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Tan N, Zhao M, Luo Z, Li Z, Zhang X, Xu J, Gu X, Wang Q, Ding S, Ying M, Xu Y. Linalool as a key component in strawberry volatile organic compounds (VOCs) modulates gut microbiota, systemic inflammation, and glucolipid metabolism. Food Chem 2024; 460:140361. [PMID: 39098193 DOI: 10.1016/j.foodchem.2024.140361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2024] [Revised: 06/14/2024] [Accepted: 07/03/2024] [Indexed: 08/06/2024]
Abstract
Strawberries are rich in volatile organic compounds (VOCs), which are increasingly recognized as potential health-promoting factors. This study explored the health effects of intaking strawberry VOC extract and its dominant terpene, linalool. The results indicated that linalool and strawberry VOC extract significantly increased the abundance of beneficial bacteria like Lactobacillus, Bacillus, and Alistipes in mice. Moreover, mice treated with linalool and strawberry VOC extract exhibited notable reductions in serum pro-inflammatory cytokines; interleukin IL-6 decreased by 14.5% and 21.8%, respectively, while IL-1β levels decreased by 9.6% and 13.4%, respectively. Triglyceride levels in the treated groups were reduced by 38.3% and 58.1%, respectively. Spearman's correlation analysis revealed that Bacillus negatively correlated with glucolipid indices, and Bifidobacterium and Dubosiella negatively correlated with inflammatory factors, indicating that alterations in glucolipid metabolism might be associated with the regulation of gut microbiota and systemic inflammation.
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Affiliation(s)
- Nanfeng Tan
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Minjie Zhao
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Zisheng Luo
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China; Ningbo Research Institute, Zhejiang University, Ningbo, 315100, China
| | - Zhenbiao Li
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Xuenan Zhang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Jiayi Xu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Xinya Gu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Qingqing Wang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Shenghua Ding
- Hunan Agricultural Product Processing Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Miaomiao Ying
- College of Landscape and Hydraulic Engineering, Wenzhou Vocational College of Science and Technology, Wenzhou, China
| | - Yanqun Xu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China; Ningbo Research Institute, Zhejiang University, Ningbo, 315100, China; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, 02138, USA.
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2
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Du Q, Yu H, Zhang Y, Qiao Q, Wang J, Zhang T, Xue L, Lei J. Uncovering fruit flavor and genetic diversity across diploid wild Fragaria species via comparative metabolomics profiling. Food Chem 2024; 456:140013. [PMID: 38878536 DOI: 10.1016/j.foodchem.2024.140013] [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: 02/06/2024] [Revised: 06/04/2024] [Accepted: 06/06/2024] [Indexed: 07/24/2024]
Abstract
Wild Fragaria resources exhibit extensive genetic diversity and desirable edible traits, such as high soluble solid content and flavor compounds. However, specific metabolites in different wild strawberry fruits remain unknown. In this study, we characterized 1008 metabolites covering 11 subclasses among 13 wild diploid resources representing eight species, including F. vesca, F. nilgerrensis, F. viridis, F. nubicola, F. pentaphylla, F. mandschurica, F. chinensis, and F. emeiensis. Fifteen potential metabolite biomarkers were identified to distinguish fruit flavors among the 13 diploid wild Fragaria accessions. A total of nine distinct modules were employed to explore key metabolites related to fruit quality through weighted gene co-expression module analysis, with significant enrichment in amino acid biosynthesis pathway. Notably, the identified significantly different key metabolites highlighted the close association of amino acids, sugars, and anthocyanins with flavor formation. These findings offer valuable resources for improving fruit quality through metabolome-assisted breeding.
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Affiliation(s)
- Qiuling Du
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Haoming Yu
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Yuanyuan Zhang
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Qin Qiao
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming 650201, China
| | - Jian Wang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Ticao Zhang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Li Xue
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China.
| | - Jiajun Lei
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China.
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3
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Su D, Shu P, Hu N, Chen Y, Wu Y, Deng H, Du X, Zhang X, Wang R, Li H, Zeng Y, Li D, Xie Y, Li M, Hong Y, Liu K, Liu M. Dynamic m6A mRNA methylation reveals the involvement of AcALKBH10 in ripening-related quality regulation in kiwifruit. THE NEW PHYTOLOGIST 2024; 243:2265-2278. [PMID: 39056285 DOI: 10.1111/nph.20008] [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: 06/18/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024]
Abstract
Kiwifruit ripening is a complex and highly coordinated process that occurs in conjunction with the formation of fruit edible quality. The significance of epigenetic changes, particularly the impact of N6-methyladenosine (m6A) RNA modification on fruit ripening and quality formation, has been largely overlooked. We monitored m6A levels and gene expression changes in kiwifruit at four different stages using LC-MS/MS, MeRIP, RNA-seq, and validated the function of AcALKBH10 through heterologous transgenic expression in tomato. Notable m6A modifications occurred predominantly at the stop codons and the 3' UTRs and exhibited a gradual reduction in m6A levels during the fruit ripening process. Moreover, these m6A modifications in the aforementioned sites demonstrated a discernible inverse relationship with the levels of mRNA abundance throughout the ripening process, suggesting a repression effect of m6A modification in the modulation of kiwifruit ripening. We further demonstrated that AcALKBH10 rather than AcECT9 predominantly regulates m6A levels in ripening-related genes, thereby exerting the regulatory control over the ripening process and the accumulation of soluble sugars and organic acids, ultimately influencing fruit ripening and quality formation. In conclusion, our findings illuminate the epi-regulatory mechanism involving m6A in kiwifruit ripening, offering a fresh perspective for cultivating high-quality kiwifruit with enhanced nutritional attributes.
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Affiliation(s)
- Dan Su
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Peng Shu
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
- Clinical Medical Research Center, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Nan Hu
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, 455000, Henan, China
| | - Yuan Chen
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Yi Wu
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Heng Deng
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Xiaofei Du
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Xumeng Zhang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Ruochen Wang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Huajia Li
- Institute of Agro-Products Processing Science and Technology, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Yunliu Zeng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dawei Li
- Wuhan Botanical Garden, Chinese Academy of Sciences, Jiufeng 1 Road, Wuhan, 430074, Hubei, China
| | - Yue Xie
- China-New Zealand the Belt and Road Joint Laboratory on Kiwifruit, Kiwifruit Breeding and Utilization Key Laboratory of Sichuan Province, Sichuan Academy of Natural Resource Sciences, Chengdu, 610041, China
| | - Mingzhang Li
- China-New Zealand the Belt and Road Joint Laboratory on Kiwifruit, Kiwifruit Breeding and Utilization Key Laboratory of Sichuan Province, Sichuan Academy of Natural Resource Sciences, Chengdu, 610041, China
| | - Yiguo Hong
- School of Science and the Environment, University of Worcester, Worcester, WR2 6AJ, UK
- State Key Laboratory of North China Crop Improvement and Regulation, College of Horticulture, Hebei Agricultural University, Baoding, 071000, China
| | - Kaidong Liu
- Life Science and Technology School, Lingnan Normal University, Zhanjiang, 524048, China
| | - Mingchun Liu
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
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4
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Fan W, Sun M, Zheng Y, Song S, Zhang Z, Bian Y. Karyotypic and phenotypic condensation in allotetraploid wheats accompanied with reproductive strategy transformation: from natural evolution to domestication. PLANTA 2024; 260:83. [PMID: 39212743 DOI: 10.1007/s00425-024-04514-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: 04/15/2024] [Accepted: 08/19/2024] [Indexed: 09/04/2024]
Abstract
MAIN CONCLUSION Allotetraploid wheat reflects evolutionary divergence and domestication convergence in the karyotypic and phenotypic evolution, accompanied with the transformation from r- strategy to K- strategy in reproductive fitness. Allotetraploid wheat, the progenitor of hexaploidy bread wheat, has undergone 300,000 years of natural evolution and 10,000 years of domestication. The variations in karyotype and phenotype as well as fertility fitness have not been systematically linked. Here, by combining fluorescent in situ hybridization with the quantification of phenotypic and reproductive traits, we compared the karyotype, vegetative growth phenotype and reproductive fitness among synthesized, wild and domesticated accessions of allotetraploid wheat. We detected that the wild accessions showed dramatically high frequencies of homologous recombination and copy number variations of simple sequence repeats (SSR) comparing with synthetic and domesticated accessions. The phenotypic traits reflected significant differences among the populations shaped by distinct evolutionary processes. The diversity observed in wild accessions was significantly greater than that in domesticated ones, particularly in traits associated with vegetative growth and spike morphology. We found that the active pollen of domesticated accessions exhibited greater potential of germination, despite a lower rate of active pollen compared with the wild accessions, indicating a transformation in reproductive fitness strategy for pollen development in domesticated accessions compared to the wild accessions, from r-strategy to K-strategy. Our results demonstrate the condensation of karyotype and phenotype from natural wild accessions to domesticated accessions in allotetraploid wheats. Ecological strategy transformation should be seriously considered from evolution to domestication in polyploid plants, especially crops, which may provide a perspective on the adaptive evolution of polyploid plants.
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Affiliation(s)
- Wei Fan
- College of Life Sciences, Liaoning Normal University, Dalian, 116000, People's Republic of China
| | - Meiqi Sun
- College of Life Sciences, Liaoning Normal University, Dalian, 116000, People's Republic of China
| | - Yongbao Zheng
- College of Life Sciences, Liaoning Normal University, Dalian, 116000, People's Republic of China
- Key Laboratory of Plant Biotechnology in Liaoning Province, Dalian, 116000, People's Republic of China
| | - Siwen Song
- College of Life Sciences, Liaoning Normal University, Dalian, 116000, People's Republic of China
| | - Zeyao Zhang
- College of Life Sciences, Liaoning Normal University, Dalian, 116000, People's Republic of China
| | - Yao Bian
- College of Life Sciences, Liaoning Normal University, Dalian, 116000, People's Republic of China.
- Key Laboratory of Plant Biotechnology in Liaoning Province, Dalian, 116000, People's Republic of China.
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5
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Wang T, van Dijk ADJ, Zhao R, Bonnema G, Wang X. Contribution of homoeologous exchange to domestication of polyploid Brassica. Genome Biol 2024; 25:231. [PMID: 39192349 DOI: 10.1186/s13059-024-03370-z] [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: 12/10/2023] [Accepted: 08/10/2024] [Indexed: 08/29/2024] Open
Abstract
BACKGROUND Polyploidy is widely recognized as a significant evolutionary force in the plant kingdom, contributing to the diversification of plants. One of the notable features of allopolyploidy is the occurrence of homoeologous exchange (HE) events between the subgenomes, causing changes in genomic composition, gene expression, and phenotypic variations. However, the role of HE in plant adaptation and domestication remains unclear. RESULTS Here we analyze the whole-genome resequencing data from Brassica napus accessions representing the different morphotypes and ecotypes, to investigate the role of HE in domestication. Our findings demonstrate frequent occurrence of HEs in Brassica napus, with substantial HE patterns shared across populations, indicating their potential role in promoting crop domestication. HE events are asymmetric, with the A genome more frequently replacing C genome segments. These events show a preference for specific genomic regions and vary among populations. We also identify candidate genes in HE regions specific to certain populations, which likely contribute to flowering-time diversification across diverse morphotypes and ecotypes. In addition, we assemble a new genome of a swede accession, confirming the HE signals on the genome and their potential involvement in root tuber development. By analyzing HE in another allopolyploid species, Brassica juncea, we characterize a potential broader role of HE in allopolyploid crop domestication. CONCLUSIONS Our results provide novel insights into the domestication of polyploid Brassica species and highlight homoeologous exchange as a crucial mechanism for generating variations that are selected for crop improvement in polyploid species.
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Affiliation(s)
- Tianpeng Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
- Bioinformatics Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Aalt D J van Dijk
- Bioinformatics Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Ranze Zhao
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guusje Bonnema
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands.
| | - Xiaowu Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.
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6
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Súnico V, Higuera JJ, Amil-Ruiz F, Arjona-Girona I, López-Herrera CJ, Muñoz-Blanco J, Maldonado-Alconada AM, Caballero JL. FaNPR3 Members of the NPR1-like Gene Family Negatively Modulate Strawberry Fruit Resistance against Colletotrichum acutatum. PLANTS (BASEL, SWITZERLAND) 2024; 13:2261. [PMID: 39204697 PMCID: PMC11360474 DOI: 10.3390/plants13162261] [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: 07/17/2024] [Revised: 08/08/2024] [Accepted: 08/09/2024] [Indexed: 09/04/2024]
Abstract
Strawberry fruit is highly appreciated worldwide for its organoleptic and healthy properties. However, this plant is attacked by many pathogenic fungi, which significantly affect fruit production and quality at pre- and post-harvest stages, making chemical applications the most effective but undesirable strategy to control diseases that has been found so far. Alternatively, genetic manipulation, employing plant key genes involved in defense, such as members of the NPR-like gene family, has been successful in many crops to improve resistance. The identification and use of the endogenous counterpart genes in the plant of interest (as it is the case of strawberry) is desirable as it would increase the favorable outcome and requires prior knowledge of their defense-related function. Using RNAi technology in strawberry, transient silencing of Fragaria ananassa NPR3 members in fruit significantly reduced tissue damage after Colletotrichum acutatum infection, whereas the ectopic expression of either FaNPR3.1 or FaNPR3.2 did not have an apparent effect. Furthermore, the ectopic expression of FaNPR3.2 in Arabidopsis thaliana double-mutant npr3npr4 reverted the disease resistance phenotype to Pseudomonas syringe to wild-type levels. Therefore, the results revealed that members of the strawberry FaNPR3 clade negatively regulate the defense response to pathogens, as do their Arabidopsis AtNPR3/AtNPR4 orthologs. Also, evidence was found showing that FaNPR3 members act in strawberry (F. ananassa) as positive regulators of WRKY genes, FaWRKY19 and FaWRKY24; additionally, in Arabidopsis, FaNPR3.2 negatively regulates its orthologous genes AtNPR3/AtNPR4. We report for the first time the functional characterization of FaNPR3 members in F. ananassa, which provides a relevant molecular basis for the improvement of resistance in this species through new breeding technologies.
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Affiliation(s)
- Victoria Súnico
- Biotechnology and Plant Pharmacognosy (BIO-278), Department of Biochemistry and Molecular Biology, Campus de Rabanales, Severo Ochoa building-C6, University of Córdoba, UCO-CeiA3, 14071 Córdoba, Spain; (V.S.); (J.J.H.); (J.M.-B.)
| | - José Javier Higuera
- Biotechnology and Plant Pharmacognosy (BIO-278), Department of Biochemistry and Molecular Biology, Campus de Rabanales, Severo Ochoa building-C6, University of Córdoba, UCO-CeiA3, 14071 Córdoba, Spain; (V.S.); (J.J.H.); (J.M.-B.)
| | - Francisco Amil-Ruiz
- Bioinformatics Unit, Central Research Support Service (SCAI), University of Córdoba, 14071 Córdoba, Spain;
| | - Isabel Arjona-Girona
- Department of Crop Protection, Institute for Sustainable Agriculture (CSIC), Alameda del Obispo s/n, 14004 Córdoba, Spain; (I.A.-G.); (C.J.L.-H.)
| | - Carlos J. López-Herrera
- Department of Crop Protection, Institute for Sustainable Agriculture (CSIC), Alameda del Obispo s/n, 14004 Córdoba, Spain; (I.A.-G.); (C.J.L.-H.)
| | - Juan Muñoz-Blanco
- Biotechnology and Plant Pharmacognosy (BIO-278), Department of Biochemistry and Molecular Biology, Campus de Rabanales, Severo Ochoa building-C6, University of Córdoba, UCO-CeiA3, 14071 Córdoba, Spain; (V.S.); (J.J.H.); (J.M.-B.)
| | - Ana María Maldonado-Alconada
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, 14014 Córdoba, Spain
| | - José L. Caballero
- Biotechnology and Plant Pharmacognosy (BIO-278), Department of Biochemistry and Molecular Biology, Campus de Rabanales, Severo Ochoa building-C6, University of Córdoba, UCO-CeiA3, 14071 Córdoba, Spain; (V.S.); (J.J.H.); (J.M.-B.)
