygosity genome. Therefore, information on the different haplotypes is particularly relevant to understand the genetic basis of trait variability in this species. However, although reference genomes for several almond varieties exist, none of them is phased and has genome information at the haplotype level. Here, we present a phased assembly of genome of the almond cv. Texas. This new assembly has 13% more assembled sequence than the previous version of the Texas genome and has an increased contiguity, in particular in repetitive regions such as the centromeres. Our analysis shows that the 'Texas' genome has a high degree of heterozygosity, both at SNPs, short indels, and structural variants level. Many of the SVs are the result of heterozygous transposable element insertions, and in many cases, they also contain genic sequences. In addition to the direct consequences of this genic variability on the presence/absence of genes, our results show that variants located close to genes are often associated with allele-specific gene expression, which highlights the importance of heterozygous SVs in almond.
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Affiliation(s)
- Raúl Castanera
- Centre for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, 08193, Cerdanyola del Vallès, Barcelona, Spain
| | - Carlos de Tomás
- Centre for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, 08193, Cerdanyola del Vallès, Barcelona, Spain
| | | | - Carlos Vicient
- Centre for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, 08193, Cerdanyola del Vallès, Barcelona, Spain
| | - Iban Eduardo
- Centre for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, 08193, Cerdanyola del Vallès, Barcelona, Spain
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), 08140, Caldes de Montbui, Barcelona, Spain
| | - Maria José Aranzana
- Centre for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, 08193, Cerdanyola del Vallès, Barcelona, Spain
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), 08140, Caldes de Montbui, Barcelona, Spain
| | - Pere Arús
- Centre for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, 08193, Cerdanyola del Vallès, Barcelona, Spain
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), 08140, Caldes de Montbui, Barcelona, Spain
| | - Josep M Casacuberta
- Centre for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, 08193, Cerdanyola del Vallès, Barcelona, Spain
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17
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Yu Z, Li J, Wang H, Ping B, Li X, Liu Z, Guo B, Yu Q, Zou Y, Sun Y, Ma F, Zhao T. Transposable elements in Rosaceae: insights into genome evolution, expression dynamics, and syntenic gene regulation. HORTICULTURE RESEARCH 2024; 11:uhae118. [PMID: 38919560 PMCID: PMC11197308 DOI: 10.1093/hr/uhae118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 04/17/2024] [Indexed: 06/27/2024]
Abstract
Transposable elements (TEs) exert significant influence on plant genomic structure and gene expression. Here, we explored TE-related aspects across 14 Rosaceae genomes, investigating genomic distribution, transposition activity, expression patterns, and nearby differentially expressed genes (DEGs). Analyses unveiled distinct long terminal repeat retrotransposon (LTR-RT) evolutionary patterns, reflecting varied genome size changes among nine species over the past million years. In the past 2.5 million years, Rubus idaeus showed a transposition rate twice as fast as Fragaria vesca, while Pyrus bretschneideri displayed significantly faster transposition compared with Crataegus pinnatifida. Genes adjacent to recent TE insertions were linked to adversity resistance, while those near previous insertions were functionally enriched in morphogenesis, enzyme activity, and metabolic processes. Expression analysis revealed diverse responses of LTR-RTs to internal or external conditions. Furthermore, we identified 3695 pairs of syntenic DEGs proximal to TEs in Malus domestica cv. 'Gala' and M. domestica (GDDH13), suggesting TE insertions may contribute to varietal trait differences in these apple varieties. Our study across representative Rosaceae species underscores the pivotal role of TEs in plant genome evolution within this diverse family. It elucidates how these elements regulate syntenic DEGs on a genome-wide scale, offering insights into Rosaceae-specific genomic evolution.
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Affiliation(s)
- Ze Yu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jiale Li
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hanyu Wang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Boya Ping
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xinchu Li
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhiguang Liu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Bocheng Guo
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qiaoming Yu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yangjun Zou
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yaqiang Sun
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fengwang Ma
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Tao Zhao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
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18
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Kohler AR, Scheil A, Hill JL, Allen JR, Al-Haddad JM, Goeckeritz CZ, Strader LC, Telewski FW, Hollender CA. Defying gravity: WEEP promotes negative gravitropism in peach trees by establishing asymmetric auxin gradients. PLANT PHYSIOLOGY 2024; 195:1229-1255. [PMID: 38366651 PMCID: PMC11142379 DOI: 10.1093/plphys/kiae085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 01/09/2024] [Accepted: 01/14/2024] [Indexed: 02/18/2024]
Abstract
Trees with weeping shoot architectures are valued for their beauty and are a resource for understanding how plants regulate posture control. The peach (Prunus persica) weeping phenotype, which has elliptical downward arching branches, is caused by a homozygous mutation in the WEEP gene. Little is known about the function of WEEP despite its high conservation throughout Plantae. Here, we present the results of anatomical, biochemical, biomechanical, physiological, and molecular experiments that provide insight into WEEP function. Our data suggest that weeping peach trees do not have defects in branch structure. Rather, transcriptomes from the adaxial (upper) and abaxial (lower) sides of standard and weeping branch shoot tips revealed flipped expression patterns for genes associated with early auxin response, tissue patterning, cell elongation, and tension wood development. This suggests that WEEP promotes polar auxin transport toward the lower side during shoot gravitropic response, leading to cell elongation and tension wood development. In addition, weeping peach trees exhibited steeper root systems and faster lateral root gravitropic response. This suggests that WEEP moderates root gravitropism and is essential to establishing the set-point angle of lateral roots from the gravity vector. Additionally, size exclusion chromatography indicated that WEEP proteins self-oligomerize, like other proteins with sterile alpha motif domains. Collectively, our results from weeping peach provide insight into polar auxin transport mechanisms associated with gravitropism and lateral shoot and root orientation.
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Affiliation(s)
- Andrea R Kohler
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
| | - Andrew Scheil
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
| | - Joseph L Hill
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
| | - Jeffrey R Allen
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Jameel M Al-Haddad
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Charity Z Goeckeritz
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
| | - Lucia C Strader
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Frank W Telewski
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Courtney A Hollender
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
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19
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Zhou S, Wu X, Yuan Y, Qiao X, Wang Z, Wu M, Qi K, Xie Z, Yin H, Zhang S. Evolutionary origin and gradual accumulation with plant evolution of the LACS family. BMC PLANT BIOLOGY 2024; 24:481. [PMID: 38816698 PMCID: PMC11140897 DOI: 10.1186/s12870-024-05194-2] [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: 04/11/2024] [Accepted: 05/24/2024] [Indexed: 06/01/2024]
Abstract
BACKGROUND LACS (long-chain acyl-CoA synthetase) genes are widespread in organisms and have multiple functions in plants, especially in lipid metabolism. However, the origin and evolutionary dynamics of the LACS gene family remain largely unknown. RESULTS Here, we identified 1785 LACS genes in the genomes of 166 diverse plant species and identified the clades (I, II, III, IV, V, VI) of six clades for the LACS gene family of green plants through phylogenetic analysis. Based on the evolutionary history of plant lineages, we found differences in the origins of different clades, with Clade IV originating from chlorophytes and representing the origin of LACS genes in green plants. The structural characteristics of different clades indicate that clade IV is relatively independent, while the relationships between clades (I, II, III) and clades (V, VI) are closer. Dispersed duplication (DSD) and transposed duplication (TRD) are the main forces driving the evolution of plant LACS genes. Network clustering analysis further grouped all LACS genes into six main clusters, with genes within each cluster showing significant co-linearity. Ka/Ks results suggest that LACS family genes underwent purifying selection during evolution. We analyzed the phylogenetic relationships and characteristics of six clades of the LACS gene family to explain the origin, evolutionary history, and phylogenetic relationships of different clades and proposed a hypothetical evolutionary model for the LACS family of genes in plants. CONCLUSIONS Our research provides genome-wide insights into the evolutionary history of the LACS gene family in green plants. These insights lay an important foundation for comprehensive functional characterization in future research.
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Affiliation(s)
- Siyuan Zhou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiao Wu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Yubo Yuan
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xin Qiao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zewen Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mayan Wu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China
| | - Kaijie Qi
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhihua Xie
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hao Yin
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shaoling Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China.
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20
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López ME, Denoyes B, Bucher E. Epigenomic and transcriptomic persistence of heat stress memory in strawberry (Fragaria vesca). BMC PLANT BIOLOGY 2024; 24:405. [PMID: 38750420 PMCID: PMC11096098 DOI: 10.1186/s12870-024-05093-6] [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: 03/22/2024] [Accepted: 05/02/2024] [Indexed: 05/18/2024]
Abstract
BACKGROUND In plants, epigenetic stress memory has so far been found to be largely transient. Here, we wanted to assess the heritability of heat stress-induced epigenetic and transcriptomic changes following woodland strawberry (Fragaria vesca) reproduction. Strawberry is an ideal model to study epigenetic inheritance because it presents two modes of reproduction: sexual (self-pollinated plants) and asexual (clonally propagated plants named daughter plants). Taking advantage of this model, we investigated whether heat stress-induced DNA methylation changes can be transmitted via asexual reproduction. RESULTS Our genome-wide study provides evidence for stress memory acquisition and maintenance in F. vesca. We found that specific DNA methylation marks or epimutations are stably transmitted over at least three asexual generations. Some of the epimutations were associated with transcriptional changes after heat stress. CONCLUSION Our findings show that the strawberry methylome and transcriptome respond with a high level of flexibility to heat stress. Notably, independent plants acquired the same epimutations and those were inherited by their asexual progenies. Overall, the asexual progenies can retain some information in the genome of past stresses encountered by their progenitors. This molecular memory, also documented at the transcriptional level, might be involved in functional plasticity and stress adaptation. Finally, these findings may contribute to novel breeding approaches for climate-ready plants.
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Affiliation(s)
- María-Estefanía López
- Crop Genome Dynamics Group, Agroscope, Nyon, 1260, Switzerland
- Department of Botany and Plant Biology, Faculty of Sciences, University of Geneva, Geneva, 1205, Switzerland
| | - Béatrice Denoyes
- INRAE, Biologie du Fruit et Pathologie, Univ. Bordeaux, Villenave d'Ornon, F-33140, France
| | - Etienne Bucher
- Crop Genome Dynamics Group, Agroscope, Nyon, 1260, Switzerland.
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21
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Ianiri G, Barone G, Palmieri D, Quiquero M, Gaeta I, De Curtis F, Castoria R. Transcriptomic investigation of the interaction between a biocontrol yeast, Papiliotrema terrestris strain PT22AV, and the postharvest fungal pathogen Penicillium expansum on apple. Commun Biol 2024; 7:359. [PMID: 38519651 PMCID: PMC10960036 DOI: 10.1038/s42003-024-06031-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 03/08/2024] [Indexed: 03/25/2024] Open
Abstract
Biocontrol strategies offer a promising alternative to control plant pathogens achieving food safety and security. In this study we apply a RNAseq analysis during interaction between the biocontrol agent (BCA) Papiliotrema terrestris, the pathogen Penicillium expansum, and the host Malus domestica. Analysis of the BCA finds overall 802 upregulated DEGs (differentially expressed genes) when grown in apple tissue, with the majority being involved in nutrients uptake and oxidative stress response. This suggests that these processes are crucial for the BCA to colonize the fruit wounds and outcompete the pathogen. As to P. expansum analysis, 1017 DEGs are upregulated when grown in apple tissue, with the most represented GO categories being transcription, oxidation reduction process, and transmembrane transport. Analysis of the host M. domestica finds a higher number of DEGs in response to the pathogen compared to the BCA, with overexpression of genes involved in host defense signaling pathways in the presence of both of them, and a prevalence of pattern-triggered immunity (PTI) and effector-triggered immunity (ETI) only during interaction with P. expansum. This analysis contributes to advance the knowledge on the molecular mechanisms that underlie biocontrol activity and the tritrophic interaction of the BCA with the pathogen and the host.
