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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 2024:10.1038/s41588-024-01760-4. [PMID: 38783120 DOI: 10.1038/s41588-024-01760-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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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Tan W, Zhou P, Huang X, Liao R, Wang X, Wu Y, Ni Z, Shi T, Yu X, Zhang H, Ma C, Gao F, Ma Y, Bai Y, Hayat F, Omondi OK, Coulibaly D, Gao Z. Haplotype-resolved genome of Prunus zhengheensis provides insight into its evolution and low temperature adaptation in apricot. HORTICULTURE RESEARCH 2024; 11:uhae103. [PMID: 38689698 PMCID: PMC11059810 DOI: 10.1093/hr/uhae103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 03/31/2024] [Indexed: 05/02/2024]
Abstract
Prunus zhengheensis, an extremely rare population of apricots, originated in warm South-East China and is an excellent material for genetic breeding. However, most apricots and two related species (P. sibirica, P. mandshurica) are found in the cold northern regions in China and the mechanism of their distribution is still unclear. In addition, the classification status of P. zhengheensis is controversial. Thus, we generated a high-quality haplotype-resolved genome for P. zhengheensis, exploring key genetic variations in its adaptation and the causes of phylogenetic incongruence. We found extensive phylogenetic discordances between the nuclear and organelle phylogenies of P. zhengheensis, which could be explained by incomplete lineage sorting. A 242.22-Mb pan-genome of the Armeniaca section was developed with 13 chromosomal genomes. Importantly, we identified a 566-bp insertion in the promoter of the HSFA1d gene in apricot and showed that the activity of the HSFA1d promoter increased under low temperatures. In addition, HSFA1d overexpression in Arabidopsis thaliana indicated that HSFA1d positively regulated plant growth under chilling. Therefore, we hypothesized that the insertion in the promoter of HSFA1d in apricot improved its low-temperature adaptation, allowing it to thrive in relatively cold locations. The findings help explain the weather adaptability of Armeniaca plants.
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Affiliation(s)
- Wei Tan
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Pengyu Zhou
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiao Huang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ruyu Liao
- Institute of Fruit, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
| | - Xiaoan Wang
- Institute of Fruit, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
| | - Yaoyao Wu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhaojun Ni
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ting Shi
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaqing Yu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Huiqin Zhang
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Chengdong Ma
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Feng Gao
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yufan Ma
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yang Bai
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Faisal Hayat
- Department of Pomology, College of Horticulture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Ouma Kenneth Omondi
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Department of Crops, Horticulture and Soils, Faculty of Agriculture, Egerton University, P.O. Box 536, Egerton 20115, Kenya
| | - Daouda Coulibaly
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Department of Agricultural Sciences and Techniques-Horticulture, Rural Polytechnic Institute for Training and Applied Research (IPR/IFRA) of Katibougou, Koulikoro B.P.224, Mali
| | - Zhihong Gao
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
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3
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Wang Y, Guan J, Zhang Q. Chromosome-scale genome, together with transcriptome and metabolome, provides insights into the evolution and anthocyanin biosynthesis of Rubus rosaefolius Sm. (Rosaceae). HORTICULTURE RESEARCH 2024; 11:uhae064. [PMID: 38689697 PMCID: PMC11060340 DOI: 10.1093/hr/uhae064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 02/18/2024] [Indexed: 05/02/2024]
Abstract
Rubus rosaefolius is a kind of red raspberry possessing high nutritional and pharmaceutical value. Here we present a chromosome-level draft genome of R. rosaefolius. Of the total 131 assembled scaffolds, 70 with a total size of 219.02 Mb, accounting for 99.33% of the estimated genome size, were anchored to seven pseudochromosomes. We traced a whole-genome duplication (WGD) event shared among members of the Rosaceae family, from which were derived 5090 currently detectable duplicated gene pairs (dgps). Of the WGD-dgps 75.09% underwent purifying selection, and approximately three-quarters of informative WGD-dgps expressed their two paralogs with significant differences. We detected a wide variety of anthocyanins in the berries of R. rosaefolius, and their total concentration remained relatively stable during berry development but increased rapidly during the ripening stage, mainly because of the contributions of pelargonidin-3-O-glucoside and pelargonidin-3-O-(6″-O-malonyl)glucoside. We identified many structural genes that encode enzymes, such as RrDFR, RrF3H, RrANS, and RrBZ1, and play key roles in anthocyanin biosynthesis. The expression of some of these genes significantly increased or decreased with the accumulation of pelargonidin-3-O-glucoside and pelargonidin-3-O-(6″-O-malonyl)glucoside. We also identified some transcription factors and specific methylase-encoding genes that may play a role in regulating anthocyanin biosynthesis by targeting structural genes. In conclusion, our findings provide deeper insights into the genomic evolution and molecular mechanisms underlying anthocyanin biosynthesis in berries of R. rosaefolius. This knowledge may significantly contribute to the targeted domestication and breeding of Rubus species.
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Affiliation(s)
- Yunsheng Wang
- School of Health and Life Science, Kaili University, Kaili city, Guizhou Province 566011, China
| | - Jiyuan Guan
- Botanic Garden of Guizhou Province, Guiyang city, Guizhou Province 550081, China
| | - Qunying Zhang
- Botanic Garden of Guizhou Province, Guiyang city, Guizhou Province 550081, China
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Li M, Mount SM, Liu Z. Rosaceae fruit transcriptome database (ROFT)-a useful genomic resource for comparing fruits of apple, peach, strawberry, and raspberry. HORTICULTURE RESEARCH 2023; 10:uhad240. [PMID: 38162465 PMCID: PMC10756754 DOI: 10.1093/hr/uhad240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 11/06/2023] [Indexed: 01/03/2024]
Abstract
Rosaceae is a large plant family consisting of many economically important fruit crops including peach, apple, pear, strawberry, raspberry, plum, and others. Investigations into their growth and development will promote both basic understanding and progress toward increasing fruit yield and quality. With the ever-increasing high-throughput sequencing data of Rosaceae, comparative studies are hindered by inconsistency of sample collection with regard to tissue, stage, growth conditions, and by vastly different handling of the data. Therefore, databases that enable easy access and effective utilization of directly comparable transcript data are highly desirable. Here, we describe a database for comparative analysis, ROsaceae Fruit Transcriptome database (ROFT), based on RNA-seq data generated from the same laboratory using similarly dissected and staged fruit tissues of four important Rosaceae fruit crops: apple, peach, strawberry, and red raspberry. Hence, the database is unique in allowing easy and robust comparisons among fruit gene expression across the four species. ROFT enables researchers to query orthologous genes and their expression patterns during different fruit developmental stages in the four species, identify tissue-specific and tissue-/stage-specific genes, visualize and compare ortholog expression in different fruit types, explore consensus co-expression networks, and download different data types. The database provides users access to vast amounts of RNA-seq data across the four economically important fruits, enables investigations of fruit type specification and evolution, and facilitates the selection of genes with critical roles in fruit development for further studies.
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Affiliation(s)
- Muzi Li
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Stephen M Mount
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
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5
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Zhou J, Li M, Li Y, Xiao Y, Luo X, Gao S, Ma Z, Sadowski N, Timp W, Dardick C, Callahan A, Mount SM, Liu Z. Comparison of red raspberry and wild strawberry fruits reveals mechanisms of fruit type specification. PLANT PHYSIOLOGY 2023; 193:1016-1035. [PMID: 37440715 DOI: 10.1093/plphys/kiad409] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 05/31/2023] [Accepted: 06/18/2023] [Indexed: 07/15/2023]
Abstract
Belonging to Rosaceae, red raspberry (Rubus idaeus) and wild strawberry (Fragaria vesca) are closely related species with distinct fruit types. While the numerous ovaries become the juicy drupelet fruits in raspberry, their strawberry counterparts become dry and tasteless achenes. In contrast, while the strawberry receptacle, the stem tip, enlarges to become a red fruit, the raspberry receptacle shrinks and dries. The distinct fruit-forming ability of homologous organs in these 2 species allows us to investigate fruit type determination. We assembled and annotated the genome of red raspberry (R. idaeus) and characterized its fruit development morphologically and physiologically. Subsequently, transcriptomes of dissected and staged raspberry fruit tissues were compared to those of strawberry from a prior study. Class B MADS box gene expression was negatively associated with fruit-forming ability, which suggested a conserved inhibitory role of class B heterodimers, PISTILLATA/TM6 or PISTILLATA/APETALA3, for fruit formation. Additionally, the inability of strawberry ovaries to develop into fruit flesh was associated with highly expressed lignification genes and extensive lignification of the ovary pericarp. Finally, coexpressed gene clusters preferentially expressed in the dry strawberry achenes were enriched in "cell wall biosynthesis" and "ABA signaling," while coexpressed clusters preferentially expressed in the fleshy raspberry drupelets were enriched in "protein translation." Our work provides extensive genomic resources as well as several potential mechanisms underlying fruit type specification. These findings provide the framework for understanding the evolution of different fruit types, a defining feature of angiosperms.
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Affiliation(s)
- Junhui Zhou
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences, Weifang, Shandong 2611325, China
| | - Muzi Li
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Yongping Li
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Yuwei Xiao
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Xi Luo
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Shenglan Gao
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences, Weifang, Shandong 2611325, China
| | - Zhimin Ma
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences, Weifang, Shandong 2611325, China
| | - Norah Sadowski
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Chris Dardick
- USDA-ARS, Appalachian Fruit Research Station, Kearneysville, WV 25430, USA
| | - Ann Callahan
- USDA-ARS, Appalachian Fruit Research Station, Kearneysville, WV 25430, USA
| | - Stephen M Mount
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
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6
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Gao XF, Xiong XH, Boufford DE, Gao YD, Xu B, Zhang C. Phylogeny of the Diploid Species of Rubus (Rosaceae). Genes (Basel) 2023; 14:1152. [PMID: 37372332 DOI: 10.3390/genes14061152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
Rubus L. (Rosaceae, Rosoideae) contains around 700 species distributed on all continents except Antarctica, with the highest species diversity in temperate to subtropical regions of the northern hemisphere. The taxonomy of Rubus is challenging due to the frequency of polyploidy, hybridization and apomixis. Previous studies mostly sampled sparsely and used limited DNA sequence data. The evolutionary relationships between infrageneric taxa, therefore, remain to be further clarified. In the present study, genotyping by sequencing (GBS) reduced-representation genome sequencing data from 186 accessions representing 65 species, 1 subspecies and 17 varieties of Rubus, with emphasis on diploid species, were used to infer a phylogeny using maximum likelihood and maximum parsimony methods. The major results were as follows: (1) we confirmed or reconfirmed the polyphyly or paraphyly of some traditionally circumscribed subgenera, sections and subsections; (2) 19 well-supported clades, which differed from one another on molecular, morphological and geographical grounds, were identified for the species sampled; (3) characteristics such as plants with dense bristles or not, leaves leathery or papyraceous, number of carpels, instead of inflorescences paniculate or not, aggregate fruits and leaves abaxially tomentose or not, may be of some use in classifying taxa whose drupelets are united into a thimble-shaped aggregate fruit that falls in its entirety from the dry receptacle; and (4) a preliminary classification scheme of diploid species of Rubus is proposed based on our results combined with those from previous phylogenetic analyses.
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Affiliation(s)
- Xin-Fen Gao
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Xian-Hua Xiong
- College of Life Science and Biotechnology, Mianyang Teachers' College, Mianyang 621000, China
| | - David E Boufford
- Harvard University Herbaria, Harvard University, 22 Divinity Avenue, Cambridge, MA 02138, USA
| | - Yun-Dong Gao
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Bo Xu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Cheng Zhang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
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Wang G, Guan SL, Zhu N, Li Q, Chong X, Wang T, Xuan J. Comprehensive Genomic Analysis of SnRK in Rosaceae and Expression Analysis of RoSnRK2 in Response to Abiotic Stress in Rubus occidentalis. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091784. [PMID: 37176842 PMCID: PMC10181103 DOI: 10.3390/plants12091784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/23/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023]
Abstract
The sucrose nonfermenting 1-related protein kinase (SnRK) plays an important role in responding to abiotic stresses by phosphorylating the target protein to regulate various signaling pathways. However, little is known about the characteristics, evolutionary history, and expression patterns of the SnRK family in black raspberry (Rubus occidentalis L.) or other Rosaceae family species. In this study, a total of 209 SnRK genes were identified in 7 Rosaceae species and divided into 3 subfamilies (SnRK1, SnRK2, and SnRK3) based on phylogenetic analysis and specific motifs. Whole-genome duplication (WGD) and dispersed duplication (DSD) were considered to be major contributions to the SnRK family expansion. Purifying selection was the primary driving force in the SnRK family evolution. The spatial expression indicated that the RoSnRK genes may play important roles in different tissues. In addition, the expression models of 5 RoSnRK2 genes in response to abiotic stresses were detected by qRT-PCR. The proteins encoded by RoSnRK2 genes localize to the cytoplasm and nucleus in order to perform their respective functions. Taken together, this study provided an analysis of the SnRK gene family expansion and evolution, and contributed to the current knowledge of the function of 5 RoSnRK2 genes, which in turn expanded understanding of the molecular mechanisms of black raspberry responses to abiotic stress.
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Affiliation(s)
- Guoming Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Sophia Lee Guan
- College of Computer, Mathematical, and Natural Sciences, University of Maryland, College Park, MD 20742, USA
| | - Nan Zhu
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Qionghou Li
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Xinran Chong
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Tao Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Jiping Xuan
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
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8
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Kenchanmane Raju SK, Ledford M, Niederhuth CE. DNA methylation signatures of duplicate gene evolution in angiosperms. PLANT PHYSIOLOGY 2023:kiad220. [PMID: 37061825 PMCID: PMC10400039 DOI: 10.1093/plphys/kiad220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/03/2023] [Accepted: 04/12/2023] [Indexed: 06/19/2023]
Abstract
Gene duplication is a source of evolutionary novelty. DNA methylation may play a role in the evolution of duplicate genes (paralogs) through its association with gene expression. While this relationship has been examined to varying extents in a few individual species, the generalizability of these results at either a broad phylogenetic scale with species of differing duplication histories or across a population remains unknown. We applied a comparative epigenomics approach to 43 angiosperm species across the phylogeny and a population of 928 Arabidopsis (Arabidopsis thaliana) accessions, examining the association of DNA methylation with paralog evolution. Genic DNA methylation was differentially associated with duplication type, the age of duplication, sequence evolution, and gene expression. Whole genome duplicates were typically enriched for CG-only gene-body methylated or unmethylated genes, while single-gene duplications were typically enriched for non-CG methylated or unmethylated genes. Non-CG methylation, in particular, was characteristic of more recent single-gene duplicates. Core angiosperm gene families differentiated into those which preferentially retain paralogs and 'duplication-resistant' families, which convergently reverted to singletons following duplication. Duplication-resistant families that still have paralogous copies were, uncharacteristically for core angiosperm genes, enriched for non-CG methylation. Non-CG methylated paralogs had higher rates of sequence evolution, higher frequency of presence-absence variation, and more limited expression. This suggests that silencing by non-CG methylation may be important to maintaining dosage following duplication and be a precursor to fractionation. Our results indicate that genic methylation marks differing evolutionary trajectories and fates between paralogous genes and have a role in maintaining dosage following duplication.