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7
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Liu J, Wang X, Chang J, Du P, Wu J, Hou R, Zhu S, Liu P, Miao X, Zhang P, Zhang Z. Green synthesized lignin nanoparticles for the sustainable delivery of pyraclostrobin to control strawberry diseases caused by Botrytis cinerea. Int J Biol Macromol 2024; 274:133488. [PMID: 38944092 DOI: 10.1016/j.ijbiomac.2024.133488] [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: 04/15/2024] [Revised: 06/14/2024] [Accepted: 06/26/2024] [Indexed: 07/01/2024]
Abstract
Lignin, renowned for its renewable, biocompatible, and environmentally benign characteristics, holds immense potential as a sustainable feedstock for agrochemical formulations. In this study, raw dealkaline lignin (DAL) underwent a purification process involving two sequential solvent extractions. Subsequently, an enzyme-responsive nanodelivery system (Pyr@DAL-NPs), was fabricated through the solvent self-assembly method, with pyraclostrobin (Pyr) loaded into lignin nanoparticles. The Pyr@DAL-NPs shown an average particle size of 250.4 nm, demonstrating a remarkable loading capacity of up to 54.70 % and an encapsulation efficiency of 86.15 %. Notably, in the presence of cellulase and pectinase at a concentration of 2 mg/mL, the release of Pyr from the Pyr@DAL-NPs reached 92.66 % within 120 h. Furthermore, the photostability of Pyr@DAL-NPs was significantly improved, revealing a 2.92-fold enhancement compared to the commercially available fungicide suspension (Pyr SC). Bioassay results exhibited that the Pyr@DAL-NPs revealed superior fungicidal activity against Botrytis cinerea over Pyr SC, with an EC50 value of 0.951 mg/L. Additionally, biosafety assessments indicated that the Pyr@DAL-NPs effectively declined the acute toxicity of Pyr towards zebrafish and posed no negative effects on the healthy growth of strawberry plants. In conclusion, this study presents a viable and promising strategy for developing environmentally friendly controlled-release systems for pesticides, offering the unique properties of lignin.
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Affiliation(s)
- Jun Liu
- National Key Laboratory of Green Pesticide, South China Agricultural University, Guangzhou 510642, China
| | - Xin Wang
- National Key Laboratory of Green Pesticide, South China Agricultural University, Guangzhou 510642, China
| | - Jinzhe Chang
- National Key Laboratory of Green Pesticide, South China Agricultural University, Guangzhou 510642, China
| | - Pengrui Du
- National Key Laboratory of Green Pesticide, South China Agricultural University, Guangzhou 510642, China
| | - Jian Wu
- National Key Laboratory of Green Pesticide, South China Agricultural University, Guangzhou 510642, China
| | - Ruiquan Hou
- National Key Laboratory of Green Pesticide, South China Agricultural University, Guangzhou 510642, China
| | - Shiqi Zhu
- National Key Laboratory of Green Pesticide, South China Agricultural University, Guangzhou 510642, China
| | - Pengpeng Liu
- National Key Laboratory of Green Pesticide, South China Agricultural University, Guangzhou 510642, China
| | - Xiaoran Miao
- National Key Laboratory of Green Pesticide, South China Agricultural University, Guangzhou 510642, China
| | - Peiwen Zhang
- National Key Laboratory of Green Pesticide, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan 512005, China.
| | - Zhixiang Zhang
- National Key Laboratory of Green Pesticide, South China Agricultural University, Guangzhou 510642, China.
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8
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Sun Y, Yang X, Wu R, Lv S, Li Y, Jia H, Yang Y, Li B, Chen W, Allan AC, Jiang G, Shi YN, Chen K. DNA methylation controlling abscisic acid catabolism responds to light to mediate strawberry fruit ripening. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:1718-1734. [PMID: 38896078 DOI: 10.1111/jipb.13681] [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: 01/30/2024] [Accepted: 05/02/2024] [Indexed: 06/21/2024]
Abstract
Phytohormones, epigenetic regulation and environmental factors regulate fruit ripening but their interplay during strawberry fruit ripening remains to be determined. In this study, bagged strawberry fruit exhibited delayed ripening compared with fruit grown in normal light, correlating with reduced abscisic acid (ABA) accumulation. Transcription of the key ABA catabolism gene, ABA 8'-hydroxylase FaCYP707A4, was induced in bagged fruit. With light exclusion whole genome DNA methylation levels were up-regulated, corresponding to a delayed ripening process, while DNA methylation levels in the promoter of FaCYP707A4 were suppressed, correlating with increases in transcript and decreased ABA content. Experiments indicated FaCRY1, a blue light receptor repressed in bagged fruit and FaAGO4, a key protein involved in RNA-directed DNA methylation, could bind to the promoter of FaCYP707A4. The interaction between FaCRY1 and FaAGO4, and an increased enrichment of FaAGO4 directed to the FaCYP707A4 promoter in fruit grown under light suggests FaCRY1 may influence FaAGO4 to modulate the DNA methylation status of the FaCYP707A4 promoter. Furthermore, transient overexpression of FaCRY1, or an increase in FaCRY1 transcription by blue light treatment, increases the methylation level of the FaCYP707A4 promoter, while transient RNA interference of FaCRY1 displayed opposite phenotypes. These findings reveal a mechanism by which DNA methylation influences ABA catabolism, and participates in light-mediated strawberry ripening.
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Affiliation(s)
- Yunfan Sun
- College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Xiaofang Yang
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Rongrong Wu
- College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Shouzheng Lv
- College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Yunduan Li
- College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Haoran Jia
- College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Yuying Yang
- College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Baijun Li
- College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Wenbo Chen
- College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Andrew C Allan
- New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Guihua Jiang
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Yan-Na Shi
- College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Kunsong Chen
- College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
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9
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Whitener MR, Mangelson H, Sweigart AL. Patterns of genomic variation reveal a single evolutionary origin of the wild allotetraploid Mimulus sookensis. Evolution 2024; 78:1464-1477. [PMID: 38766685 DOI: 10.1093/evolut/qpae079] [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: 09/17/2023] [Revised: 03/12/2024] [Accepted: 05/17/2024] [Indexed: 05/22/2024]
Abstract
Polyploidy occurs across the tree of life and is especially common in plants. Because newly formed cytotypes are often incompatible with their progenitors, polyploidy is also said to trigger "instantaneous" speciation. If a polyploid can self-fertilize or reproduce asexually, it is even possible for one individual to produce an entirely new lineage, but how often this scenario occurs is unclear. Here, we investigate the evolutionary history of the wild allotetraploid Mimulus sookensis, which was formed through hybridization between self-compatible, diploid species in the Mimulus guttatus complex. We generate a chromosome-scale reference assembly for M. sookensis and define its distinct subgenomes. Despite previous reports suggesting multiple origins of this highly selfing polyploid, we discover patterns of population genomic variation that provide unambiguous support for a single origin. One M. sookensis subgenome is clearly derived from the selfer Mimulus nasutus, which organellar variation suggests is the maternal progenitor. The ancestor of the other subgenome is less certain, but it shares variation with both Mimulus decorus and M. guttatus, two outcrossing diploids with geographic ranges that overlap broadly with M. sookensis. This study establishes M. sookensis as an example of instantaneous speciation, likely facilitated by the polyploid's predisposition to self-fertilize.
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Affiliation(s)
- Makenzie R Whitener
- Department of Genetics, University of Georgia, Athens, GA 30602, United States
| | | | - Andrea L Sweigart
- Department of Genetics, University of Georgia, Athens, GA 30602, United States
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10
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Aufiero G, Fruggiero C, D’Angelo D, D’Agostino N. Homoeologs in Allopolyploids: Navigating Redundancy as Both an Evolutionary Opportunity and a Technical Challenge-A Transcriptomics Perspective. Genes (Basel) 2024; 15:977. [PMID: 39202338 PMCID: PMC11353593 DOI: 10.3390/genes15080977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 07/22/2024] [Accepted: 07/23/2024] [Indexed: 09/03/2024] Open
Abstract
Allopolyploidy in plants involves the merging of two or more distinct parental genomes into a single nucleus, a significant evolutionary process in the plant kingdom. Transcriptomic analysis provides invaluable insights into allopolyploid plants by elucidating the fate of duplicated genes, revealing evolutionary novelties and uncovering their environmental adaptations. By examining gene expression profiles, scientists can discern how duplicated genes have evolved to acquire new functions or regulatory roles. This process often leads to the development of novel traits and adaptive strategies that allopolyploid plants leverage to thrive in diverse ecological niches. Understanding these molecular mechanisms not only enhances our appreciation of the genetic complexity underlying allopolyploidy but also underscores their importance in agriculture and ecosystem resilience. However, transcriptome profiling is challenging due to genomic redundancy, which is further complicated by the presence of multiple chromosomes sets and the variations among homoeologs and allelic genes. Prior to transcriptome analysis, sub-genome phasing and homoeology inference are essential for obtaining a comprehensive view of gene expression. This review aims to clarify the terminology in this field, identify the most challenging aspects of transcriptome analysis, explain their inherent difficulties, and suggest reliable analytic strategies. Furthermore, bulk RNA-seq is highlighted as a primary method for studying allopolyploid gene expression, focusing on critical steps like read mapping and normalization in differential gene expression analysis. This approach effectively captures gene expression from both parental genomes, facilitating a comprehensive analysis of their combined profiles. Its sensitivity in detecting low-abundance transcripts allows for subtle differences between parental genomes to be identified, crucial for understanding regulatory dynamics and gene expression balance in allopolyploids.
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Affiliation(s)
| | | | | | - Nunzio D’Agostino
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy; (G.A.); (C.F.); (D.D.)
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11
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Decena MÁ, Sancho R, Inda LA, Pérez-Collazos E, Catalán P. Expansions and contractions of repetitive DNA elements reveal contrasting evolutionary responses to the polyploid genome shock hypothesis in Brachypodium model grasses. FRONTIERS IN PLANT SCIENCE 2024; 15:1419255. [PMID: 39049853 PMCID: PMC11266827 DOI: 10.3389/fpls.2024.1419255] [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: 04/17/2024] [Accepted: 06/19/2024] [Indexed: 07/27/2024]
Abstract
Brachypodium grass species have been selected as model plants for functional genomics of grass crops, and to elucidate the origins of allopolyploidy and perenniality in monocots, due to their small genome sizes and feasibility of cultivation. However, genome sizes differ greatly between diploid or polyploid Brachypodium lineages. We have used genome skimming sequencing data to uncover the composition, abundance, and phylogenetic value of repetitive elements in 44 representatives of the major Brachypodium lineages and cytotypes. We also aimed to test the possible mechanisms and consequences of the "polyploid genome shock hypothesis" (PGSH) under three different evolutionary scenarios of variation in repeats and genome sizes of Brachypodium allopolyploids. Our data indicated that the proportion of the genome covered by the repeatome in the Brachypodium species showed a 3.3-fold difference between the highest content of B. mexicanum-4x (67.97%) and the lowest of B. stacei-2x (20.77%), and that changes in the sizes of their genomes were a consequence of gains or losses in their repeat elements. LTR-Retand and Tekay retrotransposons were the most frequent repeat elements in the Brachypodium genomes, while Ogre retrotransposons were found exclusively in B. mexicanum. The repeatome phylogenetic network showed a high topological congruence with plastome and nuclear rDNA and transcriptome trees, differentiating the ancestral outcore lineages from the recently evolved core-perennial lineages. The 5S rDNA graph topologies had a strong match with the ploidy levels and nature of the subgenomes of the Brachypodium polyploids. The core-perennial B. sylvaticum presents a large repeatome and characteristics of a potential post-polyploid diploidized origin. Our study evidenced that expansions and contractions in the repeatome were responsible for the three contrasting responses to the PGSH. The exacerbated genome expansion of the ancestral allotetraploid B. mexicanum was a consequence of chromosome-wide proliferation of TEs and not of WGD, the additive repeatome pattern of young allotetraploid B. hybridum of stabilized post-WGD genome evolution, and the genomecontraction of recent core-perennials polyploids (B. pinnatum, B. phoenicoides) of repeat losses through recombination of these highly hybridizing lineages. Our analyses have contributed to unraveling the evolution of the repeatome and the genome size variation in model Brachypodium grasses.
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Affiliation(s)
- María Ángeles Decena
- Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Huesca, Spain
- Grupo de Bioquímica, Biofísica y Biología Computacional (Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) Universidad de Zaragoza), Unidad Asociada al Consejo Superior de Investigaciones Científicas (CSIC), Zaragoza, Spain
| | - Rubén Sancho
- Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Huesca, Spain
- Grupo de Bioquímica, Biofísica y Biología Computacional (Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) Universidad de Zaragoza), Unidad Asociada al Consejo Superior de Investigaciones Científicas (CSIC), Zaragoza, Spain
| | - Luis A. Inda
- Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Huesca, Spain
- Centro de Investigaciones Tecnológicas y Agroalimentarias de Aragón (CITA), Zaragoza, Spain
| | - Ernesto Pérez-Collazos
- Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Huesca, Spain
- Grupo de Bioquímica, Biofísica y Biología Computacional (Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) Universidad de Zaragoza), Unidad Asociada al Consejo Superior de Investigaciones Científicas (CSIC), Zaragoza, Spain
| | - Pilar Catalán
- Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Huesca, Spain
- Grupo de Bioquímica, Biofísica y Biología Computacional (Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) Universidad de Zaragoza), Unidad Asociada al Consejo Superior de Investigaciones Científicas (CSIC), Zaragoza, Spain
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12
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Zhao M, Hu R, Lin Y, Yang Y, Chen Q, Li M, Zhang Y, Zhang Y, Wang Y, He W, Wang X, Tang H, Luo Y. Genome-Wide Analysis of Polygalacturonase Gene Family Reveals Its Role in Strawberry Softening. PLANTS (BASEL, SWITZERLAND) 2024; 13:1838. [PMID: 38999678 PMCID: PMC11244104 DOI: 10.3390/plants13131838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 06/18/2024] [Accepted: 07/02/2024] [Indexed: 07/14/2024]
Abstract
Fruit softening is a prominent attribute governing both longevity on shelves and commercial worth. Polygalacturonase (PG) plays a major role in strawberry fruit softening. However, the PG gene family in strawberry has not been comprehensively analyzed. In this study, 75 FaPG genes were identified in the octoploid strawberry genome, which were classified into three groups according to phylogenetic analysis. Subcellular localization prediction indicated that FaPGs are mostly localized to the plasma membrane, cytoplasm, and chloroplasts. Moreover, the expression of FaPGs during strawberry development and ripening of 'Benihoppe' and its softer mutant was estimated. The results showed that among all 75 FaPGs, most genes exhibited low expression across developmental stages, while two group c members (FxaC_21g15770 and FxaC_20g05360) and one group b member, FxaC_19g05040, displayed relatively higher and gradual increases in their expression trends during strawberry ripening and softening. FxaC_21g15770 was selected for subsequent silencing to validate its role in strawberry softening due to the fact that it exhibited the highest and most changed expression level across different developmental stages in 'Benihoppe' and its mutant. Silencing FxaC_21g15770 could significantly improve strawberry fruit firmness without affecting fruit color, soluble solids, cellulose, and hemicellulose. Conversely, silencing FxaC_21g15770 could significantly suppress the expression of other genes related to pectin degradation such as FaPG-like, FaPL, FaPME, FaCX, FaCel, FaGlu, FaXET, and FaEG. These findings provide basic information on the FaPG gene family for further functional research and indicate that FxaC_21g15770 plays a vital role in strawberry fruit softening.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Ya Luo
- College of Horticulture, Sichuan Agricultural University, Chengdu 625014, China; (M.Z.); (R.H.); (Y.L.); (Y.Y.); (Q.C.); (M.L.); (Y.Z.); (Y.Z.); (Y.W.); (W.H.); (X.W.); (H.T.)