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Affiliation(s)
- Giuseppe Ianiri
- Department of Agricultural, Environmental and Food Sciences, University of Molise, via F. De Sanctis snc, 86100, Campobasso, Italy.
| | - Giuseppe Barone
- Department of Agricultural, Environmental and Food Sciences, University of Molise, via F. De Sanctis snc, 86100, Campobasso, Italy
| | - Davide Palmieri
- Department of Agricultural, Environmental and Food Sciences, University of Molise, via F. De Sanctis snc, 86100, Campobasso, Italy
| | - Michela Quiquero
- Department of Agricultural, Environmental and Food Sciences, University of Molise, via F. De Sanctis snc, 86100, Campobasso, Italy
| | - Ilenia Gaeta
- Department of Agricultural, Environmental and Food Sciences, University of Molise, via F. De Sanctis snc, 86100, Campobasso, Italy
| | - Filippo De Curtis
- Department of Agricultural, Environmental and Food Sciences, University of Molise, via F. De Sanctis snc, 86100, Campobasso, Italy
| | - Raffaello Castoria
- Department of Agricultural, Environmental and Food Sciences, University of Molise, via F. De Sanctis snc, 86100, Campobasso, Italy.
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22
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Hadish JA, Hargarten HL, Zhang H, Mattheis JP, Honaas LA, Ficklin SP. Towards identification of postharvest fruit quality transcriptomic markers in Malus domestica. PLoS One 2024; 19:e0297015. [PMID: 38446822 PMCID: PMC10917293 DOI: 10.1371/journal.pone.0297015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 12/27/2023] [Indexed: 03/08/2024] Open
Abstract
Gene expression is highly impacted by the environment and can be reflective of past events that affected developmental processes. It is therefore expected that gene expression can serve as a signal of a current or future phenotypic traits. In this paper we identify sets of genes, which we call Prognostic Transcriptomic Biomarkers (PTBs), that can predict firmness in Malus domestica (apple) fruits. In apples, all individuals of a cultivar are clones, and differences in fruit quality are due to the environment. The apples transcriptome responds to these differences in environment, which makes PTBs an attractive predictor of future fruit quality. PTBs have the potential to enhance supply chain efficiency, reduce crop loss, and provide higher and more consistent quality for consumers. However, several questions must be addressed. In this paper we answer the question of which of two common modeling approaches, Random Forest or ElasticNet, outperforms the other. We answer if PTBs with few genes are efficient at predicting traits. This is important because we need few genes to perform qPCR, and we answer the question if qPCR is a cost-effective assay as input for PTBs modeled using high-throughput RNA-seq. To do this, we conducted a pilot study using fruit texture in the 'Gala' variety of apples across several postharvest storage regiments. Fruit texture in 'Gala' apples is highly controllable by post-harvest treatments and is therefore a good candidate to explore the use of PTBs. We find that the RandomForest model is more consistent than an ElasticNet model and is predictive of firmness (r2 = 0.78) with as few as 15 genes. We also show that qPCR is reasonably consistent with RNA-seq in a follow up experiment. Results are promising for PTBs, yet more work is needed to ensure that PTBs are robust across various environmental conditions and storage treatments.
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Affiliation(s)
- John A. Hadish
- Molecular Plant Science Department, Washington State University, Pullman, Washington, United States of America
- Department of Horticulture, Washington State University, Pullman, Washington, United States of America
| | - Heidi L. Hargarten
- USDA Agricultural Research Service Physiology and Pathology of Tree Fruits Research, Wenatchee, Washington, United States of America
| | - Huiting Zhang
- Department of Horticulture, Washington State University, Pullman, Washington, United States of America
| | - James P. Mattheis
- USDA Agricultural Research Service Physiology and Pathology of Tree Fruits Research, Wenatchee, Washington, United States of America
| | - Loren A. Honaas
- USDA Agricultural Research Service Physiology and Pathology of Tree Fruits Research, Wenatchee, Washington, United States of America
| | - Stephen P. Ficklin
- Molecular Plant Science Department, Washington State University, Pullman, Washington, United States of America
- Department of Horticulture, Washington State University, Pullman, Washington, United States of America
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23
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Dong W, Sun L, Jiao B, Zhao P, Ma C, Gao J, Zhou S. Evaluation of aphid resistance on different rose cultivars and transcriptome analysis in response to aphid infestation. BMC Genomics 2024; 25:232. [PMID: 38438880 PMCID: PMC10910744 DOI: 10.1186/s12864-024-10100-z] [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: 05/12/2023] [Accepted: 02/08/2024] [Indexed: 03/06/2024] Open
Abstract
BACKGROUND The rose is one of the most important ornamental flowers in the world for its aesthetic beauty but can be attacked by many pests such as aphids. Aphid infestation causes tremendous damage on plant tissues leading to harmed petals and leaves. Rose cultivars express different levels of resistance to aphid infestation yet the information remains unclear. Not only that, studies about the transcriptional analysis on defending mechanisms against aphids in rose are limited so far. RESULTS In this study, the aphid resistance of 20 rose cultivars was evaluated, and they could be sorted into six levels based on the number ratio of aphids. And then, a transcriptome analysis was conducted after aphid infestation in one high resistance (R, Harmonie) and one highly susceptibility (S, Carefree Wonder) rose cultivar. In open environment the majority of rose cultivars had the highest aphid number at May 6th or May 15th in 2020 and the resistance to infestation could be classified into six levels. Differential expression analysis revealed that there were 1,626 upregulated and 767 downregulated genes in the R cultivar and 481 upregulated and 63 downregulated genes in the S cultivar after aphid infestation. Pathway enrichment analysis of the differentially expressed genes revealed that upregulated genes in R and S cultivars were both enriched in defense response, biosynthesis of secondary metabolites (phenylpropanoid, alkaloid, and flavonoid), carbohydrate metabolism (galactose, starch, and sucrose metabolism) and lipid processing (alpha-linolenic acid and linolenic acid metabolism) pathways. In the jasmonic acid metabolic pathway, linoleate 13S-lipoxygenase was specifically upregulated in the R cultivar, while genes encoding other crucial enzymes, allene oxide synthase, allene oxide cyclase, and 12-oxophytodienoate reductase were upregulated in both cultivars. Transcription factor analysis and transcription factor binding search showed that WRKY transcription factors play a pivotal role during aphid infestation in the R cultivar. CONCLUSIONS Our study indicated the potential roles of jasmonic acid metabolism and WRKY transcription factors during aphid resistance in rose, providing clues for future research.
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Affiliation(s)
- Wenqi Dong
- Hebei Key Laboratory of Plant Genetic Engineering, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050051, China
- Department of Ornamental Horticulture, State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Lei Sun
- Hebei Key Laboratory of Plant Genetic Engineering, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050051, China
| | - Bo Jiao
- Hebei Key Laboratory of Plant Genetic Engineering, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050051, China
| | - Pu Zhao
- Hebei Key Laboratory of Plant Genetic Engineering, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050051, China
| | - Chunhong Ma
- Hebei Key Laboratory of Plant Genetic Engineering, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050051, China
| | - Junping Gao
- Department of Ornamental Horticulture, State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Shuo Zhou
- Hebei Key Laboratory of Plant Genetic Engineering, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050051, China.
- Department of Ornamental Horticulture, State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China.
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24
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Zhu J, Li Y, Zhang Y, Xia L, Hu W, Huang X, Li K, He X, Luo C. Overexpression of MiSPL3a and MiSPL3b confers early flowering and stress tolerance in Arabidopsis thaliana. Int J Biol Macromol 2024; 262:129913. [PMID: 38336312 DOI: 10.1016/j.ijbiomac.2024.129913] [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: 11/01/2023] [Revised: 01/11/2024] [Accepted: 01/31/2024] [Indexed: 02/12/2024]
Abstract
SQUAMOSA promoter-binding protein-like (SPL) family genes play an important role in regulating plant flowering and resistance to stress. However, understanding the function of the SPL family in mango is still limited. In a previous study, two MiSPL3 genes, MiSPL3a and MiSPL3b (MiSPL3a/b), were identified in 'SiJiMi' mango and exhibited the highest expression in flowers at the initial flowering stage [24]. Therefore, in this study, we further investigated the expression pattern and gene function of MiSPL3a/b. The results showed that the expression of MiSPL3a was greatest at the end of floral bud differentiation, and MiSPL3b was expressed mainly during the flowering induction and vegetative growth stages. Subcellular localization showed that MiSPL3a/b localized to the nucleus. In addition, ectopic expression of MiSPL3a/b promoted earlier flowering in Arabidopsis thaliana by 3 d-6 d than in wild-type (WT) plants, which increased the expression of SUPPRESSOR OF CONSTANS1 (AtSOC1), FRUITFULL (AtFUL), and APETALA1 (AtAP1). MiSPL3a/b transgenic lines exhibited increased tolerance to drought, GA3, and abscisic acid (ABA) treatments but were sensitive to Pro-Ca treatment. Furthermore, protein interaction analysis revealed that MiSPL3a/b could interact with several stress-related proteins, flowering-related proteins, and the bridge protein 14-3-3. Taken together, MiSPL3a and MiSPL3b acted as positive regulators of flowering time and stress tolerance in transgenic Arabidopsis.
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Affiliation(s)
- Jiawei Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, Guangxi, China; College of Horticulture, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Yuze Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, Guangxi, China
| | - Yili Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, Guangxi, China
| | - LiMing Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, Guangxi, China
| | - Wanli Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, Guangxi, China
| | - Xing Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, Guangxi, China
| | - Kaijiang Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, Guangxi, China
| | - Xinhua He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, Guangxi, China.
| | - Cong Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, Guangxi, China.