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Affiliation(s)
| | | | - Chad E Niederhuth
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
- AgBioResearch, Michigan State University, East Lansing, MI 48824, USA
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9
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Cai Y, Tang C, Lv S, Chen Q, Zhu X, Li X, Qi K, Xie Z, Zhang S, Wang P, Wu J. Elucidation of the GAUT gene family in eight Rosaceae species and function analysis of PbrGAUT22 in pear pollen tube growth. PLANTA 2023; 257:68. [PMID: 36853424 DOI: 10.1007/s00425-023-04103-5] [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: 01/10/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
The phylogenetic relationship and evolutionary history of the GAUT gene family were identified in 8 Rosaseae species. PbrGAUT22 was involved in controlling pollen tube growth by regulating the content of pectins. In plants, galacturonosyltransferases (GAUTs) were involved in homogalacturonan biosynthesis and functioned in maintaining pollen tube cell wall integrity. However, the feature and evolutionary history of the GAUT gene family in Rosaceae species and candidates in pear pollen tube growth remain unclear. Here, we identified 190 GAUT genes in 8 Rosaceae species, including Chinese white pear (Pyrus bretschneideri), European pear (Pyrus communis), apple (Malus × domestica), peach (Prunus persica), Japanese apricot (Prunus mume), sweet cherry (Prunus avium), woodland strawberry (Fragaria vesca) and black raspberry (Rubus occidentalis). Members in GAUT gene family were divided into 4 subfamilies according to the phylogenetic and structural analysis. Whole-genome duplication events and dispersed duplicates drove the expansion of the GAUT gene family. Among 23 pollen-expressed PbrGAUT genes in pear, PbrGAUT22 showed increased expression level during 1-6 h post-cultured pollen tubes. PbrGAUT22 was localized to the cytoplasm and plasma membrane. Knockdown of PbrGAUT22 expression in pollen tubes caused the decrease of pectin content and inhibited pear pollen tubes growth. Taken together, we investigated the identification and evolution of the GAUT gene family in Rosaceae species, and found that PbrGAUT22 played an essential role in the synthesis of pectin and the growth of pear pollen tubes.
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Affiliation(s)
- Yiling Cai
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chao Tang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China
- Hainan Yazhou Bay Seed Lab, Sanya, 572024, China
| | - Shouzheng Lv
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qiming Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaoxuan Zhu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xian Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China
| | - Kaijie Qi
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhihua Xie
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shaoling Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China
| | - Peng Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China
| | - Juyou Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095, China.
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, 210014, China.
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10
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Brůna T, Aryal R, Dudchenko O, Sargent DJ, Mead D, Buti M, Cavallini A, Hytönen T, Andrés J, Pham M, Weisz D, Mascagni F, Usai G, Natali L, Bassil N, Fernandez GE, Lomsadze A, Armour M, Olukolu B, Poorten T, Britton C, Davik J, Ashrafi H, Aiden EL, Borodovsky M, Worthington M. A chromosome-length genome assembly and annotation of blackberry (Rubus argutus, cv. "Hillquist"). G3 (BETHESDA, MD.) 2023; 13:jkac289. [PMID: 36331334 PMCID: PMC9911083 DOI: 10.1093/g3journal/jkac289] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 10/03/2022] [Indexed: 11/06/2022]
Abstract
Blackberries (Rubus spp.) are the fourth most economically important berry crop worldwide. Genome assemblies and annotations have been developed for Rubus species in subgenus Idaeobatus, including black raspberry (R. occidentalis), red raspberry (R. idaeus), and R. chingii, but very few genomic resources exist for blackberries and their relatives in subgenus Rubus. Here we present a chromosome-length assembly and annotation of the diploid blackberry germplasm accession "Hillquist" (R. argutus). "Hillquist" is the only known source of primocane-fruiting (annual-fruiting) in tetraploid fresh-market blackberry breeding programs and is represented in the pedigree of many important cultivars worldwide. The "Hillquist" assembly, generated using Pacific Biosciences long reads scaffolded with high-throughput chromosome conformation capture sequencing, consisted of 298 Mb, of which 270 Mb (90%) was placed on 7 chromosome-length scaffolds with an average length of 38.6 Mb. Approximately 52.8% of the genome was composed of repetitive elements. The genome sequence was highly collinear with a novel maternal haplotype-resolved linkage map of the tetraploid blackberry selection A-2551TN and genome assemblies of R. chingii and red raspberry. A total of 38,503 protein-coding genes were predicted, of which 72% were functionally annotated. Eighteen flowering gene homologs within a previously mapped locus aligning to an 11.2 Mb region on chromosome Ra02 were identified as potential candidate genes for primocane-fruiting. The utility of the "Hillquist" genome has been demonstrated here by the development of the first genotyping-by-sequencing-based linkage map of tetraploid blackberry and the identification of possible candidate genes for primocane-fruiting. This chromosome-length assembly will facilitate future studies in Rubus biology, genetics, and genomics and strengthen applied breeding programs.
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Affiliation(s)
- Tomáš Brůna
- School of Biological Sciences, Center for Bioinformatics and Computational Genomics, Georgia Tech, Atlanta, GA 30332, USA
| | - Rishi Aryal
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Computer Science, Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
| | - Daniel James Sargent
- Department of Genetics, Genomics and Breeding, NIAB-EMR, East Malling, Kent, UK
- Natural Resources Institute, University of Greenwich, Medway Campus, Chatham Maritime, Kent, UK
| | - Daniel Mead
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- Owlstone Medical Ltd, Cambridge CB4 0GJ, UK
| | - Matteo Buti
- Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Florence, Italy
| | - Andrea Cavallini
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Timo Hytönen
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, 00790 Helsinki, Finland
| | - Javier Andrés
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, 00790 Helsinki, Finland
| | - Melanie Pham
- Department of Molecular and Human Genetics, Baylor College of Medicine, The Center for Genome Architecture, Houston, TX 77030, USA
| | - David Weisz
- Department of Molecular and Human Genetics, Baylor College of Medicine, The Center for Genome Architecture, Houston, TX 77030, USA
| | - Flavia Mascagni
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Gabriele Usai
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Lucia Natali
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Nahla Bassil
- USDA-ARS, National Clonal Germplasm Repository, Corvallis, OR 97333, USA
| | - Gina E Fernandez
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607, USA
| | - Alexandre Lomsadze
- Department of Biomedical Engineering, Center for Bioinformatics and Computational Genomics, Georgia Tech, Atlanta, GA 30332, USA
| | - Mitchell Armour
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA
| | - Bode Olukolu
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA
| | | | | | - Jahn Davik
- Department of Molecular Plant Biology, Norwegian Institute of Bioeconomy Research, N-1431 Ås, Norway
| | - Hamid Ashrafi
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695, USA
| | - Erez Lieberman Aiden
- Department of Computer Science, Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, The Center for Genome Architecture, Houston, TX 77030, USA
- UWA School of Agriculture and Environment, The University of Western Australia, Crawley, WA 6009, Australia
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech, Pudong 201210, China
| | - Mark Borodovsky
- Department of Biomedical Engineering, School of Computational Science and Engineering, Center for Bioinformatics and Computational Genomics, Georgia Tech, Atlanta, GA 30332USA
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11
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Chromosome-Level Assembly of Flowering Cherry ( Prunus campanulata) Provides Insight into Anthocyanin Accumulation. Genes (Basel) 2023; 14:genes14020389. [PMID: 36833316 PMCID: PMC9957189 DOI: 10.3390/genes14020389] [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: 01/05/2023] [Revised: 01/28/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
The flowering cherries (genus Prunus, subgenus Cerasus) are popular ornamental trees in China, Japan, Korea, and elsewhere. Prunus campanulata Maxim. is an important species of flowering cherry native to Southern China, which is also distributed in Taiwan, the Ryukyu Islands of Japan, and Vietnam. It produces bell-shaped flowers with colors ranging from bright pink to crimson during the Chinese Spring Festival from January to March each year. We selected the P. campanulata cultivar "Lianmeiren", with only 0.54% of heterozygosity, as the focus of this study, and generated a high-quality chromosome-scale genome assembly of P. campanulata by combining Pacific Biosciences (PacBio) single-molecule sequencing, 10× Genomics sequencing, and high-throughput chromosome conformation capture (Hi-C) technology. We first assembled a 300.48 Mb genome assembly with a contig N50 length of 2.02 Mb. In total, 28,319 protein-coding genes were predicted from the genome, 95.8% of which were functionally annotated. Phylogenetic analyses indicated that P. campanulata diverged from a common ancestor of cherry approximately 15.1 million years ago. Comparative genomic analyses showed that the expanded gene families were significantly involved in ribosome biogenesis, diterpenoid biosynthesis, flavonoid biosynthesis, and circadian rhythm. Furthermore, we identified 171 MYB genes from the P. campanulata genome. Based on the RNA-seq of five organs at three flowering stages, expression analyses revealed that the majority of the MYB genes exhibited tissue-specific expression patterns, and some genes were identified as being associated with anthocyanin accumulation. This reference sequence is an important resource for further studies of floral morphology and phenology, and comparative genomics of the subgenera Cerasus and Prunus.
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Nguyen HM, Putterill J, Dare AP, Plunkett BJ, Cooney J, Peng Y, Souleyre EJF, Albert NW, Espley RV, Günther CS. Two genes, ANS and UFGT2, from Vaccinium spp. are key steps for modulating anthocyanin production. FRONTIERS IN PLANT SCIENCE 2023; 14:1082246. [PMID: 36818839 PMCID: PMC9933871 DOI: 10.3389/fpls.2023.1082246] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 01/11/2023] [Indexed: 06/18/2023]
Abstract
Anthocyanins are a major group of red to blue spectrum plant pigments with many consumer health benefits. Anthocyanins are derived from the flavonoid pathway and diversified by glycosylation and methylation, involving the concerted action of specific enzymes. Blueberry and bilberry (Vaccinium spp.) are regarded as 'superfruits' owing to their high content of flavonoids, especially anthocyanins. While ripening-related anthocyanin production in bilberry (V. myrtillus) and blueberry (V. corymbosum) is regulated by the transcriptional activator MYBA1, the role of specific structural genes in determining the concentration and composition of anthocyanins has not been functionally elucidated. We isolated three candidate genes, CHALCONE SYNTHASE (VmCHS1), ANTHOCYANIDIN SYNTHASE (VmANS) and UDP-GLUCOSE : FLAVONOID-3-O-GLYCOSYLTRANSFERASE (VcUFGT2), from Vaccinium, which were predominantly expressed in pigmented fruit skin tissue and showed high homology between bilberry and blueberry. Agrobacterium-mediated transient expression of Nicotiana benthamiana showed that overexpression of VcMYBA1 in combination with VmANS significantly increased anthocyanin concentration (3-fold). Overexpression of VmCHS1 showed no effect above that induced by VcMYBA1, while VcUFGT2 modulated anthocyanin composition to produce delphinidin-3-galactosylrhamnoside, not naturally produced in tobacco. In strawberry (Fragaria × ananassa), combined transient overexpression of VcUFGT2 with a FLAVONOID 3´,5´-HYDROXYLASE from kiwifruit (Actinidia melanandra) modulated the anthocyanin profile to include galactosides and arabinosides of delphinidin and cyanidin, major anthocyanins in blueberry and bilberry. These findings provide insight into the role of the final steps of biosynthesis in modulating anthocyanin production in Vaccinium and may contribute to the targeted breeding of new cultivars with improved nutritional properties.
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Affiliation(s)
- Han M. Nguyen
- The New Zealand Institute for Plant and Food Research Ltd, Auckland, New Zealand
- University of Auckland, School of Biological Sciences, Auckland, New Zealand
| | - Joanna Putterill
- University of Auckland, School of Biological Sciences, Auckland, New Zealand
| | - Andrew P. Dare
- The New Zealand Institute for Plant and Food Research Ltd, Auckland, New Zealand
| | - Blue J. Plunkett
- The New Zealand Institute for Plant and Food Research Ltd, Auckland, New Zealand
| | - Janine Cooney
- The New Zealand Institute for Plant and Food Research Ltd, Hamilton, New Zealand
| | - Yongyan Peng
- The New Zealand Institute for Plant and Food Research Ltd, Auckland, New Zealand
| | | | - Nick W. Albert
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Richard V. Espley
- The New Zealand Institute for Plant and Food Research Ltd, Auckland, New Zealand
| | - Catrin S. Günther
- The New Zealand Institute for Plant and Food Research Ltd, Hamilton, New Zealand
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13
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Liu Z, Zhu X, Liu W, Qi K, Xie Z, Zhang S, Wu J, Wang P. Characterization of the REVEILLE family in Rosaceae and role of PbLHY in flowering time regulation. BMC Genomics 2023; 24:49. [PMID: 36707756 PMCID: PMC9883883 DOI: 10.1186/s12864-023-09144-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 01/19/2023] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND The circadian clock integrates endogenous and exogenous signals and regulates various physiological processes in plants. REVEILLE (RVE) proteins play critical roles in circadian clock system, especially CCA1 (CIRCADIAN CLOCK ASSOCIATED 1) and LHY (LATE ELONGATED HYPOCOTYL), which also participate in flowering regulation. However, little is known about the evolution and function of the RVE family in Rosaceae species, especially in Pyrus bretschneideri. RESULTS In this study, we performed a genome-wide analysis and identified 51 RVE genes in seven Rosaceae species. The RVE family members were classified into two groups based on phylogenetic analysis. Dispersed duplication events and purifying selection were the main drivers of evolution in the RVE family. Moreover, the expression patterns of ten PbRVE genes were diverse in P. bretschneideri tissues. All PbRVE genes showed diurnal rhythms under light/dark cycles in P. bretschneideri leaves. Four PbRVE genes also displayed robust rhythms under constant light conditions. PbLHY, the gene with the highest homology to AtCCA1 and AtLHY in P. bretschneideri, is localized in the nucleus. Ectopic overexpression of PbLHY in Arabidopsis delayed flowering time and repressed the expression of flowering time-related genes. CONCLUSION These results contribute to improving the understanding and functional research of RVE genes in P. bretschneideri.
