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Jara-Cornejo K, Zúñiga PE, Rivera-Mora C, Bustos E, Garrido-Bigotes A, Ruiz-Lara S, Figueroa CR. YABBY transcription factor family in the octoploid Fragaria × ananassa and five diploid Fragaria species. PLANT BIOLOGY (STUTTGART, GERMANY) 2024; 26:735-748. [PMID: 38924267 DOI: 10.1111/plb.13656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 04/02/2024] [Indexed: 06/28/2024]
Abstract
YABBY genes encode specific TFs of seed plants involved in development and formation of leaves, flowers, and fruit. In the present work, genome-wide and expression analyses of the YABBY gene family were performed in six species of the Fragaria genus: Fragaria × ananassa, F. daltoniana, F. nilgerrensis, F. pentaphylla, F. viridis, and F. vesca. The chromosomal location, synteny pattern, gene structure, and phylogenetic analyses were carried out. By combining RNA-seq data and RT-qPCR analysis we explored specific expression of YABBYs in F. × ananassa and F. vesca. We also analysed the promoter regions of FaYABBYs and performed MeJA application to F. × ananassa fruit to observe effects on gene expression. We identified and characterized 25 YABBY genes in F. × ananassa and six in each of the other five species, which belong to FIL/YAB3 (YABBY1), YAB2 (YABBY2), YAB5 (YABBY5), CRC, and INO clades previously described. Division of the YABBY1 clade into YABBY1.1 and YABBY1.2 subclades is reported. We observed differential expression according to tissue, where some FaYABBYs are expressed mainly in leaves and flowers and to a minor extent during fruit development of F. × ananassa. Specifically, the FaINO genes contain jasmonate-responsive cis-acting elements in their promoters which may be functional since FaINOs are upregulated in F. × ananassa fruit under MeJA treatment. This study suggests that YABBY TFs play an important role in the development- and environment-associated responses of the Fragaria genus.
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Affiliation(s)
- K Jara-Cornejo
- Laboratory of Plant Molecular Physiology, Institute of Biological Sciences, Campus Talca, Universidad de Talca, Talca, Chile
- Doctoral Program in Sciences mention in Plant Biology and Biotechnology, Institute of Biological Sciences, Campus Talca, Universidad de Talca, Talca, Chile
- Functional Genomics Laboratory, Institute of Biological Sciences, Campus Talca, Universidad de Talca, Talca, Chile
- Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, Chile
| | - P E Zúñiga
- Laboratory of Plant Molecular Physiology, Institute of Biological Sciences, Campus Talca, Universidad de Talca, Talca, Chile
- Doctoral Program in Sciences mention in Plant Biology and Biotechnology, Institute of Biological Sciences, Campus Talca, Universidad de Talca, Talca, Chile
- Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, Chile
| | - C Rivera-Mora
- Laboratory of Plant Molecular Physiology, Institute of Biological Sciences, Campus Talca, Universidad de Talca, Talca, Chile
- Doctoral Program in Sciences mention in Plant Biology and Biotechnology, Institute of Biological Sciences, Campus Talca, Universidad de Talca, Talca, Chile
- Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, Chile
| | - E Bustos
- Laboratory of Plant Molecular Physiology, Institute of Biological Sciences, Campus Talca, Universidad de Talca, Talca, Chile
- Doctoral Program in Sciences mention in Plant Biology and Biotechnology, Institute of Biological Sciences, Campus Talca, Universidad de Talca, Talca, Chile
- Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, Chile
| | - A Garrido-Bigotes
- Laboratorio de Epigenética Vegetal, Departamento de Silvicultura, Facultad de Ciencias Forestales, Universidad de Concepción, Concepción, Chile
| | - S Ruiz-Lara
- Functional Genomics Laboratory, Institute of Biological Sciences, Campus Talca, Universidad de Talca, Talca, Chile
- Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, Chile
| | - C R Figueroa
- Laboratory of Plant Molecular Physiology, Institute of Biological Sciences, Campus Talca, Universidad de Talca, Talca, Chile
- Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, Chile
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2
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Garg V, Bohra A, Mascher M, Spannagl M, Xu X, Bevan MW, Bennetzen JL, Varshney RK. Unlocking plant genetics with telomere-to-telomere genome assemblies. Nat Genet 2024:10.1038/s41588-024-01830-7. [PMID: 39048791 DOI: 10.1038/s41588-024-01830-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 06/12/2024] [Indexed: 07/27/2024]
Abstract
Contiguous genome sequence assemblies will help us to realize the full potential of crop translational genomics. Recent advances in sequencing technologies, especially long-read sequencing strategies, have made it possible to construct gapless telomere-to-telomere (T2T) assemblies, thus offering novel insights into genome organization and function. Plant genomes pose unique challenges, such as a continuum of ancient to recent polyploidy and abundant highly similar and long repetitive elements. Owing to progress in sequencing approaches, for most crop plants, chromosome-scale reference genome assemblies are available, but T2T assembly construction remains challenging. Here we describe methods for haplotype-resolved, gapless T2T assembly construction in plants, including various crop species. We outline the impact of T2T assemblies in elucidating the roles of repetitive elements in gene regulation, as well as in pangenomics, functional genomics, genome-assisted breeding and targeted genome manipulation. In conjunction with sequence-enriched germplasm repositories, T2T assemblies thus hold great promise for basic and applied plant sciences.
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Affiliation(s)
- Vanika Garg
- WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Abhishek Bohra
- WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
- ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Seeland, Germany
| | - Manuel Spannagl
- WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
- Plant Genome and Systems Biology, German Research Center for Environmental Health, Helmholtz Zentrum München, Neuherberg, Germany
| | - Xun Xu
- WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
- BGI-Shenzhen, Shenzhen, China
| | | | | | - Rajeev K Varshney
- WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia.
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3
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Miga KH. From complete genomes to pangenomes. Am J Hum Genet 2024; 111:1265-1268. [PMID: 38996470 DOI: 10.1016/j.ajhg.2024.05.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 07/14/2024] Open
Abstract
Highlighting the Distinguished Speakers Symposium on "The Future of Human Genetics and Genomics," this collection of articles is based on presentations at the ASHG 2023 Annual Meeting in Washington, DC, in celebration of all our field has accomplished in the past 75 years, since the founding of ASHG in 1948.