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13
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Saez D, Rodríguez-Arriaza F, Urra G, Fabi JP, Hormazábal-Abarza F, Méndez-Yáñez A, Castro E, Bustos D, Ramos P, Morales-Quintana L. Unraveling the key step in the aroma puzzle: Insights into alcohol acyltransferases in strawberries. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 212:108668. [PMID: 38823091 DOI: 10.1016/j.plaphy.2024.108668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 03/27/2024] [Accepted: 04/25/2024] [Indexed: 06/03/2024]
Abstract
Alcohol acyltransferases (AATs) play a crucial role in catalyzing the transfer of acyl groups, contributing to the diverse aroma of fruits, including strawberries. In this research we identified nine AAT genes in strawberries through a comprehensive analysis involving phylogenetics, gene structure, conserved motifs, and structural protein model examinations. The study used the 'Camarosa' strawberry genome database, and experiments were conducted with fruits harvested at different developmental and ripening stages. The transcriptional analysis revealed differential expression patterns among the AAT genes during fruit ripening, with only four genes (SAAT, FaAAT2, FaAAT7, and FaAAT9) showing increased transcript accumulation correlated with total AAT enzyme activity. Additionally, the study employed in silico methods, including sequence alignment, phylogenetic analysis, and structural modeling, to gain insights into the AAT protein model structures with increase expression pattern during fruit ripening. The four modeled AAT proteins exhibited structural similarities, including conserved catalytic sites and solvent channels. Furthermore, the research investigated the interaction of AAT proteins with different substrates, highlighting the enzymes' promiscuity in substrate preferences. The study contributes with valuable information to unveil AAT gene family members in strawberries, providing scientific background for further exploration of their biological characteristics and their role in aroma biosynthesis during fruit ripening.
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Affiliation(s)
- Darwin Saez
- Multidisciplinary Agroindustry Research Laboratory, Instituto de Ciencias Biomédicas, Facultad de Ciencias de La Salud, Universidad Autónoma de Chile, Cinco Poniente #1670, Talca, Región del Maule, 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, Región del Maule, Chile
| | - Gabriela Urra
- Laboratorio de Bioinformática y Química Computacional, Departamento de Medicina Traslacional, Facultad de Medicina, Universidad Católica Del Maule, Talca, 3480094, Chile
| | - João Paulo Fabi
- Department of Food Science and Experimental Nutrition, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Francisca Hormazábal-Abarza
- Multidisciplinary Agroindustry Research Laboratory, Instituto de Ciencias Biomédicas, Facultad de Ciencias de La Salud, Universidad Autónoma de Chile, Cinco Poniente #1670, Talca, Región del Maule, Chile
| | - 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, Región del Maule, Chile
| | - Egle Castro
- Multidisciplinary Agroindustry Research Laboratory, Instituto de Ciencias Biomédicas, Facultad de Ciencias de La Salud, Universidad Autónoma de Chile, Cinco Poniente #1670, Talca, Región del Maule, Chile
| | - Daniel Bustos
- Laboratorio de Bioinformática y Química Computacional, Departamento de Medicina Traslacional, Facultad de Medicina, Universidad Católica Del Maule, Talca, 3480094, Chile.
| | - Patricio Ramos
- Plant Microorganism Interaction Laboratory, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, 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, Región del Maule, Chile.
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14
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Session AM. Allopolyploid subgenome identification and implications for evolutionary analysis. Trends Genet 2024; 40:621-631. [PMID: 38637269 DOI: 10.1016/j.tig.2024.03.008] [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: 11/17/2023] [Revised: 03/21/2024] [Accepted: 03/21/2024] [Indexed: 04/20/2024]
Abstract
Whole-genome duplications (WGDs) are widespread genomic events in eukaryotes that are hypothesized to contribute to the evolutionary success of many lineages, including flowering plants, Saccharomyces yeast, and vertebrates. WGDs generally can be classified into autopolyploids (ploidy increase descended from one species) or allopolyploids (ploidy increase descended from multiple species). Assignment of allopolyploid progenitor species (called subgenomes in the polyploid) is important to understanding the biology and evolution of polyploids, including the asymmetric subgenome evolution following hybridization (biased fractionation). Here, I review the different methodologies used to identify the ancestors of allopolyploid subgenomes, discuss the advantages and disadvantages of these methods, and outline the implications of how these methods affect the subsequent evolutionary analysis of these genomes.
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Affiliation(s)
- Adam M Session
- Department of Biological Sciences, Binghamton University, Binghamton, NY 13902, USA.
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15
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Prohaska A, Rey-Serra P, Petit J, Petit A, Perrotte J, Rothan C, Denoyes B. Exploration of a European-centered strawberry diversity panel provides markers and candidate genes for the control of fruit quality traits. HORTICULTURE RESEARCH 2024; 11:uhae137. [PMID: 38988619 PMCID: PMC11233882 DOI: 10.1093/hr/uhae137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 05/05/2024] [Indexed: 07/12/2024]
Abstract
Fruit quality traits are major breeding targets in cultivated strawberry (Fragaria × ananassa). Taking into account the requirements of both growers and consumers when selecting high-quality cultivars is a real challenge. Here, we used a diversity panel enriched with unique European accessions and the 50 K FanaSNP array to highlight the evolution of strawberry diversity over the past 160 years, investigate the molecular basis of 12 major fruit quality traits by genome-wide association studies (GWAS), and provide genetic markers for breeding. Results show that considerable improvements of key breeding targets including fruit weight, firmness, composition, and appearance occurred simultaneously in European and American cultivars. Despite the high genetic diversity of our panel, we observed a drop in nucleotide diversity in certain chromosomal regions, revealing the impact of selection. GWAS identified 71 associations with 11 quality traits and, while validating known associations (firmness, sugar), highlighted the predominance of new quantitative trait locus (QTL), demonstrating the value of using untapped genetic resources. Three of the six selective sweeps detected are related to glossiness or skin resistance, two little-studied traits important for fruit attractiveness and, potentially, postharvest shelf life. Moreover, major QTL for firmness, glossiness, skin resistance, and susceptibility to bruising are found within a low diversity region of chromosome 3D. Stringent search for candidate genes underlying QTL uncovered strong candidates for fruit color, firmness, sugar and acid composition, glossiness, and skin resistance. Overall, our study provides a potential avenue for extending shelf life without compromising flavor and color as well as the genetic markers needed to achieve this goal.
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Affiliation(s)
- Alexandre Prohaska
- Univ. Bordeaux, INRAE, UMR BFP, F-33140 Villenave d'Ornon, France
- Invenio, MIN de Brienne, 110 Quai de Paludate, 33000 Bordeaux, France
| | - Pol Rey-Serra
- Univ. Bordeaux, INRAE, UMR BFP, F-33140 Villenave d'Ornon, France
| | - Johann Petit
- Univ. Bordeaux, INRAE, UMR BFP, F-33140 Villenave d'Ornon, France
| | - Aurélie Petit
- Invenio, MIN de Brienne, 110 Quai de Paludate, 33000 Bordeaux, France
| | - Justine Perrotte
- Invenio, MIN de Brienne, 110 Quai de Paludate, 33000 Bordeaux, France
| | | | - Béatrice Denoyes
- Univ. Bordeaux, INRAE, UMR BFP, F-33140 Villenave d'Ornon, France
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16
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Li F, Hou Z, Xu S, Han D, Li B, Hu H, Liu J, Cai S, Gan Z, Gu Y, Zhang X, Zhou X, Wang S, Zhao J, Mei Y, Zhang J, Wang Z, Wang J. Haplotype-resolved genomes of octoploid species in Phyllanthaceae family reveal a critical role for polyploidization and hybridization in speciation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:348-363. [PMID: 38606539 DOI: 10.1111/tpj.16767] [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: 10/21/2023] [Revised: 03/14/2024] [Accepted: 03/31/2024] [Indexed: 04/13/2024]
Abstract
The Phyllanthaceae family comprises a diverse range of plants with medicinal, edible, and ornamental value, extensively cultivated worldwide. Polyploid species commonly occur in Phyllanthaceae. Due to the rather complex genomes and evolutionary histories, their speciation process has been still lacking in research. In this study, we generated chromosome-scale haplotype-resolved genomes of two octoploid species (Phyllanthus emblica and Sauropus spatulifolius) in Phyllanthaceae family. Combined with our previously reported one tetraploid (Sauropus androgynus) and one diploid species (Phyllanthus cochinchinensis) from the same family, we explored their speciation history. The three polyploid species were all identified as allopolyploids with subgenome A/B. Each of their two distinct subgenome groups from various species was uncovered to independently share a common diploid ancestor (Ancestor-AA and Ancestor-BB). Via different evolutionary routes, comprising various scenarios of bifurcating divergence, allopolyploidization (hybrid polyploidization), and autopolyploidization, they finally evolved to the current tetraploid S. androgynus, and octoploid S. spatulifolius and P. emblica, respectively. We further discuss the variations in copy number of alleles and the potential impacts within the two octoploids. In addition, we also investigated the fluctuation of metabolites with medical values and identified the key factor in its biosynthesis process in octoploids species. Our study reconstructed the evolutionary history of these Phyllanthaceae species, highlighting the critical roles of polyploidization and hybridization in their speciation processes. The high-quality genomes of the two octoploid species provide valuable genomic resources for further research of evolution and functional genomics.
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Affiliation(s)
- Fangping Li
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crop Research Institute, Guangdong Academy of Agriculture Sciences, Guangzhou, 510640, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Ecology and Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Zhuangwei Hou
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crop Research Institute, Guangdong Academy of Agriculture Sciences, Guangzhou, 510640, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Shiqiang Xu
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crop Research Institute, Guangdong Academy of Agriculture Sciences, Guangzhou, 510640, China
| | - Danlu Han
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, 510631, Guangzhou, China
| | - Bin Li
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crop Research Institute, Guangdong Academy of Agriculture Sciences, Guangzhou, 510640, China
| | - Haifei Hu
- Rice Research Institute & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Jieying Liu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Shike Cai
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crop Research Institute, Guangdong Academy of Agriculture Sciences, Guangzhou, 510640, China
| | - Zhenpeng Gan
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Yan Gu
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crop Research Institute, Guangdong Academy of Agriculture Sciences, Guangzhou, 510640, China
| | - Xiufeng Zhang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Xiaofan Zhou
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Shaokui Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Junliang Zhao
- Rice Research Institute & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Yu Mei
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crop Research Institute, Guangdong Academy of Agriculture Sciences, Guangzhou, 510640, China
| | - Jisen Zhang
- State Key Lab for Conservation and Utilization of Subtropical Agric-Biological Resources, Guangxi University, Nanning, 530005, China
| | - Zefu Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Ecology and Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Jihua Wang
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crop Research Institute, Guangdong Academy of Agriculture Sciences, Guangzhou, 510640, China
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17
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Phillips AR. Variant calling in polyploids for population and quantitative genetics. APPLICATIONS IN PLANT SCIENCES 2024; 12:e11607. [PMID: 39184203 PMCID: PMC11342233 DOI: 10.1002/aps3.11607] [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: 11/27/2023] [Revised: 03/03/2024] [Accepted: 04/10/2024] [Indexed: 08/27/2024]
Abstract
Advancements in genome assembly and sequencing technology have made whole genome sequence (WGS) data and reference genomes accessible to study polyploid species. Compared to popular reduced-representation sequencing approaches, the genome-wide coverage and greater marker density provided by WGS data can greatly improve our understanding of polyploid species and polyploid biology. However, biological features that make polyploid species interesting also pose challenges in read mapping, variant identification, and genotype estimation. Accounting for characteristics in variant calling like allelic dosage uncertainty, homology between subgenomes, and variance in chromosome inheritance mode can reduce errors. Here, I discuss the challenges of variant calling in polyploid WGS data and discuss where potential solutions can be integrated into a standard variant calling pipeline.
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Affiliation(s)
- Alyssa R. Phillips
- Department of Evolution and EcologyUniversity of California, DavisDavis95616CaliforniaUSA
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18
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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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19
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Winter MR, Taranto AP, Yimer HZ, Coomer Blundell A, Siddique S, Williamson VM, Lunt DH. Phased chromosome-scale genome assembly of an asexual, allopolyploid root-knot nematode reveals complex subgenomic structure. PLoS One 2024; 19:e0302506. [PMID: 38843263 PMCID: PMC11156385 DOI: 10.1371/journal.pone.0302506] [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: 05/08/2023] [Accepted: 04/05/2024] [Indexed: 06/09/2024] Open
Abstract
We present the chromosome-scale genome assembly of the allopolyploid root-knot nematode Meloidogyne javanica. We show that the M. javanica genome is predominantly allotetraploid, comprising two subgenomes, A and B, that most likely originated from hybridisation of two ancestral parental species. The assembly was annotated using full-length non-chimeric transcripts, comparison to reference databases, and ab initio prediction techniques, and the subgenomes were phased using ancestral k-mer spectral analysis. Subgenome B appears to show fission of chromosomal contigs, and while there is substantial synteny between subgenomes, we also identified regions lacking synteny that may have diverged in the ancestral genomes prior to or following hybridisation. This annotated and phased genome assembly forms a significant resource for understanding the origins and genetics of these globally important plant pathogens.
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Affiliation(s)
- Michael R. Winter
- School of Natural Sciences, University of Hull, Hull, United Kingdom
| | - Adam P. Taranto
- Department of Plant Pathology, University of California Davis, Davis, CA, United States of America
| | - Henok Zemene Yimer
- Department of Entomology and Nematology, University of California Davis, Davis, CA, United States of America
| | - Alison Coomer Blundell
- Department of Plant Pathology, University of California Davis, Davis, CA, United States of America
| | - Shahid Siddique
- Department of Entomology and Nematology, University of California Davis, Davis, CA, United States of America
| | - Valerie M. Williamson
- Department of Plant Pathology, University of California Davis, Davis, CA, United States of America
| | - David H. Lunt
- School of Natural Sciences, University of Hull, Hull, United Kingdom
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20
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Wang Y, Li Y, Wu W, Shao S, Fang Q, Xu S, Guo Z, Shi S, He Z. The evolution history of an allotetraploid mangrove tree analysed with a new tool Allo4D. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1491-1503. [PMID: 38157253 PMCID: PMC11123425 DOI: 10.1111/pbi.14281] [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: 06/08/2023] [Revised: 12/10/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024]
Abstract
Mangrove species are broadly classified as true mangroves and mangrove associates. The latter are amphibious plants that can survive in the intertidal zone and reproduce naturally in terrestrial environments. Their widespread distribution and extensive adaptability make them ideal research materials for exploring adaptive evolution. In this study, we de novo assembled two genomes of mangrove associates (the allotetraploid Barringtonia racemosa (2n = 4x = 52) and diploid Barringtonia asiatica (2n = 2x = 26)) to investigate the role of allopolyploidy in the evolutionary history of mangrove species. We developed a new allotetraploid-dividing tool Allo4D to distinguish between allotetraploid scaffold-scale subgenomes and verified its accuracy and reliability using real and simulated data. According to the two subgenomes of allotetraploid B. racemosa divided using Allo4D, the allopolyploidization event was estimated to have occurred approximately one million years ago (Mya). We found that B. racemosa, B. asiatica, and Diospyros lotus shared a whole genome duplication (WGD) event during the K-Pg (Cretaceous-Paleozoic) period. K-Pg WGD and recent allopolyploidization events contributed to the speciation of B. racemosa and its adaptation to coastal habitats. We found that genes in the glucosinolates (GSLs) pathway, an essential pathway in response to various biotic and abiotic stresses, expanded rapidly in B. racemosa during polyploidization. In summary, this study provides a typical example of the adaptation of allopolyploid plants to extreme environmental conditions. The newly developed tool, Allo4D, can effectively divide allotetraploid subgenomes and explore the evolutionary history of polyploid plants, especially for species whose ancestors are unknown or extinct.