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Affiliation(s)
- Zhe Liu
- grid.254020.10000 0004 1798 4253Department of Pharmacy, Changzhi Medical College, Changzhi, 046000 China ,grid.27871.3b0000 0000 9750 7019Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China ,Shanxi Province Key Laboratory of Functional Food with Homologous of Medicine and Food, Changzhi, China
| | - Xiaoxuan Zhu
- grid.27871.3b0000 0000 9750 7019Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Weijuan Liu
- grid.27871.3b0000 0000 9750 7019Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Kaijie Qi
- grid.27871.3b0000 0000 9750 7019Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Zhihua Xie
- grid.27871.3b0000 0000 9750 7019Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Shaoling Zhang
- grid.27871.3b0000 0000 9750 7019Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Juyou Wu
- grid.27871.3b0000 0000 9750 7019Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China ,Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, China
| | - Peng Wang
- grid.27871.3b0000 0000 9750 7019Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
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14
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Price RJ, Davik J, Fernandéz Fernandéz F, Bates HJ, Lynn S, Nellist CF, Buti M, Røen D, Šurbanovski N, Alsheikh M, Harrison RJ, Sargent DJ. Chromosome-scale genome sequence assemblies of the 'Autumn Bliss' and 'Malling Jewel' cultivars of the highly heterozygous red raspberry (Rubus idaeus L.) derived from long-read Oxford Nanopore sequence data. PLoS One 2023; 18:e0285756. [PMID: 37192177 DOI: 10.1371/journal.pone.0285756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 05/01/2023] [Indexed: 05/18/2023] Open
Abstract
Red raspberry (Rubus idaeus L.) is an economically valuable soft-fruit species with a relatively small (~300 Mb) but highly heterozygous diploid (2n = 2x = 14) genome. Chromosome-scale genome sequences are a vital tool in unravelling the genetic complexity controlling traits of interest in crop plants such as red raspberry, as well as for functional genomics, evolutionary studies, and pan-genomics diversity studies. In this study, we developed genome sequences of a primocane fruiting variety ('Autumn Bliss') and a floricane variety ('Malling Jewel'). The use of long-read Oxford Nanopore Technologies sequencing data yielded long read lengths that permitted well resolved genome sequences for the two cultivars to be assembled. The de novo assemblies of 'Malling Jewel' and 'Autumn Bliss' contained 79 and 136 contigs respectively, and 263.0 Mb of the 'Autumn Bliss' and 265.5 Mb of the 'Malling Jewel' assembly could be anchored unambiguously to a previously published red raspberry genome sequence of the cultivar 'Anitra'. Single copy ortholog analysis (BUSCO) revealed high levels of completeness in both genomes sequenced, with 97.4% of sequences identified in 'Autumn Bliss' and 97.7% in 'Malling Jewel'. The density of repetitive sequence contained in the 'Autumn Bliss' and 'Malling Jewel' assemblies was significantly higher than in the previously published assembly and centromeric and telomeric regions were identified in both assemblies. A total of 42,823 protein coding regions were identified in the 'Autumn Bliss' assembly, whilst 43,027 were identified in the 'Malling Jewel' assembly. These chromosome-scale genome sequences represent an excellent genomics resource for red raspberry, particularly around the highly repetitive centromeric and telomeric regions of the genome that are less complete in the previously published 'Anitra' genome sequence.
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Affiliation(s)
- R Jordan Price
- Cambridge Crop Research, NIAB, Cambridge, United Kingdom
| | - Jahn Davik
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research, Ås, Norway
| | | | - Helen J Bates
- Cambridge Crop Research, NIAB, Cambridge, United Kingdom
| | - Samantha Lynn
- Department of Genetics, Genomics and Breeding, NIAB, East Malling, Kent, United Kingdom
| | | | - Matteo Buti
- Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Florence, Italy
| | - Dag Røen
- Graminor Breeding Ltd., Ridabu, Norway
| | - Nada Šurbanovski
- Department of Genetics, Genomics and Breeding, NIAB, East Malling, Kent, United Kingdom
| | | | | | - Daniel James Sargent
- Department of Genetics, Genomics and Breeding, NIAB, East Malling, Kent, United Kingdom
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15
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Zhang H, Wafula EK, Eilers J, Harkess A, Ralph PE, Timilsena PR, dePamphilis CW, Waite JM, Honaas LA. Building a foundation for gene family analysis in Rosaceae genomes with a novel workflow: A case study in Pyrus architecture genes. FRONTIERS IN PLANT SCIENCE 2022; 13:975942. [PMID: 36452099 PMCID: PMC9702816 DOI: 10.3389/fpls.2022.975942] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 09/21/2022] [Indexed: 05/26/2023]
Abstract
The rapid development of sequencing technologies has led to a deeper understanding of plant genomes. However, direct experimental evidence connecting genes to important agronomic traits is still lacking in most non-model plants. For instance, the genetic mechanisms underlying plant architecture are poorly understood in pome fruit trees, creating a major hurdle in developing new cultivars with desirable architecture, such as dwarfing rootstocks in European pear (Pyrus communis). An efficient way to identify genetic factors for important traits in non-model organisms can be to transfer knowledge across genomes. However, major obstacles exist, including complex evolutionary histories and variable quality and content of publicly available plant genomes. As researchers aim to link genes to traits of interest, these challenges can impede the transfer of experimental evidence across plant species, namely in the curation of high-quality, high-confidence gene models in an evolutionary context. Here we present a workflow using a collection of bioinformatic tools for the curation of deeply conserved gene families of interest across plant genomes. To study gene families involved in tree architecture in European pear and other rosaceous species, we used our workflow, plus a draft genome assembly and high-quality annotation of a second P. communis cultivar, 'd'Anjou.' Our comparative gene family approach revealed significant issues with the most recent 'Bartlett' genome - primarily thousands of missing genes due to methodological bias. After correcting assembly errors on a global scale in the 'Bartlett' genome, we used our workflow for targeted improvement of our genes of interest in both P. communis genomes, thus laying the groundwork for future functional studies in pear tree architecture. Further, our global gene family classification of 15 genomes across 6 genera provides a valuable and previously unavailable resource for the Rosaceae research community. With it, orthologs and other gene family members can be easily identified across any of the classified genomes. Importantly, our workflow can be easily adopted for any other plant genomes and gene families of interest.
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Affiliation(s)
- Huiting Zhang
- Tree Fruit Research Laboratory, Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Wenatchee, WA, United States
- Department of Horticulture, Washington State University, Pullman, WA, United States
| | - Eric K. Wafula
- Department of Biology, The Pennsylvania State University, University Park, PA, United States
| | - Jon Eilers
- Tree Fruit Research Laboratory, Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Wenatchee, WA, United States
| | - Alex E. Harkess
- College of Agriculture, Auburn University, Auburn, AL, United States
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Paula E. Ralph
- Department of Biology, The Pennsylvania State University, University Park, PA, United States
| | - Prakash Raj Timilsena
- Department of Biology, The Pennsylvania State University, University Park, PA, United States
| | - Claude W. dePamphilis
- Department of Biology, The Pennsylvania State University, University Park, PA, United States
| | - Jessica M. Waite
- Tree Fruit Research Laboratory, Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Wenatchee, WA, United States
| | - Loren A. Honaas
- Tree Fruit Research Laboratory, Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Wenatchee, WA, United States
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16
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Senger E, Osorio S, Olbricht K, Shaw P, Denoyes B, Davik J, Predieri S, Karhu S, Raubach S, Lippi N, Höfer M, Cockerton H, Pradal C, Kafkas E, Litthauer S, Amaya I, Usadel B, Mezzetti B. Towards smart and sustainable development of modern berry cultivars in Europe. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1238-1251. [PMID: 35751152 DOI: 10.1111/tpj.15876] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/15/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
Fresh berries are a popular and important component of the human diet. The demand for high-quality berries and sustainable production methods is increasing globally, challenging breeders to develop modern berry cultivars that fulfill all desired characteristics. Since 1994, research projects have characterized genetic resources, developed modern tools for high-throughput screening, and published data in publicly available repositories. However, the key findings of different disciplines are rarely linked together, and only a limited range of traits and genotypes has been investigated. The Horizon2020 project BreedingValue will address these challenges by studying a broader panel of strawberry, raspberry and blueberry genotypes in detail, in order to recover the lost genetic diversity that has limited the aroma and flavor intensity of recent cultivars. We will combine metabolic analysis with sensory panel tests and surveys to identify the key components of taste, flavor and aroma in berries across Europe, leading to a high-resolution map of quality requirements for future berry cultivars. Traits linked to berry yields and the effect of environmental stress will be investigated using modern image analysis methods and modeling. We will also use genetic analysis to determine the genetic basis of complex traits for the development and optimization of modern breeding technologies, such as molecular marker arrays, genomic selection and genome-wide association studies. Finally, the results, raw data and metadata will be made publicly available on the open platform Germinate in order to meet FAIR data principles and provide the basis for sustainable research in the future.
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Affiliation(s)
- Elisa Senger
- Institute of Bio- and Geosciences, IBG-4 Bioinformatics, BioSC, CEPLAS, Forschungszentrum Jülich, Jülich, Germany
| | - Sonia Osorio
- Departamento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Campus de Teatinos, Málaga, Spain
| | | | - Paul Shaw
- Department of Information and Computational Sciences, The James Hutton Institute, Invergowrie, Scotland, UK
| | - Béatrice Denoyes
- Université de Bordeaux, UMR BFP, INRAE, Villenave d'Ornon, France
| | - Jahn Davik
- Department of Molecular Plant Biology, Norwegian Institute of Bioeconomy Research (NIBIO), Ås, Norway
| | - Stefano Predieri
- Bio-Agrofood Department, Institute for Bioeconomy, IBE-CNR, Italian National Research Council, Bologna, Italy
| | - Saila Karhu
- Natural Resources Institute Finland (Luke), Turku, Finland
| | - Sebastian Raubach
- Department of Information and Computational Sciences, The James Hutton Institute, Invergowrie, Scotland, UK
| | - Nico Lippi
- Bio-Agrofood Department, Institute for Bioeconomy, IBE-CNR, Italian National Research Council, Bologna, Italy
| | - Monika Höfer
- Institute of Breeding Research on Fruit Crops, Federal Research Centre for Cultivated Plants (JKI), Dresden, Germany
| | - Helen Cockerton
- Genetics, Genomics and Breeding Department, NIAB, East Malling, UK
| | - Christophe Pradal
- CIRAD and UMR AGAP Institute, Montpellier, France
- INRIA and LIRMM, University Montpellier, CNRS, Montpellier, France
| | - Ebru Kafkas
- Department of Horticulture, Faculty of Agriculture, Çukurova University, Balcalı, Adana, Turkey
| | | | - Iraida Amaya
- Unidad Asociada deI + D + i IFAPA-CSIC Biotecnología y Mejora en Fresa, Málaga, Spain
- Laboratorio de Genómica y Biotecnología, Centro IFAPA de Málaga, Instituto Andaluz de Investigación y Formación Agraria y Pesquera, Málaga, Spain
| | - Björn Usadel
- Institute of Bio- and Geosciences, IBG-4 Bioinformatics, BioSC, CEPLAS, Forschungszentrum Jülich, Jülich, Germany
- Institute for Biological Data Science, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Bruno Mezzetti
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy
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Grimplet J. Genomic and Bioinformatic Resources for Perennial Fruit Species. Curr Genomics 2022; 23:217-233. [PMID: 36777875 PMCID: PMC9875543 DOI: 10.2174/1389202923666220428102632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 03/12/2022] [Accepted: 03/12/2022] [Indexed: 11/22/2022] Open
Abstract
In the post-genomic era, data management and development of bioinformatic tools are critical for the adequate exploitation of genomics data. In this review, we address the actual situation for the subset of crops represented by the perennial fruit species. The agronomical singularity of these species compared to plant and crop model species provides significant challenges on the implementation of good practices generally not addressed in other species. Studies are usually performed over several years in non-controlled environments, usage of rootstock is common, and breeders heavily rely on vegetative propagation. A reference genome is now available for all the major species as well as many members of the economically important genera for breeding purposes. Development of pangenome for these species is beginning to gain momentum which will require a substantial effort in term of bioinformatic tool development. The available tools for genome annotation and functional analysis will also be presented.
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Affiliation(s)
- Jérôme Grimplet
- Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Unidad de Hortofruticultura, Gobierno de Aragón, Avda. Montañana, Zaragoza, Spain;,Instituto Agroalimentario de Aragón–IA2 (CITA-Universidad de Zaragoza), Calle Miguel Servet, Zaragoza, Spain,Address correspondence to this author at the Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Unidad de Hortofruticultura, Gobierno de Aragón, Avda. Montañana, Zaragoza, Spain; Instituto Agroalimentario de Aragón–IA2 (CITA-Universidad de Zaragoza), Calle Miguel Servet, Zaragoza, Spain; Tel: +34976713635; E-mail:
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Belal MA, Ezzat M, Zhang Y, Xu Z, Cao Y, Han Y. Integrative Analysis of the DICER-like (DCL) Genes From Peach (Prunus persica): A Critical Role in Response to Drought Stress. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.923166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
DICER-likes (DCLs) proteins are the core component for non-coding RNA (ncRNA) biogenesis, playing essential roles in some biological processes. The DCL family has been characterized in model plants, such as Arabidopsis, rice, and poplar. However, the evolutionary aspect and the expression mechanism under drought stress were scarce and have never been reported and characterized in one of the most important worldwide cultivated fruit trees, peach (Prunus persica). Eight DCLs genes in the Prunus persica genome were detected, in addition to 51 DCLs in the other seven Rosaceae genomes. The phylogenetic analysis with Arabidopsis thaliana and RTL1 gene as outgroups suggested that DCL members are divided into four clades: DCL1, DCL2, DCL3, and DCL4 with several gene gain/loss events of DCL gene copies through the evolutionary tract of the Rosacea family. The number of homologous DCL copies within each clade, along with the chromosomal location indicated gene duplication event of the DCL2 gene occurred once for the subfamily Amygdaloideae and twice for Pyrus communis and Prunus dulics and trice for the P. persica on Chromosome number 7 genes. Another duplication event was found for the DCL3 gene that occurred once for all the eight Rosaceae species with no match in A. thaliana. The DCL genetic similarity and activity was evaluated using BLASTp and previously published RNA-seq data among different tissues and over different time points of peach trees exposed to drought conditions. Finally, the expression pattern of PrupeDCLs in response to drought stress was identified, and two of these members, Prupe.7G047900 and Prupe.6G363600, were found as main candidate genes for response to drought stress. Our data presented here provide useful information for a better understanding of the molecular evolution of DCL genes in Rosaceae genomes, and the function of DCLs in P. persica.