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Affiliation(s)
- Karen H Miga
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
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4
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Wei Y, Kong Y, Li H, Yao A, Han J, Zhang W, Li X, Li W, Han D. Genome-Wide Characterization and Expression Profiling of the AP2/ERF Gene Family in Fragaria vesca L. Int J Mol Sci 2024; 25:7614. [PMID: 39062854 PMCID: PMC11277216 DOI: 10.3390/ijms25147614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 07/08/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
The wild strawberry (Fragaria vesca L.; F. vesca) represents a resilient and extensively studied model organism. While the AP2/ERF gene family plays a pivotal role in plant development, its exploration within F. vesca remains limited. In this study, we characterized the AP2/ERF gene family in wild strawberries using the recently released genomic data (F. vesca V6.0). We conducted an analysis of the gene family expansion pattern, we examined gene expression in stem segments and leaves under cold conditions, and we explored its functional attributes. Our investigation revealed that the FvAP2/ERF family comprises 86 genes distributed among four subfamilies: AP2 (17), RAV (6), ERF (62), and Soloist (1). Tandem and segmental duplications significantly contributed to the growth of this gene family. Furthermore, predictive analysis identified several cis-acting elements in the promoter region associated with meristematic tissue expression, hormone regulation, and resistance modulation. Transcriptomic analysis under cold stress unveiled diverse responses among multiple FvAP2/ERFs in stem segments and leaves. Real-time fluorescence quantitative reverse transcription PCR (RT-qPCR) results confirmed elevated expression levels of select genes following the cold treatment. Additionally, overexpression of FvERF23 in Arabidopsis enhanced cold tolerance, resulting in significantly increased fresh weight and root length compared to the wild-type control. These findings lay the foundation for further exploration into the functional roles of FvAP2/ERF genes.
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Affiliation(s)
| | | | | | | | | | | | | | - Wenhui Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (Y.W.); (Y.K.); (H.L.); (A.Y.); (J.H.); (W.Z.); (X.L.)
| | - Deguo Han
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (Y.W.); (Y.K.); (H.L.); (A.Y.); (J.H.); (W.Z.); (X.L.)
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5
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Li F, Hou Z, Xu S, Han D, Li B, Hu H, Liu J, Cai S, Gan Z, Gu Y, Zhang X, Zhou X, Wang S, Zhao J, Mei Y, Zhang J, Wang Z, Wang J. Haplotype-resolved genomes of octoploid species in Phyllanthaceae family reveal a critical role for polyploidization and hybridization in speciation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:348-363. [PMID: 38606539 DOI: 10.1111/tpj.16767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 03/14/2024] [Accepted: 03/31/2024] [Indexed: 04/13/2024]
Abstract
The Phyllanthaceae family comprises a diverse range of plants with medicinal, edible, and ornamental value, extensively cultivated worldwide. Polyploid species commonly occur in Phyllanthaceae. Due to the rather complex genomes and evolutionary histories, their speciation process has been still lacking in research. In this study, we generated chromosome-scale haplotype-resolved genomes of two octoploid species (Phyllanthus emblica and Sauropus spatulifolius) in Phyllanthaceae family. Combined with our previously reported one tetraploid (Sauropus androgynus) and one diploid species (Phyllanthus cochinchinensis) from the same family, we explored their speciation history. The three polyploid species were all identified as allopolyploids with subgenome A/B. Each of their two distinct subgenome groups from various species was uncovered to independently share a common diploid ancestor (Ancestor-AA and Ancestor-BB). Via different evolutionary routes, comprising various scenarios of bifurcating divergence, allopolyploidization (hybrid polyploidization), and autopolyploidization, they finally evolved to the current tetraploid S. androgynus, and octoploid S. spatulifolius and P. emblica, respectively. We further discuss the variations in copy number of alleles and the potential impacts within the two octoploids. In addition, we also investigated the fluctuation of metabolites with medical values and identified the key factor in its biosynthesis process in octoploids species. Our study reconstructed the evolutionary history of these Phyllanthaceae species, highlighting the critical roles of polyploidization and hybridization in their speciation processes. The high-quality genomes of the two octoploid species provide valuable genomic resources for further research of evolution and functional genomics.
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Affiliation(s)
- Fangping Li
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crop Research Institute, Guangdong Academy of Agriculture Sciences, Guangzhou, 510640, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Ecology and Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Zhuangwei Hou
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crop Research Institute, Guangdong Academy of Agriculture Sciences, Guangzhou, 510640, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Shiqiang Xu
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crop Research Institute, Guangdong Academy of Agriculture Sciences, Guangzhou, 510640, China
| | - Danlu Han
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, 510631, Guangzhou, China
| | - Bin Li
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crop Research Institute, Guangdong Academy of Agriculture Sciences, Guangzhou, 510640, China
| | - Haifei Hu
- Rice Research Institute & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Jieying Liu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Shike Cai
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crop Research Institute, Guangdong Academy of Agriculture Sciences, Guangzhou, 510640, China
| | - Zhenpeng Gan
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Yan Gu
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crop Research Institute, Guangdong Academy of Agriculture Sciences, Guangzhou, 510640, China
| | - Xiufeng Zhang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Xiaofan Zhou
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Shaokui Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Junliang Zhao
- Rice Research Institute & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Yu Mei
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crop Research Institute, Guangdong Academy of Agriculture Sciences, Guangzhou, 510640, China
| | - Jisen Zhang
- State Key Lab for Conservation and Utilization of Subtropical Agric-Biological Resources, Guangxi University, Nanning, 530005, China
| | - Zefu Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Ecology and Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Jihua Wang
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crop Research Institute, Guangdong Academy of Agriculture Sciences, Guangzhou, 510640, China
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6
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Song Y, Zhang Y, Wang X, Yu X, Liao Y, Zhang H, Li L, Wang Y, Liu B, Li W. Telomere-to-telomere reference genome for Panax ginseng highlights the evolution of saponin biosynthesis. HORTICULTURE RESEARCH 2024; 11:uhae107. [PMID: 38883331 PMCID: PMC11179851 DOI: 10.1093/hr/uhae107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 03/31/2024] [Indexed: 06/18/2024]
Abstract
Ginseng (Panax ginseng) is a representative of Chinese traditional medicine, also used worldwide, while the triterpene saponin ginsenoside is the most important effective compound within it. Ginseng is an allotetraploid, with complex genetic background, making the study of its metabolic evolution challenging. In this study, we assembled a telomere-to-telomere ginseng reference genome, constructed of 3.45 Gb with 24 chromosomes and 77 266 protein-coding genes. Additionally, the reference genome was divided into two subgenomes, designated as subgenome A and B. Subgenome A contains a larger number of genes, whereas subgenome B has a general expression advantage, suggesting that ginseng subgenomes experienced asymmetric gene loss with biased gene expression. The two subgenomes separated approximately 6.07 million years ago, and subgenome B shows the closest relation to Panax vietnamensis var. fuscidiscus. Comparative genomics revealed an expansion of gene families associated with ginsenoside biosynthesis in both ginseng subgenomes. Furthermore, both tandem duplications and proximal duplications play crucial roles in ginsenoside biosynthesis. We also screened functional genes identified in previous research and found that some of these genes located in colinear regions between subgenomes have divergence functions, revealing an unbalanced evolution in both subgenomes and the saponin biosynthesis pathway in ginseng. Our work provides important resources for future genetic studies and breeding programs of ginseng, as well as the biosynthesis of ginsenosides.