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25
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Lin Y, She M, Zhao M, Yu H, Xiao W, Zhang Y, Li M, Chen Q, Zhang Y, Wang Y, He W, Wang X, Tang H, Luo Y. Genome-wide analysis and functional validation reveal the role of late embryogenesis abundant genes in strawberry (Fragaria × ananassa) fruit ripening. BMC Genomics 2024; 25:228. [PMID: 38429694 PMCID: PMC10908092 DOI: 10.1186/s12864-024-10085-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 02/02/2024] [Indexed: 03/03/2024] Open
Abstract
BACKGROUND Late embryogenesis abundant (LEA) proteins play important roles in plant growth and development, as well as stresses responsiveness. Nowadays, it has been found that LEAs also have function in fruit ripening. However, the comprehensive analysis on a genome-wide basis of LEA family remains limited, and the role of LEA in fruit ripening has not been fully explored yet, especially in strawberry, an economic important plant and ideal material for studying fruit ripening. RESULTS In this study, a total of 266 putative LEA proteins were identified and characterized in strawberry genome. Subcellular localization prediction indicated that they were mostly localized in chloroplast, cytoplasm and nucleus. Duplication events detection revealed that whole genome duplication or segmental was the main driver for the expansion of LEA family in strawberry. The phylogenetic analysis suggested that FaLEAs were classified into eight groups, among which, LEA2 was the largest subgroup with 179 members, followed by LEA3, dehydrin (DHN), LEA4 and SMP (seed maturation protein). The LEA1 and DHN groups were speculated to play dominant roles in strawberry fruit development and ripening, according to their larger proportion of members detected as differentially expressed genes during such process. Notably, the expression of FaLEA167 belonging to LEA1 group was altered by strawberry maturation, and inhibited by overexpression of negative regulators of ripening (a cytosolic/plastid glyceraldehyde-3-phosphate dehydrogenase, FaGAPC2 and a cytosolic pyruvate kinase, FaPKc2.2). Subsequently, overexpression of FaLEA167 significantly increased the percentage of fruit at green stage, while reduced the full red fruit proportion. In consistent, the anthocyanins content and the fruit skin color variable reflecting a range from greenness to redness (a* value) were significantly reduced. Whereas, FaLEA167 overexpression apparently up-regulated citric acid, soluble protein and malondialdehyde content, but had no obvious effects on total soluble solids, sugar, flavonoids, phenolics content and antioxidant capacity. CONCLUSIONS These findings not only provided basic information of FaLEA family for further functional research, but also revealed the involvement of FaLEA167 in negatively regulating strawberry fruit ripening, giving new insights into understanding of FaLEA functions.
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Affiliation(s)
- Yuanxiu Lin
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Musha She
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Mantong Zhao
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Hong Yu
- Hangzhou Academy of Agricultural Sciences, Hangzhou, 310024, Zhejiang, China
| | - Wenfei Xiao
- Hangzhou Academy of Agricultural Sciences, Hangzhou, 310024, Zhejiang, China
| | - Yunting Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Mengyao Li
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Qing Chen
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yong Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yan Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Wen He
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xiaorong Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Haoru Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
| | - Ya Luo
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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26
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Gunaseelan K, Schröder R, Rebstock R, Ninan AS, Deng C, Khanal BP, Favre L, Tomes S, Dragulescu MA, O'Donoghue EM, Hallett IC, Schaffer RJ, Knoche M, Brummell DA, Atkinson RG. Constitutive expression of apple endo-POLYGALACTURONASE1 in fruit induces early maturation, alters skin structure and accelerates softening. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1413-1431. [PMID: 38038980 DOI: 10.1111/tpj.16571] [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: 06/06/2023] [Revised: 10/25/2023] [Accepted: 11/20/2023] [Indexed: 12/02/2023]
Abstract
During fruit ripening, polygalacturonases (PGs) are key contributors to the softening process in many species. Apple is a crisp fruit that normally exhibits only minor changes to cell walls and limited fruit softening. Here, we explore the effects of PG overexpression during fruit development using transgenic apple lines overexpressing the ripening-related endo-POLYGALACTURONASE1 gene. MdPG1-overexpressing (PGox) fruit displayed early maturation/ripening with black seeds, conversion of starch to sugars and ethylene production occurring by 80 days after pollination (DAP). PGox fruit exhibited a striking, white-skinned phenotype that was evident from 60 DAP and most likely resulted from increased air spaces and separation of cells in the hypodermis due to degradation of the middle lamellae. Irregularities in the integrity of the epidermis and cuticle were also observed. By 120 DAP, PGox fruit cracked and showed lenticel-associated russeting. Increased cuticular permeability was associated with microcracks in the cuticle around lenticels and was correlated with reduced cortical firmness at all time points and extensive post-harvest water loss from the fruit, resulting in premature shrivelling. Transcriptomic analysis suggested that early maturation was associated with upregulation of genes involved in stress responses, and overexpression of MdPG1 also altered the expression of genes involved in cell wall metabolism (e.g. β-galactosidase, MD15G1221000) and ethylene biosynthesis (e.g. ACC synthase, MD14G1111500). The results show that upregulation of PG not only has dramatic effects on the structure of the fruit outer cell layers, indirectly affecting water status and turgor, but also has unexpected consequences for fruit development.
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Affiliation(s)
- Kularajathevan Gunaseelan
- The New Zealand Institute for Plant and Food Research Limited (Plant and Food Research), Mount Albert Research Centre, Private Bag 92169, Auckland, 1142, New Zealand
| | - Roswitha Schröder
- The New Zealand Institute for Plant and Food Research Limited (Plant and Food Research), Mount Albert Research Centre, Private Bag 92169, Auckland, 1142, New Zealand
| | - Ria Rebstock
- The New Zealand Institute for Plant and Food Research Limited (Plant and Food Research), Mount Albert Research Centre, Private Bag 92169, Auckland, 1142, New Zealand
| | - Annu S Ninan
- The New Zealand Institute for Plant and Food Research Limited (Plant and Food Research), Mount Albert Research Centre, Private Bag 92169, Auckland, 1142, New Zealand
| | - Cecilia Deng
- The New Zealand Institute for Plant and Food Research Limited (Plant and Food Research), Mount Albert Research Centre, Private Bag 92169, Auckland, 1142, New Zealand
| | - Bishnu P Khanal
- Institute for Horticultural Production Systems, Leibniz-University Hannover, Herrenhäuser Straße 2, 30419, Hannover, Germany
| | - Laurie Favre
- Plant and Food Research, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - Sumathi Tomes
- The New Zealand Institute for Plant and Food Research Limited (Plant and Food Research), Mount Albert Research Centre, Private Bag 92169, Auckland, 1142, New Zealand
| | - Monica A Dragulescu
- The New Zealand Institute for Plant and Food Research Limited (Plant and Food Research), Mount Albert Research Centre, Private Bag 92169, Auckland, 1142, New Zealand
| | - Erin M O'Donoghue
- Plant and Food Research, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - Ian C Hallett
- The New Zealand Institute for Plant and Food Research Limited (Plant and Food Research), Mount Albert Research Centre, Private Bag 92169, Auckland, 1142, New Zealand
| | | | - Moritz Knoche
- Institute for Horticultural Production Systems, Leibniz-University Hannover, Herrenhäuser Straße 2, 30419, Hannover, Germany
| | - David A Brummell
- Plant and Food Research, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - Ross G Atkinson
- The New Zealand Institute for Plant and Food Research Limited (Plant and Food Research), Mount Albert Research Centre, Private Bag 92169, Auckland, 1142, New Zealand
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27
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de los Cobos FP, García-Gómez BE, Orduña-Rubio L, Batlle I, Arús P, Matus JT, Eduardo I. Exploring large-scale gene coexpression networks in peach ( Prunus persica L.): a new tool for predicting gene function. HORTICULTURE RESEARCH 2024; 11:uhad294. [PMID: 38487296 PMCID: PMC10939413 DOI: 10.1093/hr/uhad294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 12/17/2023] [Indexed: 03/17/2024]
Abstract
Peach is a model for Prunus genetics and genomics, however, identifying and validating genes associated to peach breeding traits is a complex task. A gene coexpression network (GCN) capable of capturing stable gene-gene relationships would help researchers overcome the intrinsic limitations of peach genetics and genomics approaches and outline future research opportunities. In this study, we created four GCNs from 604 Illumina RNA-Seq libraries. We evaluated the performance of every GCN in predicting functional annotations using an algorithm based on the 'guilty-by-association' principle. The GCN with the best performance was COO300, encompassing 21 956 genes. To validate its performance predicting gene function, we performed two case studies. In case study 1, we used two genes involved in fruit flesh softening: the endopolygalacturonases PpPG21 and PpPG22. Genes coexpressing with both genes were extracted and referred to as melting flesh (MF) network. Finally, we performed an enrichment analysis of MF network and compared the results with the current knowledge regarding peach fruit softening. The MF network mostly included genes involved in cell wall expansion and remodeling, and with expressions triggered by ripening-related phytohormones, such as ethylene, auxin, and methyl jasmonate. In case study 2, we explored potential targets of the anthocyanin regulator PpMYB10.1 by comparing its gene-centered coexpression network with that of its grapevine orthologues, identifying a common regulatory network. These results validated COO300 as a powerful tool for peach and Prunus research. This network, renamed as PeachGCN v1.0, and the scripts required to perform a function prediction analysis are available at https://github.com/felipecobos/PeachGCN.
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Affiliation(s)
- Felipe Pérez de los Cobos
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA) , Mas Bové, Ctra. Reus-El Morell Km 3,8 43120 Constantí Tarragona, Spain
- Centre de Recerca en Agrigenòmica (CRAG), Institut de Recerca i Tecnologia Agroalimentàries (IRTA), CSIC-IRTA-UAB-UB. Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | - Beatriz E García-Gómez
- Centre de Recerca en Agrigenòmica (CRAG), Institut de Recerca i Tecnologia Agroalimentàries (IRTA), CSIC-IRTA-UAB-UB. Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | - Luis Orduña-Rubio
- Institute for Integrative Systems Biology (I2SysBio), Universitat de Valencia-CSIC, Paterna, 46908, Valencia, Spain
| | - Ignasi Batlle
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA) , Mas Bové, Ctra. Reus-El Morell Km 3,8 43120 Constantí Tarragona, Spain
| | - Pere Arús
- Centre de Recerca en Agrigenòmica (CRAG), Institut de Recerca i Tecnologia Agroalimentàries (IRTA), CSIC-IRTA-UAB-UB. Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | - José Tomás Matus
- Institute for Integrative Systems Biology (I2SysBio), Universitat de Valencia-CSIC, Paterna, 46908, Valencia, Spain
| | - Iban Eduardo
- Centre de Recerca en Agrigenòmica (CRAG), Institut de Recerca i Tecnologia Agroalimentàries (IRTA), CSIC-IRTA-UAB-UB. Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
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28
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Sammarco I, Díez Rodríguez B, Galanti D, Nunn A, Becker C, Bossdorf O, Münzbergová Z, Latzel V. DNA methylation in the wild: epigenetic transgenerational inheritance can mediate adaptation in clones of wild strawberry (Fragaria vesca). THE NEW PHYTOLOGIST 2024; 241:1621-1635. [PMID: 38058250 DOI: 10.1111/nph.19464] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/20/2023] [Indexed: 12/08/2023]
Abstract
Due to the accelerating climate change, it is crucial to understand how plants adapt to rapid environmental changes. Such adaptation may be mediated by epigenetic mechanisms like DNA methylation, which could heritably alter phenotypes without changing the DNA sequence, especially across clonal generations. However, we are still missing robust evidence of the adaptive potential of DNA methylation in wild clonal populations. Here, we studied genetic, epigenetic and transcriptomic variation of Fragaria vesca, a predominantly clonally reproducing herb. We examined samples from 21 natural populations across three climatically distinct geographic regions, as well as clones of the same individuals grown in a common garden. We found that epigenetic variation was partly associated with climate of origin, particularly in non-CG contexts. Importantly, a large proportion of this variation was heritable across clonal generations. Additionally, a subset of these epigenetic changes affected the expression of genes mainly involved in plant growth and responses to pathogen and abiotic stress. These findings highlight the potential influence of epigenetic changes on phenotypic traits. Our findings indicate that variation in DNA methylation, which can be environmentally inducible and heritable, may enable clonal plant populations to adjust to their environmental conditions even in the absence of genetic adaptation.