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Meng Q, Manghwar H, Hu W. Study on Supergenus Rubus L.: Edible, Medicinal, and Phylogenetic Characterization. PLANTS (BASEL, SWITZERLAND) 2022; 11:1211. [PMID: 35567211 PMCID: PMC9102695 DOI: 10.3390/plants11091211] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 06/15/2023]
Abstract
Rubus L. is one of the most diverse genera belonging to Rosaceae; it consists of more than 700 species with a worldwide distribution. It thus provides an ideal natural "supergenus" for studying the importance of its edible, medicinal, and phylogenetic characteristics for application in our daily lives and fundamental scientific studies. The Rubus genus includes many economically important species, such as blackberry (R. fruticosus L.), red raspberry (R. ideaus L.), black raspberry (R. occidentalis L.), and raspberry (R. chingii Hu), which are widely utilized in the fresh fruit market and the medicinal industry. Although Rubus species have existed in human civilization for hundreds of years, their utilization as fruit and in medicine is still largely inadequate, and many questions on their complex phylogenetic relationships need to be answered. In this review, we briefly summarize the history and progress of studies on Rubus, including its domestication as a source of fresh fruit, its medicinal uses in pharmacology, and its systematic position in the phylogenetic tree. Recent available evidence indicates that (1) thousands of Rubus cultivars were bred via time- and labor-consuming methods from only a few wild species, and new breeding strategies and germplasms were thus limited; (2) many kinds of species in Rubus have been used as medicinal herbs, though only a few species (R. ideaus L., R. chingii Hu, and R. occidentalis L.) have been well studied; (3) the phylogeny of Rubus is very complex, with the main reason for this possibly being the existence of multiple reproductive strategies (apomixis, hybridization, and polyploidization). Our review addresses the utilization of Rubus, summarizing major relevant achievements and proposing core prospects for future application, and thus could serve as a useful roadmap for future elite cultivar breeding and scientific studies.
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Affiliation(s)
- Qinglin Meng
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China; (Q.M.); (H.M.)
| | - Hakim Manghwar
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China; (Q.M.); (H.M.)
| | - Weiming Hu
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China; (Q.M.); (H.M.)
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20
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Comparative Analysis of Transposable Elements and the Identification of Candidate Centromeric Elements in the Prunus Subgenus Cerasus and Its Relatives. Genes (Basel) 2022; 13:genes13040641. [PMID: 35456447 PMCID: PMC9028240 DOI: 10.3390/genes13040641] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/29/2022] [Accepted: 03/31/2022] [Indexed: 12/04/2022] Open
Abstract
The subgenus Cerasus and its relatives include many crucial economic drupe fruits and ornamental plants. Repetitive elements make up a large part of complex genomes, and some of them play an important role in gene regulation that can affect phenotypic variation. However, the variation in their genomes remains poorly understood. This work conducted a comprehensive repetitive sequence identification across the draft genomes of eight taxa of the genus Prunus, including four of the Prunus subgenus Cerasus (Prunus pseudocerasus, P. avium, P. yedoensis and P. × yedoensis) as well as congeneric species (Prunus salicina, P. armeniaca, P. dulcis and P. persica). Annotation results showed high proportions of transposable elements in their genomes, ranging from 52.28% (P. armeniaca) to 61.86% (P. pseudocerasus). The most notable differences in the contents of long terminal repeat retrotransposons (LTR-RTs) and tandem repeats (TRs) were confirmed with de novo identification based on the structure of each genome, which significantly contributed to their genome size variation, especially in P. avium and P.salicina. Sequence comparisons showed many similar LTR-RTs closely related to their phylogenetic relationships, and a highly similar monomer unit of the TR sequence was conserved among species. Additionally, the predicted centromere-associated sequence was located in centromeric regions with FISH in the 12 taxa of Prunus. It presented significantly different signal intensities, even within the diverse interindividual phenotypes for Prunus tomentosa. This study provides insight into the LTR-RT and TR variation within Prunus and increases our knowledge about its role in genome evolution.
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Analysis of a Multi-Environment Trial for Black Raspberry (Rubus occidentalis L.) Quality Traits. Genes (Basel) 2022; 13:genes13030418. [PMID: 35327972 PMCID: PMC8950803 DOI: 10.3390/genes13030418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/21/2022] [Accepted: 02/24/2022] [Indexed: 02/01/2023] Open
Abstract
U.S. black raspberry (BR) production is currently limited by narrowly adapted, elite germplasm. An improved understanding of genetic control and the stability of pomological traits will inform the development of improved BR germplasm and cultivars. To this end, the analysis of a multiple-environment trial of a BR mapping population derived from a cross that combines wild ancestors introgressed with commercial cultivars on both sides of its pedigree has provided insights into genetic variation, genotype-by-environment interactions, quantitative trait loci (QTL), and QTL-by-environment interactions (QEI) of fruit quality traits among diverse field environments. The genetic components and stability of four fruit size traits and six fruit biochemistry traits were characterized in this mapping population following their evaluation over three years at four distinct locations representative of current U.S. BR production. This revealed relatively stable genetic control of the four fruit size traits across the tested production environments and less stable genetic control of the fruit biochemistry traits. Of the fifteen total QTL, eleven exhibited significant QEI. Closely overlapping QTL revealed the linkage of several fruit size traits: fruit mass, drupelet count, and seed fraction. These and related findings are expected to guide further genetic characterization of BR fruit quality, management of breeding germplasm, and development of improved BR cultivars for U.S. production.
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22
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Villamor DEV, Keller KE, Martin RR, Tzanetakis IE. Comparison of High Throughput Sequencing to Standard Protocols for Virus Detection in Berry Crops. PLANT DISEASE 2022; 106:518-525. [PMID: 34282931 DOI: 10.1094/pdis-05-21-0949-re] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We completed a comprehensive study comparing virus detection between high throughput sequencing (HTS) and standard protocols in 30 berry selections (12 Fragaria, 10 Vaccinium, and eight Rubus) with known virus profiles. The study examined temporal detection of viruses at four sampling times encompassing two growing seasons. Within the standard protocols, reverse transcription (RT) PCR proved better than biological indexing. Detection of known viruses by HTS and RT-PCR nearly mirrored each other. HTS provided superior detection compared with RT-PCR on a wide spectrum of variants and discovery of novel viruses. More importantly, in most cases in which the two protocols showed parallel virus detection, 11 viruses in 16 selections were not consistently detected by both methods at all sampling points. Based on these data, we propose a testing requirement of four sampling times over two growing seasons for berry and potentially other crops, to ensure that no virus remains undetected independent of titer, distribution, or other virus-virus or virus-host interactions.
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Affiliation(s)
- D E V Villamor
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
| | - K E Keller
- U.S. Department of Agriculture Agricultural Research Service, Corvallis, OR 97330
| | - R R Martin
- U.S. Department of Agriculture Agricultural Research Service, Corvallis, OR 97330
| | - I E Tzanetakis
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
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23
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Zahid G, Aka Kaçar Y, Dönmez D, Küden A, Giordani T. Perspectives and recent progress of genome-wide association studies (GWAS) in fruits. Mol Biol Rep 2022; 49:5341-5352. [PMID: 35064403 DOI: 10.1007/s11033-021-07055-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/06/2021] [Indexed: 11/25/2022]
Abstract
BACKGROUND Earlier next-generation sequencing technologies are being vastly used to explore, administer, and investigate the gene space with accurate profiling of nucleotide variations in the germplasm. OVERVIEW AND PROGRESS: Recently, novel advancements in high-throughput sequencing technologies allow a genotyping-by-sequencing approach that has opened up new horizons for extensive genotyping exploiting single-nucleotide-polymorphisms (SNPs). This method acts as a bridge to support and minimize a genotype to phenotype gap allowing genetic selection at the genome-wide level, named genomic selection that could facilitate the selection of traits also in the pomology sector. In addition to this, genome-wide genotyping is a prerequisite for genome-wide association studies that have been used successfully to discover the genes, which control polygenic traits including the genetic loci, associated with the trait of interest in fruit crops. AIMS AND PROSPECTS This review article emphasizes the role of genome-wide approaches to unlock and explore the genetic potential along with the detection of SNPs affecting the phenotype of fruit crops and highlights the prospects of genome-wide association studies in fruits.
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Affiliation(s)
- Ghassan Zahid
- Department of Biotechnology, Institute of Natural and Applied Sciences, Çukurova University, 01330, Adana, Turkey.
| | - Yıldız Aka Kaçar
- Department of Horticulture, Faculty of Agriculture, Çukurova University, 01330, Adana, Turkey
| | - Dicle Dönmez
- Biotechnology Research and Application Center, Çukurova University, 01330, Adana, Turkey
| | - Ayzin Küden
- Department of Horticulture, Faculty of Agriculture, Çukurova University, 01330, Adana, Turkey
| | - Tommaso Giordani
- Department of Agriculture, Food and Environment, University of Pisa, 56124, Pisa, Italy
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24
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Chromosome-length genome assemblies of six legume species provide insights into genome organization, evolution, and agronomic traits for crop improvement. J Adv Res 2021; 42:315-329. [PMID: 36513421 PMCID: PMC9788938 DOI: 10.1016/j.jare.2021.10.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/20/2021] [Accepted: 10/24/2021] [Indexed: 12/27/2022] Open
Abstract
INTRODUCTION Legume crops are an important source of protein and oil for human health and in fixing atmospheric N2 for soil enrichment. With an objective to accelerate much-needed genetic analyses and breeding applications, draft genome assemblies were generated in several legume crops; many of them are not high quality because they are mainly based on short reads. However, the superior quality of genome assembly is crucial for a detailed understanding of genomic architecture, genome evolution, and crop improvement. OBJECTIVES Present study was undertaken with an objective of developing improved chromosome-length genome assemblies in six different legumes followed by their systematic investigation to unravel different aspects of genome organization and legume evolution. METHODS We employed in situ Hi-C data to improve the existing draft genomes and performed different evolutionary and comparative analyses using improved genome assemblies. RESULTS We have developed chromosome-length genome assemblies in chickpea, pigeonpea, soybean, subterranean clover, and two wild progenitor species of cultivated groundnut (A. duranensis and A. ipaensis). A comprehensive comparative analysis of these genome assemblies offered improved insights into various evolutionary events that shaped the present-day legume species. We highlighted the expansion of gene families contributing to unique traits such as nodulation in legumes, gravitropism in groundnut, and oil biosynthesis in oilseed legume crops such as groundnut and soybean. As examples, we have demonstrated the utility of improved genome assemblies for enhancing the resolution of "QTL-hotspot" identification for drought tolerance in chickpea and marker-trait associations for agronomic traits in pigeonpea through genome-wide association study. Genomic resources developed in this study are publicly available through an online repository, 'Legumepedia'. CONCLUSION This study reports chromosome-length genome assemblies of six legume species and demonstrates the utility of these assemblies in crop improvement. The genomic resources developed here will have significant role in accelerating genetic improvement applications of legume crops.
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25
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Ireland HS, Wu C, Deng CH, Hilario E, Saei A, Erasmuson S, Crowhurst RN, David KM, Schaffer RJ, Chagné D. The Gillenia trifoliata genome reveals dynamics correlated with growth and reproduction in Rosaceae. HORTICULTURE RESEARCH 2021; 8:233. [PMID: 34719690 PMCID: PMC8558331 DOI: 10.1038/s41438-021-00662-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/28/2021] [Accepted: 07/30/2021] [Indexed: 05/03/2023]
Abstract
The Rosaceae family has striking phenotypic diversity and high syntenic conservation. Gillenia trifoliata is sister species to the Maleae tribe of apple and ~1000 other species. Gillenia has many putative ancestral features, such as herb/sub-shrub habit, dry fruit-bearing and nine base chromosomes. This coalescence of ancestral characters in a phylogenetically important species, positions Gillenia as a 'rosetta stone' for translational science within Rosaceae. We present genomic and phenological resources to facilitate the use of Gillenia for this purpose. The Gillenia genome is the first fully annotated chromosome-level assembly with an ancestral genome complement (x = 9), and with it we developed an improved model of the Rosaceae ancestral genome. MADS and NAC gene family analyses revealed genome dynamics correlated with growth and reproduction and we demonstrate how Gillenia can be a negative control for studying fleshy fruit development in Rosaceae.
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Affiliation(s)
- Hilary S Ireland
- The New Zealand Institute for Plant and Food Research Ltd, Private Bag 92196, Auckland Mail Centre, Auckland, 1142, New Zealand
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland Mail Centre, Auckland, 1142, New Zealand
| | - Chen Wu
- The New Zealand Institute for Plant and Food Research Ltd, Private Bag 92196, Auckland Mail Centre, Auckland, 1142, New Zealand
- Genomics Aotearoa, ℅ Department of Biochemistry, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - Cecilia H Deng
- The New Zealand Institute for Plant and Food Research Ltd, Private Bag 92196, Auckland Mail Centre, Auckland, 1142, New Zealand
- Genomics Aotearoa, ℅ Department of Biochemistry, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - Elena Hilario
- The New Zealand Institute for Plant and Food Research Ltd, Private Bag 92196, Auckland Mail Centre, Auckland, 1142, New Zealand
- Genomics Aotearoa, ℅ Department of Biochemistry, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - Ali Saei
- Genomics Aotearoa, ℅ Department of Biochemistry, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
- The New Zealand Institute for Plant and Food Research Ltd, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - Sylvia Erasmuson
- The New Zealand Institute for Plant and Food Research Ltd, Private Bag 4704, Christchurch Mail Centre, Christchurch, 8140, New Zealand
| | - Ross N Crowhurst
- The New Zealand Institute for Plant and Food Research Ltd, Private Bag 92196, Auckland Mail Centre, Auckland, 1142, New Zealand
- Genomics Aotearoa, ℅ Department of Biochemistry, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - Karine M David
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland Mail Centre, Auckland, 1142, New Zealand
| | - Robert J Schaffer
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland Mail Centre, Auckland, 1142, New Zealand
- The New Zealand Institute for Plant and Food Research Ltd, 55 Old Mill Road, RD 3, Motueka, 7198, New Zealand
| | - David Chagné
- Genomics Aotearoa, ℅ Department of Biochemistry, University of Otago, PO Box 56, Dunedin, 9054, New Zealand.