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Affiliation(s)
- Yuan Wang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life SciencesSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Yulong Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life SciencesSun Yat‐sen UniversityGuangzhouGuangdongChina
- School of EcologySun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Weihong Wu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life SciencesSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Shao Shao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life SciencesSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Qi Fang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life SciencesSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Shaohua Xu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life SciencesSun Yat‐sen UniversityGuangzhouGuangdongChina
- School of EcologySun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Zixiao Guo
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life SciencesSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Suhua Shi
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life SciencesSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Ziwen He
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life SciencesSun Yat‐sen UniversityGuangzhouGuangdongChina
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21
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Khan AW, Garg V, Sun S, Gupta S, Dudchenko O, Roorkiwal M, Chitikineni A, Bayer PE, Shi C, Upadhyaya HD, Bohra A, Bharadwaj C, Mir RR, Baruch K, Yang B, Coyne CJ, Bansal KC, Nguyen HT, Ronen G, Aiden EL, Veneklaas E, Siddique KHM, Liu X, Edwards D, Varshney RK. Cicer super-pangenome provides insights into species evolution and agronomic trait loci for crop improvement in chickpea. Nat Genet 2024; 56:1225-1234. [PMID: 38783120 DOI: 10.1038/s41588-024-01760-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 04/18/2024] [Indexed: 05/25/2024]
Abstract
Chickpea (Cicer arietinum L.)-an important legume crop cultivated in arid and semiarid regions-has limited genetic diversity. Efforts are being undertaken to broaden its diversity by utilizing its wild relatives, which remain largely unexplored. Here, we present the Cicer super-pangenome based on the de novo genome assemblies of eight annual Cicer wild species. We identified 24,827 gene families, including 14,748 core, 2,958 softcore, 6,212 dispensable and 909 species-specific gene families. The dispensable genome was enriched for genes related to key agronomic traits. Structural variations between cultivated and wild genomes were used to construct a graph-based genome, revealing variations in genes affecting traits such as flowering time, vernalization and disease resistance. These variations will facilitate the transfer of valuable traits from wild Cicer species into elite chickpea varieties through marker-assisted selection or gene-editing. This study offers valuable insights into the genetic diversity and potential avenues for crop improvement in chickpea.
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Affiliation(s)
- Aamir W Khan
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- School of Biological Sciences, University of Western Australia, Perth, Western Australia, Australia
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, USA
| | - Vanika Garg
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Centre for Crop and Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | | | - Saurabh Gupta
- Curtin Health Innovation Research Institute (CHIRI), Curtin Medical School, Curtin University, Perth, Western Australia, Australia
| | - Olga Dudchenko
- Department of Molecular and Human Genetics, Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA
| | - Manish Roorkiwal
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Annapurna Chitikineni
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Centre for Crop and Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Philipp E Bayer
- School of Biological Sciences, University of Western Australia, Perth, Western Australia, Australia
| | | | - Hari D Upadhyaya
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Plant Genome Mapping Laboratory, The University of Georgia, Athens, GA, USA
| | - Abhishek Bohra
- Centre for Crop and Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | | | - Reyazul Rouf Mir
- Division of Genetics and Plant Breeding, Faculty of Agriculture (FoA), SKUAST-Kashmir,Wadura Campus, Kashmir, India
| | | | | | - Clarice J Coyne
- USDA-ARS Plant Germplasm Introduction and Testing, Washington State University, Pullman, WA, USA
| | - Kailash C Bansal
- National Academy of Agricultural Sciences (NAAS), NASC Complex, New Delhi, India
| | - Henry T Nguyen
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, USA
| | - Gil Ronen
- NRGene Ltd, Park HaMada, Ness Ziona, Israel
| | - Erez Lieberman Aiden
- Department of Molecular and Human Genetics, Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA
| | - Erik Veneklaas
- School of Biological Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - Kadambot H M Siddique
- UWA Institute of Agriculture, and School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Xin Liu
- BGI Research, Qingdao, China.
- BGI Research, Shenzhen, China.
| | - David Edwards
- School of Biological Sciences, University of Western Australia, Perth, Western Australia, Australia.
| | - Rajeev K Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.
- Centre for Crop and Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia.
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22
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Sun C, Wu J, Zhou X, Fu S, Liu H, Xue Z, Wang X, Peng Q, Gao J, Chen F, Zhang W, Hu M, Fu T, Wang Y, Yi B, Zhang J. Homoeologous exchanges contribute to branch angle variations in rapeseed: Insights from transcriptome, QTL-seq and gene functional analysis. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1636-1648. [PMID: 38308663 PMCID: PMC11123428 DOI: 10.1111/pbi.14292] [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: 10/18/2023] [Revised: 12/10/2023] [Accepted: 01/08/2024] [Indexed: 02/05/2024]
Abstract
Branch angle (BA) is a critical morphological trait that significantly influences planting density, light interception and ultimately yield in plants. Despite its importance, the regulatory mechanism governing BA in rapeseed remains poorly understood. In this study, we generated 109 transcriptome data sets for 37 rapeseed accessions with divergent BA phenotypes. Relative to adaxial branch segments, abaxial segments accumulated higher levels of auxin and exhibited lower expression of six TCP1 homologues and one GA20ox3. A co-expression network analysis identified two modules highly correlated with BA. The modules contained homologues to known BA control genes, such as FUL, YUCCA6, TCP1 and SGR3. Notably, a homoeologous exchange (HE), occurring at the telomeres of A09, was prevalent in large BA accessions, while an A02-C02 HE was common in small BA accessions. In their corresponding regions, these HEs explained the formation of hub gene hotspots in the two modules. QTL-seq analysis confirmed that the presence of a large A07-C06 HE (~8.1 Mb) was also associated with a small BA phenotype, and BnaA07.WRKY40.b within it was predicted as candidate gene. Overexpressing BnaA07.WRKY40.b in rapeseed increased BA by up to 20°, while RNAi- and CRISPR-mediated mutants (BnaA07.WRKY40.b and BnaC06.WRKY40.b) exhibited decreased BA by up to 11.4°. BnaA07.WRKY40.b was exclusively localized to the nucleus and exhibited strong expression correlations with many genes related to gravitropism and plant architecture. Taken together, our study highlights the influence of HEs on rapeseed plant architecture and confirms the role of WRKY40 homologues as novel regulators of BA.
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Affiliation(s)
- Chengming Sun
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs/Key Laboratory of Jiangsu Province for Agrobiology/Institute of Industrial CropsJiangsu Academy of Agricultural SciencesNanjingChina
| | - Jian Wu
- Key Laboratory of Plant Functional Genomics of the Ministry of EducationYangzhou UniversityYangzhouChina
| | - Xiaoying Zhou
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs/Key Laboratory of Jiangsu Province for Agrobiology/Institute of Industrial CropsJiangsu Academy of Agricultural SciencesNanjingChina
| | - Sanxiong Fu
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs/Key Laboratory of Jiangsu Province for Agrobiology/Institute of Industrial CropsJiangsu Academy of Agricultural SciencesNanjingChina
| | - Huimin Liu
- Key Laboratory of Plant Functional Genomics of the Ministry of EducationYangzhou UniversityYangzhouChina
| | - Zhifei Xue
- National Key Laboratory of Crop Genetic Improvement/National Center of Rapeseed Improvement/Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Xiaodong Wang
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs/Key Laboratory of Jiangsu Province for Agrobiology/Institute of Industrial CropsJiangsu Academy of Agricultural SciencesNanjingChina
| | - Qi Peng
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs/Key Laboratory of Jiangsu Province for Agrobiology/Institute of Industrial CropsJiangsu Academy of Agricultural SciencesNanjingChina
| | - Jianqin Gao
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs/Key Laboratory of Jiangsu Province for Agrobiology/Institute of Industrial CropsJiangsu Academy of Agricultural SciencesNanjingChina
| | - Feng Chen
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs/Key Laboratory of Jiangsu Province for Agrobiology/Institute of Industrial CropsJiangsu Academy of Agricultural SciencesNanjingChina
| | - Wei Zhang
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs/Key Laboratory of Jiangsu Province for Agrobiology/Institute of Industrial CropsJiangsu Academy of Agricultural SciencesNanjingChina
| | - Maolong Hu
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs/Key Laboratory of Jiangsu Province for Agrobiology/Institute of Industrial CropsJiangsu Academy of Agricultural SciencesNanjingChina
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement/National Center of Rapeseed Improvement/Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Youping Wang
- Key Laboratory of Plant Functional Genomics of the Ministry of EducationYangzhou UniversityYangzhouChina
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement/National Center of Rapeseed Improvement/Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Jiefu Zhang
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs/Key Laboratory of Jiangsu Province for Agrobiology/Institute of Industrial CropsJiangsu Academy of Agricultural SciencesNanjingChina
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23
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Zhang C, Tang Y, Tang S, Chen L, Li T, Yuan H, Xu Y, Zhou Y, Zhang S, Wang J, Wen H, Jiang W, Pang Y, Deng X, Cao X, Zhou J, Song X, Liu Q. An inducible CRISPR activation tool for accelerating plant regeneration. PLANT COMMUNICATIONS 2024; 5:100823. [PMID: 38243597 PMCID: PMC11121170 DOI: 10.1016/j.xplc.2024.100823] [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: 11/29/2023] [Revised: 01/09/2024] [Accepted: 01/12/2024] [Indexed: 01/21/2024]
Abstract
The inducible CRISPR activation (CRISPR-a) system offers unparalleled precision and versatility for regulating endogenous genes, making it highly sought after in plant research. In this study, we developed a chemically inducible CRISPR-a tool for plants called ER-Tag by combining the LexA-VP16-ER inducible system with the SunTag CRISPR-a system. We systematically compared different induction strategies and achieved high efficiency in target gene activation. We demonstrated that guide RNAs can be multiplexed and pooled for large-scale screening of effective morphogenic genes and gene pairs involved in plant regeneration. Further experiments showed that induced activation of these morphogenic genes can accelerate regeneration and improve regeneration efficiency in both eudicot and monocot plants, including alfalfa, woodland strawberry, and sheepgrass. Our study expands the CRISPR toolset in plants and provides a powerful new strategy for studying gene function when constitutive expression is not feasible or ideal.
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Affiliation(s)
- Cuimei Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Yajun Tang
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong 261000, China
| | - Shanjie Tang
- National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Lei Chen
- National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Tong Li
- National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Haidi Yuan
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong 261000, China
| | - Yujun Xu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Yangyan Zhou
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Shuaibin Zhang
- National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianli Wang
- Grass and Science Institute of Heilongjiang Academy of Agricultural Sciences, Heilongjiang 150086, China
| | - Hongyu Wen
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Wenbo Jiang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yongzhen Pang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xian Deng
- Key Laboratory of Seed Innovation and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaofeng Cao
- National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Junhui Zhou
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong 261000, China.
| | - Xianwei Song
- Key Laboratory of Seed Innovation and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Qikun Liu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China.
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24
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Masters LE, Tomaszewska P, Schwarzacher T, Hackel J, Zuntini AR, Heslop-Harrison P, Vorontsova MS. Phylogenomic analysis reveals five independently evolved African forage grass clades in the genus Urochloa. ANNALS OF BOTANY 2024; 133:725-742. [PMID: 38365451 PMCID: PMC11082517 DOI: 10.1093/aob/mcae022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/21/2024] [Indexed: 02/18/2024]
Abstract
BACKGROUND AND AIMS The grass genus Urochloa (Brachiaria) sensu lato includes forage crops that are important for beef and dairy industries in tropical and sub-tropical Africa, South America and Oceania/Australia. Economically important species include U. brizantha, U. decumbens, U. humidicola, U. mutica, U. arrecta, U. trichopus, U. mosambicensis and Megathyrsus maximus, all native to the African continent. Perennial growth habits, large, fast growing palatable leaves, intra- and interspecific morphological variability, apomictic reproductive systems and frequent polyploidy are widely shared within the genus. The combination of these traits probably favoured the selection for forage domestication and weediness, but trait emergence across Urochloa cannot be modelled, as a robust phylogenetic assessment of the genus has not been conducted. We aim to produce a phylogeny for Urochloa that includes all important forage species, and identify their closest wild relatives (crop wild relatives). Finally, we will use our phylogeny and available trait data to infer the ancestral states of important forage traits across Urochloa s.l. and model the evolution of forage syndromes across the genus. METHODS Using a target enrichment sequencing approach (Angiosperm 353), we inferred a species-level phylogeny for Urochloa s.l., encompassing 54 species (~40 % of the genus) and outgroups. Phylogenies were inferred using a multispecies coalescent model and maximum likelihood method. We determined the phylogenetic placement of agriculturally important species and identified their closest wild relatives, or crop wild relatives, based on well-supported monophyly. Further, we mapped key traits associated with Urochloa forage crops to the species tree and estimated ancestral states for forage traits along branch lengths for continuous traits and at ancestral nodes in discrete traits. KEY RESULTS Agricultural species belong to five independent clades, including U. brizantha and U. decumbens lying in a previously defined species complex. Crop wild relatives were identified for these clades supporting previous sub-generic groupings in Urochloa based on morphology. Using ancestral trait estimation models, we find that five morphological traits that correlate with forage potential (perennial growth habits, culm height, leaf size, a winged rachis and large seeds) independently evolved in forage clades. CONCLUSIONS Urochloa s.l. is a highly diverse genus that contains numerous species with agricultural potential, including crop wild relatives that are currently underexploited. All forage species and their crop wild relatives naturally occur on the African continent and their conservation across their native distributions is essential. Genomic and phenotypic diversity in forage clade species and their wild relatives need to be better assessed both to develop conservation strategies and to exploit the diversity in the genus for improved sustainability in Urochloa cultivar production.
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Affiliation(s)
- Lizo E Masters
- Department of Genetics and Genome Biology, Institute for Environmental Futures, University of Leicester, Leicester LE17RH, UK
- Accelerated Taxonomy/Trait Diversity and Function, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
| | - Paulina Tomaszewska
- Department of Genetics and Genome Biology, Institute for Environmental Futures, University of Leicester, Leicester LE17RH, UK
- Department of Genetics and Cell Physiology, University of Wroclaw, 50-328 Wroclaw, Poland
| | - Trude Schwarzacher
- Department of Genetics and Genome Biology, Institute for Environmental Futures, University of Leicester, Leicester LE17RH, UK
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Jan Hackel
- Accelerated Taxonomy/Trait Diversity and Function, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
- Department of Biology, University of Marburg, Karl-von-Frisch-Straße 8, 35043 Marburg, Germany
| | - Alexandre R Zuntini
- Accelerated Taxonomy/Trait Diversity and Function, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
| | - Pat Heslop-Harrison
- Department of Genetics and Genome Biology, Institute for Environmental Futures, University of Leicester, Leicester LE17RH, UK
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Maria S Vorontsova
- Accelerated Taxonomy/Trait Diversity and Function, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
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25
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Fan Z, Whitaker VM. Genomic signatures of strawberry domestication and diversification. THE PLANT CELL 2024; 36:1622-1636. [PMID: 38113879 PMCID: PMC11062436 DOI: 10.1093/plcell/koad314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/20/2023] [Accepted: 11/25/2023] [Indexed: 12/21/2023]
Abstract
Cultivated strawberry (Fragaria × ananassa) has a brief history of less than 300 yr, beginning with the hybridization of octoploids Fragaria chiloensis and Fragaria virginiana. Here we explored the genomic signatures of early domestication and subsequent diversification for different climates using whole-genome sequences of 289 wild, heirloom, and modern varieties from two major breeding programs in the United States. Four nonadmixed wild octoploid populations were identified, with recurrent introgression among the sympatric populations. The proportion of F. virginiana ancestry increased by 20% in modern varieties over initial hybrids, and the proportion of F. chiloensis subsp. pacifica rose from 0% to 3.4%. Effective population size rapidly declined during early breeding. Meanwhile, divergent selection for distinct environments reshaped wild allelic origins in 21 out of 28 chromosomes. Overlapping divergent selective sweeps in natural and domesticated populations revealed 16 convergent genomic signatures that may be important for climatic adaptation. Despite 20 breeding cycles since initial hybridization, more than half of loci underlying yield and fruit size are still not under artificial selection. These insights add clarity to the domestication and breeding history of what is now the most widely cultivated fruit in the world.