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Affiliation(s)
- Iris Sammarco
- Institute of Botany, Czech Academy of Sciences, Zámek 1, 252 43, Průhonice, Czechia
| | - Bárbara Díez Rodríguez
- Natural Resources and Climate Area, CARTIF Technology Centre, Parque Tecnológico de Boecillo, parc. 205, 47151, Boecillo, Valladolid, Spain
- Department of Biology, Philipps-University Marburg, Karl-von-Frisch Strasse 8, D-35043, Marburg, Germany
- Department of Forest Genetics, Albert-Ludwigs-Universität Freiburg, Bertoldstraße 17, 79098, Freiburg i. Br., Germany
| | - Dario Galanti
- Royal Botanic Gardens, Kew, Richmond, UK
- Plant Evolutionary Ecology, Institute of Evolution and Ecology, University of Tübingen, Auf der Morgenstelle 5, 72076, Tübingen, Germany
| | - Adam Nunn
- ecSeq Bioinformatics GmbH, Sternwartenstraße 29, 04103, Saxony, Germany
- Department of Computer Science, University of Leipzig, Härtelstraße 16-18, Leipzig, 04107, Germany
| | - Claude Becker
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr Bohr-Gasse 3, 1030, Vienna, Austria
- LMU Biocenter, Faculty of Biology, Ludwig Maximilians University Munich, Grosshaderner Str. 2-4, 82152, Martinsried, Germany
| | - Oliver Bossdorf
- Plant Evolutionary Ecology, Institute of Evolution and Ecology, University of Tübingen, Auf der Morgenstelle 5, 72076, Tübingen, Germany
| | - Zuzana Münzbergová
- Institute of Botany, Czech Academy of Sciences, Zámek 1, 252 43, Průhonice, Czechia
- Department of Botany, Faculty of Science, Charles University, Benátská 2, 128 01, Prague, Czechia
| | - Vít Latzel
- Institute of Botany, Czech Academy of Sciences, Zámek 1, 252 43, Průhonice, Czechia
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29
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Dujak C, Coleto-Alcudia V, Aranzana MJ. Genomic analysis of fruit size and shape traits in apple: unveiling candidate genes through GWAS analysis. HORTICULTURE RESEARCH 2024; 11:uhad270. [PMID: 38419968 PMCID: PMC10901474 DOI: 10.1093/hr/uhad270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 12/05/2023] [Indexed: 03/02/2024]
Abstract
Genomic tools facilitate the efficient selection of improved genetic materials within a breeding program. Here, we focus on two apple fruit quality traits: shape and size. We utilized data from 11 fruit morphology parameters gathered across three years of harvest from 355 genotypes of the apple REFPOP collection, which serves as a representative sample of the genetic variability present in European-cultivated apples. The data were then employed for genome-wide association studies (GWAS) using the FarmCPU and the BLINK models. The analysis identified 59 SNPs associated with fruit size and shape traits (35 with FarmCPU and 45 with BLINK) responsible for 71 QTNs. These QTNs were distributed across all chromosomes except for chromosomes 10 and 15. Thirty-four QTNs, identified by 27 SNPs, were related for size traits, and 37 QTNs, identified by 26 SNPs, were related to shape attributes. The definition of the haploblocks containing the most relevant SNPs served to propose candidate genes, among them the genes of the ovate family protein MdOFP17 and MdOFP4 that were in a 9.7kb haploblock on Chromosome 11. RNA-seq data revealed low or null expression of these genes in the oblong cultivar "Skovfoged" and higher expression in the flat "Grand'mere." The Gene Ontology enrichment analysis support a role of OFPs and hormones in shape regulation. In conclusion, this comprehensive GWAS analysis of the apple REFPOP collection has revealed promising genetic markers and candidate genes associated with apple fruit shape and size attributes, providing valuable insights that could enhance the efficiency of future breeding programs.
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Affiliation(s)
- Christian Dujak
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UABUB, Plant and Animal Genomics, Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Veredas Coleto-Alcudia
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UABUB, Plant and Animal Genomics, Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Maria José Aranzana
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UABUB, Plant and Animal Genomics, Campus UAB, 08193 Bellaterra, Barcelona, Spain
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Genomics and Biotechnology, 08140 Caldes de Montbui, Barcelona, Spain
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30
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da Silva Linge C, Fu W, Calle A, Rawandoozi Z, Cai L, Byrne DH, Worthington M, Gasic K. Ppe.RPT/SSC-1: from QTL mapping to a predictive KASP test for ripening time and soluble solids concentration in peach. Sci Rep 2024; 14:1453. [PMID: 38228692 PMCID: PMC10791670 DOI: 10.1038/s41598-024-51599-2] [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: 11/06/2023] [Accepted: 01/07/2024] [Indexed: 01/18/2024] Open
Abstract
Genomic regions associated with ripening time (RPT) and soluble solids concentration (SSC) were mapped using a pedigreed population including multiple F1 and F2 families from the Clemson University peach breeding program (CUPBP). RPT and SSC QTLs were consistently identified in two seasons (2011 and 2012) and the average datasets (average of two seasons). A target region spanning 10,981,971-11,298,736 bp on chromosome 4 of peach reference genome used for haplotype analysis revealed four haplotypes with significant differences in trait values among different diplotype combinations. Favorable alleles at the target region for both RPT and SSC were determined and a DNA test for predicting RPT and SSC was developed. Two Kompetitive Allele Specific PCR (KASP) assays were validated on 84 peach cultivars and 163 seedlings from the CUPBP, with only one assay (Ppe.RPT/SSC-1) needed to predict between early and late-season ripening cultivars and low and high SSC. These results advance our understanding of the genetic basis of RPT and SSC and facilitate selection of new peach cultivars with the desired RPT and SSC.
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Affiliation(s)
- Cassia da Silva Linge
- Department of Plant and Environmental Sciences, College of Agriculture, Forestry and Life Sciences, Clemson University, Clemson, SC, 29634, USA
- Department of Agriculture and Environmental Sciences, University of Milan, Milan, Italy
| | - Wanfang Fu
- Department of Plant and Environmental Sciences, College of Agriculture, Forestry and Life Sciences, Clemson University, Clemson, SC, 29634, USA
| | - Alejandro Calle
- Department of Plant and Environmental Sciences, College of Agriculture, Forestry and Life Sciences, Clemson University, Clemson, SC, 29634, USA
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Fruitcentre, PCiTAL, Gardeny Park, Fruitcentre Building, 25003, Lleida, Spain
| | - Zena Rawandoozi
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Lichun Cai
- Department of Plant and Environmental Sciences, College of Agriculture, Forestry and Life Sciences, Clemson University, Clemson, SC, 29634, USA
| | - David H Byrne
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Margaret Worthington
- Department of Horticulture, University of Arkansas System Division of Agriculture, Fayetteville, AR, 72701, USA
| | - Ksenija Gasic
- Department of Plant and Environmental Sciences, College of Agriculture, Forestry and Life Sciences, Clemson University, Clemson, SC, 29634, USA.
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31
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Waite JM, Hollender CA, Eilers JR, Burchard E, Dardick C. Peach LAZY1 and DRO1 protein-protein interactions and co-expression with PRAF/RLD family support conserved gravity-related protein interactions across plants. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.000995. [PMID: 38287925 PMCID: PMC10823791 DOI: 10.17912/micropub.biology.000995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/12/2023] [Accepted: 01/09/2024] [Indexed: 01/31/2024]
Abstract
IGT/LAZY proteins play a central role in determining gravitropic set point angle and orientation of lateral organs across plant species. Recent work in model systems has demonstrated that interactions between IGT/LAZY proteins and BREVIS RADIX (BRX)-domain containing proteins, such as PH, RCC1, AND FYVE/RCC1-LIKE DOMAIN (PRAF/RLD), and BREVIS RADIX LIKE (BRXL) family members, are mechanistically important for setting gravitropic set point angle. Here, we identified peach PRAF/RLD proteins as interactors of the peach IGT/LAZY proteins PpeLAZY1 and DEEPER ROOTING 1 (PpeDRO1) from a yeast-two-hybrid screen. We also show that the BRX domains of these interacting proteins have high sequence similarity with PRAF/RLD and BRX family proteins from rice and Arabidopsis. Further, PpeLAZY1 and the peach PRAF/RLD interactors are all expressed at relatively high levels in leaf, meristem, and shoot tip tissues. Together, this evidence supports the importance and conservation of IGT/LAZY-BRX-domain interactions, which underlie setting gravitropic set point angle across angiosperms.
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Affiliation(s)
| | | | - Jon R. Eilers
- USDA ARS Tree Fruit Research Laboratory, Wenatchee, WA
| | - Erik Burchard
- USDA ARS Appalachian Fruit Research Station, Kearneysville, WV
| | - Chris Dardick
- USDA ARS Appalachian Fruit Research Station, Kearneysville, WV
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32
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Lang X, Yu C, Shen M, Gu L, Qian Q, Zhou D, Tan J, Li Y, Peng X, Diao S, Deng Z, Ruan Z, Xu Z, Xing J, Li C, Wang R, Ding C, Cao Y, Liu Q. PRMD: an integrated database for plant RNA modifications. Nucleic Acids Res 2024; 52:D1597-D1613. [PMID: 37831097 PMCID: PMC10768107 DOI: 10.1093/nar/gkad851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 08/23/2023] [Accepted: 09/23/2023] [Indexed: 10/14/2023] Open
Abstract
The scope and function of RNA modifications in model plant systems have been extensively studied, resulting in the identification of an increasing number of novel RNA modifications in recent years. Researchers have gradually revealed that RNA modifications, especially N6-methyladenosine (m6A), which is one of the most abundant and commonly studied RNA modifications in plants, have important roles in physiological and pathological processes. These modifications alter the structure of RNA, which affects its molecular complementarity and binding to specific proteins, thereby resulting in various of physiological effects. The increasing interest in plant RNA modifications has necessitated research into RNA modifications and associated datasets. However, there is a lack of a convenient and integrated database with comprehensive annotations and intuitive visualization of plant RNA modifications. Here, we developed the Plant RNA Modification Database (PRMD; http://bioinformatics.sc.cn/PRMD and http://rnainformatics.org.cn/PRMD) to facilitate RNA modification research. This database contains information regarding 20 plant species and provides an intuitive interface for displaying information. Moreover, PRMD offers multiple tools, including RMlevelDiff, RMplantVar, RNAmodNet and Blast (for functional analyses), and mRNAbrowse, RNAlollipop, JBrowse and Integrative Genomics Viewer (for displaying data). Furthermore, PRMD is freely available, making it useful for the rapid development and promotion of research on plant RNA modifications.