- The New Zealand Institute for Plant and Food Research Ltd, Private Bag 11600, Palmerston North, 4442, New Zealand.
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Zhou XJ, Li JT, Wang HL, Han JW, Zhang K, Dong SW, Zhang YZ, Ya HY, Cheng YW, Sun SS. The chromosome-scale genome assembly, annotation and evolution of Rhododendron henanense subsp. lingbaoense. Mol Ecol Resour 2021; 22:988-1001. [PMID: 34652864 DOI: 10.1111/1755-0998.13529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 10/10/2021] [Accepted: 10/11/2021] [Indexed: 01/21/2023]
Abstract
Rhododendron henanense subsp. lingbaoense (hereafter referred to as R. henanense) is an endemic species naturally distributed in the Henan province, China, with high horticultural, ornamental and medicinal value. Herein, we report a de novo genome assembly for R. henanense using a combination of PacBio long read and Illumina short read sequencing technologies. In total, we assembled 634.07 Mb with a contig N50 of 2.5 Mb, representing ~96.93% of the estimated genome size. By applying Hi-C data, 13 pseudochromosomes of R. henanense genome were assembled, covering ~98.21% of the genome assembly. The genome was composed of ~65.76% repetitive sequences and 31,098 protein-coding genes, 88.77% of which could be functionally annotated. Rhododendron henanense displayed a high level of synteny with other Rhododendron species from the Hymenanthes subgenus. Our data also suggests that R. henanense genes related to stress responses have undergone expansion, which may underly the unique abiotic and biotic stress resistance of the species. This alpine Rhododendron chromosome-scale genome assembly provides fundamental molecular resources for germplasm conservation, breeding efforts, evolutionary studies, and elucidating the unique biological characteristics of R. henanense.
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Affiliation(s)
- Xiao-Jun Zhou
- Life Science College, Luoyang Normal University, Luoyang, China
| | - Jian-Tao Li
- Wuhan Frasergen Bioinformatics Co., Ltd., Wuhan, China
| | - Hai-Liang Wang
- Henan Xiaoqinling National Nature Reserve Management Bureau, Sanmenxia, China
| | - Jun-Wang Han
- Henan Xiaoqinling National Nature Reserve Management Bureau, Sanmenxia, China
| | - Kai Zhang
- Henan Xiaoqinling National Nature Reserve Management Bureau, Sanmenxia, China
| | - Shuai-Wei Dong
- Henan Xiaoqinling National Nature Reserve Management Bureau, Sanmenxia, China
| | - Yan-Zhao Zhang
- Life Science College, Luoyang Normal University, Luoyang, China
| | - Hui-Yuan Ya
- Life Science College, Luoyang Normal University, Luoyang, China
| | - Yan-Wei Cheng
- Life Science College, Luoyang Normal University, Luoyang, China
| | - Shan-Shan Sun
- Life Science College, Luoyang Normal University, Luoyang, China
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Chen Z, Jiang J, Shu L, Li X, Huang J, Qian B, Wang X, Li X, Chen J, Xu H. Combined transcriptomic and metabolic analyses reveal potential mechanism for fruit development and quality control of Chinese raspberry (Rubus chingii Hu). PLANT CELL REPORTS 2021; 40:1923-1946. [PMID: 34333679 DOI: 10.1007/s00299-021-02758-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 07/15/2021] [Indexed: 05/09/2023]
Abstract
Combined transcriptomic and metabolic analyses reveal that fruit of Rubus chingii Hu launches biosynthesis of phenolic acids and flavonols at beginning of fruit set and then coordinately accumulated or converted to their derivatives. Rubus chingii Hu (Chinese raspberry) is an important dual functional food with nutraceutical and pharmaceutical values. Comprehensively understanding the mechanisms of fruit development and bioactive components synthesis and regulation could accelerate genetic analysis and molecular breeding for the unique species. Combined transcriptomic and metabolic analyses of R. chingii fruits from different developmental stages, including big green, green-to-yellow, yellow-to-orange, and red stages, were conducted. A total of 89,188 unigenes were generated and 57,545 unigenes (64.52%) were annotated. Differential expression genes (DEGs) and differentially accumulated metabolites (DAMs) were mainly involved in the biosynthesis of secondary metabolites. The fruit launched the biosynthesis of phenolic acids and flavonols at the very beginning of fruit set and then coordinately accumulated or converted to their derivatives. This was tightly regulated by expressions of the related genes and MYB and bHLH transcription factors. The core genes products participated in the biosynthesis of ellagic acid (EA) and kaempferol-3-O-rutinoside (K-3-R), such as DAHPS, DQD/SDH, PAL, 4CL, CHS, CHI, F3H, F3'H, FLS, and UGT78D2, and their corresponding metabolites were elaborately characterized. Our research reveals the molecular and chemical mechanisms of the fruit development of R. chingii. The results provide a solid foundation for the genetic analysis, functional genes isolation, fruit quality improvement and modifiable breeding of R. chingii.
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Affiliation(s)
- Zhen Chen
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, College of Life Sciences, Taizhou University, 1139 Civic Road, Taizhou, 318000, Zhejiang, People's Republic of China.
| | - Jingyong Jiang
- Institute of Horticulture, Taizhou Academy of Agricultural Sciences, Linhai, 317000, People's Republic of China
| | - Liangzuo Shu
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, College of Life Sciences, Taizhou University, 1139 Civic Road, Taizhou, 318000, Zhejiang, People's Republic of China
| | - Xiaobai Li
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People's Republic of China
| | - Jing Huang
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, College of Life Sciences, Taizhou University, 1139 Civic Road, Taizhou, 318000, Zhejiang, People's Republic of China
| | - Baoying Qian
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, College of Life Sciences, Taizhou University, 1139 Civic Road, Taizhou, 318000, Zhejiang, People's Republic of China
| | - Xiaoyan Wang
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, College of Life Sciences, Taizhou University, 1139 Civic Road, Taizhou, 318000, Zhejiang, People's Republic of China
| | - Xin Li
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, College of Life Sciences, Taizhou University, 1139 Civic Road, Taizhou, 318000, Zhejiang, People's Republic of China
| | - Jiangxia Chen
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, College of Life Sciences, Taizhou University, 1139 Civic Road, Taizhou, 318000, Zhejiang, People's Republic of China
| | - Haidan Xu
- School of Pharmaceutical, Chemical and Materials Engineering, Taizhou University, Taizhou, 318000, People's Republic of China
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Allan AC, Chagné D. Plant biology: Environmental extremes induce a jump in peach fitness. Curr Biol 2021; 31:R1046-R1048. [PMID: 34520715 DOI: 10.1016/j.cub.2021.07.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
A new study reports that adaptation to climate extremes appears to be driven by replication of a class of transposable elements in peaches and related species. Advanced genomic sequencing techniques may reveal similar events in other plants exposed to extreme stress.
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Affiliation(s)
- Andrew C Allan
- The New Zealand Institute for Plant and Food Research Limited (Plant and Food Research), Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand; School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand.
| | - David Chagné
- The New Zealand Institute for Plant and Food Research Limited (Plant and Food Research), Private Bag 11030, Manawatu Mail Centre, Palmerston North 4442, New Zealand; Genomics Aotearoa, https://www.genomics-aotearoa.org.nz/
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Gao Y, Yang Q, Yan X, Wu X, Yang F, Li J, Wei J, Ni J, Ahmad M, Bai S, Teng Y. High-quality genome assembly of 'Cuiguan' pear (Pyrus pyrifolia) as a reference genome for identifying regulatory genes and epigenetic modifications responsible for bud dormancy. HORTICULTURE RESEARCH 2021; 8:197. [PMID: 34465760 PMCID: PMC8408243 DOI: 10.1038/s41438-021-00632-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 06/09/2021] [Accepted: 06/13/2021] [Indexed: 05/26/2023]
Abstract
Dormancy-associated MADS-box (DAM) genes serve as crucial regulators of the endodormancy cycle in rosaceous plants. Although pear DAM genes have been identified previously, the lack of a high-quality reference genome and techniques to study gene function have prevented accurate genome-wide analysis and functional verification of such genes. Additionally, the contribution of other genes to the regulation of endodormancy release remains poorly understood. In this study, a high-quality genome assembly for 'Cuiguan' pear (Pyrus pyrifolia), which is a leading cultivar with a low chilling requirement cultivated in China, was constructed using PacBio and Hi-C technologies. Using this genome sequence, we revealed that pear DAM genes were tandemly clustered on Chr8 and Chr15 and were differentially expressed in the buds between 'Cuiguan' and the high-chilling-requirement cultivar 'Suli' during the dormancy cycle. Using a virus-induced gene silencing system, we determined the repressive effects of DAM genes on bud break. Several novel genes potentially involved in the regulation of endodormancy release were identified by RNA sequencing and H3K4me3 chromatin immunoprecipitation sequencing analyses of 'Suli' buds during artificial chilling using the new reference genome. Our findings enrich the knowledge of the regulatory mechanism underlying endodormancy release and chilling requirements and provide a foundation for the practical regulation of dormancy release in fruit trees as an adaptation to climate change.
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Affiliation(s)
- Yuhao Gao
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Qinsong Yang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- Key Laboratory for Silviculture and Conservation, Ministry of Education, Beijing Forestry University, Haidian District, Beijing, 100083, China
| | - Xinhui Yan
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Xinyue Wu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Feng Yang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Jianzhao Li
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- College of Agriculture, Ludong University, Yantai, Shandong, 264025, China
| | - Jia Wei
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Junbei Ni
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Mudassar Ahmad
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Songling Bai
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Yuanwen Teng
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- Hainan Institute of Zhejiang University, Sanya, Hainan, 572000, China
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Wang L, Lei T, Han G, Yue J, Zhang X, Yang Q, Ruan H, Gu C, Zhang Q, Qian T, Zhang N, Qian W, Wang Q, Pang X, Shu Y, Gao L, Wang Y. The chromosome-scale reference genome of Rubus chingii Hu provides insight into the biosynthetic pathway of hydrolyzable tannins. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1466-1477. [PMID: 34174125 DOI: 10.1111/tpj.15394] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 06/05/2021] [Accepted: 06/21/2021] [Indexed: 05/09/2023]
Abstract
Rubus chingii Hu (Fu-Pen-Zi), a perennial woody plant in the Rosaceae family, is a characteristic traditional Chinese medicinal plant because of its unique pharmacological effects. There are abundant hydrolyzable tannin (HT) components in R. chingii that provide health benefits. Here, an R. chingii chromosome-scale genome and related functional analysis provide insights into the biosynthetic pathway of HTs. In total, sequence data of 231.21 Mb (155 scaffolds with an N50 of 8.2 Mb) were assembled into seven chromosomes with an average length of 31.4 Mb, and 33 130 protein-coding genes were predicted, 89.28% of which were functionally annotated. Evolutionary analysis showed that R. chingii was most closely related to Rubus occidentalis, from which it was predicted to have diverged 22.46 million years ago (Table S8). Comparative genomic analysis showed that there was a tandem gene cluster of UGT, carboxylesterase (CXE) and SCPL genes on chromosome 02 of R. chingii, including 11 CXE, eight UGT, and six SCPL genes, which may be critical for the synthesis of HTs. In vitro enzyme assays indicated that the proteins encoded by the CXE (LG02.4273) and UGT (LG02.4102) genes have tannin hydrolase and gallic acid glycosyltransferase functions, respectively. The genomic sequence of R. chingii will be a valuable resource for comparative genomic analysis within the Rosaceae family and will be useful for understanding the biosynthesis of HTs.
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Affiliation(s)
- Longji Wang
- Life Science College, Anhui Agricultural University, Hefei, 230036, China
- State Key Laboratory of Tea Plant Biology, Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Ting Lei
- Life Science College, Anhui Agricultural University, Hefei, 230036, China
- State Key Laboratory of Tea Plant Biology, Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Guomin Han
- Life Science College, Anhui Agricultural University, Hefei, 230036, China
| | - Junyang Yue
- Horticulture College, Anhui Agricultural University, Hefei, 230036, China
| | - Xueru Zhang
- GrandOmics Biosciences, Wuhan, 430073, China
| | - Qi Yang
- GrandOmics Biosciences, Wuhan, 430073, China
| | - Haixiang Ruan
- Life Science College, Anhui Agricultural University, Hefei, 230036, China
| | - Chunyang Gu
- Life Science College, Anhui Agricultural University, Hefei, 230036, China
| | - Qiang Zhang
- Life Science College, Anhui Agricultural University, Hefei, 230036, China
| | - Tao Qian
- Life Science College, Anhui Agricultural University, Hefei, 230036, China
| | - Niuniu Zhang
- Life Science College, Anhui Agricultural University, Hefei, 230036, China
| | - Wei Qian
- Life Science College, Anhui Agricultural University, Hefei, 230036, China
| | - Qi Wang
- Life Science College, Anhui Agricultural University, Hefei, 230036, China
| | - Xiaojing Pang
- Life Science College, Anhui Agricultural University, Hefei, 230036, China
| | - Yue Shu
- Life Science College, Anhui Agricultural University, Hefei, 230036, China
| | - Liping Gao
- Life Science College, Anhui Agricultural University, Hefei, 230036, China
- State Key Laboratory of Tea Plant Biology, Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Yunsheng Wang
- Life Science College, Anhui Agricultural University, Hefei, 230036, China
- State Key Laboratory of Tea Plant Biology, Utilization, Anhui Agricultural University, Hefei, 230036, China
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31
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Wang X, Liu S, Zuo H, Zheng W, Zhang S, Huang Y, Pingcuo G, Ying H, Zhao F, Li Y, Liu J, Yi TS, Zan Y, Larkin RM, Deng X, Zeng X, Xu Q. Genomic basis of high-altitude adaptation in Tibetan Prunus fruit trees. Curr Biol 2021; 31:3848-3860.e8. [PMID: 34314676 DOI: 10.1016/j.cub.2021.06.062] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 02/25/2021] [Accepted: 06/22/2021] [Indexed: 01/03/2023]
Abstract
The Great Himalayan Mountains and their foothills are believed to be the place of origin and development of many plant species. The genetic basis of adaptation to high plateaus is a fascinating topic that is poorly understood at the population level. We comprehensively collected and sequenced 377 accessions of Prunus germplasm along altitude gradients ranging from 2,067 to 4,492 m in the Himalayas. We de novo assembled three high-quality genomes of Tibetan Prunus species. A comparative analysis of Prunus genomes indicated a remarkable expansion of the SINE retrotransposons occurred in the genomes of Tibetan species. We observed genetic differentiation between Tibetan peaches from high and low altitudes and that genes associated with light stress signaling, especially UV stress signaling, were enriched in the differentiated regions. By profiling the metabolomes of Tibetan peach fruit, we determined 379 metabolites had significant genetic correlations with altitudes and that in particular phenylpropanoids were positively correlated with altitudes. We identified 62 Tibetan peach-specific SINEs that colocalized with metabolites differentially accumualted in Tibetan relative to cultivated peach. We demonstrated that two SINEs were inserted in a locus controlling the accumulation of 3-O-feruloyl quinic acid. SINE1 was specific to Tibetan peach. SINE2 was predominant in high altitudes and associated with the accumulation of 3-O-feruloyl quinic acid. These genomic and metabolic data for Prunus populations native to the Himalayan region indicate that the expansion of SINE retrotransposons helped Tibetan Prunus species adapt to the harsh environment of the Himalayan plateau by promoting the accumulation of beneficial metabolites.