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Affiliation(s)
- Yiting Song
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yating Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Xu Wang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Xikai Yu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yi Liao
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Hao Zhang
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Linfeng Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of Yangtze River Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Songhu Road 2005, Shanghai 200433, China
| | - Yingping Wang
- State-Local Joint Engineering Research Center of Ginseng Breeding and Application, Jilin Agricultural University, Changchun 130118, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Wei Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Kunpeng Institute of Modern Agriculture at Foshan, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
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7
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Wijesundara UK, Masouleh AK, Furtado A, Dillon NL, Henry RJ. A chromosome-level genome of mango exclusively from long-read sequence data. THE PLANT GENOME 2024; 17:e20441. [PMID: 38462715 DOI: 10.1002/tpg2.20441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/28/2024] [Accepted: 02/04/2024] [Indexed: 03/12/2024]
Abstract
Improvements in long-read sequencing techniques have greatly accelerated plant genome sequencing. Current de novo assemblies are routinely achieved by assembling long-read sequence data into contigs that are assembled to chromosome level by chromatin conformation capture. We report here a chromosome-level mango genome using only PacBio high-fidelity (HiFi) long reads. HiFi reads at high coverage (204x) resulted in the assembly of 17 chromosomes, each as a single contig with telomeres at both ends. The remaining three chromosomes were represented each by two contigs, with telomeres at one end and ribosomal repeats at the other end. Analyzing contig ends allowed them to be paired and linked to generate the remaining three complete chromosomes, telomere-to-telomere but with ribosomal repeats of uncertain length. The assembled genome was 365 Mb with 100% completeness as assessed by Benchmarking Universal Single-Copy Orthologs analysis. The haplotypes assembled demonstrated extensive structural differences. This approach using very high genome coverage may be useful for assembling high-quality genomes for many other plants.
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Affiliation(s)
- Upendra Kumari Wijesundara
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Queensland, Australia
| | - Ardashir Kharabian Masouleh
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Queensland, Australia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Queensland, Australia
| | - Natalie L Dillon
- Department of Agriculture and Fisheries, Mareeba, Queensland, Australia
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Queensland, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Queensland, Brisbane, Queensland, Australia
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8
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Vondracek K, Altpeter F, Liu T, Lee S. Advances in genomics and genome editing for improving strawberry ( Fragaria ×ananassa). Front Genet 2024; 15:1382445. [PMID: 38706796 PMCID: PMC11066249 DOI: 10.3389/fgene.2024.1382445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 04/04/2024] [Indexed: 05/07/2024] Open
Abstract
The cultivated strawberry, Fragaria ×ananassa, is a recently domesticated fruit species of economic interest worldwide. As such, there is significant interest in continuous varietal improvement. Genomics-assisted improvement, including the use of DNA markers and genomic selection have facilitated significant improvements of numerous key traits during strawberry breeding. CRISPR/Cas-mediated genome editing allows targeted mutations and precision nucleotide substitutions in the target genome, revolutionizing functional genomics and crop improvement. Genome editing is beginning to gain traction in the more challenging polyploid crops, including allo-octoploid strawberry. The release of high-quality reference genomes and comprehensive subgenome-specific genotyping and gene expression profiling data in octoploid strawberry will lead to a surge in trait discovery and modification by using CRISPR/Cas. Genome editing has already been successfully applied for modification of several strawberry genes, including anthocyanin content, fruit firmness and tolerance to post-harvest disease. However, reports on many other important breeding characteristics associated with fruit quality and production are still lacking, indicating a need for streamlined genome editing approaches and tools in Fragaria ×ananassa. In this review, we present an overview of the latest advancements in knowledge and breeding efforts involving CRISPR/Cas genome editing for the enhancement of strawberry varieties. Furthermore, we explore potential applications of this technology for improving other Rosaceous plant species.
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Affiliation(s)
- Kaitlyn Vondracek
- Gulf Coast Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Wimauma, FL, United States
- University of Florida, Horticultural Sciences Department, Institute of Food and Agricultural Sciences, Gainesville, FL, United States
| | - Fredy Altpeter
- University of Florida, Agronomy Department, Institute of Food and Agricultural Sciences, Gainesville, FL, United States
| | - Tie Liu
- University of Florida, Horticultural Sciences Department, Institute of Food and Agricultural Sciences, Gainesville, FL, United States
| | - Seonghee Lee
- Gulf Coast Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Wimauma, FL, United States
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9
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Xie L, Gong X, Yang K, Huang Y, Zhang S, Shen L, Sun Y, Wu D, Ye C, Zhu QH, Fan L. Technology-enabled great leap in deciphering plant genomes. NATURE PLANTS 2024; 10:551-566. [PMID: 38509222 DOI: 10.1038/s41477-024-01655-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 02/20/2024] [Indexed: 03/22/2024]
Abstract
Plant genomes provide essential and vital basic resources for studying many aspects of plant biology and applications (for example, breeding). From 2000 to 2020, 1,144 genomes of 782 plant species were sequenced. In the past three years (2021-2023), 2,373 genomes of 1,031 plant species, including 793 newly sequenced species, have been assembled, representing a great leap. The 2,373 newly assembled genomes, of which 63 are telomere-to-telomere assemblies and 921 have been generated in pan-genome projects, cover the major phylogenetic clades. Substantial advances in read length, throughput, accuracy and cost-effectiveness have notably simplified the achievement of high-quality assemblies. Moreover, the development of multiple software tools using different algorithms offers the opportunity to generate more complete and complex assemblies. A database named N3: plants, genomes, technologies has been developed to accommodate the metadata associated with the 3,517 genomes that have been sequenced from 1,575 plant species since 2000. We also provide an outlook for emerging opportunities in plant genome sequencing.