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Affiliation(s)
- Zhen Fan
- Horticultural Sciences Department, University of Florida, IFAS Gulf Coast Research and Education Center, Wimauma, FL 33597, USA
| | - Vance M Whitaker
- Horticultural Sciences Department, University of Florida, IFAS Gulf Coast Research and Education Center, Wimauma, FL 33597, USA
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Vondracek K, Altpeter F, Liu T, Lee S. Advances in genomics and genome editing for improving strawberry ( Fragaria ×ananassa). Front Genet 2024; 15:1382445. [PMID: 38706796 PMCID: PMC11066249 DOI: 10.3389/fgene.2024.1382445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 04/04/2024] [Indexed: 05/07/2024] Open
Abstract
The cultivated strawberry, Fragaria ×ananassa, is a recently domesticated fruit species of economic interest worldwide. As such, there is significant interest in continuous varietal improvement. Genomics-assisted improvement, including the use of DNA markers and genomic selection have facilitated significant improvements of numerous key traits during strawberry breeding. CRISPR/Cas-mediated genome editing allows targeted mutations and precision nucleotide substitutions in the target genome, revolutionizing functional genomics and crop improvement. Genome editing is beginning to gain traction in the more challenging polyploid crops, including allo-octoploid strawberry. The release of high-quality reference genomes and comprehensive subgenome-specific genotyping and gene expression profiling data in octoploid strawberry will lead to a surge in trait discovery and modification by using CRISPR/Cas. Genome editing has already been successfully applied for modification of several strawberry genes, including anthocyanin content, fruit firmness and tolerance to post-harvest disease. However, reports on many other important breeding characteristics associated with fruit quality and production are still lacking, indicating a need for streamlined genome editing approaches and tools in Fragaria ×ananassa. In this review, we present an overview of the latest advancements in knowledge and breeding efforts involving CRISPR/Cas genome editing for the enhancement of strawberry varieties. Furthermore, we explore potential applications of this technology for improving other Rosaceous plant species.
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Affiliation(s)
- Kaitlyn Vondracek
- Gulf Coast Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Wimauma, FL, United States
- University of Florida, Horticultural Sciences Department, Institute of Food and Agricultural Sciences, Gainesville, FL, United States
| | - Fredy Altpeter
- University of Florida, Agronomy Department, Institute of Food and Agricultural Sciences, Gainesville, FL, United States
| | - Tie Liu
- University of Florida, Horticultural Sciences Department, Institute of Food and Agricultural Sciences, Gainesville, FL, United States
| | - Seonghee Lee
- Gulf Coast Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Wimauma, FL, United States
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27
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Zhang T, Huang W, Zhang L, Li DZ, Qi J, Ma H. Phylogenomic profiles of whole-genome duplications in Poaceae and landscape of differential duplicate retention and losses among major Poaceae lineages. Nat Commun 2024; 15:3305. [PMID: 38632270 PMCID: PMC11024178 DOI: 10.1038/s41467-024-47428-9] [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: 07/13/2023] [Accepted: 04/02/2024] [Indexed: 04/19/2024] Open
Abstract
Poaceae members shared a whole-genome duplication called rho. However, little is known about the evolutionary pattern of the rho-derived duplicates among Poaceae lineages and implications in adaptive evolution. Here we present phylogenomic/phylotranscriptomic analyses of 363 grasses covering all 12 subfamilies and report nine previously unknown whole-genome duplications. Furthermore, duplications from a single whole-genome duplication were mapped to multiple nodes on the species phylogeny; a whole-genome duplication was likely shared by woody bamboos with possible gene flow from herbaceous bamboos; and recent paralogues of a tetraploid Oryza are implicated in tolerance of seawater submergence. Moreover, rho duplicates showing differential retention among subfamilies include those with functions in environmental adaptations or morphogenesis, including ACOT for aquatic environments (Oryzoideae), CK2β for cold responses (Pooideae), SPIRAL1 for rapid cell elongation (Bambusoideae), and PAI1 for drought/cold responses (Panicoideae). This study presents a Poaceae whole-genome duplication profile with evidence for multiple evolutionary mechanisms that contribute to gene retention and losses.
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Affiliation(s)
- Taikui Zhang
- Department of Biology, the Eberly College of Science, and the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, State College, PA, 16802, USA
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Weichen Huang
- Department of Biology, the Eberly College of Science, and the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, State College, PA, 16802, USA
| | - Lin Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Ji Qi
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China.
| | - Hong Ma
- Department of Biology, the Eberly College of Science, and the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, State College, PA, 16802, USA.
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28
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Salojärvi J, Rambani A, Yu Z, Guyot R, Strickler S, Lepelley M, Wang C, Rajaraman S, Rastas P, Zheng C, Muñoz DS, Meidanis J, Paschoal AR, Bawin Y, Krabbenhoft TJ, Wang ZQ, Fleck SJ, Aussel R, Bellanger L, Charpagne A, Fournier C, Kassam M, Lefebvre G, Métairon S, Moine D, Rigoreau M, Stolte J, Hamon P, Couturon E, Tranchant-Dubreuil C, Mukherjee M, Lan T, Engelhardt J, Stadler P, Correia De Lemos SM, Suzuki SI, Sumirat U, Wai CM, Dauchot N, Orozco-Arias S, Garavito A, Kiwuka C, Musoli P, Nalukenge A, Guichoux E, Reinout H, Smit M, Carretero-Paulet L, Filho OG, Braghini MT, Padilha L, Sera GH, Ruttink T, Henry R, Marraccini P, Van de Peer Y, Andrade A, Domingues D, Giuliano G, Mueller L, Pereira LF, Plaisance S, Poncet V, Rombauts S, Sankoff D, Albert VA, Crouzillat D, de Kochko A, Descombes P. The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars. Nat Genet 2024; 56:721-731. [PMID: 38622339 PMCID: PMC11018527 DOI: 10.1038/s41588-024-01695-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 02/23/2024] [Indexed: 04/17/2024]
Abstract
Coffea arabica, an allotetraploid hybrid of Coffea eugenioides and Coffea canephora, is the source of approximately 60% of coffee products worldwide, and its cultivated accessions have undergone several population bottlenecks. We present chromosome-level assemblies of a di-haploid C. arabica accession and modern representatives of its diploid progenitors, C. eugenioides and C. canephora. The three species exhibit largely conserved genome structures between diploid parents and descendant subgenomes, with no obvious global subgenome dominance. We find evidence for a founding polyploidy event 350,000-610,000 years ago, followed by several pre-domestication bottlenecks, resulting in narrow genetic variation. A split between wild accessions and cultivar progenitors occurred ~30.5 thousand years ago, followed by a period of migration between the two populations. Analysis of modern varieties, including lines historically introgressed with C. canephora, highlights their breeding histories and loci that may contribute to pathogen resistance, laying the groundwork for future genomics-based breeding of C. arabica.
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Affiliation(s)
- Jarkko Salojärvi
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland.
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.
| | - Aditi Rambani
- Boyce Thompson Institute, Cornell University, Ithaca, NY, USA
| | - Zhe Yu
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada
| | - Romain Guyot
- Institut de Recherche pour le Développement (IRD), Université de Montpellier, Montpellier, France
- Department of Electronics and Automation, Universidad Autónoma de Manizales, Manizales, Colombia
| | - Susan Strickler
- Boyce Thompson Institute, Cornell University, Ithaca, NY, USA
| | - Maud Lepelley
- Société des Produits Nestlé SA, Nestlé Research, Tours, France
| | - Cui Wang
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Sitaram Rajaraman
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Pasi Rastas
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Chunfang Zheng
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada
| | - Daniella Santos Muñoz
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada
| | - João Meidanis
- Institute of Computing, University of Campinas, Campinas, Brazil
| | - Alexandre Rossi Paschoal
- Department of Computer Science, The Federal University of Technology - Paraná (UTFPR), Cornélio Procópio, Brazil
| | - Yves Bawin
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | | | - Zhen Qin Wang
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
| | - Steven J Fleck
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
| | - Rudy Aussel
- Société des Produits Nestlé SA, Nestlé Research, Tours, France
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, Marseille, France
| | | | - Aline Charpagne
- Société des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland
| | - Coralie Fournier
- Société des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland
| | - Mohamed Kassam
- Société des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland
| | - Gregory Lefebvre
- Société des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland
| | - Sylviane Métairon
- Société des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland
| | - Déborah Moine
- Société des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland
| | - Michel Rigoreau
- Société des Produits Nestlé SA, Nestlé Research, Tours, France
| | - Jens Stolte
- Société des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland
| | - Perla Hamon
- Institut de Recherche pour le Développement (IRD), Université de Montpellier, Montpellier, France
| | - Emmanuel Couturon
- Institut de Recherche pour le Développement (IRD), Université de Montpellier, Montpellier, France
| | | | - Minakshi Mukherjee
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
| | - Tianying Lan
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
| | - Jan Engelhardt
- Department of Computer Science, University of Leipzig, Leipzig, Germany
| | - Peter Stadler
- Department of Computer Science, University of Leipzig, Leipzig, Germany
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
| | | | | | - Ucu Sumirat
- Indonesian Coffee and Cocoa Research Institute (ICCRI), Jember, Indonesia
| | - Ching Man Wai
- University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Nicolas Dauchot
- Research Unit in Plant Cellular and Molecular Biology, University of Namur, Namur, Belgium
| | - Simon Orozco-Arias
- Department of Electronics and Automation, Universidad Autónoma de Manizales, Manizales, Colombia
| | - Andrea Garavito
- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad de Caldas, Manizales, Colombia
| | - Catherine Kiwuka
- National Agricultural Research Organization (NARO), Entebbe, Uganda
| | - Pascal Musoli
- National Agricultural Research Organization (NARO), Entebbe, Uganda
| | - Anne Nalukenge
- National Agricultural Research Organization (NARO), Entebbe, Uganda
| | - Erwan Guichoux
- Biodiversité Gènes & Communautés, INRA, Bordeaux, France
| | | | - Martin Smit
- Hortus Botanicus Amsterdam, Amsterdam, the Netherlands
| | | | - Oliveiro Guerreiro Filho
- Instituto Agronômico (IAC) Centro de Café 'Alcides Carvalho', Fazenda Santa Elisa, Campinas, Brazil
| | - Masako Toma Braghini
- Instituto Agronômico (IAC) Centro de Café 'Alcides Carvalho', Fazenda Santa Elisa, Campinas, Brazil
| | - Lilian Padilha
- Embrapa Café/Instituto Agronômico (IAC) Centro de Café 'Alcides Carvalho', Fazenda Santa Elisa, Campinas, Brazil
| | | | - Tom Ruttink
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Queensland, Australia
| | - Pierre Marraccini
- CIRAD - UMR DIADE (IRD-CIRAD-Université de Montpellier) BP 64501, Montpellier, France
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Alan Andrade
- Embrapa Café/Inovacafé Laboratory of Molecular Genetics Campus da UFLA-MG, Lavras, Brazil
| | - Douglas Domingues
- Group of Genomics and Transcriptomes in Plants, São Paulo State University, UNESP, Rio Claro, Brazil
| | - Giovanni Giuliano
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development, ENEA Casaccia Research Center, Rome, Italy
| | - Lukas Mueller
- Boyce Thompson Institute, Cornell University, Ithaca, NY, USA
| | - Luiz Filipe Pereira
- Embrapa Café/Lab. Biotecnologia, Área de Melhoramento Genético, Londrina, Brazil
| | | | - Valerie Poncet
- Institut de Recherche pour le Développement (IRD), Université de Montpellier, Montpellier, France
| | - Stephane Rombauts
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - David Sankoff
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada
| | - Victor A Albert
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA.
| | | | - Alexandre de Kochko
- Institut de Recherche pour le Développement (IRD), Université de Montpellier, Montpellier, France.
| | - Patrick Descombes
- Société des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland.
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29
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Ma PF, Liu YL, Guo C, Jin G, Guo ZH, Mao L, Yang YZ, Niu LZ, Wang YJ, Clark LG, Kellogg EA, Xu ZC, Ye XY, Liu JX, Zhou MY, Luo Y, Yang Y, Soltis DE, Bennetzen JL, Soltis PS, Li DZ. Genome assemblies of 11 bamboo species highlight diversification induced by dynamic subgenome dominance. Nat Genet 2024; 56:710-720. [PMID: 38491323 PMCID: PMC11018529 DOI: 10.1038/s41588-024-01683-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 02/08/2024] [Indexed: 03/18/2024]
Abstract
Polyploidy (genome duplication) is a pivotal force in evolution. However, the interactions between parental genomes in a polyploid nucleus, frequently involving subgenome dominance, are poorly understood. Here we showcase analyses of a bamboo system (Poaceae: Bambusoideae) comprising a series of lineages from diploid (herbaceous) to tetraploid and hexaploid (woody), with 11 chromosome-level de novo genome assemblies and 476 transcriptome samples. We find that woody bamboo subgenomes exhibit stunning karyotype stability, with parallel subgenome dominance in the two tetraploid clades and a gradual shift of dominance in the hexaploid clade. Allopolyploidization and subgenome dominance have shaped the evolution of tree-like lignified culms, rapid growth and synchronous flowering characteristic of woody bamboos as large grasses. Our work provides insights into genome dominance in a remarkable polyploid system, including its dependence on genomic context and its ability to switch which subgenomes are dominant over evolutionary time.
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Affiliation(s)
- Peng-Fei Ma
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Yun-Long Liu
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Cen Guo
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Center for Integrative Conservation & Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, China
| | - Guihua Jin
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Zhen-Hua Guo
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Ling Mao
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Yi-Zhou Yang
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Liang-Zhong Niu
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Yu-Jiao Wang
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Lynn G Clark
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, 345 Bessey, Ames, IA, USA
| | | | - Zu-Chang Xu
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Xia-Ying Ye
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Jing-Xia Liu
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Meng-Yuan Zhou
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Yan Luo
- Center for Integrative Conservation & Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, China
| | - Yang Yang
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| | | | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - De-Zhu Li
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China.
- Key Laboratory for Plant Diversity and Biogeography in East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.