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Affiliation(s)
- Xia Wang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Horticultural Crop (Fruit trees) Biology and Genetic Improvement (Ministry of Agriculture and Rural Affairs), Huazhong Agricultural University, Wuhan 430070, China
| | - Shengjun Liu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Horticultural Crop (Fruit trees) Biology and Genetic Improvement (Ministry of Agriculture and Rural Affairs), Huazhong Agricultural University, Wuhan 430070, China
| | - Hao Zuo
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Horticultural Crop (Fruit trees) Biology and Genetic Improvement (Ministry of Agriculture and Rural Affairs), Huazhong Agricultural University, Wuhan 430070, China
| | - Weikang Zheng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Horticultural Crop (Fruit trees) Biology and Genetic Improvement (Ministry of Agriculture and Rural Affairs), Huazhong Agricultural University, Wuhan 430070, China
| | - Shanshan Zhang
- Qinghai-Tibet Plateau Fruit Trees Scientific Observation Test Station (Ministry of Agriculture and Rural Affairs), Lhasa, Tibet 850032, China; Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China
| | - Yue Huang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Horticultural Crop (Fruit trees) Biology and Genetic Improvement (Ministry of Agriculture and Rural Affairs), Huazhong Agricultural University, Wuhan 430070, China
| | - Gesang Pingcuo
- Qinghai-Tibet Plateau Fruit Trees Scientific Observation Test Station (Ministry of Agriculture and Rural Affairs), Lhasa, Tibet 850032, China; Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China
| | - Hong Ying
- Qinghai-Tibet Plateau Fruit Trees Scientific Observation Test Station (Ministry of Agriculture and Rural Affairs), Lhasa, Tibet 850032, China; Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China
| | - Fan Zhao
- Qinghai-Tibet Plateau Fruit Trees Scientific Observation Test Station (Ministry of Agriculture and Rural Affairs), Lhasa, Tibet 850032, China; Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China
| | - Yuanrong Li
- Qinghai-Tibet Plateau Fruit Trees Scientific Observation Test Station (Ministry of Agriculture and Rural Affairs), Lhasa, Tibet 850032, China; Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China
| | - Junwei Liu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Horticultural Crop (Fruit trees) Biology and Genetic Improvement (Ministry of Agriculture and Rural Affairs), Huazhong Agricultural University, Wuhan 430070, China
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Yanjun Zan
- Department of Forestry Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå 90736, Sweden
| | - Robert M Larkin
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China
| | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China; Key Laboratory of Horticultural Crop (Fruit trees) Biology and Genetic Improvement (Ministry of Agriculture and Rural Affairs), Huazhong Agricultural University, Wuhan 430070, China
| | - Xiuli Zeng
- Qinghai-Tibet Plateau Fruit Trees Scientific Observation Test Station (Ministry of Agriculture and Rural Affairs), Lhasa, Tibet 850032, China; Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China.
| | - Qiang Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China; Key Laboratory of Horticultural Crop (Fruit trees) Biology and Genetic Improvement (Ministry of Agriculture and Rural Affairs), Huazhong Agricultural University, Wuhan 430070, China.
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32
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Feng C, Wang J, Harris AJ, Folta KM, Zhao M, Kang M. Tracing the Diploid Ancestry of the Cultivated Octoploid Strawberry. Mol Biol Evol 2021; 38:478-485. [PMID: 32941604 PMCID: PMC7826170 DOI: 10.1093/molbev/msaa238] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The commercial strawberry, Fragaria × ananassa, is a recent allo-octoploid that is cultivated worldwide. However, other than Fragaria vesca, which is universally accepted one of its diploid ancestors, its other early diploid progenitors remain unclear. Here, we performed comparative analyses of the genomes of five diploid strawberries, F. iinumae, F. vesca, F. nilgerrensis, F. nubicola, and F. viridis, of which the latter three are newly sequenced. We found that the genomes of these species share highly conserved gene content and gene order. Using an alignment-based approach, we show that F. iinumae and F. vesca are the diploid progenitors to the octoploid F. × ananassa, whereas the other three diploids that we analyzed in this study are not parental species. We generated a fully resolved, dated phylogeny of Fragaria, and determined that the genus arose ∼6.37 Ma. Our results effectively resolve conflicting hypotheses regarding the putative diploid progenitors of the cultivated strawberry, establish a reliable backbone phylogeny for the genus, and provide genetic resources for molecular breeding.
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Affiliation(s)
- Chao Feng
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
| | - Jing Wang
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, China
| | - A J Harris
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China.,Department of Biology, Oberlin College, Oberlin, OH
| | - Kevin M Folta
- Horticultural Sciences Department, University of Florida, Gainesville, FL
| | - Mizhen Zhao
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, China
| | - Ming Kang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
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33
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Zhu X, Tang C, Li Q, Qiao X, Li X, Cai Y, Wang P, Sun Y, Zhang H, Zhang S, Wu J. Characterization of the pectin methylesterase inhibitor gene family in Rosaceae and role of PbrPMEI23/39/41 in methylesterified pectin distribution in pear pollen tube. PLANTA 2021; 253:118. [PMID: 33961146 DOI: 10.1007/s00425-021-03638-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 05/01/2021] [Indexed: 05/02/2023]
Abstract
Pectin methylesterase inhibitor gene family in the seven Rosaceae species (including three pear cultivars) is characterized and three pectin methylesterase inhibitor genes are identified to regulate pollen tube growth in pear. Pectin methylesterase inhibitor (PMEI) participates in a variety of biological processes in plants. However, the information and function of PMEI genes in Rosaceae are largely unknown. In this study, a total of 423 PMEI genes are identified in the genomes of seven Rosaceae species. The PMEI genes in pear are categorized into five subfamilies based on structural analysis and evolutionary analysis. WGD and TD are the main duplication events in the PMEI gene family of pear. Quantitative real-time PCR analysis indicates that PbrPMEI23, PbrPMEI39, and PbrPMEI41 are increasingly expressed during pear pollen tube growth. Under the treatment of recombinant proteins PbrPMEI23, PbrPMEI39 or PbrPMEI41, the content of methylesterified pectin at the region 5-20 μm from the pollen tube tip significantly increases, and the growth of pear pollen tubes is promoted. These results indicate that PMEI regulates the growth of pollen tubes by changing the distribution of methylesterified pectin in the apex.
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Affiliation(s)
- Xiaoxuan Zhu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chao Tang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qionghou Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xin Qiao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xian Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yilin Cai
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing, 210095, China
| | - Peng Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yangyang Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hua Zhang
- Shanghai Vocational College of Agriculture and Forestry, Shanghai, 201699, China
| | - Shaoling Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing, 210095, China
| | - Juyou Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing, 210095, China.
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, 210014, China.
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Park YS, Park JY, Kang JH, Lee WH, Yang TJ. Diversity and authentication of Rubus accessions revealed by complete plastid genome and rDNA sequences. Mitochondrial DNA B Resour 2021; 6:1454-1459. [PMID: 33969195 PMCID: PMC8079122 DOI: 10.1080/23802359.2021.1911712] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 03/26/2021] [Indexed: 11/06/2022] Open
Abstract
Complete plastid genome (plastome) and ribosomal DNA (rDNA) sequences of three Rubus accessions (two Rubus longisepalus and one R. hirsutus) were newly assembled using Illumina whole-genome sequences. Rubus longisepalus Nakai and R. longisepalus var. tozawai, described as different varieties, have identical plastomes and rDNA sequences. The plastomes are 155,957 bp and 156,005 bp and the 45S rDNA transcription unit sizes are 5809 bp and 5811 bp in R. longisepalus and R. hirsutus, respectively. The 5S rDNA transcription unit is an identical 121 bp in three Rubus accessions. We developed three DNA markers to authenticate R. longisepalus and R. hirsutus based on plastome diversity. Phylogenomic analysis revealed that the Rubus species classified as two clades and R. longisepalus, R. hirsutus, and R. chingii are the most closely related species in clade 1.
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Affiliation(s)
- Young Sang Park
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Jee Young Park
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | | | | | - Tae-Jin Yang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
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Li M, Xiao Y, Mount S, Liu Z. An Atlas of Genomic Resources for Studying Rosaceae Fruits and Ornamentals. FRONTIERS IN PLANT SCIENCE 2021; 12:644881. [PMID: 33868343 PMCID: PMC8047320 DOI: 10.3389/fpls.2021.644881] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/22/2021] [Indexed: 05/12/2023]
Abstract
Rosaceae, a large plant family of more than 3,000 species, consists of many economically important fruit and ornamental crops, including peach, apple, strawberry, raspberry, cherry, and rose. These horticultural crops are not only important economic drivers in many regions of the world, but also major sources of human nutrition. Additionally, due to the diversity of fruit types in Rosaceae, this plant family offers excellent opportunities for investigations into fleshy fruit diversity, evolution, and development. With the development of high-throughput sequencing technologies and computational tools, an increasing number of high-quality genomes and transcriptomes of Rosaceae species have become available and will greatly facilitate Rosaceae research and breeding. This review summarizes major genomic resources and genome research progress in Rosaceae, highlights important databases, and suggests areas for further improvement. The availability of these big data resources will greatly accelerate research progress and enhance the agricultural productivity of Rosaceae.
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Affiliation(s)
| | | | | | - Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, United States
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36
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Zhang M, Li P, Yan X, Wang J, Cheng T, Zhang Q. Genome-wide characterization of PEBP family genes in nine Rosaceae tree species and their expression analysis in P. mume. BMC Ecol Evol 2021; 21:32. [PMID: 33622244 PMCID: PMC7901119 DOI: 10.1186/s12862-021-01762-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 02/08/2021] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Phosphatidylethanolamine-binding proteins (PEBPs) constitute a common gene family found among animals, plants and microbes. Plant PEBP proteins play an important role in regulating flowering time, plant architecture as well as seed dormancy. Though PEBP family genes have been well studied in Arabidopsis and other model species, less is known about these genes in perennial trees. RESULTS To understand the evolution of PEBP genes and their functional roles in flowering control, we identified 56 PEBP members belonging to three gene clades (MFT-like, FT-like, and TFL1-like) and five lineages (FT, BFT, CEN, TFL1, and MFT) across nine Rosaceae perennial species. Structural analysis revealed highly conserved gene structure and protein motifs among Rosaceae PEBP proteins. Codon usage analysis showed slightly biased codon usage across five gene lineages. With selection pressure analysis, we detected strong purifying selection constraining divergence within most lineages, while positive selection driving the divergence of FT-like and TFL1-like genes from the MFT-like gene clade. Spatial and temporal expression analyses revealed the essential role of FT in regulating floral bud breaking and blooming in P. mume. By employing a weighted gene co-expression network approach, we inferred a putative FT regulatory module required for dormancy release and blooming in P. mume. CONCLUSIONS We have characterized the PEBP family genes in nine Rosaceae species and examined their phylogeny, genomic syntenic relationship, duplication pattern, and expression profiles during flowering process. These results revealed the evolutionary history of PEBP genes and their functions in regulating floral bud development and blooming among Rosaceae tree species.
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Affiliation(s)
- Man Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Ping Li
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
| | - Xiaolan Yan
- Mei Germplasm Research Center, Wuhan, 430073, China
| | - Jia Wang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Tangren Cheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Qixiang Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China.
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.
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Mayrose I, Lysak MA. The Evolution of Chromosome Numbers: Mechanistic Models and Experimental Approaches. Genome Biol Evol 2020; 13:5923296. [PMID: 33566095 PMCID: PMC7875004 DOI: 10.1093/gbe/evaa220] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2020] [Indexed: 12/16/2022] Open
Abstract
Chromosome numbers have been widely used to describe the most fundamental genomic attribute of an organism or a lineage. Although providing strong phylogenetic signal, chromosome numbers vary remarkably among eukaryotes at all levels of taxonomic resolution. Changes in chromosome numbers regularly serve as indication of major genomic events, most notably polyploidy and dysploidy. Here, we review recent advancements in our ability to make inferences regarding historical events that led to alterations in the number of chromosomes of a lineage. We first describe the mechanistic processes underlying changes in chromosome numbers, focusing on structural chromosomal rearrangements. Then, we focus on experimental procedures, encompassing comparative cytogenomics and genomics approaches, and on computational methodologies that are based on explicit models of chromosome-number evolution. Together, these tools offer valuable predictions regarding historical events that have changed chromosome numbers and genome structures, as well as their phylogenetic and temporal placements.