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Affiliation(s)
- Lingjuan Xie
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou, China
- Hainan Institute of Zhejiang University, Yazhou Bay, Shanya, China
| | - Xiaojiao Gong
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou, China
| | - Kun Yang
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou, China
| | - Yujie Huang
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou, China
| | - Shiyu Zhang
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou, China
| | - Leti Shen
- Hainan Institute of Zhejiang University, Yazhou Bay, Shanya, China
| | - Yanqing Sun
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou, China
| | - Dongya Wu
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou, China
| | - Chuyu Ye
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou, China
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, Black Mountain Laboratories, Canberra, Australia
| | - Longjiang Fan
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou, China.
- Hainan Institute of Zhejiang University, Yazhou Bay, Shanya, China.
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10
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He S, Dong W, Chen J, Zhang J, Lin W, Yang S, Xu D, Zhou Y, Miao B, Wang W, Chen F. DataColor: unveiling biological data relationships through distinctive color mapping. HORTICULTURE RESEARCH 2024; 11:uhad273. [PMID: 38333729 PMCID: PMC10852383 DOI: 10.1093/hr/uhad273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 12/06/2023] [Indexed: 02/10/2024]
Abstract
In the era of rapid advancements in high-throughput omics technologies, the visualization of diverse data types with varying orders of magnitude presents a pressing challenge. To bridge this gap, we introduce DataColor, an all-encompassing software solution meticulously crafted to address this challenge. Our aim is to empower users with the ability to handle a wide array of data types through an assortment of tools, while simultaneously streamlining parameter selection for rapid insights and detailed enhancements. DataColor stands as a robust toolkit, encompassing 23 distinct tools coupled with over 600 parameters. The defining characteristic of this toolkit is its adept utilization of the color spectrum, allowing for the representation of data spanning diverse types and magnitudes. Through the integration of advanced algorithms encompassing data clustering, normalization, squarified layouts, and customizable parameters, DataColor unveils an abundance of insights that lay hidden within the intricate relationships embedded in the data. Whether you find yourself navigating the analysis of expansive datasets or embarking on the quest to visualize intricate patterns, DataColor stands as the comprehensive and potent solution. We extend the availability of DataColor to all users at no cost, accessible through the following link: https://github.com/frankgenome/DataColor.
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Affiliation(s)
- Shuang He
- Sanya Institute of Breeding and Multiplication, National Key Laboratory for Tropical Crop Breeding, Hainan University, Sanya 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Wei Dong
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou 510055, China
| | - Junhao Chen
- Department of Biology, Saint Louis University, St Louis, MO 63103, USA
| | - Junyu Zhang
- Sanya Institute of Breeding and Multiplication, National Key Laboratory for Tropical Crop Breeding, Hainan University, Sanya 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Weiwei Lin
- Merkle Business Information Consultancy (Nanjing) Co., Ltd, Nanjing 210032, China
| | - Shuting Yang
- Sanya Institute of Breeding and Multiplication, National Key Laboratory for Tropical Crop Breeding, Hainan University, Sanya 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Dong Xu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Yuhan Zhou
- State Key Laboratory of Rice Biology & Breeding, Zhejiang Provincial Key Laboratory of Crop Germplasm, The Advanced Seed Institute, Zhejiang University, Hangzhou 310058, China
| | - Benben Miao
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, Fujian, China
| | - Wenquan Wang
- Sanya Institute of Breeding and Multiplication, National Key Laboratory for Tropical Crop Breeding, Hainan University, Sanya 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Fei Chen
- Sanya Institute of Breeding and Multiplication, National Key Laboratory for Tropical Crop Breeding, Hainan University, Sanya 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
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11
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Wang X, Tu M, Wang Y, Zhang Y, Yin W, Fang J, Gao M, Li Z, Zhan W, Fang Y, Song J, Xi Z, Wang X. Telomere-to-telomere and gap-free genome assembly of a susceptible grapevine species (Thompson Seedless) to facilitate grape functional genomics. HORTICULTURE RESEARCH 2024; 11:uhad260. [PMID: 38288254 PMCID: PMC10822838 DOI: 10.1093/hr/uhad260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 11/26/2023] [Indexed: 01/31/2024]
Abstract
Grapes are globally recognized as economically significant fruit trees. Among grape varieties, Thompson Seedless holds paramount influence for fresh consumption and for extensive applications in winemaking, drying, and juicing. This variety is one of the most efficient genotypes for grape genetic modification. However, the lack of a high-quality genome has impeded effective breeding efforts. Here, we present the high-quality reference genome of Thompson Seedless with all 19 chromosomes represented as 19 contiguous sequences (N50 = 27.1 Mb) with zero gaps and prediction of all telomeres and centromeres. Compared with the previous assembly (TSv1 version), the new assembly incorporates an additional 31.5 Mb of high-quality sequenced data with annotation of a total of 30 397 protein-coding genes. We also performed a meticulous analysis to identify nucleotide-binding leucine-rich repeat genes (NLRs) in Thompson Seedless and two wild grape varieties renowned for their disease resistance. Our analysis revealed a significant reduction in the number of two types of NLRs, TIR-NB-LRR (TNL) and CC-NB-LRR (CNL), in Thompson Seedless, which may have led to its sensitivity to many fungal diseases, such as powdery mildew, and an increase in the number of a third type, RPW8 (resistance to powdery mildew 8)-NB-LRR (RNL). Subsequently, transcriptome analysis showed significant enrichment of NLRs during powdery mildew infection, emphasizing the pivotal role of these elements in grapevine's defense against powdery mildew. The successful assembly of a high-quality Thompson Seedless reference genome significantly contributes to grape genomics research, providing insight into the importance of seedlessness, disease resistance, and color traits, and these data can be used to facilitate grape molecular breeding efforts.