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Affiliation(s)
- Xiaoqiang Lang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Chunyan Yu
- Frontiers Science Center for Disease-related Molecular Network, Laboratory of Omics Technology and Bioinformatics, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Mengyuan Shen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China
| | - Lei Gu
- Epigenetics Laboratory, Max Planck Institute for Heart and Lung Research & Cardiopulmonary Institute (CPI). Parkstr.1 61231 Bad Nauheim Germany
| | - Qian Qian
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China
| | - Degui Zhou
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China
| | - Jiantao Tan
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China
| | - Yiliang Li
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization/Guangdong Academy of Forestry, Guangzhou, Guangdong 510520, China
| | - Xin Peng
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China
| | - Shu Diao
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Zhujun Deng
- Precision Medicine Center, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Zhaohui Ruan
- Sun Yat-sen University Cancer Center, State Key Laboratory Oncology in South China, Collaborative Innovation Center of Cancer Medicine, 510060, Guangzhou, China
| | - Zhi Xu
- Guangxi Key Laboratory of Images and Graphics Intelligent Processing, Guilin University of Electronics Technology, Guilin, 541004, China
| | - Junlian Xing
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China
| | - Chen Li
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China
| | - Runfeng Wang
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Changjun Ding
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Yi Cao
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Qi Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China
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Gupta P, Elser J, Hooks E, D’Eustachio P, Jaiswal P, Naithani S. Plant Reactome Knowledgebase: empowering plant pathway exploration and OMICS data analysis. Nucleic Acids Res 2024; 52:D1538-D1547. [PMID: 37986220 PMCID: PMC10767815 DOI: 10.1093/nar/gkad1052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 11/22/2023] Open
Abstract
Plant Reactome (https://plantreactome.gramene.org) is a freely accessible, comprehensive plant pathway knowledgebase. It provides curated reference pathways from rice (Oryza sativa) and gene-orthology-based pathway projections to 129 additional species, spanning single-cell photoautotrophs, non-vascular plants, and higher plants, thus encompassing a wide-ranging taxonomic diversity. Currently, Plant Reactome houses a collection of 339 reference pathways, covering metabolic and transport pathways, hormone signaling, genetic regulations of developmental processes, and intricate transcriptional networks that orchestrate a plant's response to abiotic and biotic stimuli. Beyond being a mere repository, Plant Reactome serves as a dynamic data discovery platform. Users can analyze and visualize omics data, such as gene expression, gene-gene interaction, proteome, and metabolome data, all within the rich context of plant pathways. Plant Reactome is dedicated to fostering data interoperability, upholding global data standards, and embracing the tenets of the Findable, Accessible, Interoperable and Re-usable (FAIR) data policy.
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Affiliation(s)
- Parul Gupta
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Justin Elser
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Elizabeth Hooks
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | | | - Pankaj Jaiswal
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Sushma Naithani
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
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Liang Z, Ye H, Ma J, Wei Z, Wang Y, Zhang Y, Huang D, Song B, Meng J, Rigden DJ, Chen K. m6A-Atlas v2.0: updated resources for unraveling the N6-methyladenosine (m6A) epitranscriptome among multiple species. Nucleic Acids Res 2024; 52:D194-D202. [PMID: 37587690 PMCID: PMC10768109 DOI: 10.1093/nar/gkad691] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/02/2023] [Accepted: 08/10/2023] [Indexed: 08/18/2023] Open
Abstract
N 6-Methyladenosine (m6A) is one of the most abundant internal chemical modifications on eukaryote mRNA and is involved in numerous essential molecular functions and biological processes. To facilitate the study of this important post-transcriptional modification, we present here m6A-Atlas v2.0, an updated version of m6A-Atlas. It was expanded to include a total of 797 091 reliable m6A sites from 13 high-resolution technologies and two single-cell m6A profiles. Additionally, three methods (exomePeaks2, MACS2 and TRESS) were used to identify >16 million m6A enrichment peaks from 2712 MeRIP-seq experiments covering 651 conditions in 42 species. Quality control results of MeRIP-seq samples were also provided to help users to select reliable peaks. We also estimated the condition-specific quantitative m6A profiles (i.e. differential methylation) under 172 experimental conditions for 19 species. Further, to provide insights into potential functional circuitry, the m6A epitranscriptomics were annotated with various genomic features, interactions with RNA-binding proteins and microRNA, potentially linked splicing events and single nucleotide polymorphisms. The collected m6A sites and their functional annotations can be freely queried and downloaded via a user-friendly graphical interface at: http://rnamd.org/m6a.
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Affiliation(s)
- Zhanmin Liang
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian 350004, China
- Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
| | - Haokai Ye
- Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, Liverpool, UK
| | - Jiongming Ma
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian 350004, China
- Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, Liverpool, UK
| | - Zhen Wei
- Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
- Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Yue Wang
- Department of Mathematical Sciences, Xi’an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
- Department of Computer Science, University of Liverpool, Liverpool L69 7ZB, UK
| | - Yuxin Zhang
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian 350004, China
- Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, Liverpool, UK
| | - Daiyun Huang
- Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
- Department of Computer Science, University of Liverpool, Liverpool L69 7ZB, UK
| | - Bowen Song
- Department of Public Health, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Jia Meng
- Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
- AI University Research Centre, Xi’an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, Liverpool, UK
| | - Daniel J Rigden
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, Liverpool, UK
| | - Kunqi Chen
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian 350004, China
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Lawrence BT, Calle A, Saski CA, Melgar JC. Differential Gene Expression Patterns in Peach Roots under Non-Uniform Soil Conditions in Response to Organic Matter. Genes (Basel) 2024; 15:70. [PMID: 38254960 PMCID: PMC10815151 DOI: 10.3390/genes15010070] [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: 10/26/2023] [Revised: 12/01/2023] [Accepted: 01/01/2024] [Indexed: 01/24/2024] Open
Abstract
Organic matter (OM) amendments are often encouraged in sustainable agriculture programs but can create heterogeneous soil environments when applied to perennial crops such as peaches (Prunus persica (L.) Batsch). To better understand the responses of peach roots to non-uniform soil conditions, transcriptomic analysis was performed in a split-root study using uniform soil (the same soil type for all roots) or non-uniform soil (different soil types for each half of the root system) from either (1) autoclaved sand (S), (2) autoclaved sand with autoclaved compost (A), or (3) autoclaved sand with compost which included inherent biological soil life (B). Each uniform soil type (S, A, and B) was grouped and compared by uniform and non-uniform soil comparisons for a total of nine treatments. Comparisons revealed peach roots had differentially expressed genes (DEGs) and gene ontology terms between soil groups, with the S and B groups having a range of 106-411 DEGs and the A group having a range of 19-94 DEGs. Additionally, six modules were identified and correlated (p > 0.69) for six of the nine treatment combinations. This study broadly highlights the complexity of how OM and biological life in the rhizosphere interact with immediate and distant roots and sheds light on how non-homogenous soil conditions can influence peach root gene expression.
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Affiliation(s)
- Brian T. Lawrence
- Department of Plant and Environmental Sciences, Clemson University, 105 Collings Street, Clemson, SC 29634, USA
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA
| | - Alejandro Calle
- Department of Plant and Environmental Sciences, Clemson University, 105 Collings Street, Clemson, SC 29634, USA
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Fruitcentre, PCiTAL, Gardeny Park, Fruitcentre Building, 25003 Lleida, Spain
| | - Christopher A. Saski
- Department of Plant and Environmental Sciences, Clemson University, 105 Collings Street, Clemson, SC 29634, USA
| | - Juan Carlos Melgar
- Department of Plant and Environmental Sciences, Clemson University, 105 Collings Street, Clemson, SC 29634, USA
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Rodrigues M, Ordoñez-Trejo EJ, Rasori A, Varotto S, Ruperti B, Bonghi C. Dissecting postharvest chilling injuries in pome and stone fruit through integrated omics. FRONTIERS IN PLANT SCIENCE 2024; 14:1272986. [PMID: 38235207 PMCID: PMC10791837 DOI: 10.3389/fpls.2023.1272986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024]
Abstract
Lowering the storage temperature is an effective method to extend the postharvest and shelf life of fruits. Nevertheless, this technique often leads to physiological disorders, commonly known as chilling injuries. Apples and pears are susceptible to chilling injuries, among which superficial scald is the most economically relevant. Superficial scald is due to necrotic lesions of the first layers of hypodermis manifested through skin browning. In peaches and nectarines, chilling injuries are characterized by internal symptoms, such as mealiness. Fruits with these aesthetic or compositional/structural defects are not suitable for fresh consumption. Genetic variation is a key factor in determining fruit susceptibility to chilling injuries; however, physiological, or technical aspects such as harvest maturity and storage conditions also play a role. Multi-omics approaches have been used to provide an integrated explanation of chilling injury development. Metabolomics in pome fruits specifically targets the identification of ethylene, phenols, lipids, and oxidation products. Genomics and transcriptomics have revealed interesting connections with metabolomic datasets, pinpointing specific genes linked to cold stress, wax synthesis, farnesene metabolism, and the metabolic pathways of ascorbate and glutathione. When applied to Prunus species, these cutting-edge approaches have uncovered that the development of mealiness symptoms is linked to ethylene signaling, cell wall synthesis, lipid metabolism, cold stress genes, and increased DNA methylation levels. Emphasizing the findings from multi-omics studies, this review reports how the integration of omics datasets can provide new insights into understanding of chilling injury development. This new information is essential for successfully creating more resilient fruit varieties and developing novel postharvest strategies.
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Affiliation(s)
| | | | | | | | - Benedetto Ruperti
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Legnaro, Italy
| | - Claudio Bonghi
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Legnaro, Italy
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Fan Y, Gao P, Zhou T, Pang S, Zhang J, Yang T, Zhang W, Dong J, Che D. Genome-Wide Identification and Expression Analysis of the Trehalose-6-phosphate Synthase and Trehalose-6-phosphate Phosphatase Gene Families in Rose ( Rosa hybrida cv 'Carola') under Different Light Conditions. PLANTS (BASEL, SWITZERLAND) 2023; 13:114. [PMID: 38202423 PMCID: PMC10780518 DOI: 10.3390/plants13010114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/20/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024]
Abstract
Trehalose, trehalose-6-phosphate synthase (TPS),and trehalose-6-phosphatase (TPP) have been reported to play important roles in plant abiotic stress and growth development. However, their functions in the flowering process of Rosa hybrida have not been characterized. In this study we found that, under a short photoperiod or weak light intensity, the content of trehalose in the shoot apical meristem of Rosa hybrida cv 'Carola' significantly decreased, leading to delayed flowering time. A total of nine RhTPSs and seven RhTPPs genes were identified in the genome. Cis-element analysis suggested that RhTPS and RhTPP genes were involved in plant hormones and environmental stress responses. Transcriptome data analysis reveals significant differences in the expression levels of RhTPSs and RhTPPs family genes in different tissues and indicates that RhTPPF and RhTPPJ are potential key genes involved in rose flower bud development under different light environments. The results of quantitative real-time reverse transcription (qRT-PCR) further indicate that under short photoperiod and weak light intensity all RhTPP members were significantly down-regulated. Additionally, RhTPS1a, RhTPS10, and RhTPS11 were up-regulated under a short photoperiod and showed a negative correlation with flowering time and trehalose content decrease. Under weak light intensity, RhTPS11 was up-regulated and negatively regulated flowering, while RhTPS5, RhTPS6, RhTPS7b, RhTPS9, and RhTPS10 were down-regulated and positively regulated flowering. This work lays the foundation for revealing the functions of RhTPS and RhTPP gene families in the regulation of rose trehalose.