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Affiliation(s)
- Itay Mayrose
- School of Plant Sciences and Food Security, George S. Wise Faculty of Life Sciences, Tel Aviv University, Israel
| | - Martin A Lysak
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
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A Rosaceae Family-Level Approach To Identify Loci Influencing Soluble Solids Content in Blackberry for DNA-Informed Breeding. G3-GENES GENOMES GENETICS 2020; 10:3729-3740. [PMID: 32769135 PMCID: PMC7534445 DOI: 10.1534/g3.120.401449] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A Rosaceae family-level candidate gene approach was used to identify genes associated with sugar content in blackberry (Rubus subgenus Rubus). Three regions conserved among apple (Malus × domestica), peach (Prunus persica), and alpine strawberry (Fragaria vesca) were identified that contained previously detected sweetness-related quantitative trait loci (QTL) in at least two of the crops. Sugar related genes from these conserved regions and 789 sugar-associated apple genes were used to identify 279 Rubus candidate transcripts. A Hyb-Seq approach was used in conjunction with PacBio sequencing to generate haplotype level sequence information of sugar-related genes for 40 cultivars with high and low soluble solids content from the University of Arkansas and USDA blackberry breeding programs. Polymorphisms were identified relative to the ‘Hillquist’ blackberry (R. argutus) and ORUS 4115-3 black raspberry (R. occidentalis) genomes and tested for their association with soluble solids content (SSC). A total of 173 alleles were identified that were significantly (α = 0.05) associated with SSC. KASP genotyping was conducted for 92 of these alleles on a validation set of blackberries from each breeding program and 48 markers were identified that were significantly associated with SSC. One QTL, qSSC-Ruh-ch1.1, identified in both breeding programs accounted for an increase of 1.5 °Brix and the polymorphisms were detected in the intron space of a sucrose synthase gene. This discovery represents the first environmentally stable sweetness QTL identified in blackberry. The approach demonstrated in this study can be used to develop breeding tools for other crops that have not yet benefited directly from the genomics revolution.
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Yang Y, Ma K, Zhang T, Li L, Wang J, Cheng T, Zhang Q. Characteristics and Expression Analyses of Trehalose-6-Phosphate Synthase Family in Prunus mume Reveal Genes Involved in Trehalose Biosynthesis and Drought Response. Biomolecules 2020; 10:biom10101358. [PMID: 32977584 PMCID: PMC7598203 DOI: 10.3390/biom10101358] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/20/2020] [Accepted: 09/21/2020] [Indexed: 11/16/2022] Open
Abstract
Trehalose and its key synthase (trehalose-6-phosphate synthase, TPS) can improve the drought tolerance of plants. However, little is known about the roles of trehalose and the TPS family in Prunus mume response to drought. In our study, we discovered that the trehalose content in leaf, root, and stem tissues significantly increased in P. mume in response to drought. Therefore, the characteristics and functions of the TPS family are worth investigating in P. mume. We identified nine TPS family members in P. mume, which were divided into two sub-families and characterized by gene structure, promoter elements, protein conserved domains, and protein motifs. We found that the Hydrolase_3 domain and several motifs were highly conserved in Group II instead of Group I. The distinctions between the two groups may result from selective constraints, which we estimated by the dN/dS (ω) ratio. The ω values of all the PmTPS family gene pairs were evaluated as less than 1, indicating that purity selection facilitated their divergence. A phylogenetic tree was constructed using 92 TPSs from 10 Rosaceae species, which were further divided into five clusters. Based on evolutionary analyses, the five clusters of TPS family proteins mainly underwent varied purity selection. The expression patterns of PmTPSs under drought suggested that the TPS family played an important role in the drought tolerance of P. mume. Combining the expression patterns of PmTPSs and the trehalose content changes in leaf, stem, and root tissues under normal conditions and drought stress, we found that the PmTPS2 and PmTPS6 mainly function in the trehalose biosynthesis in P. mume. Our findings not only provide valuable information about the functions of trehalose and TPSs in the drought response of P. mume, but they also contribute to the future drought breeding of P. mume.
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Affiliation(s)
- Yongjuan Yang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; (Y.Y.); (T.Z.); (L.L.)
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing 100083, China; (K.M.); (J.W.); (T.C.)
- National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing 100083, China
- Engineering Research Center of Landscape Environment of Ministry of Education, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing 100083, China
- School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Kaifeng Ma
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing 100083, China; (K.M.); (J.W.); (T.C.)
- National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing 100083, China
- Engineering Research Center of Landscape Environment of Ministry of Education, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing 100083, China
- School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Tengxun Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; (Y.Y.); (T.Z.); (L.L.)
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing 100083, China; (K.M.); (J.W.); (T.C.)
- National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing 100083, China
- Engineering Research Center of Landscape Environment of Ministry of Education, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing 100083, China
- School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Lulu Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; (Y.Y.); (T.Z.); (L.L.)
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing 100083, China; (K.M.); (J.W.); (T.C.)
- National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing 100083, China
- Engineering Research Center of Landscape Environment of Ministry of Education, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing 100083, China
- School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Jia Wang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing 100083, China; (K.M.); (J.W.); (T.C.)
- National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing 100083, China
- Engineering Research Center of Landscape Environment of Ministry of Education, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing 100083, China
- School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Tangren Cheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing 100083, China; (K.M.); (J.W.); (T.C.)
- National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing 100083, China
- Engineering Research Center of Landscape Environment of Ministry of Education, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing 100083, China
- School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Qixiang Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; (Y.Y.); (T.Z.); (L.L.)
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing 100083, China; (K.M.); (J.W.); (T.C.)
- National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing 100083, China
- Engineering Research Center of Landscape Environment of Ministry of Education, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing 100083, China
- School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
- Correspondence: ; Tel.: +86-010-6233-8005
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Barrera-Redondo J, Piñero D, Eguiarte LE. Genomic, Transcriptomic and Epigenomic Tools to Study the Domestication of Plants and Animals: A Field Guide for Beginners. Front Genet 2020; 11:742. [PMID: 32760427 PMCID: PMC7373799 DOI: 10.3389/fgene.2020.00742] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 06/22/2020] [Indexed: 01/07/2023] Open
Abstract
In the last decade, genomics and the related fields of transcriptomics and epigenomics have revolutionized the study of the domestication process in plants and animals, leading to new discoveries and new unresolved questions. Given that some domesticated taxa have been more studied than others, the extent of genomic data can range from vast to nonexistent, depending on the domesticated taxon of interest. This review is meant as a rough guide for students and academics that want to start a domestication research project using modern genomic tools, as well as for researchers already conducting domestication studies that are interested in following a genomic approach and looking for alternate strategies (cheaper or more efficient) and future directions. We summarize the theoretical and technical background needed to carry out domestication genomics, starting from the acquisition of a reference genome and genome assembly, to the sampling design for population genomics, paleogenomics, transcriptomics, epigenomics and experimental validation of domestication-related genes. We also describe some examples of the aforementioned approaches and the relevant discoveries they made to understand the domestication of the studied taxa.
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Affiliation(s)
| | | | - Luis E. Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
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Wang J, Liu W, Zhu D, Zhou X, Hong P, Zhao H, Tan Y, Chen X, Zong X, Xu L, Zhang L, Wei H, Liu Q. A de novo assembly of the sweet cherry ( Prunus avium cv. Tieton) genome using linked-read sequencing technology. PeerJ 2020; 8:e9114. [PMID: 32547856 PMCID: PMC7278891 DOI: 10.7717/peerj.9114] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 04/10/2020] [Indexed: 11/20/2022] Open
Abstract
The sweet cherry (Prunus avium) is one of the most economically important fruit species in the world. However, there is a limited amount of genetic information available for this species, which hinders breeding efforts at a molecular level. We were able to describe a high-quality reference genome assembly and annotation of the diploid sweet cherry (2n = 2x = 16) cv. Tieton using linked-read sequencing technology. We generated over 750 million clean reads, representing 112.63 GB of raw sequencing data. The Supernova assembler produced a more highly-ordered and continuous genome sequence than the current P. avium draft genome, with a contig N50 of 63.65 KB and a scaffold N50 of 2.48 MB. The final scaffold assembly was 280.33 MB in length, representing 82.12% of the estimated Tieton genome. Eight chromosome-scale pseudomolecules were constructed, completing a 214 MB sequence of the final scaffold assembly. De novo, homology-based, and RNA-seq methods were used together to predict 30,975 protein-coding loci. 98.39% of core eukaryotic genes and 97.43% of single copy orthologues were identified in the embryo plant, indicating the completeness of the assembly. Linked-read sequencing technology was effective in constructing a high-quality reference genome of the sweet cherry, which will benefit the molecular breeding and cultivar identification in this species.
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Affiliation(s)
- Jiawei Wang
- Scientific Observation and Experiment Station of Fruits in Huang-huai Area, Ministry of Agriculture, Shandong Institute of Pomology, Taian, Shandong, China
| | - Weizhen Liu
- School of Computer Science and Technology, Wuhan University of Technology, Wuhan, Hubei, China
| | - Dongzi Zhu
- Scientific Observation and Experiment Station of Fruits in Huang-huai Area, Ministry of Agriculture, Shandong Institute of Pomology, Taian, Shandong, China
| | - Xiang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Po Hong
- Scientific Observation and Experiment Station of Fruits in Huang-huai Area, Ministry of Agriculture, Shandong Institute of Pomology, Taian, Shandong, China
| | - Hongjun Zhao
- Scientific Observation and Experiment Station of Fruits in Huang-huai Area, Ministry of Agriculture, Shandong Institute of Pomology, Taian, Shandong, China
| | - Yue Tan
- Scientific Observation and Experiment Station of Fruits in Huang-huai Area, Ministry of Agriculture, Shandong Institute of Pomology, Taian, Shandong, China
| | - Xin Chen
- Scientific Observation and Experiment Station of Fruits in Huang-huai Area, Ministry of Agriculture, Shandong Institute of Pomology, Taian, Shandong, China
| | - Xiaojuan Zong
- Scientific Observation and Experiment Station of Fruits in Huang-huai Area, Ministry of Agriculture, Shandong Institute of Pomology, Taian, Shandong, China
| | - Li Xu
- Scientific Observation and Experiment Station of Fruits in Huang-huai Area, Ministry of Agriculture, Shandong Institute of Pomology, Taian, Shandong, China
| | - Lisi Zhang
- Scientific Observation and Experiment Station of Fruits in Huang-huai Area, Ministry of Agriculture, Shandong Institute of Pomology, Taian, Shandong, China
| | - Hairong Wei
- Scientific Observation and Experiment Station of Fruits in Huang-huai Area, Ministry of Agriculture, Shandong Institute of Pomology, Taian, Shandong, China
| | - Qingzhong Liu
- Scientific Observation and Experiment Station of Fruits in Huang-huai Area, Ministry of Agriculture, Shandong Institute of Pomology, Taian, Shandong, China
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Liu Z, Ma H, Jung S, Main D, Guo L. Developmental Mechanisms of Fleshy Fruit Diversity in Rosaceae. ANNUAL REVIEW OF PLANT BIOLOGY 2020; 71:547-573. [PMID: 32442388 DOI: 10.1146/annurev-arplant-111119-021700] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Rosaceae (the rose family) is an economically important family that includes species prized for high-value fruits and ornamentals. The family also exhibits diverse fruit types, including drupe (peach), pome (apple), drupetum (raspberry), and achenetum (strawberry). Phylogenetic analysis and ancestral fruit-type reconstruction suggest independent evolutionary paths of multiple fleshy fruit types from dry fruits. A recent whole genome duplication in the Maleae/Pyreae tribe (with apple, pear, hawthorn, and close relatives; referred to as Maleae here) may have contributed to the evolution of pome fruit. MADS-box genes, known to regulate floral organ identity, are emerging as important regulators of fruit development. The differential competence of floral organs to respond to fertilization signals may explain the different abilities of floral organs to form fleshy fruit. Future comparative genomics and functional studies in closely related Rosaceae species with distinct fruit types will test hypotheses and provide insights into mechanisms of fleshy fruit diversity. These efforts will be facilitated by the wealth of genome data and resources in Rosaceae.
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Affiliation(s)
- Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742, USA; ,
| | - Hong Ma
- Department of Biology, Eberly College of Science, and The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA;
| | - Sook Jung
- Department of Horticulture, Washington State University, Pullman, Washington 99164, USA; ,
| | - Dorrie Main
- Department of Horticulture, Washington State University, Pullman, Washington 99164, USA; ,
| | - Lei Guo
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742, USA; ,
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Jayakumar V, Ishii H, Seki M, Kumita W, Inoue T, Hase S, Sato K, Okano H, Sasaki E, Sakakibara Y. An improved de novo genome assembly of the common marmoset genome yields improved contiguity and increased mapping rates of sequence data. BMC Genomics 2020; 21:243. [PMID: 32241258 PMCID: PMC7114785 DOI: 10.1186/s12864-020-6657-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 03/09/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The common marmoset (Callithrix jacchus) is one of the most studied primate model organisms. However, the marmoset genomes available in the public databases are highly fragmented and filled with sequence gaps, hindering research advances related to marmoset genomics and transcriptomics. RESULTS Here we utilize single-molecule, long-read sequence data to improve and update the existing genome assembly and report a near-complete genome of the common marmoset. The assembly is of 2.79 Gb size, with a contig N50 length of 6.37 Mb and a chromosomal scaffold N50 length of 143.91 Mb, representing the most contiguous and high-quality marmoset genome up to date. Approximately 90% of the assembled genome was represented in contigs longer than 1 Mb, with approximately 104-fold improvement in contiguity over the previously published marmoset genome. More than 98% of the gaps from the previously published genomes were filled successfully, which improved the mapping rates of genomic and transcriptomic data on to the assembled genome. CONCLUSIONS Altogether the updated, high-quality common marmoset genome assembly provide improvements at various levels over the previous versions of the marmoset genome assemblies. This will allow researchers working on primate genomics to apply the genome more efficiently for their genomic and transcriptomic sequence data.