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30
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Fang C, Jiang N, Teresi SJ, Platts AE, Agarwal G, Niederhuth C, Edger PP, Jiang J. Dynamics of accessible chromatin regions and subgenome dominance in octoploid strawberry. Nat Commun 2024; 15:2491. [PMID: 38509076 PMCID: PMC10954716 DOI: 10.1038/s41467-024-46861-0] [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: 08/07/2023] [Accepted: 03/12/2024] [Indexed: 03/22/2024] Open
Abstract
Subgenome dominance has been reported in diverse allopolyploid species, where genes from one subgenome are preferentially retained and are more highly expressed than those from other subgenome(s). However, the molecular mechanisms responsible for subgenome dominance remain poorly understood. Here, we develop genome-wide map of accessible chromatin regions (ACRs) in cultivated strawberry (2n = 8x = 56, with A, B, C, D subgenomes). Each ACR is identified as an MNase hypersensitive site (MHS). We discover that the dominant subgenome A contains a greater number of total MHSs and MHS per gene than the submissive B/C/D subgenomes. Subgenome A suffers fewer losses of MHS-related DNA sequences and fewer MHS fragmentations caused by insertions of transposable elements. We also discover that genes and MHSs related to stress response have been preferentially retained in subgenome A. We conclude that preservation of genes and their cognate ACRs, especially those related to stress responses, play a major role in the establishment of subgenome dominance in octoploid strawberry.
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Affiliation(s)
- Chao Fang
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Ning Jiang
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- Michigan State University AgBioResearch, East Lansing, MI, 48824, USA
- Genetics and Genome Sciences Program, Michigan State University, East Lansing, MI, 48824, USA
| | - Scott J Teresi
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- Genetics and Genome Sciences Program, Michigan State University, East Lansing, MI, 48824, USA
| | - Adrian E Platts
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Gaurav Agarwal
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Chad Niederhuth
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- Michigan State University AgBioResearch, East Lansing, MI, 48824, USA
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA.
- Michigan State University AgBioResearch, East Lansing, MI, 48824, USA.
- Genetics and Genome Sciences Program, Michigan State University, East Lansing, MI, 48824, USA.
| | - Jiming Jiang
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA.
- Michigan State University AgBioResearch, East Lansing, MI, 48824, USA.
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31
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Martínez-Rivas FJ, Fernie AR. Metabolomics to understand metabolic regulation underpinning fruit ripening, development, and quality. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1726-1740. [PMID: 37864494 PMCID: PMC10938048 DOI: 10.1093/jxb/erad384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 09/28/2023] [Indexed: 10/23/2023]
Abstract
Classically fruit ripening and development was studied using genetic approaches, with understanding of metabolic changes that occurred in concert largely focused on a handful of metabolites including sugars, organic acids, cell wall components, and phytohormones. The advent and widespread application of metabolomics has, however, led to far greater understanding of metabolic components that play a crucial role not only in this process but also in influencing the organoleptic and nutritive properties of the fruits. Here we review how the study of natural variation, mutants, transgenics, and gene-edited fruits has led to a considerable increase in our understanding of these aspects. We focus on fleshy fruits such as tomato but also review berries, receptacle fruits, and stone-bearing fruits. Finally, we offer a perspective as to how comparative analyses and machine learning will likely further improve our comprehension of the functional importance of various metabolites in the future.
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Affiliation(s)
- Félix Juan Martínez-Rivas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Edificio Severo Ochoa, Campus de Rabanales, E-14014, Córdoba, Spain
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
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Feldmann MJ, Pincot DDA, Vachev MV, Famula RA, Cole GS, Knapp SJ. Accelerating genetic gains for quantitative resistance to verticillium wilt through predictive breeding in strawberry. THE PLANT GENOME 2024; 17:e20405. [PMID: 37961831 DOI: 10.1002/tpg2.20405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 10/12/2023] [Indexed: 11/15/2023]
Abstract
Verticillium wilt (VW), a devastating vascular wilt disease of strawberry (Fragaria × $\times$ ananassa), has caused economic losses for nearly a century. This disease is caused by the soil-borne pathogen Verticillium dahliae, which occurs nearly worldwide and causes disease in numerous agriculturally important plants. The development of VW-resistant cultivars is critically important for the sustainability of strawberry production. We previously showed that a preponderance of the genetic resources (asexually propagated hybrid individuals) preserved in public germplasm collections were moderately to highly susceptible and that genetic gains for increased resistance to VW have been negligible over the last 60 years. To more fully understand the challenges associated with breeding for increased quantitative resistance to this pathogen, we developed and phenotyped a training population of hybrids (n = 564 $n = 564$ ) among elite parents with a wide range of resistance phenotypes. When these data were combined with training data from a population of elite and exotic hybrids (n = 386 $n = 386$ ), genomic prediction accuracies of 0.47-0.48 were achieved and were predicted to explain 70%-75% of the additive genetic variance for resistance. We concluded that breeding values for resistance to VW can be predicted with sufficient accuracy for effective genomic selection with routine updating of training populations.
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Affiliation(s)
- Mitchell J Feldmann
- Department of Plant Sciences, University of California Davis, Davis, California, USA
| | - Dominique D A Pincot
- Department of Plant Sciences, University of California Davis, Davis, California, USA
| | - Mishi V Vachev
- Department of Plant Sciences, University of California Davis, Davis, California, USA
| | - Randi A Famula
- Department of Plant Sciences, University of California Davis, Davis, California, USA
| | - Glenn S Cole
- Department of Plant Sciences, University of California Davis, Davis, California, USA
| | - Steven J Knapp
- Department of Plant Sciences, University of California Davis, Davis, California, USA
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33
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Runemark A, Moore EC, Larson EL. Hybridization and gene expression: Beyond differentially expressed genes. Mol Ecol 2024:e17303. [PMID: 38411307 DOI: 10.1111/mec.17303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 02/06/2024] [Accepted: 02/15/2024] [Indexed: 02/28/2024]
Abstract
Gene expression has a key role in reproductive isolation, and studies of hybrid gene expression have identified mechanisms causing hybrid sterility. Here, we review the evidence for altered gene expression following hybridization and outline the mechanisms shown to contribute to altered gene expression in hybrids. Transgressive gene expression, transcending that of both parental species, is pervasive in early generation sterile hybrids, but also frequently observed in viable, fertile hybrids. We highlight studies showing that hybridization can result in transgressive gene expression, also in established hybrid lineages or species. Such extreme patterns of gene expression in stabilized hybrid taxa suggest that altered hybrid gene expression may result in hybridization-derived evolutionary novelty. We also conclude that while patterns of misexpression in hybrids are well documented, the understanding of the mechanisms causing misexpression is lagging. We argue that jointly assessing differences in cell composition and cell-specific changes in gene expression in hybrids, in addition to assessing changes in chromatin and methylation, will significantly advance our understanding of the basis of altered gene expression. Moreover, uncovering to what extent evolution of gene expression results in altered expression for individual genes, or entire networks of genes, will advance our understanding of how selection moulds gene expression. Finally, we argue that jointly studying the dual roles of altered hybrid gene expression, serving both as a mechanism for reproductive isolation and as a substrate for hybrid ecological adaptation, will lead to significant advances in our understanding of the evolution of gene expression.
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Affiliation(s)
- Anna Runemark
- Department of Biology, Lund University, Lund, Sweden
| | - Emily C Moore
- Department of Biological Sciences, University of Denver, Denver, Colorado, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Erica L Larson
- Department of Biological Sciences, University of Denver, Denver, Colorado, USA
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Meca E, Díez CM, Gaut BS. Modeling transposable elements dynamics during polyploidization in plants. J Theor Biol 2024; 579:111701. [PMID: 38128754 DOI: 10.1016/j.jtbi.2023.111701] [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: 02/27/2023] [Revised: 11/24/2023] [Accepted: 12/08/2023] [Indexed: 12/23/2023]
Abstract
In this work we study the proliferation of transposable elements (TEs) and the epigenetic response of plants during the process of polyploidization. Through a deterministic model, expanding on our previous work on TE proliferation under epigenetic regulation, we study the long-term TE distribution and TE stability in the subgenomes of both autopolyploids and allopolyploids. We also explore different small-interfering RNA (siRNA) action modes on the subgenomes, including a model where siRNAs are not directed to specific genomes and one where siRNAs are directed - i.e. more active - in subgenomes with higher TE loads. In the autopolyploid case, we find long-term stable equilbria that tend to equilibrate the number of active TEs between subgenomes. In the allopolyploid case, directed siRNA action is fundamental to avoid a "winner takes all" outcome of the competition between the TEs in the different subgenomes. We also show that decaying oscillations in the number of TEs occur naturally in all cases, perhaps explaining some of the observed features of 'genomic shock' after hybridization events, and that the balance in the dynamics of the different types of siRNA is determinant for the synchronization of these oscillations.
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Affiliation(s)
- Esteban Meca
- Departamento de Física Aplicada, Radiología y Medicina Física, Universidad de Córdoba, Campus Universitario de Rabanales, Edificio Albert Einstein (C2), 14014 Córdoba, Spain.
| | - Concepción M Díez
- Departamento de Agronomía, Universidad de Córdoba, Campus Universitario de Rabanales, Edificio Celestino Mutis (C4), 14014 Córdoba, Spain.
| | - Brandon S Gaut
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697-3875, United States of America.
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Li H, Liu Y, Fan P, Dai Z, Hao J, Duan W, Liang Z, Wang Y. The Genome of Vitis zhejiang-adstricta Strengthens the Protection and Utilization of the Endangered Ancient Grape Endemic to China. PLANT & CELL PHYSIOLOGY 2024; 65:216-227. [PMID: 37930871 PMCID: PMC10873524 DOI: 10.1093/pcp/pcad140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 11/08/2023]
Abstract
Vitis zhejiang-adstricta (V. zhejiang-adstricta) is one of the most important and endangered wild grapes. It is a national key protected wild, rare and endangered ancient grape endemic to China and used as a candidate material for resistance breeding owing to its excellent significant disease resistance. Here, we present a high-quality chromosome-level assembly of V. zhejiang-adstricta (IB-VB-01), comprising 506.66 Mb assembled into 19 pseudo-chromosomes. The contig N50 length is 3.91 Mb with 31,196 annotated protein-coding genes. Comparative genome and evolutionary analyses illustrated that V. zhejiang-adstricta has a specific position in the evolution of East Asian Vitis and shared a common ancestor with Vitis vinifera during the divergence of the two species about 10.42 (between 9.34 and 11.12) Mya. The expanded gene families compared with those in plants were related to disease resistance, and constructed gene families were related to plant growth and primary metabolism. With the analysis of gene family expansion and contraction, the evolution of environmental adaptability and especially the NBS-LRR gene family of V. zhejiang-adstricta was elucidated based on the pathways of resistance genes (R genes), unique genes and structural variations. The near-complete and accurate diploid V. zhejiang-adstricta reference genome obtained herein serves as an important complement to wild grape genomes and will provide valuable genomic resources for investigating the genomic architecture of V. zhejiang-adstricta as well as for improving disease resistance breeding strategies in grape.
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Affiliation(s)
- Huayang Li
- Beijing Key Laboratory of Grape Science and Enology, CAS Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, China
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
- China National Botanical Garden, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
- University of Chinese Academy of Sciences, 19 Yuquan Rd, Beijing 100049, PR China
| | - Yongbo Liu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, 8 Dayangfang, Beijing 100012, PR China
| | - Peige Fan
- Beijing Key Laboratory of Grape Science and Enology, CAS Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, China
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
- China National Botanical Garden, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
| | - Zhanwu Dai
- Beijing Key Laboratory of Grape Science and Enology, CAS Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, China
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
- China National Botanical Garden, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
| | - Jiachen Hao
- China National Botanical Garden, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
| | - Wei Duan
- Beijing Key Laboratory of Grape Science and Enology, CAS Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, China
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
- China National Botanical Garden, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
| | - Zhenchang Liang
- Beijing Key Laboratory of Grape Science and Enology, CAS Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, China
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
- China National Botanical Garden, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
| | - Yi Wang
- Beijing Key Laboratory of Grape Science and Enology, CAS Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, China
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
- China National Botanical Garden, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
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36
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Zhang F, Wang Y, Lin Y, Wang H, Wu Y, Ren W, Wang L, Yang Y, Zheng P, Wang S, Yue J, Liu Y. Haplotype-resolved genome assembly provides insights into evolutionary history of the Actinidia arguta tetraploid. MOLECULAR HORTICULTURE 2024; 4:4. [PMID: 38317251 PMCID: PMC10845759 DOI: 10.1186/s43897-024-00083-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 01/23/2024] [Indexed: 02/07/2024]
Abstract
Actinidia arguta, known as hardy kiwifruit, is a widely cultivated species with distinct botanical characteristics such as small and smooth-fruited, rich in beneficial nutrients, rapid softening and tolerant to extremely low temperatures. It contains the most diverse ploidy types, including diploid, tetraploid, hexaploid, octoploid, and decaploid. Here we report a haplotype-resolved tetraploid genome (A. arguta cv. 'Longcheng No.2') containing four haplotypes, each with 40,859, 41,377, 39,833 and 39,222 protein-coding genes. We described the phased genome structure, synteny, and evolutionary analyses to identify and date possible WGD events. Ks calculations for both allelic and paralogous genes pairs throughout the assembled haplotypic individuals showed its tetraploidization is estimated to have formed ~ 1.03 Mya following Ad-α event occurred ~ 18.7 Mya. Detailed annotations of NBS-LRRs or CBFs highlight the importance of genetic variations coming about after polyploidization in underpinning ability of immune responses or environmental adaptability. WGCNA analysis of postharvest quality indicators in combination with transcriptome revealed several transcription factors were involved in regulating ripening kiwi berry texture. Taking together, the assembly of an A. arguta tetraploid genome provides valuable resources in deciphering complex genome structure and facilitating functional genomics studies and genetic improvement for kiwifruit and other crops.
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Affiliation(s)
- Feng Zhang
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Yingzhen Wang
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
- School of Forestry Science and Technology, Lishui Vocational and Technical College, Lishui, 323000, China
| | - Yunzhi Lin
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610064, China
| | - Hongtao Wang
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Ying Wu
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Wangmei Ren
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Lihuan Wang
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Ying Yang
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Pengpeng Zheng
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Songhu Wang
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Junyang Yue
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, China.
| | - Yongsheng Liu
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, China.
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610064, China.
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37
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Yan M, Li M, Wang Y, Wang X, Moeinzadeh MH, Quispe-Huamanquispe DG, Fan W, Fang Y, Wang Y, Nie H, Wang Z, Tanaka A, Heider B, Kreuze JF, Gheysen G, Wang H, Vingron M, Bock R, Yang J. Haplotype-based phylogenetic analysis and population genomics uncover the origin and domestication of sweetpotato. MOLECULAR PLANT 2024; 17:277-296. [PMID: 38155570 DOI: 10.1016/j.molp.2023.12.019] [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: 06/07/2023] [Revised: 11/10/2023] [Accepted: 12/25/2023] [Indexed: 12/30/2023]
Abstract
The hexaploid sweetpotato (Ipomoea batatas) is one of the most important root crops worldwide. However, its genetic origin remains controversial, and its domestication history remains unknown. In this study, we used a range of genetic evidence and a newly developed haplotype-based phylogenetic analysis to identify two probable progenitors of sweetpotato. The diploid progenitor was likely closely related to Ipomoea aequatoriensis and contributed the B1 subgenome, IbT-DNA2, and the lineage 1 type of chloroplast genome to sweetpotato. The tetraploid progenitor of sweetpotato was most likely I. batatas 4x, which donated the B2 subgenome, IbT-DNA1, and the lineage 2 type of chloroplast genome. Sweetpotato most likely originated from reciprocal crosses between the diploid and tetraploid progenitors, followed by a subsequent whole-genome duplication. In addition, we detected biased gene exchanges between the subgenomes; the rate of B1 to B2 subgenome conversions was nearly three times higher than that of B2 to B1 subgenome conversions. Our analyses revealed that genes involved in storage root formation, maintenance of genome stability, biotic resistance, sugar transport, and potassium uptake were selected during the speciation and domestication of sweetpotato. This study sheds light on the evolution of sweetpotato and paves the way for improvement of this crop.