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Affiliation(s)
- Xianhang Wang
- College of Enology, College of Food Science and Engineering, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Shaanxi Engineering Research Center for Viti-Viniculture, Heyang Viti-Viniculture Station, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mingxing Tu
- College of Enology, College of Food Science and Engineering, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Shaanxi Engineering Research Center for Viti-Viniculture, Heyang Viti-Viniculture Station, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ya Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yali Zhang
- College of Enology, College of Food Science and Engineering, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Shaanxi Engineering Research Center for Viti-Viniculture, Heyang Viti-Viniculture Station, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wuchen Yin
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jinghao Fang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Min Gao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhi Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wei Zhan
- Xi'an Haorui Genomics Technology Co., Ltd, Xi'an 710116, China
| | - Yulin Fang
- College of Enology, College of Food Science and Engineering, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Shaanxi Engineering Research Center for Viti-Viniculture, Heyang Viti-Viniculture Station, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Junyang Song
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhumei Xi
- College of Enology, College of Food Science and Engineering, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Shaanxi Engineering Research Center for Viti-Viniculture, Heyang Viti-Viniculture Station, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiping Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
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12
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Song Y, Peng Y, Liu L, Li G, Zhao X, Wang X, Cao S, Muyle A, Zhou Y, Zhou H. Phased gap-free genome assembly of octoploid cultivated strawberry illustrates the genetic and epigenetic divergence among subgenomes. HORTICULTURE RESEARCH 2024; 11:uhad252. [PMID: 38269295 PMCID: PMC10807706 DOI: 10.1093/hr/uhad252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 11/18/2023] [Indexed: 01/26/2024]
Abstract
The genetic and epigenetic mechanisms underlying the coexistence and coordination of the four diverged subgenomes (ABCD) in octoploid strawberries (Fragaria × ananassa) remains poorly understood. In this study, we have assembled a haplotype-phased gap-free octoploid genome for the strawberry, which allowed us to uncover the sequence, structure, and epigenetic divergences among the subgenomes. The diploid progenitors of the octoploid strawberry, apart from subgenome A (Fragaria vesca), have been a subject of public controversy. Phylogenomic analyses revealed a close relationship between diploid species Fragaria iinumae and subgenomes B, C, and D. Subgenome A, closely related to F. vesca, retains the highest number of genes, exhibits the lowest content of transposable elements (TEs), experiences the strongest purifying selection, shows the lowest DNA methylation levels, and displays the highest expression level compared to the other three subgenomes. Transcriptome and DNA methylome analyses revealed that subgenome A-biased genes were enriched in fruit development biological processes. In contrast, although subgenomes B, C, and D contain equivalent amounts of repetitive sequences, they exhibit diverged methylation levels, particularly for TEs located near genes. Taken together, our findings provide valuable insights into the evolutionary patterns of subgenome structure, divergence and epigenetic dynamics in octoploid strawberries, which could be utilized in strawberry genetics and breeding research.
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Affiliation(s)
- Yanhong Song
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Yanling Peng
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Lifeng Liu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Gang Li
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Xia Zhao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Xu Wang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Shuo Cao
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Aline Muyle
- CEFE, University of Montpellier, CNRS, EPHE, IRD, Montpellier 34000, France
| | - Yongfeng Zhou
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- National Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 570000, China
| | - Houcheng Zhou
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
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13
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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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14
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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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15
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Xu XD, Zhao RP, Xiao L, Lu L, Gao M, Luo YH, Zhou ZW, Ye SY, Qian YQ, Fan BL, Shang X, Shi P, Zeng W, Cao S, Wu Z, Yan H, Chen LL, Song JM. Telomere-to-telomere assembly of cassava genome reveals the evolution of cassava and divergence of allelic expression. HORTICULTURE RESEARCH 2023; 10:uhad200. [PMID: 38023477 PMCID: PMC10673656 DOI: 10.1093/hr/uhad200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 09/28/2023] [Indexed: 12/01/2023]
Abstract
Cassava is a crucial crop that makes a significant contribution to ensuring human food security. However, high-quality telomere-to-telomere cassava genomes have not been available up to now, which has restricted the progress of haploid molecular breeding for cassava. In this study, we constructed two nearly complete haploid resolved genomes and an integrated, telomere-to-telomere gap-free reference genome of an excellent cassava variety, 'Xinxuan 048', thereby providing a new high-quality genomic resource. Furthermore, the evolutionary history of several species within the Euphorbiaceae family was revealed. Through comparative analysis of haploid genomes, it was found that two haploid genomes had extensive differences in linear structure, transcriptome features, and epigenetic characteristics. Genes located within the highly divergent regions and differentially expressed alleles are enriched in the functions of auxin response and the starch synthesis pathway. The high heterozygosity of cassava 'Xinxuan 048' leads to rapid trait segregation in the first selfed generation. This study provides a theoretical basis and genomic resource for molecular breeding of cassava haploids.
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Affiliation(s)
- Xin-Dong Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Ru-Peng Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Liang Xiao
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Liuying Lu
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Min Gao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Yu-Hong Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Zu-Wen Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Si-Ying Ye
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Yong-Qing Qian
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Bing-Liang Fan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Xiaohong Shang
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Pingli Shi
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Wendan Zeng
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Sheng Cao
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Zhengdan Wu
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Huabing Yan
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Ling-Ling Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Jia-Ming Song
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
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16
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Zeng T, He Z, He J, Lv W, Huang S, Li J, Zhu L, Wan S, Zhou W, Yang Z, Zhang Y, Luo C, He J, Wang C, Wang L. The telomere-to-telomere gap-free reference genome of wild blueberry ( Vaccinium duclouxii) provides its high soluble sugar and anthocyanin accumulation. HORTICULTURE RESEARCH 2023; 10:uhad209. [PMID: 38023474 PMCID: PMC10681038 DOI: 10.1093/hr/uhad209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 10/19/2023] [Indexed: 12/01/2023]
Abstract
Vaccinium duclouxii, endemic to southwestern China, is a berry-producing shrub or small tree belonging to the Ericaceae family, with high nutritive, medicinal, and ornamental value, abundant germplasm resources, and good edible properties. In addition, V. duclouxii exhibits strong tolerance to adverse environmental conditions, making it a promising candidate for research and offering wide-ranging possibilities for utilization. However, the lack of V. duclouxii genome sequence has hampered its development and utilization. Here, a high-quality telomere-to-telomere genome sequence of V. duclouxii was de novo assembled and annotated. All of 12 chromosomes were assembled into gap-free single contigs, providing the highest integrity and quality assembly reported so far for blueberry. The V. duclouxii genome is 573.67 Mb, which encodes 41 953 protein-coding genes. Combining transcriptomics and metabolomics analyses, we have uncovered the molecular mechanisms involved in sugar and acid accumulation and anthocyanin biosynthesis in V. duclouxii. This provides essential molecular information for further research on the quality of V. duclouxii. Moreover, the high-quality telomere-to-telomere assembly of the V. duclouxii genome will provide insights into the genomic evolution of Vaccinium and support advancements in blueberry genetics and molecular breeding.