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Affiliation(s)
- Yingdong Fan
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (Y.F.); (P.G.)
- Key Laboratory of Cold Region Landscape Plants and Applications, Harbin 150030, China
| | - Peng Gao
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (Y.F.); (P.G.)
- Key Laboratory of Cold Region Landscape Plants and Applications, Harbin 150030, China
| | - Tong Zhou
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (Y.F.); (P.G.)
- Key Laboratory of Cold Region Landscape Plants and Applications, Harbin 150030, China
| | - Siyu Pang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (Y.F.); (P.G.)
- Key Laboratory of Cold Region Landscape Plants and Applications, Harbin 150030, China
| | - Jinzhu Zhang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (Y.F.); (P.G.)
- Key Laboratory of Cold Region Landscape Plants and Applications, Harbin 150030, China
| | - Tao Yang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (Y.F.); (P.G.)
- Key Laboratory of Cold Region Landscape Plants and Applications, Harbin 150030, China
| | - Wuhua Zhang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (Y.F.); (P.G.)
- Key Laboratory of Cold Region Landscape Plants and Applications, Harbin 150030, China
| | - Jie Dong
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (Y.F.); (P.G.)
- Key Laboratory of Cold Region Landscape Plants and Applications, Harbin 150030, China
| | - Daidi Che
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (Y.F.); (P.G.)
- Key Laboratory of Cold Region Landscape Plants and Applications, Harbin 150030, China
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Xiang N, Chang X, Qin L, Li K, Wang S, Guo X. Insights into tissue-specific anthocyanin accumulation in Japanese plum ( Prunus salicina L.) fruits: A comparative study of three cultivars. FOOD CHEMISTRY. MOLECULAR SCIENCES 2023; 7:100178. [PMID: 37554520 PMCID: PMC10404606 DOI: 10.1016/j.fochms.2023.100178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/22/2023] [Accepted: 07/22/2023] [Indexed: 08/10/2023]
Abstract
In the present study, three matured Japanese plum cultivars with different colored peel and flesh were selected to mine the key transcription factors regulating anthocyanin formation in tissues. Results showed that PsMYB10 was correlated with structural genes C4H, F3H, and ANS. PsMYB6 could positively regulate C4H (r = 0.732) and accumulated anthocyanins in Sanhua plum's flesh. Sanhua plum has the highest phenolic and anthocyanin contents (10.24 ± 0.37 gallic acid equivalent mg g-1 dry weight (DW) and 68.95 ± 1.03 μg g-1 DW), resulting itself superior biological activity as 367.1 ± 42.9 Trolox equivalent mg g-1 DW in oxygen radical absorbance capacity value and 72.79 ± 4.34 quercetin equivalent mg g-1 DW in cellular antioxidant activity value. The present work provides new insights into the regulatory mechanism of tissue-specific anthocyanin biosynthesis, confirming the pivotal role of anthocyanins in the biological activity of plums, providing essential support for the development of horticultural products enriched with anthocyanins.
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Affiliation(s)
- Nan Xiang
- School of Food Science and Engineering, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, Engineering Research Center of Starch and Vegetable Protein Processing Ministry of Education, Research Institute for Food Nutrition and Human Health, South China University of Technology, Guangzhou 510640, China
- Department of Food, Nutrition, and Health, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Xiaoxiao Chang
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China
| | - Liuwei Qin
- School of Food Science and Engineering, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, Engineering Research Center of Starch and Vegetable Protein Processing Ministry of Education, Research Institute for Food Nutrition and Human Health, South China University of Technology, Guangzhou 510640, China
| | - Kun Li
- Crop Research Institute, Key Laboratory of Crops Genetics Improvement of Guangdong Province, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Siyun Wang
- Department of Food, Nutrition, and Health, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Xinbo Guo
- School of Food Science and Engineering, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, Engineering Research Center of Starch and Vegetable Protein Processing Ministry of Education, Research Institute for Food Nutrition and Human Health, South China University of Technology, Guangzhou 510640, China
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Švara A, Sun H, Fei Z, Khan A. Chromosome-level phased genome assembly of "Antonovka" identified candidate apple scab-resistance genes highly homologous to HcrVf2 and HcrVf1 on linkage group 1. G3 (BETHESDA, MD.) 2023; 14:jkad253. [PMID: 37936323 PMCID: PMC10755186 DOI: 10.1093/g3journal/jkad253] [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: 08/07/2023] [Revised: 10/12/2023] [Accepted: 10/20/2023] [Indexed: 11/09/2023]
Abstract
Apple scab, a fungal disease caused by Venturia inaequalis, leads to losses in both yield and fruit quality of apples (Malus domestica Borkh.). Most commercial apple cultivars, including those containing the well-characterized Rvi6-scab-resistance locus on linkage group (LG) 1, are susceptible to scab. HcrVf2 and HcrVf1 are considered the main paralogs of the Rvi6 locus. The major apple scab-resistance loci Vhc1 in "Honeycrisp" and Rvi17 in "Antonovka," were identified in close proximity to HcrVf2. In this study, we used long-read sequencing and in silico gene sequence characterization to identify candidate resistance genes homologous to HcrVf2 and HcrVf1 in Honeycrisp and Antonovka. Previously published chromosome-scale phased assembly of Honeycrisp and a newly assembled phased genome of Antonovka 172670-B were used to identify HcrVf2 and HcrVf1 homologs spanning Vhc1 and Rvi17 loci. In combination with 8 available Malus assemblies, 43 and 46 DNA sequences highly homologous to HcrVf2 and HcrVf1, respectively, were identified on LG 1 and 6, with identity and coverage ranging between 87-95 and 81-95%, respectively. Among these homologs, 2 candidate genes in Antonovka and Honeycrisp haplome A are located in close physical proximity to the scab-resistance marker Ch-Vf1 on LG 1. They showed the highest identity and coverage (95%) of HcrVf2 and only minor changes in the protein motifs. They were identical by state between each other, but not with HcrVf2. This study offers novel genomic resources and insights into the Vhc1 and Rvi17 loci on LG 1 and identifies candidate genes for further resistance characterization.
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Affiliation(s)
- Anže Švara
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA
| | - Honghe Sun
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
- USDA-ARS Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
| | - Awais Khan
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA
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Deng CH, Naithani S, Kumari S, Cobo-Simón I, Quezada-Rodríguez EH, Skrabisova M, Gladman N, Correll MJ, Sikiru AB, Afuwape OO, Marrano A, Rebollo I, Zhang W, Jung S. Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences. Database (Oxford) 2023; 2023:baad088. [PMID: 38079567 PMCID: PMC10712715 DOI: 10.1093/database/baad088] [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: 04/13/2023] [Revised: 10/17/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023]
Abstract
Large-scale genotype and phenotype data have been increasingly generated to identify genetic markers, understand gene function and evolution and facilitate genomic selection. These datasets hold immense value for both current and future studies, as they are vital for crop breeding, yield improvement and overall agricultural sustainability. However, integrating these datasets from heterogeneous sources presents significant challenges and hinders their effective utilization. We established the Genotype-Phenotype Working Group in November 2021 as a part of the AgBioData Consortium (https://www.agbiodata.org) to review current data types and resources that support archiving, analysis and visualization of genotype and phenotype data to understand the needs and challenges of the plant genomic research community. For 2021-22, we identified different types of datasets and examined metadata annotations related to experimental design/methods/sample collection, etc. Furthermore, we thoroughly reviewed publicly funded repositories for raw and processed data as well as secondary databases and knowledgebases that enable the integration of heterogeneous data in the context of the genome browser, pathway networks and tissue-specific gene expression. Based on our survey, we recommend a need for (i) additional infrastructural support for archiving many new data types, (ii) development of community standards for data annotation and formatting, (iii) resources for biocuration and (iv) analysis and visualization tools to connect genotype data with phenotype data to enhance knowledge synthesis and to foster translational research. Although this paper only covers the data and resources relevant to the plant research community, we expect that similar issues and needs are shared by researchers working on animals. Database URL: https://www.agbiodata.org.
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Affiliation(s)
- Cecilia H Deng
- Molecular and Digital Breeding, New Cultivar Innovation, The New Zealand Institute for Plant and Food Research Limited, 120 Mt Albert Road, Auckland 1025, New Zealand
| | - Sushma Naithani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Sunita Kumari
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, New York, NY 11724, USA
| | - Irene Cobo-Simón
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
- Institute of Forest Science (ICIFOR-INIA, CSIC), Madrid, Spain
| | - Elsa H Quezada-Rodríguez
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana-Xochimilco, Ciudad de México, México
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Maria Skrabisova
- Department of Biochemistry, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Nick Gladman
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, New York, NY 11724, USA
- U.S. Department of Agriculture-Agricultural Research Service, NEA Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, NY 14853, USA
| | - Melanie J Correll
- Agricultural and Biological Engineering Department, University of Florida, 1741 Museum Rd, Gainesville, FL 32611, USA
| | | | | | - Annarita Marrano
- Phoenix Bioinformatics, 39899 Balentine Drive, Suite 200, Newark, CA 94560, USA
| | | | - Wentao Zhang
- National Research Council Canada, 110 Gymnasium Pl, Saskatoon, Saskatchewan S7N 0W9, Canada
| | - Sook Jung
- Department of Horticulture, Washington State University, 303c Plant Sciences Building, Pullman, WA 99164-6414, USA
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41
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Li M, Mount SM, Liu Z. Rosaceae fruit transcriptome database (ROFT)-a useful genomic resource for comparing fruits of apple, peach, strawberry, and raspberry. HORTICULTURE RESEARCH 2023; 10:uhad240. [PMID: 38162465 PMCID: PMC10756754 DOI: 10.1093/hr/uhad240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 11/06/2023] [Indexed: 01/03/2024]
Abstract
Rosaceae is a large plant family consisting of many economically important fruit crops including peach, apple, pear, strawberry, raspberry, plum, and others. Investigations into their growth and development will promote both basic understanding and progress toward increasing fruit yield and quality. With the ever-increasing high-throughput sequencing data of Rosaceae, comparative studies are hindered by inconsistency of sample collection with regard to tissue, stage, growth conditions, and by vastly different handling of the data. Therefore, databases that enable easy access and effective utilization of directly comparable transcript data are highly desirable. Here, we describe a database for comparative analysis, ROsaceae Fruit Transcriptome database (ROFT), based on RNA-seq data generated from the same laboratory using similarly dissected and staged fruit tissues of four important Rosaceae fruit crops: apple, peach, strawberry, and red raspberry. Hence, the database is unique in allowing easy and robust comparisons among fruit gene expression across the four species. ROFT enables researchers to query orthologous genes and their expression patterns during different fruit developmental stages in the four species, identify tissue-specific and tissue-/stage-specific genes, visualize and compare ortholog expression in different fruit types, explore consensus co-expression networks, and download different data types. The database provides users access to vast amounts of RNA-seq data across the four economically important fruits, enables investigations of fruit type specification and evolution, and facilitates the selection of genes with critical roles in fruit development for further studies.