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Affiliation(s)
- Mengxiao Yan
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
| | - Ming Li
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China; Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610061, China
| | - Yunze Wang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Xinyi Wang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - M-Hossein Moeinzadeh
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | | | - Weijuan Fan
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
| | - Yijie Fang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Yuqin Wang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Haozhen Nie
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
| | - Zhangying Wang
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crop Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Aiko Tanaka
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan
| | | | | | | | - Hongxia Wang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; CAS Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China.
| | - Martin Vingron
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany.
| | - Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
| | - Jun Yang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; CAS Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China.
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38
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Hormazábal-Abarza F, Bustos D, Rodríguez-Arriaza F, Sáez D, Urra G, Parra-Palma C, Méndez-Yáñez Á, Ramos P, Morales-Quintana L. Structural and transcriptional characterization of pyruvate decarboxylase (PDC) gene family during strawberry fruit ripening process. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 207:108417. [PMID: 38354527 DOI: 10.1016/j.plaphy.2024.108417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 01/17/2024] [Accepted: 02/01/2024] [Indexed: 02/16/2024]
Abstract
Strawberry is one of the most popular fruits in the world, because their high fruit quality, especially with respect to the combination of aroma, flavor, color, and nutritional compounds. Pyruvate decarboxylase (PDC) is the first of two enzymes specifically required for ethanolic fermentation and catalyzes the decarboxylation of pyruvate to yield acetaldehyde and CO2. The ethanol, an important alcohol which acts as a precursor for the ester and other alcohols formation in strawberry, is produced by the PDC. The objective was found all different PDCs genes present in the strawberry genome and investigate PDC gene expression and ligand-protein interactions in strawberry fruit. Volatile organic compounds were evaluated during the development of the fruit. After this, eight FaPDC were identified with four genes that increase the relative expression during fruit ripening process. Molecular dynamics simulations were performed to analyze the behavior of Pyr and TPP ligands within the catalytic and regulatory sites of the PDC proteins. Results indicated that energy-restrained simulations exhibited minor fluctuations in ligand-protein interactions, while unrestrained simulations revealed crucial insights into ligand affinity. TPP consistently displayed strong interactions with the catalytic site, emphasizing its pivotal role in enzymatic activity. However, FaPDC6 and FaPDC9 exhibited decreased pyruvate affinity initially, suggesting unique binding characteristics requiring further investigation. Finally, the present study contributes significantly to understanding PDC gene expression and the intricate molecular dynamics underlying strawberry fruit ripening, shedding light on potential targets for further research in this critical biological pathway.
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Affiliation(s)
- Francisca Hormazábal-Abarza
- Multidisciplinary Agroindustry Research Laboratory, Instituto de Ciencias Biomédicas, Facultad de Ciencias de La Salud, Universidad Autónoma de Chile, Cinco Poniente #1670 Talca, Región Del Maule, Chile
| | - Daniel Bustos
- Laboratorio de Bioinformática y Química Computacional, Departamento de Medicina Traslacional, Facultad de Medicina, Universidad Católica Del Maule, Talca, 3480094, Chile; Vicerrectoría de Investigación y Postgrado, Universidad Católica Del Maule, Talca, 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, Región Del Maule, 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, Región Del Maule, Chile; Programa de Doctorado en Ciencias Biomédicas, Instituto de Ciencias Biomédicas, Facultad de Ciencias de La Salud, Universidad Autónoma de Chile, Chile
| | - Gabriela Urra
- Vicerrectoría de Investigación y Postgrado, Universidad Católica Del Maule, Talca, Chile
| | - Carolina Parra-Palma
- Multidisciplinary Agroindustry Research Laboratory, Instituto de Ciencias Biomédicas, Facultad de Ciencias de La Salud, Universidad Autónoma de Chile, Cinco Poniente #1670 Talca, Región Del Maule, Chile
| | - Ángela Méndez-Yáñez
- Multidisciplinary Agroindustry Research Laboratory, Instituto de Ciencias Biomédicas, Facultad de Ciencias de La Salud, Universidad Autónoma de Chile, Cinco Poniente #1670 Talca, Región Del Maule, Chile
| | - Patricio Ramos
- Vicerrectoría de Investigación y Postgrado, Universidad Católica Del Maule, Talca, Chile; Plant Microorganism Interaction Laboratory, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, 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, Región Del Maule, Chile.
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Yang J, Song J, Jeong BR. Flowering and Runnering of Seasonal Strawberry under Different Photoperiods Are Affected by Intensity of Supplemental or Night-Interrupting Blue Light. PLANTS (BASEL, SWITZERLAND) 2024; 13:375. [PMID: 38337908 PMCID: PMC10857185 DOI: 10.3390/plants13030375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024]
Abstract
The strawberry (Fragaria × ananassa Duch.) "Sulhyang" is a typical seasonal flowering (SF) strawberry that produces flower buds in day lengths shorter than a critical limit (variable, but often defined as <12 h). There is a trade-off between photoperiod-controlled flowering and gibberellin (GA) signaling pathway-mediated runnering. Some related genes (such as CO, FT1, SOC1, and TFL1) participating in light signaling and circadian rhythm in plants are altered under blue light (BL). Sugars for flowering and runnering are mainly produced by photosynthetic carbon assimilation. The intensity of light could affect photosynthesis, thereby regulating flowering and runnering. Here, we investigated the effect of the intensity of supplemental blue light (S-BL) or night-interrupting blue light (NI-BL) in photoperiodic flowering and runnering regulation by applying 4 h of S-BL or NI-BL with either 0, 10, 20, 30, or 40 μmol·m-2·s-1 photosynthetic photon flux density (PPFD) in a 10 h short-day (SD10) (SD10 + S-BL4 or + NI-BL4 (0, 10, 20, 30, or 40)) or 14 h long-day (LD14) conditions (LD14 + S-BL4 or + NI-BL4 (0, 10, 20, 30, or 40)). Approximately 45 days after the photoperiodic light treatment, generally, whether S-BL or NI-BL, BL (20) was the most promotive in runnering, leading to more runners in both the LD and SD conditions. For flowering, except the treatment LD14 + S-BL, BL (20) was still the key light, either from BL (20) or BL (40), promoting flowering, especially when BL acted as the night-interrupting light, regardless of the photoperiod. At the harvest stage, larger numbers of inflorescences and runners were observed in the LD14 + NI-BL4 treatment, and the most were observed in the LD14 + NI-BL (20). Moreover, the SD10 + NI-BL4 was slightly inferior to the LD14 + NI-BL4 in increasing the numbers of inflorescences and runners, but it caused earlier flowering. Additionally, the circadian rhythm expression of flowering-related genes was affected differently by the S-BL and NI-BL. After the application of BL in LD conditions, the expression of an LD-specific floral activator FaFT1 was stimulated, while that of a flowering suppressor FaTFL1 was inhibited, resetting the balance of expression between these two opposite flowering regulators. The SD runnering was caused by BL in non-runnering SD conditions associated with the stimulation of two key genes that regulate runner formation in the GA pathway, FaGRAS32 and FaGA20ox4. In addition, the positive effects of BL on enhancing photosynthesis and carbohydrate production also provided an abundant energy supply for the flowering and runnering processes.
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Affiliation(s)
- Jingli Yang
- Shandong Provincial University Laboratory for Protected Horticulture, Weifang University of Science and Technology, Shouguang 262700, China or (J.Y.); (J.S.)
- Department of Horticulture, Division of Applied Life Science (BK21 Four), Graduate School, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Jinnan Song
- Shandong Provincial University Laboratory for Protected Horticulture, Weifang University of Science and Technology, Shouguang 262700, China or (J.Y.); (J.S.)
- Department of Horticulture, Division of Applied Life Science (BK21 Four), Graduate School, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Byoung Ryong Jeong
- Department of Horticulture, Division of Applied Life Science (BK21 Four), Graduate School, Gyeongsang National University, Jinju 52828, Republic of Korea
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea
- Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea
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40
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Xiao Y, Xi Z, Wang F, Wang J. Genomic asymmetric epigenetic modification of transposable elements is involved in gene expression regulation of allopolyploid Brassica napus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:226-241. [PMID: 37797206 DOI: 10.1111/tpj.16491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 09/20/2023] [Accepted: 09/25/2023] [Indexed: 10/07/2023]
Abstract
Polyploids are common and have a wide geographical distribution and environmental adaptability. Allopolyploidy may lead to the activation of transposable elements (TE). However, the mechanism of epigenetic modification of TEs in the establishment and evolution of allopolyploids remains to be explored. We focused on the TEs of model allopolyploid Brassica napus (An An Cn Cn ), exploring the TE characteristics of the genome, epigenetic modifications of TEs during allopolyploidization, and regulation of gene expression by TE methylation. In B. napus, approximately 50% of the genome was composed of TEs. TEs increased with proximity to genes, especially DNA transposons. TE methylation levels were negatively correlated with gene expression, and changes in TE methylation levels were able to regulate the expression of neighboring genes related to responses to light intensity and stress, which promoted powerful adaptation of allopolyploids to new environments. TEs can be synergistically regulated by RNA-directed DNA methylation pathways and histone modifications. The epigenetic modification levels of TEs tended to be similar to those of the diploid parents during the genome evolution of B. napus. The TEs of the An subgenome were more likely to be modified, and the imbalance in TE number and epigenetic modification level in the An and Cn subgenomes may lead to the establishment of subgenome dominance. Our study analyzed the characteristics of TE location, DNA methylation, siRNA, and histone modification in B. napus and highlighted the importance of TE epigenetic modifications during the allopolyploidy process, providing support for revealing the mechanism of allopolyploid formation and evolution.
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Affiliation(s)
- Yafang Xiao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zengde Xi
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Fei Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jianbo Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
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Song Y, Peng Y, Liu L, Li G, Zhao X, Wang X, Cao S, Muyle A, Zhou Y, Zhou H. Phased gap-free genome assembly of octoploid cultivated strawberry illustrates the genetic and epigenetic divergence among subgenomes. HORTICULTURE RESEARCH 2024; 11:uhad252. [PMID: 38269295 PMCID: PMC10807706 DOI: 10.1093/hr/uhad252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 11/18/2023] [Indexed: 01/26/2024]
Abstract
The genetic and epigenetic mechanisms underlying the coexistence and coordination of the four diverged subgenomes (ABCD) in octoploid strawberries (Fragaria × ananassa) remains poorly understood. In this study, we have assembled a haplotype-phased gap-free octoploid genome for the strawberry, which allowed us to uncover the sequence, structure, and epigenetic divergences among the subgenomes. The diploid progenitors of the octoploid strawberry, apart from subgenome A (Fragaria vesca), have been a subject of public controversy. Phylogenomic analyses revealed a close relationship between diploid species Fragaria iinumae and subgenomes B, C, and D. Subgenome A, closely related to F. vesca, retains the highest number of genes, exhibits the lowest content of transposable elements (TEs), experiences the strongest purifying selection, shows the lowest DNA methylation levels, and displays the highest expression level compared to the other three subgenomes. Transcriptome and DNA methylome analyses revealed that subgenome A-biased genes were enriched in fruit development biological processes. In contrast, although subgenomes B, C, and D contain equivalent amounts of repetitive sequences, they exhibit diverged methylation levels, particularly for TEs located near genes. Taken together, our findings provide valuable insights into the evolutionary patterns of subgenome structure, divergence and epigenetic dynamics in octoploid strawberries, which could be utilized in strawberry genetics and breeding research.
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Affiliation(s)
- Yanhong Song
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Yanling Peng
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Lifeng Liu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Gang Li
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Xia Zhao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Xu Wang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Shuo Cao
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Aline Muyle
- CEFE, University of Montpellier, CNRS, EPHE, IRD, Montpellier 34000, France
| | - Yongfeng Zhou
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- National Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 570000, China
| | - Houcheng Zhou
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
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42
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An H, Pires JC, Conant GC. Gene expression bias between the subgenomes of allopolyploid hybrids is an emergent property of the kinetics of expression. PLoS Comput Biol 2024; 20:e1011803. [PMID: 38227592 PMCID: PMC10817154 DOI: 10.1371/journal.pcbi.1011803] [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: 08/17/2023] [Revised: 01/26/2024] [Accepted: 01/06/2024] [Indexed: 01/18/2024] Open
Abstract
Hybridization coupled to polyploidy, or allopolyploidy, has dramatically shaped the evolution of flowering plants, teleost fishes, and other lineages. Studies of recently formed allopolyploid plants have shown that the two subgenomes that merged to form that new allopolyploid do not generally express their genes equally. Instead, one of the two subgenomes expresses its paralogs more highly on average. Meanwhile, older allopolyploidy events tend to show biases in duplicate losses, with one of the two subgenomes retaining more genes than the other. Since reduced expression is a pathway to duplicate loss, understanding the origins of expression biases may help explain the origins of biased losses. Because we expect gene expression levels to experience stabilizing selection, our conceptual frameworks for how allopolyploid organisms form tend to assume that the new allopolyploid will show balanced expression between its subgenomes. It is then necessary to invoke phenomena such as differences in the suppression of repetitive elements to explain the observed expression imbalances. Here we show that, even for phenotypically identical diploid progenitors, the inherent kinetics of gene expression give rise to biases between the expression levels of the progenitor genes in the hybrid. Some of these biases are expected to be gene-specific and not give rise to global differences in progenitor gene expression. However, particularly in the case of allopolyploids formed from progenitors with different genome sizes, global expression biases favoring one subgenome are expected immediately on formation. Hence, expression biases are arguably the expectation upon allopolyploid formation rather than a phenomenon needing explanation. In the future, a deeper understanding of the kinetics of allopolyploidy may allow us to better understand both biases in duplicate losses and hybrid vigor.
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Affiliation(s)
- Hong An
- MU Bioinformatics and Analytics Core, University of Missouri, Columbia, Missouri, United States of America
| | - J. Chris Pires
- Department of Soil and Crop Science, Colorado State University, Fort Collins, Colorado, United States of America
| | - Gavin C. Conant
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, United States of America
- Program in Genetics, North Carolina State University, Raleigh, North Carolina, United States of America
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
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43
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Xu MRX, Liao ZY, Brock JR, Du K, Li GY, Chen ZQ, Wang YH, Gao ZN, Agarwal G, Wei KHC, Shao F, Pang S, Platts AE, van de Velde J, Lin HM, Teresi SJ, Bird K, Niederhuth CE, Xu JG, Yu GH, Yang JY, Dai SF, Nelson A, Braasch I, Zhang XG, Schartl M, Edger PP, Han MJ, Zhang HH. Maternal dominance contributes to subgenome differentiation in allopolyploid fishes. Nat Commun 2023; 14:8357. [PMID: 38102128 PMCID: PMC10724154 DOI: 10.1038/s41467-023-43740-y] [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: 02/16/2023] [Accepted: 11/17/2023] [Indexed: 12/17/2023] Open
Abstract
Teleost fishes, which are the largest and most diverse group of living vertebrates, have a rich history of ancient and recent polyploidy. Previous studies of allotetraploid common carp and goldfish (cyprinids) reported a dominant subgenome, which is more expressed and exhibits biased gene retention. However, the underlying mechanisms contributing to observed 'subgenome dominance' remains poorly understood. Here we report high-quality genomes of twenty-one cyprinids to investigate the origin and subsequent subgenome evolution patterns following three independent allopolyploidy events. We identify the closest extant relatives of the diploid progenitor species, investigate genetic and epigenetic differences among subgenomes, and conclude that observed subgenome dominance patterns are likely due to a combination of maternal dominance and transposable element densities in each polyploid. These findings provide an important foundation to understanding subgenome dominance patterns observed in teleost fishes, and ultimately the role of polyploidy in contributing to evolutionary innovations.
