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Yu Z, Li J, Wang H, Ping B, Li X, Liu Z, Guo B, Yu Q, Zou Y, Sun Y, Ma F, Zhao T. Transposable elements in Rosaceae: insights into genome evolution, expression dynamics, and syntenic gene regulation. HORTICULTURE RESEARCH 2024; 11:uhae118. [PMID: 38919560 PMCID: PMC11197308 DOI: 10.1093/hr/uhae118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 04/17/2024] [Indexed: 06/27/2024]
Abstract
Transposable elements (TEs) exert significant influence on plant genomic structure and gene expression. Here, we explored TE-related aspects across 14 Rosaceae genomes, investigating genomic distribution, transposition activity, expression patterns, and nearby differentially expressed genes (DEGs). Analyses unveiled distinct long terminal repeat retrotransposon (LTR-RT) evolutionary patterns, reflecting varied genome size changes among nine species over the past million years. In the past 2.5 million years, Rubus idaeus showed a transposition rate twice as fast as Fragaria vesca, while Pyrus bretschneideri displayed significantly faster transposition compared with Crataegus pinnatifida. Genes adjacent to recent TE insertions were linked to adversity resistance, while those near previous insertions were functionally enriched in morphogenesis, enzyme activity, and metabolic processes. Expression analysis revealed diverse responses of LTR-RTs to internal or external conditions. Furthermore, we identified 3695 pairs of syntenic DEGs proximal to TEs in Malus domestica cv. 'Gala' and M. domestica (GDDH13), suggesting TE insertions may contribute to varietal trait differences in these apple varieties. Our study across representative Rosaceae species underscores the pivotal role of TEs in plant genome evolution within this diverse family. It elucidates how these elements regulate syntenic DEGs on a genome-wide scale, offering insights into Rosaceae-specific genomic evolution.
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Affiliation(s)
- Ze Yu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jiale Li
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hanyu Wang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Boya Ping
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xinchu Li
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhiguang Liu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Bocheng Guo
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qiaoming Yu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yangjun Zou
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yaqiang Sun
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fengwang Ma
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Tao Zhao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
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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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Chwil M, Matraszek-Gawron R, Kostryco M, Różańska-Boczula M. Nutritionally Important Pro-Health Active Ingredients and Antioxidant Properties of Fruits and Fruit Juice of Selected Biennial Fruiting Rubus idaeus L. Cultivars. Pharmaceuticals (Basel) 2023; 16:1698. [PMID: 38139824 PMCID: PMC10747748 DOI: 10.3390/ph16121698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/02/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
Raspberry fruits are an important source of many biologically active chemical compounds exerting nutritional and pro-health effects. The study presents a comparative analysis of nutritionally important bioactive chemical compounds-polyphenols; flavonoids, including anthocyanins; vitamin C; amino acids; fatty acids; and primary metabolites-contained in the fruits of three biennial fruiting cultivars, R. idaeus 'Glen Ample', 'Laszka', and 'Radziejowa', i.e., common cultivars in Poland and Europe. The antioxidant activity of fresh fruits and juice was determined with five methods. The analyses revealed the strong free radical scavenging potential of the fruits and juice, confirmed by the high concentration of nutrients, e.g., polyphenols, anthocyanins, vitamin C, amino acids, and fatty acids. The antioxidant activity of the juice determined with the ferric reducing antioxidant power (FRAP) and OH radical methods was from 2.5 to 4.0 times higher than that of the fruits. The following orders of total polyphenol contents were established in the analyzed cultivars: 'Glen Ample' < 'Laszka' < 'Radziejowa' in the fruits and 'Glen Ample' < 'Radziejowa' < 'Laszka' in the juice. The highest antioxidant activity was exhibited by the 'Radziejowa' fruits. Given their high content of dietary fiber, the fruits of the analyzed raspberry cultivars can be consumed by dieting subjects. The concentrations of vitamin C (28-34 mg/100 g) and anthocyanins (20-34 mg/100 g) indicate the biological and pharmacological activity of these fruits. The main unsaturated fatty acids in the fruits were gamma-linoleic acid (C18:2n6c) and alpha-linolenic acid (C18:3n3), which neutralize excess free radicals. The amino acids nutritionally essential to humans were dominated by leucine, arginine, and phenylalanine. This is the first comparative analysis of the antioxidant activity of fruits and juice and the contents of selected active compounds in the fruits of biennial fruiting cultivars of R. idaeus, i.e., a highly commercialized crop in Europe.
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Affiliation(s)
- Mirosława Chwil
- Department of Botany and Plant Physiology, University of Life Sciences in Lublin, Akademicka 15, 20-950 Lublin, Poland;
| | - Renata Matraszek-Gawron
- Department of Botany and Plant Physiology, University of Life Sciences in Lublin, Akademicka 15, 20-950 Lublin, Poland;
| | - Mikołaj Kostryco
- Department of Botany and Plant Physiology, University of Life Sciences in Lublin, Akademicka 15, 20-950 Lublin, Poland;
| | - Monika Różańska-Boczula
- Department of Applied Mathematics and Computer Science, University of Life Sciences in Lublin, Akademicka 13, 20-950 Lublin, Poland;
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Zhang RG, Shang HY, Jia KH, Ma YP. Subgenome phasing for complex allopolyploidy: case-based benchmarking and recommendations. Brief Bioinform 2023; 25:bbad513. [PMID: 38189536 PMCID: PMC10772947 DOI: 10.1093/bib/bbad513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/27/2023] [Accepted: 12/13/2023] [Indexed: 01/09/2024] Open
Abstract
Accurate subgenome phasing is crucial for understanding the origin, evolution and adaptive potential of polyploid genomes. SubPhaser and WGDI software are two common methodologies for subgenome phasing in allopolyploids, particularly in scenarios lacking known diploid progenitors. Triggered by a recent debate over the subgenomic origins of the cultivated octoploid strawberry, we examined four well-documented complex allopolyploidy cases as benchmarks, to evaluate and compare the accuracy of the two software. Our analysis demonstrates that the subgenomic structure phased by both software is in line with prior research, effectively tracing complex allopolyploid evolutionary trajectories despite the limitations of each software. Furthermore, using these validated methodologies, we revisited the controversial issue regarding the progenitors of the octoploid strawberry. The results of both methodologies reaffirm Fragaria vesca and Fragaria iinumae as progenitors of the octoploid strawberry. Finally, we propose recommendations for enhancing the accuracy of subgenome phasing in future studies, recognizing the potential of integrated tools for advanced complex allopolyploidy research and offering a new roadmap for robust subgenome-based phylogenetic analysis.
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Affiliation(s)
- Ren-Gang Zhang
- State Key Laboratory of Plant Diversity and Specialty Crops/Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201 Yunnan, China
- University of Chinese Academy of Sciences, Beijing 101408 Beijing, China
| | - Hong-Yun Shang
- State Key Laboratory of Plant Diversity and Specialty Crops/Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201 Yunnan, China
| | - Kai-Hua Jia
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan 250100 Shandong, China
| | - Yong-Peng Ma
- State Key Laboratory of Plant Diversity and Specialty Crops/Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201 Yunnan, China
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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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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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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: 1] [Impact Index Per Article: 1.0] [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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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: 9] [Impact Index Per Article: 4.5] [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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