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Affiliation(s)
- Muzi Li
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Stephen M Mount
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
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Lyu K, Xiao J, Lyu S, Liu R. Comparative Analysis of Transposable Elements in Strawberry Genomes of Different Ploidy Levels. Int J Mol Sci 2023; 24:16935. [PMID: 38069258 PMCID: PMC10706760 DOI: 10.3390/ijms242316935] [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: 10/27/2023] [Revised: 11/25/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Transposable elements (TEs) make up a large portion of plant genomes and play a vital role in genome structure, function, and evolution. Cultivated strawberry (Fragaria x ananassa) is one of the most important fruit crops, and its octoploid genome was formed through several rounds of genome duplications from diploid ancestors. Here, we built a pan-genome TE library for the Fragaria genus using ten published strawberry genomes at different ploidy levels, including seven diploids, one tetraploid, and two octoploids, and performed comparative analysis of TE content in these genomes. The TEs comprise 51.83% (F. viridis) to 60.07% (F. nilgerrensis) of the genomes. Long terminal repeat retrotransposons (LTR-RTs) are the predominant TE type in the Fragaria genomes (20.16% to 34.94%), particularly in F. iinumae (34.94%). Estimating TE content and LTR-RT insertion times revealed that species-specific TEs have shaped each strawberry genome. Additionally, the copy number of different LTR-RT families inserted in the last one million years reflects the genetic distance between Fragaria species. Comparing cultivated strawberry subgenomes to extant diploid ancestors showed that F. vesca and F. iinumae are likely the diploid ancestors of the cultivated strawberry, but not F. viridis. These findings provide new insights into the TE variations in the strawberry genomes and their roles in strawberry genome evolution.
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Affiliation(s)
- Keliang Lyu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (K.L.); (S.L.)
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Jiajing Xiao
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Shiheng Lyu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (K.L.); (S.L.)
| | - Renyi Liu
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
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Zhang L, Zhang C, An Y, Zhu Q, Wang M. A High-Quality Reference Genome Assembly of Prinsepia uniflora (Rosaceae). Genes (Basel) 2023; 14:2035. [PMID: 38002978 PMCID: PMC10671140 DOI: 10.3390/genes14112035] [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: 09/27/2023] [Revised: 10/26/2023] [Accepted: 11/01/2023] [Indexed: 11/26/2023] Open
Abstract
This study introduces a meticulously constructed genome assembly at the chromosome level for the Rosaceae family species Prinsepia uniflora, a traditional Chinese medicinal herb. The final assembly encompasses 1272.71 megabases (Mb) distributed across 16 pseudochromosomes, boasting contig and super-scaffold N50 values of 2.77 and 79.32 Mb, respectively. Annotated within this genome is a substantial 875.99 Mb of repetitive sequences, with transposable elements occupying 777.28 Mb, constituting 61.07% of the entire genome. Our predictive efforts identified 49,261 protein-coding genes within the repeat-masked assembly, with 45,256 (91.87%) having functional annotations, 5127 (10.41%) demonstrating tandem duplication, and 2373 (4.82%) classified as transcription factor genes. Additionally, our investigation unveiled 3080 non-coding RNAs spanning 0.51 Mb of the genome sequences. According to our evolutionary study, P. uniflora underwent recent whole-genome duplication following its separation from Prunus salicina. The presented reference-level genome assembly and annotation for P. uniflora will significantly facilitate the in-depth exploration of genomic information pertaining to this species, offering substantial utility in comparative genomics and evolutionary analyses involving Rosaceae species.
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Affiliation(s)
- Lei Zhang
- Key Laboratory of Ecological Protection of Agro-Pastoral Ecotones in the Yellow River Basin, National Ethnic Affairs Commission of the People’s Republic of China, College of Biological Science & Engineering, North Minzu University, Yinchuan 750021, China; (L.Z.); (C.Z.); (Y.A.)
| | - Chaopan Zhang
- Key Laboratory of Ecological Protection of Agro-Pastoral Ecotones in the Yellow River Basin, National Ethnic Affairs Commission of the People’s Republic of China, College of Biological Science & Engineering, North Minzu University, Yinchuan 750021, China; (L.Z.); (C.Z.); (Y.A.)
| | - Yajing An
- Key Laboratory of Ecological Protection of Agro-Pastoral Ecotones in the Yellow River Basin, National Ethnic Affairs Commission of the People’s Republic of China, College of Biological Science & Engineering, North Minzu University, Yinchuan 750021, China; (L.Z.); (C.Z.); (Y.A.)
| | - Qiang Zhu
- State Key Laboratory of Efficient Production of Forest Resources, Ningxia Forestry Institute, Yinchuan 750001, China;
| | - Mingcheng Wang
- Institute for Advanced Study, Chengdu University, No. 2025 Chengluo Road, Chengdu 610106, China
- Engineering Research Center of Sichuan-Tibet Traditional Medicinal Plant, Chengdu 610106, China
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Mansfeld BN, Yocca A, Ou S, Harkess A, Burchard E, Gutierrez B, van Nocker S, Gottschalk C. A haplotype resolved chromosome-scale assembly of North American wild apple Malus fusca and comparative genomics of the fire blight Mfu10 locus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:989-1002. [PMID: 37639371 DOI: 10.1111/tpj.16433] [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: 03/22/2023] [Revised: 07/08/2023] [Accepted: 08/12/2023] [Indexed: 08/31/2023]
Abstract
SUMMARYThe Pacific crabapple (Malus fusca) is a wild relative of the commercial apple (Malus × domestica). With a range extending from Alaska to Northern California, M. fusca is extremely hardy and disease resistant. The species represents an untapped genetic resource for the development of new apple cultivars with enhanced stress resistance. However, gene discovery and utilization of M. fusca have been hampered by the lack of genomic resources. Here, we present a high‐quality, haplotype‐resolved, chromosome‐scale genome assembly and annotation for M. fusca. The genome was assembled using high‐fidelity long‐reads and scaffolded using genetic maps and high‐throughput chromatin conformation capture sequencing, resulting in one of the most contiguous apple genomes to date. We annotated the genome using public transcriptomic data from the same species taken from diverse plant structures and developmental stages. Using this assembly, we explored haplotypic structural variation within the genome of M. fusca, identifying thousands of large variants. We further showed high sequence co‐linearity with other domesticated and wild Malus species. Finally, we resolve a known quantitative trait locus associated with resistance to fire blight (Erwinia amylovora). Insights gained from the assembly of a reference‐quality genome of this hardy wild apple relative will be invaluable as a tool to facilitate DNA‐informed introgression breeding.
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Affiliation(s)
- Ben N Mansfeld
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Alan Yocca
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Shujun Ou
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, USA
| | - Alex Harkess
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Erik Burchard
- USDA ARS, Appalachian Fruit Research Station, Kearneysville, West Virginia, USA
| | | | - Steve van Nocker
- Department of Horticulture, Michigan State University, East Lansing, Michigan, USA
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Denoyes B, Prohaska A, Petit J, Rothan C. Deciphering the genetic architecture of fruit color in strawberry. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6306-6320. [PMID: 37386925 PMCID: PMC10627153 DOI: 10.1093/jxb/erad245] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/28/2023] [Indexed: 07/01/2023]
Abstract
Fruits of Fragaria species usually have an appealing bright red color due to the accumulation of anthocyanins, water-soluble flavonoid pigments. Octoploid cultivated strawberry (Fragaria × ananassa) is a major horticultural crop for which fruit color and associated nutritional value are main breeding targets. Great diversity in fruit color intensity and pattern is observed not only in cultivated strawberry but also in wild relatives such as its octoploid progenitor F. chiloensis or the diploid woodland strawberry F. vesca, a model for fruit species in the Rosaceae. This review examines our understanding of fruit color formation in strawberry and how ongoing developments will advance it. Natural variations of fruit color as well as color changes during fruit development or in response to several cues have been used to explore the anthocyanin biosynthetic pathway and its regulation. So far, the successful identification of causal genetic variants has been largely driven by the availability of high-throughput genotyping tools and high-quality reference genomes of F. vesca and F. × ananassa. The current completion of haplotype-resolved genomes of F. × ananassa combined with QTL mapping will accelerate the exploitation of the untapped genetic diversity of fruit color and help translate the findings into strawberry improvement.
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Affiliation(s)
- Béatrice Denoyes
- INRAE and Univ. of Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, F-33140 Villenave d’Ornon, France
| | - Alexandre Prohaska
- INRAE and Univ. of Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, F-33140 Villenave d’Ornon, France
- INVENIO, MIN de Brienne, Bordeaux, France
| | - Johann Petit
- INRAE and Univ. of Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, F-33140 Villenave d’Ornon, France
| | - Christophe Rothan
- INRAE and Univ. of Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, F-33140 Villenave d’Ornon, France
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Pérez-Rojas M, Díaz-Ramírez D, Ortíz-Ramírez CI, Galaz-Ávalos RM, Loyola-Vargas VM, Ferrándiz C, Abraham-Juárez MDR, Marsch-Martínez N. The Role of Cytokinins during the Development of Strawberry Flowers and Receptacles. PLANTS (BASEL, SWITZERLAND) 2023; 12:3672. [PMID: 37960026 PMCID: PMC10649685 DOI: 10.3390/plants12213672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/04/2023] [Accepted: 10/17/2023] [Indexed: 11/15/2023]
Abstract
Cytokinins play a relevant role in flower and fruit development and plant yield. Strawberry fruits have a high commercial value, although what is known as the "fruit" is not a "true" botanical fruit because it develops from a non-reproductive organ (receptacle) on which the true botanical fruits (achenes) are found. Given cytokinins' roles in botanical fruits, it is important to understand their participation in the development of a non-botanical or accessory "fruit". Therefore, in this work, the role of cytokinin in strawberry flowers and fruits was investigated by identifying and exploring the expression of homologous genes for different families that participate in the pathway, through publicly available genomic and expression data analyses. Next, trans-zeatin content in developing flowers and receptacles was determined. A high concentration was observed in flower buds and at anthesis and decreased as the fruit approached maturity. Moreover, the spatio-temporal expression pattern of selected CKX genes was evaluated and detected in receptacles at pre-anthesis stages. The results point to an important role and effect of cytokinins in flower and receptacle development, which is valuable both from a biological point of view and to improve yield and the quality of this fruit.