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Affiliation(s)
- Tuo Zeng
- School of Life Sciences, Guizhou Normal University, Guiyang 550000, China
| | - Zhijiao He
- Institute of Alpine Economic Plant, Yunnan Academy of Agricultural Sciences, Lijiang 674199, Yunnan, China
| | - Jiefang He
- School of Life Sciences, Guizhou Normal University, Guiyang 550000, China
| | - Wei Lv
- School of Life Sciences, Guizhou Normal University, Guiyang 550000, China
| | - Shixiang Huang
- School of Life Sciences, Guizhou Normal University, Guiyang 550000, China
| | - Jiawen Li
- School of Advanced Agricultural Sciences, Peking University, 100871 Beijing, China
| | - Liyong Zhu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Shuang Wan
- Wuhan Benagen Technology Co., Ltd, Wuhan 430070, China
| | - Wanfei Zhou
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhengsong Yang
- Institute of Alpine Economic Plant, Yunnan Academy of Agricultural Sciences, Lijiang 674199, Yunnan, China
| | - Yatao Zhang
- School of Life Sciences, Guizhou Normal University, Guiyang 550000, China
| | - Chong Luo
- School of Life Sciences, Guizhou Normal University, Guiyang 550000, China
| | - Jiawei He
- Institute of Alpine Economic Plant, Yunnan Academy of Agricultural Sciences, Lijiang 674199, Yunnan, China
| | - Caiyun Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Liangsheng Wang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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17
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Sun M, Yao C, Shu Q, He Y, Chen G, Yang G, Xu S, Liu Y, Xue Z, Wu J. Telomere-to-telomere pear ( Pyrus pyrifolia) reference genome reveals segmental and whole genome duplication driving genome evolution. HORTICULTURE RESEARCH 2023; 10:uhad201. [PMID: 38023478 PMCID: PMC10681005 DOI: 10.1093/hr/uhad201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 10/01/2023] [Indexed: 12/01/2023]
Abstract
Previously released pear genomes contain a plethora of gaps and unanchored genetic regions. Here, we report a telomere-to-telomere (T2T) gap-free genome for the red-skinned pear, 'Yunhong No. 1' (YH1; Pyrus pyrifolia), which is mainly cultivated in Yunnan Province (southwest China), the pear's primary region of origin. The YH1 genome is 501.20 Mb long with a contig N50 length of 29.26 Mb. All 17 chromosomes were assembled to the T2T level with 34 characterized telomeres. The 17 centromeres were predicted and mainly consist of centromeric-specific monomers (CEN198) and long terminal repeat (LTR) Gypsy elements (≥74.73%). By filling all unclosed gaps, the integrity of YH1 is markedly improved over previous P. pyrifolia genomes ('Cuiguan' and 'Nijisseiki'). A total of 1531 segmental duplication (SD) driven duplicated genes were identified and enriched in stress response pathways. Intrachromosomal SDs drove the expansion of disease resistance genes, suggesting the potential of SDs in adaptive pear evolution. A large proportion of duplicated gene pairs exhibit dosage effects or sub-/neo-functionalization, which may affect agronomic traits like stone cell content, sugar content, and fruit skin russet. Furthermore, as core regulators of anthocyanin biosynthesis, we found that MYB10 and MYB114 underwent various gene duplication events. Multiple copies of MYB10 and MYB114 displayed obvious dosage effects, indicating role differentiation in the formation of red-skinned pear fruit. In summary, the T2T gap-free pear genome provides invaluable resources for genome evolution and functional genomics.
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Affiliation(s)
- Manyi Sun
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, Jiangsu 210014, China
| | - Chenjie Yao
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, Jiangsu 210014, China
| | - Qun Shu
- Institute of Horticulture, Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Yingyun He
- Institute of Horticulture, Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Guosong Chen
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, Jiangsu 210014, China
| | - Guangyan Yang
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, Jiangsu 210014, China
| | - Shaozhuo Xu
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, Jiangsu 210014, China
| | - Yueyuan Liu
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, Jiangsu 210014, China
| | - Zhaolong Xue
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, Jiangsu 210014, China
| | - Jun Wu
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, Jiangsu 210014, China
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Li B, Yang Q, Yang L, Zhou X, Deng L, Qu L, Guo D, Hui R, Guo Y, Liu X, Wang T, Fan L, Li M, Yan M. A gap-free reference genome reveals structural variations associated with flowering time in rapeseed ( Brassica napus). HORTICULTURE RESEARCH 2023; 10:uhad171. [PMID: 37841499 PMCID: PMC10569240 DOI: 10.1093/hr/uhad171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/20/2023] [Indexed: 10/17/2023]
Abstract
Allopolyploid oilseed rape (Brassica napus) is an important oil crop and vegetable. However, the latest version of its reference genome, with collapsed duplications, gaps, and other issues, prevents comprehensive genomic analysis. Herein, we report a gap-free assembly of the rapeseed cv. Xiang5A genome using a combination of ONT (Oxford Nanopore Technologies) ultra-long reads, PacBio high-fidelity reads, and Hi-C datasets. It includes gap-free assemblies of all 19 chromosomes and telomere-to-telomere assemblies of eight chromosomes. Compared with previously published genomes of B. napus, our gap-free genome, with a contig N50 length of 50.70 Mb, has complete assemblies of 9 of 19 chromosomes without manual intervention, and greatly improves contiguity and completeness, thereby representing the highest quality genome assembly to date. Our results revealed that B. napus Xiang5A underwent nearly complete triplication and allotetraploidy relative to Arabidopsis thaliana. Using the gap-free assembly, we found that 917 flowering-related genes were affected by structural variation, including BnaA03.VERNALIZATION INSENSITIVE 3 and BnaC04.HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENES 1. These genes may play crucial roles in regulating flowering time and facilitating the adaptation of Xiang5A in the Yangtze River Basin of China. This reference genome provides a valuable genetic resource for rapeseed functional genomic studies and breeding.