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Affiliation(s)
- Min-Rui-Xuan Xu
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Zhen-Yang Liao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jordan R Brock
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
| | - Kang Du
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, USA
| | - Guo-Yin Li
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
| | | | - Ying-Hao Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhong-Nan Gao
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Gaurav Agarwal
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Kevin H-C Wei
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Feng Shao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University, School of Life Sciences, Chongqing, China
| | | | - Adrian E Platts
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
| | - Jozefien van de Velde
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Hong-Min Lin
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Scott J Teresi
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
| | - Kevin Bird
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
| | - Chad E Niederhuth
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Jin-Gen Xu
- Jiujiang Academy of Agricultural Sciences, Jiujiang, China
| | - Guo-Hua Yu
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Jian-Yuan Yang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Si-Fa Dai
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | | | - Ingo Braasch
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
| | - Xiao-Gu Zhang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China.
| | - Manfred Schartl
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, USA.
- Developmental Biochemistry, Biocenter, University of Würzburg, Würzburg, Bayern, Germany.
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, USA.
| | - Min-Jin Han
- State Key Laboratory of Resource Insects, Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry, Southwest University, Chongqing, China.
| | - Hua-Hao Zhang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China.
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44
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Koorevaar T, Willemsen JH, Visser RGF, Arens P, Maliepaard C. Construction of a strawberry breeding core collection to capture and exploit genetic variation. BMC Genomics 2023; 24:740. [PMID: 38053072 DOI: 10.1186/s12864-023-09824-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 11/21/2023] [Indexed: 12/07/2023] Open
Abstract
BACKGROUND Genetic diversity is crucial for the success of plant breeding programs and core collections are important resources to capture this diversity. Many core collections have already been constructed by gene banks, whose main goal is to obtain a panel of a limited number of genotypes to simplify management practices and to improve shareability while retaining as much diversity as possible. However, as gene banks have a different composition and goal than plant breeding programs, constructing a core collection for a plant breeding program should consider different aspects. RESULTS In this study, we present a novel approach for constructing a core collection by integrating both genomic and pedigree information to maximize the representation of the breeding germplasm in a minimum subset of genotypes while accounting for future genetic variation within a strawberry breeding program. Our stepwise approach starts with selecting the most important crossing parents of advanced selections and genotypes included for specific traits, to represent also future genetic variation. We then use pedigree-genomic-based relationship coefficients combined with the 'accession to nearest entry' criterion to complement the core collection and maximize its representativeness of the current breeding program. Combined pedigree-genomic-based relationship coefficients allow for accurate relationship estimation without the need to genotype every individual in the breeding program. CONCLUSIONS This stepwise construction of a core collection in a strawberry breeding program can be applied in other plant breeding programs to construct core collections for various purposes.
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Affiliation(s)
- T Koorevaar
- Wageningen University and Research Plant Breeding, Wageningen, The Netherlands.
- Fresh Forward Breeding B.V., Huissen, The Netherlands.
| | - J H Willemsen
- Fresh Forward Breeding B.V., Huissen, The Netherlands
| | - R G F Visser
- Wageningen University and Research Plant Breeding, Wageningen, The Netherlands
| | - P Arens
- Wageningen University and Research Plant Breeding, Wageningen, The Netherlands
| | - C Maliepaard
- Wageningen University and Research Plant Breeding, Wageningen, The Netherlands
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45
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Zheng S, Cai J, Huang P, Wang Y, Yang Z, Yu Y. Determination of volatile profiles of woodland strawberry (Fragaria vesca) during fruit maturation by HS-SPME GC-MS. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:7455-7468. [PMID: 37403783 DOI: 10.1002/jsfa.12827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 06/03/2023] [Accepted: 07/05/2023] [Indexed: 07/06/2023]
Abstract
BACKGROUND Aroma is an important agronomic trait for strawberries, and the improvement of fruit flavor is a key goal in current strawberry breeding programs. Fragaria vesca (also known as woodland strawberry) has become an excellent model plant with exquisite flavor, a small genome size and a short life cycle. Thus, the comprehensive identification of fruit volatiles and their accumulation pattern of F. vesca strawberries are very important and necessary to the fruit aroma study. This study examined the volatile profile changes from the fruits of three F. vesca genotypes during maturation using headspace solid-phase microextraction combined with gas chromatography-mass spectrometry with multivariate analysis. RESULTS A total of 191 putative volatile compounds were identified, while 152, 159 and 175 volatiles were detected in 20-30 DAP (days after pollination) fruits of Hawaii 4 (HW), Reugen (RG) and Yellow Wonder (YW), respectively. Aldehydes and alcohols predominated in the early time point while esters were predominant during the late time point. Ketones were the dominant compounds from F. vesca strawberries at the ripe stage. Certain genotype-characteristic volatiles were identified, including eugenol, γ-octalactone and δ-decalactone only detected in YW, and mesifurane was found in HW. CONCLUSIONS RG and YW showed very similar volatile compositions, but YW presented a greater number of volatiles and RG yielded a higher content. Differences in the volatile composition may be primarily due to genetic relationships. The metabolic changes that occurred during fruit ripening and characteristic volatiles will be a useful reference for future studies of strawberry volatiles. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Sujin Zheng
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jingjing Cai
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Peibin Huang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuqi Wang
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhenbiao Yang
- FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuan Yu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
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46
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Hardigan MA, Feldmann MJ, Carling J, Zhu A, Kilian A, Famula RA, Cole GS, Knapp SJ. A medium-density genotyping platform for cultivated strawberry using DArTag technology. THE PLANT GENOME 2023; 16:e20399. [PMID: 37940627 DOI: 10.1002/tpg2.20399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/22/2023] [Indexed: 11/10/2023]
Abstract
Genomic prediction in breeding populations containing hundreds to thousands of parents and seedlings is prohibitively expensive with current high-density genetic marker platforms designed for strawberry. We developed mid-density panels of molecular inversion probes (MIPs) to be deployed with the "DArTag" marker platform to provide a low-cost, high-throughput genotyping solution for strawberry genomic prediction. In total, 7742 target single nucleotide polymorphism (SNP) regions were used to generate MIP assays that were tested with a screening panel of 376 octoploid Fragaria accessions. We evaluated the performance of DArTag assays based on genotype segregation, amplicon coverage, and their ability to produce subgenome-specific amplicon alignments to the FaRR1 assembly and subsequent alignment-based variant calls with strong concordance to DArT's alignment-free, count-based genotype reports. We used a combination of marker performance metrics and physical distribution in the FaRR1 assembly to select 3K and 5K production panels for genotyping of large strawberry populations. We show that the 3K and 5K DArTag panels are able to target and amplify homologous alleles within subgenomic sequences with low-amplification bias between reference and alternate alleles, supporting accurate genotype calling while producing marker genotypes that can be treated as functionally diploid for quantitative genetic analysis. The 3K and 5K target SNPs show high levels of polymorphism in diverse F. × ananassa germplasm and UC Davis cultivars, with mean pairwise diversity (π) estimates of 0.40 and 0.32 and mean heterozygous genotype frequencies of 0.35 and 0.33, respectively.
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Affiliation(s)
- Michael A Hardigan
- USDA-ARS, Horticultural Crops Production and Genetic Improvement Research Unit, Corvallis, Oregon, USA
- Department of Plant Sciences, University of California Davis, Davis, California, USA
| | - Mitchell J Feldmann
- Department of Plant Sciences, University of California Davis, Davis, California, USA
| | - Jason Carling
- Diversity Arrays Technology, University of Canberra, Bruce, Australian Capital Territory, Australia
| | - Anyu Zhu
- Diversity Arrays Technology, University of Canberra, Bruce, Australian Capital Territory, Australia
| | - Andrzej Kilian
- Diversity Arrays Technology, University of Canberra, Bruce, Australian Capital Territory, Australia
| | - Randi A Famula
- Department of Plant Sciences, University of California Davis, Davis, California, USA
| | - Glenn S Cole
- Department of Plant Sciences, University of California Davis, Davis, California, USA
| | - Steven J Knapp
- Department of Plant Sciences, University of California Davis, Davis, California, USA
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47
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Mu W, Li K, Yang Y, Breiman A, Yang J, Wu Y, Zhu M, Wang S, Catalan P, Nevo E, Liu J. Subgenomic Stability of Progenitor Genomes During Repeated Allotetraploid Origins of the Same Grass Brachypodium hybridum. Mol Biol Evol 2023; 40:msad259. [PMID: 38000891 PMCID: PMC10708906 DOI: 10.1093/molbev/msad259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 10/17/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Both homeologous exchanges and homeologous expression bias are generally found in most allopolyploid species. Whether homeologous exchanges and homeologous expression bias differ between repeated allopolyploid speciation events from the same progenitor species remains unknown. Here, we detected a third independent and recent allotetraploid origin for the model grass Brachypodium hybridum. Our homeologous exchange with replacement analyses indicated the absence of significant homeologous exchanges in any of the three types of wild allotetraploids, supporting the integrity of their progenitor subgenomes and the immediate creation of the amphidiploids. Further homeologous expression bias tests did not uncover significant subgenomic dominance in different tissues and conditions of the allotetraploids. This suggests a balanced expression of homeologs under similar or dissimilar ecological conditions in their natural habitats. We observed that the density of transposons around genes was not associated with the initial establishment of subgenome dominance; rather, this feature is inherited from the progenitor genome. We found that drought response genes were highly induced in the two subgenomes, likely contributing to the local adaptation of this species to arid habitats in the third allotetraploid event. These findings provide evidence for the consistency of subgenomic stability of parental genomes across multiple allopolyploidization events that led to the same species at different periods. Our study emphasizes the importance of selecting closely related progenitor species genomes to accurately assess homeologous exchange with replacement in allopolyploids, thereby avoiding the detection of false homeologous exchanges when using less related progenitor species genomes.
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Affiliation(s)
- Wenjie Mu
- State Key Laboratory of Herbage Innovation and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Kexin Li
- State Key Laboratory of Herbage Innovation and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Yongzhi Yang
- State Key Laboratory of Herbage Innovation and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Adina Breiman
- Department of Evolutionary and Environmental Biology, University of Tel-Aviv, Tel-Aviv 6997801, Israel
| | - Jiao Yang
- State Key Laboratory of Herbage Innovation and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Ying Wu
- State Key Laboratory of Herbage Innovation and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Mingjia Zhu
- State Key Laboratory of Herbage Innovation and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Shuai Wang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Pilar Catalan
- Escuela Politecnica Superior de Huesca, Universidad de Zaragoza, Huesca 22071, Spain
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Haifa 3498838, Israel
| | - Jianquan Liu
- State Key Laboratory of Herbage Innovation and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
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48
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Wöhner TW, Emeriewen OF, Wittenberg AHJ, Nijbroek K, Wang RP, Blom EJ, Schneiders H, Keilwagen J, Berner T, Hoff KJ, Gabriel L, Thierfeldt H, Almolla O, Barchi L, Schuster M, Lempe J, Peil A, Flachowsky H. The structure of the tetraploid sour cherry 'Schattenmorelle' ( Prunus cerasus L.) genome reveals insights into its segmental allopolyploid nature. FRONTIERS IN PLANT SCIENCE 2023; 14:1284478. [PMID: 38107002 PMCID: PMC10722297 DOI: 10.3389/fpls.2023.1284478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 10/31/2023] [Indexed: 12/19/2023]
Abstract
Sour cherry (Prunus cerasus L.) is an important allotetraploid cherry species that evolved in the Caspian Sea and Black Sea regions from a hybridization of the tetraploid ground cherry (Prunus fruticosa Pall.) and an unreduced pollen of the diploid sweet cherry (P. avium L.) ancestor. Details of when and where the evolution of this species occurred are unclear, as well as the effect of hybridization on the genome structure. To gain insight, the genome of the sour cherry cultivar 'Schattenmorelle' was sequenced using Illumina NovaSeqTM and Oxford Nanopore long-read technologies, resulting in a ~629-Mbp pseudomolecule reference genome. The genome could be separated into two subgenomes, with subgenome PceS_a originating from P. avium and subgenome PceS_f originating from P. fruticosa. The genome also showed size reduction compared to ancestral species and traces of homoeologous sequence exchanges throughout. Comparative analysis confirmed that the genome of sour cherry is segmental allotetraploid and evolved very recently in the past.
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Affiliation(s)
- Thomas W. Wöhner
- Institute for Breeding Research on Fruit Crops, Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Dresden, Saxony, Germany
| | - Ofere F. Emeriewen
- Institute for Breeding Research on Fruit Crops, Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Dresden, Saxony, Germany
| | | | | | | | | | | | - Jens Keilwagen
- Institute for Biosafety in Plant Biotechnology, Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Quedlinburg, Saxony-Anhalt, Germany
| | - Thomas Berner
- Institute for Biosafety in Plant Biotechnology, Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Quedlinburg, Saxony-Anhalt, Germany
| | - Katharina J. Hoff
- Institute of Mathematics and Computer Science, University of Greifswald, Greifswald, Mecklenburg-Western Pomerania, Germany
| | - Lars Gabriel
- Institute of Mathematics and Computer Science, University of Greifswald, Greifswald, Mecklenburg-Western Pomerania, Germany
| | - Hannah Thierfeldt
- Institute of Mathematics and Computer Science, University of Greifswald, Greifswald, Mecklenburg-Western Pomerania, Germany
| | - Omar Almolla
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA) – Plant Genetics, University of Turin, Grugliasco, Italy
| | - Lorenzo Barchi
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA) – Plant Genetics, University of Turin, Grugliasco, Italy
| | - Mirko Schuster
- Institute for Breeding Research on Fruit Crops, Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Dresden, Saxony, Germany
| | - Janne Lempe
- Institute for Breeding Research on Fruit Crops, Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Dresden, Saxony, Germany
| | - Andreas Peil
- Institute for Breeding Research on Fruit Crops, Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Dresden, Saxony, Germany
| | - Henryk Flachowsky
- Institute for Breeding Research on Fruit Crops, Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Dresden, Saxony, Germany
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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 RG, Shang HY, Jia KH, Ma YP. Subgenome phasing for complex allopolyploidy: case-based benchmarking and recommendations. Brief Bioinform 2023; 25:bbad513. [PMID: 38189536 PMCID: PMC10772947 DOI: 10.1093/bib/bbad513] [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: 09/20/2023] [Revised: 11/27/2023] [Accepted: 12/13/2023] [Indexed: 01/09/2024] Open
Abstract
Accurate subgenome phasing is crucial for understanding the origin, evolution and adaptive potential of polyploid genomes. SubPhaser and WGDI software are two common methodologies for subgenome phasing in allopolyploids, particularly in scenarios lacking known diploid progenitors. Triggered by a recent debate over the subgenomic origins of the cultivated octoploid strawberry, we examined four well-documented complex allopolyploidy cases as benchmarks, to evaluate and compare the accuracy of the two software. Our analysis demonstrates that the subgenomic structure phased by both software is in line with prior research, effectively tracing complex allopolyploid evolutionary trajectories despite the limitations of each software. Furthermore, using these validated methodologies, we revisited the controversial issue regarding the progenitors of the octoploid strawberry. The results of both methodologies reaffirm Fragaria vesca and Fragaria iinumae as progenitors of the octoploid strawberry. Finally, we propose recommendations for enhancing the accuracy of subgenome phasing in future studies, recognizing the potential of integrated tools for advanced complex allopolyploidy research and offering a new roadmap for robust subgenome-based phylogenetic analysis.
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Affiliation(s)
- Ren-Gang Zhang
- State Key Laboratory of Plant Diversity and Specialty Crops/Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201 Yunnan, China
- University of Chinese Academy of Sciences, Beijing 101408 Beijing, China
| | - Hong-Yun Shang
- State Key Laboratory of Plant Diversity and Specialty Crops/Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201 Yunnan, China
| | - Kai-Hua Jia
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan 250100 Shandong, China
| | - Yong-Peng Ma
- State Key Laboratory of Plant Diversity and Specialty Crops/Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201 Yunnan, China
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