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Affiliation(s)
- Moises Pérez-Rojas
- Departamento de Biotecnología y Bioquímica, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato 36824, Mexico; (M.P.-R.); (D.D.-R.)
| | - David Díaz-Ramírez
- Departamento de Biotecnología y Bioquímica, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato 36824, Mexico; (M.P.-R.); (D.D.-R.)
| | - Clara Inés Ortíz-Ramírez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas—Universidad Politécnica de Valencia (CSIC-UPV), 46022 Valencia, Spain; (C.I.O.-R.); (C.F.)
| | - Rosa M. Galaz-Ávalos
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida 97205, Mexico; (R.M.G.-Á.); (V.M.L.-V.)
| | - Víctor M. Loyola-Vargas
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida 97205, Mexico; (R.M.G.-Á.); (V.M.L.-V.)
| | - Cristina Ferrándiz
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas—Universidad Politécnica de Valencia (CSIC-UPV), 46022 Valencia, Spain; (C.I.O.-R.); (C.F.)
| | | | - Nayelli Marsch-Martínez
- Departamento de Biotecnología y Bioquímica, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato 36824, Mexico; (M.P.-R.); (D.D.-R.)
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Lallemand T, Leduc M, Desmazières A, Aubourg S, Rizzon C, Landès C, Celton JM. Insights into the Evolution of Ohnologous Sequences and Their Epigenetic Marks Post-WGD in Malus Domestica. Genome Biol Evol 2023; 15:evad178. [PMID: 37847638 PMCID: PMC10601995 DOI: 10.1093/gbe/evad178] [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: 06/02/2023] [Revised: 08/25/2023] [Accepted: 10/02/2023] [Indexed: 10/19/2023] Open
Abstract
A Whole Genome Duplication (WGD) event occurred several Ma in a Rosaceae ancestor, giving rise to the Maloideae subfamily which includes today many pome fruits such as pear (Pyrus communis) and apple (Malus domestica). This complete and well-conserved genome duplication makes the apple an organism of choice to study the early evolutionary events occurring to ohnologous chromosome fragments. In this study, we investigated gene sequence evolution and expression, transposable elements (TE) density, and DNA methylation level. Overall, we identified 16,779 ohnologous gene pairs in the apple genome, confirming the relatively recent WGD. We identified several imbalances in QTL localization among duplicated chromosomal fragments and characterized various biases in genome fractionation, gene transcription, TE densities, and DNA methylation. Our results suggest a particular chromosome dominance in this autopolyploid species, a phenomenon that displays similarities with subgenome dominance that has only been described so far in allopolyploids.
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Affiliation(s)
- Tanguy Lallemand
- Université d’Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | - Martin Leduc
- Université d’Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | - Adèle Desmazières
- Université d’Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | - Sébastien Aubourg
- Université d’Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | - Carène Rizzon
- Laboratoire de Mathématiques et Modélisation d’Evry (LaMME), UMR CNRS 8071, ENSIIE, USC INRA, Université d’Evry Val d’Essonne, Evry, France
| | - Claudine Landès
- Université d’Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | - Jean-Marc Celton
- Université d’Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
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Jiang L, Lv J, Li K, Zhai L, Wu Y, Wu T, Zhang X, Han Z, Wang Y. MdGRF11-MdARF19-2 module acts as a positive regulator of drought resistance in apple rootstock. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 335:111782. [PMID: 37406680 DOI: 10.1016/j.plantsci.2023.111782] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 06/18/2023] [Accepted: 06/29/2023] [Indexed: 07/07/2023]
Abstract
14-3-3 proteins play an important role in the response of plants to drought resistance. In this study, 14-3-3 protein MdGRF11 was cloned from Malus xiaojinensis, and its positive regulation of drought resistance was verified using Orin calli and M. xiaojinensis plants. The transcription factor MdARF19-2 was further screened for interaction with this protein in vitro and in vivo. We also conducted experiments using Orin calli and found that the overexpression of MdARF19-2 decreased the level of reactive oxygen species (ROS) and increased the activity of enzymes that scavenge ROS in plant materials. This indicates that MdARF19-2 is a positive regulator in the drought resistance of plants. The drought tolerance was further improved by the overexpression of both MdGRF11 and MdARF19-2 in the calli. In addition, we examined several genes related to ROS scavenging with auxin response factor binding elements in their promoters and found that their level of expression was regulated by the MdGRF11-MdARF19-2 module. In conclusion, the enhancement of plant drought resistance by MdGRF11 could be owing to its accumulation at the protein level in response to drought, which then combined with MdARF19-2, affecting the expression of MdARF19-2 downstream genes. Thus, it scavenges ROS, which ultimately improves the resistance of plant to drought stress.
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Affiliation(s)
- Lizhong Jiang
- College of Horticulture, China Agricultural University, Beijing 100193, PR China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Nutrition and Physiology), Ministry of Agriculture and Rural Affairs, Beijing 100193, PR China
| | - Jiahong Lv
- College of Horticulture, China Agricultural University, Beijing 100193, PR China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Nutrition and Physiology), Ministry of Agriculture and Rural Affairs, Beijing 100193, PR China
| | - Keting Li
- College of Horticulture, China Agricultural University, Beijing 100193, PR China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Nutrition and Physiology), Ministry of Agriculture and Rural Affairs, Beijing 100193, PR China
| | - Longmei Zhai
- College of Horticulture, China Agricultural University, Beijing 100193, PR China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Nutrition and Physiology), Ministry of Agriculture and Rural Affairs, Beijing 100193, PR China
| | - Yue Wu
- College of Horticulture, China Agricultural University, Beijing 100193, PR China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Nutrition and Physiology), Ministry of Agriculture and Rural Affairs, Beijing 100193, PR China
| | - Ting Wu
- College of Horticulture, China Agricultural University, Beijing 100193, PR China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Nutrition and Physiology), Ministry of Agriculture and Rural Affairs, Beijing 100193, PR China
| | - Xinzhong Zhang
- College of Horticulture, China Agricultural University, Beijing 100193, PR China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Nutrition and Physiology), Ministry of Agriculture and Rural Affairs, Beijing 100193, PR China
| | - Zhenhai Han
- College of Horticulture, China Agricultural University, Beijing 100193, PR China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Nutrition and Physiology), Ministry of Agriculture and Rural Affairs, Beijing 100193, PR China
| | - Yi Wang
- College of Horticulture, China Agricultural University, Beijing 100193, PR China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Nutrition and Physiology), Ministry of Agriculture and Rural Affairs, Beijing 100193, PR China.
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Zhang Y, Yuan Y, Qu M, Kang C. Brassinosteroid catabolic enzyme CYP734A129 regulates the morphologies of leaves and floral organs in woodland strawberry. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 335:111788. [PMID: 37421982 DOI: 10.1016/j.plantsci.2023.111788] [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: 03/09/2023] [Revised: 07/02/2023] [Accepted: 07/04/2023] [Indexed: 07/10/2023]
Abstract
Brassinosteroids (BRs) play critical roles in plant growth and development and regulate many important agronomic traits. However, the functions of BRs in strawberry are unclear. This study identified two mutants, named P6 and R87, in woodland strawberry (Fragaria vesca) from EMS mutagenesis populations that exhibit narrow leaves, petals and sepals. Mapping by sequencing and genetic studies revealed that the F. vesca CYP734A129, encoding a putative BR catabolic enzyme, is the causative gene for both P6 and R87. Overexpression of CYP734A129 in both F. vesca and Arabidopsis causes a severe dwarf phenotype, and the BRI1-EMS-SUPPRESSOR 1 (BES1) protein is less abundant in the CYP734A129-overexpressing Arabidopsis seedlings. This suggests that CYP734A129 is functionally conserved with CYP734A1, as a BR-inactivating enzyme. Transcriptome analysis of young leaves revealed that four BR biosynthetic genes were significantly downregulated in P6 (cyp734a129), and photosynthesis-related genes were highly enriched among the up-regulated genes in P6 compared to the wild type. This further supports that CYP734A129 inactivates BRs in F. vesca. Furthermore, we showed that mutations in CYP734A129 do not affect fruit shape and color during ripening in strawberry. Overall, our results suggest that F. vesca CYP734A129 is a BR catabolic enzyme, and provide insights into the roles of CYP734A129 in strawberry.
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Affiliation(s)
- Yunming Zhang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China; Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Yingxin Yuan
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Minghao Qu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
| | - Chunying Kang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China.
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Zhang Z, Fang M, Wu R, Zong H, Huang H, Tong Y, Xie Y, Cheng S, Wei Z, Crabbe MJC, Zhang X, Wang Y. Large-Scale Biomedical Relation Extraction Across Diverse Relation Types: Model Development and Usability Study on COVID-19. J Med Internet Res 2023; 25:e48115. [PMID: 37632414 PMCID: PMC10551783 DOI: 10.2196/48115] [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: 04/11/2023] [Revised: 07/03/2023] [Accepted: 08/25/2023] [Indexed: 08/28/2023] Open
Abstract
BACKGROUND Biomedical relation extraction (RE) is of great importance for researchers to conduct systematic biomedical studies. It not only helps knowledge mining, such as knowledge graphs and novel knowledge discovery, but also promotes translational applications, such as clinical diagnosis, decision-making, and precision medicine. However, the relations between biomedical entities are complex and diverse, and comprehensive biomedical RE is not yet well established. OBJECTIVE We aimed to investigate and improve large-scale RE with diverse relation types and conduct usability studies with application scenarios to optimize biomedical text mining. METHODS Data sets containing 125 relation types with different entity semantic levels were constructed to evaluate the impact of entity semantic information on RE, and performance analysis was conducted on different model architectures and domain models. This study also proposed a continued pretraining strategy and integrated models with scripts into a tool. Furthermore, this study applied RE to the COVID-19 corpus with article topics and application scenarios of clinical interest to assess and demonstrate its biological interpretability and usability. RESULTS The performance analysis revealed that RE achieves the best performance when the detailed semantic type is provided. For a single model, PubMedBERT with continued pretraining performed the best, with an F1-score of 0.8998. Usability studies on COVID-19 demonstrated the interpretability and usability of RE, and a relation graph database was constructed, which was used to reveal existing and novel drug paths with edge explanations. The models (including pretrained and fine-tuned models), integrated tool (Docker), and generated data (including the COVID-19 relation graph database and drug paths) have been made publicly available to the biomedical text mining community and clinical researchers. CONCLUSIONS This study provided a comprehensive analysis of RE with diverse relation types. Optimized RE models and tools for diverse relation types were developed, which can be widely used in biomedical text mining. Our usability studies provided a proof-of-concept demonstration of how large-scale RE can be leveraged to facilitate novel research.
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Affiliation(s)
- Zeyu Zhang
- Research Center for Translational Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
- Department of Clinical Laboratory Medicine Center, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Meng Fang
- Department of Laboratory Medicine, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Rebecca Wu
- University of California, Berkeley, Berkeley, CA, United States
| | - Hui Zong
- Research Center for Translational Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
- Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Honglian Huang
- Research Center for Translational Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yuantao Tong
- Research Center for Translational Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yujia Xie
- Research Center for Translational Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Shiyang Cheng
- Research Center for Translational Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Ziyi Wei
- Research Center for Translational Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - M James C Crabbe
- Wolfson College, Oxford University, Oxford, United Kingdom
- Institute of Biomedical and Environmental Science & Technology, University of Bedfordshire, Luton, United Kingdom
- School of Life Sciences, Shanxi University, Taiyuan, China
| | - Xiaoyan Zhang
- Research Center for Translational Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Ying Wang
- Research Center for Translational Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
- Department of Clinical Laboratory Medicine Center, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Department of Laboratory Medicine, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, China
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