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Affiliation(s)
- Bao Li
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, Hunan 410125, China
- Hunan Hybrid Rapeseed Engineering and Technology Research Center, Changsha, Hunan 410125, China
| | - Qian Yang
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, Hunan 410125, China
- Hunan Hybrid Rapeseed Engineering and Technology Research Center, Changsha, Hunan 410125, China
| | - Lulu Yang
- Department of Cell Biology and Genetics, Wuhan Benagen Tech Solutions Company Limited, Wuhan, Hubei 430021, China
| | - Xing Zhou
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, Hunan 410125, China
- Hunan Hybrid Rapeseed Engineering and Technology Research Center, Changsha, Hunan 410125, China
| | - Lichao Deng
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, Hunan 410125, China
- Hunan Hybrid Rapeseed Engineering and Technology Research Center, Changsha, Hunan 410125, China
| | - Liang Qu
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, Hunan 410125, China
- Hunan Hybrid Rapeseed Engineering and Technology Research Center, Changsha, Hunan 410125, China
| | - Dengli Guo
- Department of Cell Biology and Genetics, Wuhan Benagen Tech Solutions Company Limited, Wuhan, Hubei 430021, China
| | - Rongkui Hui
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, Hunan 410125, China
- Hunan Hybrid Rapeseed Engineering and Technology Research Center, Changsha, Hunan 410125, China
| | - Yiming Guo
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, Hunan 410125, China
- Hunan Hybrid Rapeseed Engineering and Technology Research Center, Changsha, Hunan 410125, China
| | - Xinhong Liu
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, Hunan 410125, China
- Hunan Hybrid Rapeseed Engineering and Technology Research Center, Changsha, Hunan 410125, China
| | - Tonghua Wang
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, Hunan 410125, China
- Hunan Hybrid Rapeseed Engineering and Technology Research Center, Changsha, Hunan 410125, China
| | - Lianyi Fan
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, Hunan 410125, China
- Hunan Hybrid Rapeseed Engineering and Technology Research Center, Changsha, Hunan 410125, China
| | - Mei Li
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, Hunan 410125, China
- Hunan Hybrid Rapeseed Engineering and Technology Research Center, Changsha, Hunan 410125, China
| | - Mingli Yan
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, Hunan 410125, China
- Hunan Hybrid Rapeseed Engineering and Technology Research Center, Changsha, Hunan 410125, China
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19
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Huang X, Sun G, Wu Z, Jiang Y, Li Q, Yi Y, Yan H. Genome-wide identification and expression analyses of the pectate lyase (PL) gene family in Fragaria vesca. BMC Genomics 2023; 24:435. [PMID: 37537572 PMCID: PMC10401794 DOI: 10.1186/s12864-023-09533-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 07/26/2023] [Indexed: 08/05/2023] Open
Abstract
BACKGROUND Pectate lyase (PL, EC 4.2.2.2), as an endo-acting depolymerizing enzyme, cleaves α-1,4-glycosidic linkages in esterified pectin and involves a broad range of cell wall modifications. However, the knowledge concerning the genome-wide analysis of the PL gene family in Fragaria vesca has not been thoroughly elucidated. RESULTS In this study, sixteen PLs members in F. vesca were identified based on a genome-wide investigation. Substantial divergences existed among FvePLs in gene duplication, cis-acting elements, and tissue expression patterns. Four clusters were classified according to phylogenetic analysis. FvePL6, 8 and 13 in cluster II significantly contributed to the significant expansions during evolution by comparing orthologous PL genes from Malus domestica, Solanum lycopersicum, Arabidopsis thaliana, and Fragaria×ananassa. The cis-acting elements implicated in the abscisic acid signaling pathway were abundant in the regions of FvePLs promoters. The RNA-seq data and in situ hybridization revealed that FvePL1, 4, and 7 exhibited maximum expression in fruits at twenty days after pollination, whereas FvePL8 and FvePL13 were preferentially and prominently expressed in mature anthers and pollens. Additionally, the co-expression networks displayed that FvePLs had tight correlations with transcription factors and genes implicated in plant development, abiotic/biotic stresses, ions/Ca2+, and hormones, suggesting the potential roles of FvePLs during strawberry development. Besides, histological observations suggested that FvePL1, 4 and 7 enhanced cell division and expansion of the cortex, thus negatively influencing fruit firmness. Finally, FvePL1-RNAi reduced leaf size, altered petal architectures, disrupted normal pollen development, and rendered partial male sterility. CONCLUSION These results provide valuable information for characterizing the evolution, expansion, expression patterns and functional analysis, which help to understand the molecular mechanisms of the FvePLs in the development of strawberries.
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Affiliation(s)
- Xiaolong Huang
- School of Life Sciences, Guizhou Normal University, Guiyang, 550001, China
- Key Laboratory of Plant Physiology and Development Regulation, Guizhou Normal University, Guiyang, 550001, China
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guizhou Normal University, Guiyang, 550001, China
| | - Guilian Sun
- School of Life Sciences, Guizhou Normal University, Guiyang, 550001, China
- Key Laboratory of Plant Physiology and Development Regulation, Guizhou Normal University, Guiyang, 550001, China
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guizhou Normal University, Guiyang, 550001, China
| | - Zongmin Wu
- School of Life Sciences, Guizhou Normal University, Guiyang, 550001, China
- Key Laboratory of Plant Physiology and Development Regulation, Guizhou Normal University, Guiyang, 550001, China
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guizhou Normal University, Guiyang, 550001, China
| | - Yu Jiang
- School of Life Sciences, Guizhou Normal University, Guiyang, 550001, China
| | - Qiaohong Li
- Kiwifruit Breeding and Utilization Key Laboratory of Sichuan Province, Sichuan Provincial Academy of Natural Resource Science, Chengdu, 610015, China
| | - Yin Yi
- School of Life Sciences, Guizhou Normal University, Guiyang, 550001, China
- Key Laboratory of Plant Physiology and Development Regulation, Guizhou Normal University, Guiyang, 550001, China
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guizhou Normal University, Guiyang, 550001, China
| | - Huiqing Yan
- School of Life Sciences, Guizhou Normal University, Guiyang, 550001, China.