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Affiliation(s)
- Vasanthan Jayakumar
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa 223-8522 Japan
| | - Hiromi Ishii
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa 223-8522 Japan
| | - Misato Seki
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa 223-8522 Japan
| | - Wakako Kumita
- Department of Marmoset Biology and Medicine, Central Institute for Experimental Animals, Kawasaki, Kanagawa 210-0821 Japan
| | - Takashi Inoue
- Department of Marmoset Biology and Medicine, Central Institute for Experimental Animals, Kawasaki, Kanagawa 210-0821 Japan
| | - Sumitaka Hase
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa 223-8522 Japan
| | - Kengo Sato
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa 223-8522 Japan
| | - Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, Shinjuku, Tokyo, 160-8582 Japan
- Laboratory for Marmoset Neural Architecture, RIKEN Center for Brain Science, Wako-shi, Saitama, 351-0198 Japan
| | - Erika Sasaki
- Department of Marmoset Biology and Medicine, Central Institute for Experimental Animals, Kawasaki, Kanagawa 210-0821 Japan
| | - Yasubumi Sakakibara
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa 223-8522 Japan
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Teterina AA, Willis JH, Phillips PC. Chromosome-Level Assembly of the Caenorhabditis remanei Genome Reveals Conserved Patterns of Nematode Genome Organization. Genetics 2020; 214:769-780. [PMID: 32111628 PMCID: PMC7153949 DOI: 10.1534/genetics.119.303018] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 02/24/2020] [Indexed: 12/23/2022] Open
Abstract
The nematode Caenorhabditis elegans is one of the key model systems in biology, including possessing the first fully assembled animal genome. Whereas C. elegans is a self-reproducing hermaphrodite with fairly limited within-population variation, its relative C. remanei is an outcrossing species with much more extensive genetic variation, making it an ideal parallel model system for evolutionary genetic investigations. Here, we greatly improve on previous assemblies by generating a chromosome-level assembly of the entire C. remanei genome (124.8 Mb of total size) using long-read sequencing and chromatin conformation capture data. Like other fully assembled genomes in the genus, we find that the C. remanei genome displays a high degree of synteny with C. elegans despite multiple within-chromosome rearrangements. Both genomes have high gene density in central regions of chromosomes relative to chromosome ends and the opposite pattern for the accumulation of repetitive elements. C. elegans and C. remanei also show similar patterns of interchromosome interactions, with the central regions of chromosomes appearing to interact with one another more than the distal ends. The new C. remanei genome presented here greatly augments the use of the Caenorhabditis as a platform for comparative genomics and serves as a basis for molecular population genetics within this highly diverse species.
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Affiliation(s)
- Anastasia A Teterina
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403
- Center of Parasitology, A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow 117071, Russia
| | - John H Willis
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403
| | - Patrick C Phillips
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403
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Exploitation of Hi-C sequencing for improvement of genome assembly and in-vitro validation of differentially expressing genes in Jatropha curcas L. 3 Biotech 2020; 10:91. [PMID: 32089986 DOI: 10.1007/s13205-020-2082-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 01/20/2020] [Indexed: 10/25/2022] Open
Abstract
Jatropha curcas is one of the major sources of renewable energy due to potential use of its oil as a biofuel. The genome of this crop is constituted by the high content of repetitive elements. We employed the Hi-C proximity ligation technique to re-scaffold our existing hybrid genome assembly of an elite genotype (RJC1) developed using Illumina and Pacbio technologies. We assembled 99.81% of non-truncated reads to achieve 266.80 Mbp of the genome with an N50 value of 1.58 Mb. Furthermore, we compared the efficiency of Hi-C-augmented genome assembly with the hybrid genome assembly and observed a ~ 50% reduction in scaffolds and a tenfold increase in the N50 value. The gene ontology analysis revealed the identification of terms for molecular function (45.52%), cellular component (33.47%), and biological function (20.99%). Comparative genomic analysis of 13-plant species showed the conservation of 414 lipid metabolizing genes identified in the KEGG pathway analysis. Differential gene expression (DGE) studies were conducted in the healthy and Jatropha mosaic virus-infected leaves via RNA-seq analysis and observed gene expression changes for 2185 genes. Out of these, we observed 546 genes having more than two-fold change of transcript level and among these 259 genes were down-regulated and 287 genes were up-regulated. To validate RNA-seq data, two DEGs were selected for gene expression analysis using qRT-PCR and the data was in correlation with in silico results. RNA-seq analysis further shows the identification of some of the candidate genes and may be useful to develop JMV resistant plants after functional validation. This Hi-C genome assembly provides a detailed accurate reference genome which could be utilized to improve Jatropha and other economically important Euphorbiaceae family members.
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Wu H, Yao D, Chen Y, Yang W, Zhao W, Gao H, Tong C. De Novo Genome Assembly of Populus simonii Further Supports That Populus simonii and Populus trichocarpa Belong to Different Sections. G3 (BETHESDA, MD.) 2020; 10:455-466. [PMID: 31806765 PMCID: PMC7003099 DOI: 10.1534/g3.119.400913] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 12/03/2019] [Indexed: 11/18/2022]
Abstract
Populus simonii is an important tree in the genus Populus, widely distributed in the Northern Hemisphere and having a long cultivation history. Although this species has ecologically and economically important values, its genome sequence is currently not available, hindering the development of new varieties with wider adaptive and commercial traits. Here, we report a chromosome-level genome assembly of P. simonii using PacBio long-read sequencing data aided by Illumina paired-end reads and related genetic linkage maps. The assembly is 441.38 Mb in length and contain 686 contigs with a contig N50 of 1.94 Mb. With the linkage maps, 336 contigs were successfully anchored into 19 pseudochromosomes, accounting for 90.2% of the assembled genome size. Genomic integrity assessment showed that 1,347 (97.9%) of the 1,375 genes conserved among all embryophytes can be found in the P. simonii assembly. Genomic repeat analysis revealed that 41.47% of the P. simonii genome is composed of repetitive elements, of which 40.17% contained interspersed repeats. A total of 45,459 genes were predicted from the P. simonii genome sequence and 39,833 (87.6%) of the genes were annotated with one or more related functions. Phylogenetic analysis indicated that P. simonii and Populus trichocarpa should be placed in different sections, contrary to the previous classification according to morphology. The genome assembly not only provides an important genetic resource for the comparative and functional genomics of different Populus species, but also furnishes one of the closest reference sequences for identifying genomic variants in an F1 hybrid population derived by crossing P. simonii with other Populus species.
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Affiliation(s)
- Hainan Wu
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Dan Yao
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Yuhua Chen
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Wenguo Yang
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Wei Zhao
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Hua Gao
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Chunfa Tong
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
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Shuryak I. Review of resistance to chronic ionizing radiation exposure under environmental conditions in multicellular organisms. JOURNAL OF ENVIRONMENTAL RADIOACTIVITY 2020; 212:106128. [PMID: 31818732 DOI: 10.1016/j.jenvrad.2019.106128] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 12/02/2019] [Accepted: 12/03/2019] [Indexed: 06/10/2023]
Abstract
Ionizing radiation resistance occurs among many phylogenetic groups and its mechanisms remain incompletely understood. Tolerances to acute and chronic irradiation do not always correlate because different mechanisms may be involved. The radioresistance phenomenon becomes even more complex in the field than in the laboratory because the effects of radioactive contamination on natural populations are intertwined with those of other factors, such as bioaccumulation of radionuclides, interspecific competition, seasonal variations in environmental conditions, and land use changes due to evacuation of humans from contaminated areas. Previous reviews of studies performed in radioactive sites like the Kyshtym, Chernobyl, and Fukushima accident regions, and of protracted irradiation experiments, often focused on detecting radiation effects at low doses in radiosensitive organisms. Here we review the literature with a different purpose: to identify organisms with high tolerance to chronic irradiation under environmental conditions, which maintained abundant populations and/or outcompeted more radiosensitive species at high dose rates. Taxa for which consistent evidence for radioresistance came from multiple studies conducted in different locations and at different times were found among plants (e.g. willow and birch trees, sedges), invertebrate and vertebrate animals (e.g. rotifers, some insects, crustaceans and freshwater fish). These organisms are not specialized "extremophiles", but tend to tolerate broad ranges of environmental conditions and stresses, have small genomes, reproduce quickly and/or disperse effectively over long distances. Based on these findings, resistance to radioactive contamination can be examined in a more broad context of chronic stress responses.
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Affiliation(s)
- Igor Shuryak
- Center for Radiological Research, Columbia University Irving Medical Center, 630 West 168th Street, VC-11-234/5, New York, NY, USA.
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Menz I, Lakhwani D, Clotault J, Linde M, Foucher F, Debener T. Analysis of the Rdr1 gene family in different Rosaceae genomes reveals an origin of an R-gene cluster after the split of Rubeae within the Rosoideae subfamily. PLoS One 2020; 15:e0227428. [PMID: 31971947 PMCID: PMC6977733 DOI: 10.1371/journal.pone.0227428] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 12/18/2019] [Indexed: 11/20/2022] Open
Abstract
The Rdr1 gene confers resistance to black spot in roses and belongs to a large TNL gene family, which is organized in two major clusters at the distal end of chromosome 1. We used the recently available chromosome scale assemblies for the R. chinensis 'Old Blush' genome, re-sequencing data for nine rose species and genome data for Fragaria, Rubus, Malus and Prunus to identify Rdr1 homologs from different taxa within Rosaceae. Members of the Rdr1 gene family are organized into two major clusters in R. chinensis and at a syntenic location in the Fragaria genome. Phylogenetic analysis indicates that the two clusters existed prior to the split of Rosa and Fragaria and that one cluster has a more recent origin than the other. Genes belonging to cluster 2, such as the functional Rdr1 gene muRdr1A, were subject to a faster evolution than genes from cluster 1. As no Rdr1 homologs were found in syntenic positions for Prunus persica, Malus x domestica and Rubus occidentalis, a translocation of the Rdr1 clusters to the current positions probably happened after the Rubeae split from other groups within the Rosoideae approximately 70-80 million years ago during the Cretaceous period.
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Affiliation(s)
- Ina Menz
- Institute for Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Deepika Lakhwani
- IRHS, Agrocampus-Ouest, INRA, Université d’Angers, Beaucouzé, France
| | - Jérémy Clotault
- IRHS, Agrocampus-Ouest, INRA, Université d’Angers, Beaucouzé, France
| | - Marcus Linde
- Institute for Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Fabrice Foucher
- IRHS, Agrocampus-Ouest, INRA, Université d’Angers, Beaucouzé, France
| | - Thomas Debener
- Institute for Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
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Jibran R, Spencer J, Fernandez G, Monfort A, Mnejja M, Dzierzon H, Tahir J, Davies K, Chagné D, Foster TM. Two Loci, RiAF3 and RiAF4, Contribute to the Annual-Fruiting Trait in Rubus. FRONTIERS IN PLANT SCIENCE 2019; 10:1341. [PMID: 31708950 PMCID: PMC6824294 DOI: 10.3389/fpls.2019.01341] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 09/26/2019] [Indexed: 05/31/2023]
Abstract
Most Rubus species have a biennial cycle of flowering and fruiting with an intervening period of winter dormancy, in common with many perennial fruit crops. Annual-fruiting (AF) varieties of raspberry (Rubus idaeus and Rubus occidentalis L.) and blackberry (Rubus subgenus Rubus) are able to flower and fruit in one growing season, without the intervening dormant period normally required in biennial-fruiting (BF) varieties. We used a red raspberry (R. idaeus) population segregating for AF obtained from a cross between NC493 and 'Chilliwack' to identify genetic factors controlling AF. Genotyping by sequencing (GBS) was used to generate saturated linkage maps in both parents. Trait mapping in this population indicated that AF is controlled by two newly identified loci (RiAF3 and RiAF4) located on Rubus linkage groups (LGs) 3 and 4. The location of these loci was analyzed using single-nucleotide polymorphism (SNP) markers on independent red raspberry and blackberry populations segregating for the AF trait. This confirmed that AF in Rubus is regulated by loci on LG 3 and 4, in addition to a previously reported locus on LG 7. Comparative RNAseq analysis at the time of floral bud differentiation in an AF and a BF variety revealed candidate genes potentially regulating the trait.
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Affiliation(s)
- Rubina Jibran
- The New Zealand Institute for Plant & Food Research Limited, Palmerston North Research Centre, Palmerston North, New Zealand
| | - Jessica Spencer
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, United States
| | - Gina Fernandez
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, United States
| | - Amparo Monfort
- IRTA (Institut de Recerca I Tecnologia Agroalimentàries), Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Mourad Mnejja
- IRTA (Institut de Recerca I Tecnologia Agroalimentàries), Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Helge Dzierzon
- The New Zealand Institute for Plant & Food Research Limited, Palmerston North Research Centre, Palmerston North, New Zealand
| | - Jibran Tahir
- The New Zealand Institute for Plant & Food Research Limited, Palmerston North Research Centre, Palmerston North, New Zealand
| | - Kevin Davies
- The New Zealand Institute for Plant & Food Research Limited, Palmerston North Research Centre, Palmerston North, New Zealand
| | - David Chagné
- The New Zealand Institute for Plant & Food Research Limited, Palmerston North Research Centre, Palmerston North, New Zealand
| | - Toshi M. Foster
- The New Zealand Institute for Plant & Food Research Limited, Palmerston North Research Centre, Palmerston North, New Zealand
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50
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Foster TM, Bassil NV, Dossett M, Leigh Worthington M, Graham J. Genetic and genomic resources for Rubus breeding: a roadmap for the future. HORTICULTURE RESEARCH 2019; 6:116. [PMID: 31645970 PMCID: PMC6804857 DOI: 10.1038/s41438-019-0199-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 08/17/2019] [Accepted: 08/27/2019] [Indexed: 05/09/2023]
Abstract
Rubus fruits are high-value crops that are sought after by consumers for their flavor, visual appeal, and health benefits. To meet this demand, production of red and black raspberries (R. idaeus L. and R. occidentalis L.), blackberries (R. subgenus Rubus), and hybrids, such as Boysenberry and marionberry, is growing worldwide. Rubus breeding programmes are continually striving to improve flavor, texture, machine harvestability, and yield, provide pest and disease resistance, improve storage and processing properties, and optimize fruits and plants for different production and harvest systems. Breeders face numerous challenges, such as polyploidy, the lack of genetic diversity in many of the elite cultivars, and until recently, the relative shortage of genetic and genomic resources available for Rubus. This review will highlight the development of continually improving genetic maps, the identification of Quantitative Trait Loci (QTL)s controlling key traits, draft genomes for red and black raspberry, and efforts to improve gene models. The development of genetic maps and markers, the molecular characterization of wild species and germplasm, and high-throughput genotyping platforms will expedite breeding of improved cultivars. Fully sequenced genomes and accurate gene models facilitate identification of genes underlying traits of interest and enable gene editing technologies such as CRISPR/Cas9.
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Affiliation(s)
- Toshi M. Foster
- The New Zealand Institute for Plant and Food Research (PFR) Ltd, 55 Old Mill Road, Motueka, New Zealand
| | - Nahla V. Bassil
- USDA ARS National Clonal Germplasm Repository (NCGR), 33447 Peoria Rd., Corvallis, OR USA
| | - Michael Dossett
- Blueberry Council (in Partnership with Agriculture and Agri-Food Canada) Agassiz Food Research Centre, Columbia, BC V0M 1A0 Canada
| | - Margaret Leigh Worthington
- Department of Horticulture, University of Arkansas, 316 Plant Science Building, Fayetteville, AR 72701 USA
| | - Julie Graham
- The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA Scotland
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