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20
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Lin Y, Ye C, Li X, Chen Q, Wu Y, Zhang F, Pan R, Zhang S, Chen S, Wang X, Cao S, Wang Y, Yue Y, Liu Y, Yue J. quarTeT: a telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification. HORTICULTURE RESEARCH 2023; 10:uhad127. [PMID: 37560017 PMCID: PMC10407605 DOI: 10.1093/hr/uhad127] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 06/05/2023] [Indexed: 08/11/2023]
Abstract
A high-quality genome is the basis for studies on functional, evolutionary, and comparative genomics. The majority of attention has been paid to the solution of complex chromosome structures and highly repetitive sequences, along with the emergence of a new 'telomere-to-telomere (T2T) assembly' era. However, the bioinformatic tools for the automatic construction and/or characterization of T2T genome are limited. Here, we developed a user-friendly web toolkit, quarTeT, which currently includes four modules: AssemblyMapper, GapFiller, TeloExplorer, and CentroMiner. First, AssemblyMapper is designed to assemble phased contigs into the chromosome-level genome by referring to a closely related genome. Then, GapFiller would endeavor to fill all unclosed gaps in a given genome with the aid of additional ultra-long sequences. Finally, TeloExplorer and CentroMiner are applied to identify candidate telomere and centromere as well as their localizations on each chromosome. These four modules can be used alone or in combination with each other for T2T genome assembly and characterization. As a case study, by adopting the entire modular functions of quarTeT, we have achieved the Actinidia chinensis genome assembly that is of a quality comparable to the reported genome Hongyang v4.0, which was assembled with the addition of manual handling. Further evaluation of CentroMiner by searching centromeres in Arabidopsis thaliana and Oryza sativa genomes showed that quarTeT is capable of identifying all the centromeric regions that have been previously detected by experimental methods. Collectively, quarTeT is an efficient toolkit for studies of large-scale T2T genomes and can be accessed at http://www.atcgn.com:8080/quarTeT/home.html without registration.
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Affiliation(s)
- Yunzhi Lin
- College of Life Science, Sichuan University, Chengdu, Sichuan 610064, China
- School of Horticulture, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Chen Ye
- School of Information and Computer, Anhui Agricultural University, Hefei, Anhui 230036, China
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Xingzhu Li
- School of Horticulture, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Qinyao Chen
- School of Horticulture, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Ying Wu
- School of Horticulture, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Feng Zhang
- School of Horticulture, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Rui Pan
- School of Horticulture, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Sijia Zhang
- School of Horticulture, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Shuxia Chen
- School of Information and Computer, Anhui Agricultural University, Hefei, Anhui 230036, China
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Xu Wang
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, China
| | - Shuo Cao
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, China
- Key Laboratory of Horticultural Plant Biology Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yingzhen Wang
- School of Horticulture, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Yi Yue
- School of Information and Computer, Anhui Agricultural University, Hefei, Anhui 230036, China
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Yongsheng Liu
- College of Life Science, Sichuan University, Chengdu, Sichuan 610064, China
- School of Horticulture, Anhui Agricultural University, Hefei, Anhui 230036, China
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Junyang Yue
- School of Horticulture, Anhui Agricultural University, Hefei, Anhui 230036, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, China
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21
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Wang R, Li W, He Q, Zhang H, Wang M, Zheng X, Liu Z, Wang Y, Du C, Du H, Xing L. The genome of okra ( Abelmoschus esculentus) provides insights into its genome evolution and high nutrient content. HORTICULTURE RESEARCH 2023; 10:uhad120. [PMID: 37554345 PMCID: PMC10405168 DOI: 10.1093/hr/uhad120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 05/26/2023] [Indexed: 08/10/2023]
Abstract
Okra (Abelmoschus esculentus) is an important vegetable crop with high nutritional value. However, the mechanism underlying its high nutrient content remains poorly understood. Here, we present a chromosome-scale genome of okra with a size of 1.19 Gb. Comparative genomics analysis revealed the phylogenetic status of A. esculentus, as well as whole-genome duplication (WGD) events that have occurred widely across the Malvaceae species. We found that okra has experienced three additional WGDs compared with the diploid cotton Gossypium raimondii, resulting in a large chromosome number (2n = 130). After three WGDs, okra has undergone extensive genomic deletions and retained substantial numbers of genes related to secondary metabolite biosynthesis and environmental adaptation, resulting in significant differences between okra and G. raimondii in the gene families related to cellulose synthesis. Combining transcriptomic and metabolomic analysis, we revealed the relationship between gene expression and metabolite content change across different okra developmental stages. Furthermore, the sinapic acid/S-lignin biosynthesis-related gene families have experienced remarkable expansion in okra, and the expression of key enzymes involved in the sinapic acid/S-lignin biosynthesis pathway vary greatly across developmental periods, which partially explains the differences in metabolite content across the different stages. Our study gains insights into the comprehensive evolutionary history of Malvaceae species and the genetic basis that underlies the nutrient content changes in okra, which will facilitate the functional study and genetic improvement of okra varieties.
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Affiliation(s)
- Ruyu Wang
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071000, China
| | - Wei Li
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071000, China
- Hebei Basic Science Center for Biotic Interaction, Institute of Life Sciences and Green Development, Hebei University, Baoding 071000, China
| | - Qiang He
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071000, China
- Hebei Basic Science Center for Biotic Interaction, Institute of Life Sciences and Green Development, Hebei University, Baoding 071000, China
| | - Hongyu Zhang
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071000, China
| | - Meijia Wang
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071000, China
| | - Xinyuan Zheng
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071000, China
| | - Ze Liu
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071000, China
| | - Yu Wang
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071000, China
| | - Cailian Du
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071000, China
| | - Huilong Du
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071000, China
- Hebei Basic Science Center for Biotic Interaction, Institute of Life Sciences and Green Development, Hebei University, Baoding 071000, China
| | - Longsheng Xing
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071000, China
- Hebei Basic Science Center for Biotic Interaction, Institute of Life Sciences and Green Development, Hebei University, Baoding 071000, China
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22
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Ma B, Wang H, Liu J, Chen L, Xia X, Wei W, Yang Z, Yuan J, Luo Y, He N. The gap-free genome of mulberry elucidates the architecture and evolution of polycentric chromosomes. HORTICULTURE RESEARCH 2023; 10:uhad111. [PMID: 37786730 PMCID: PMC10541557 DOI: 10.1093/hr/uhad111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/15/2023] [Indexed: 10/04/2023]
Abstract
Mulberry is a fundamental component of the global sericulture industry, and its positive impact on our health and the environment cannot be overstated. However, the mulberry reference genomes reported previously remained unassembled or unplaced sequences. Here, we report the assembly and analysis of the telomere-to-telomere gap-free reference genome of the mulberry species, Morus notabilis, which has emerged as an important reference in mulberry gene function research and genetic improvement. The mulberry gap-free reference genome produced here provides an unprecedented opportunity for us to study the structure and function of centromeres. Our results revealed that all mulberry centromeric regions share conserved centromeric satellite repeats with different copies. Strikingly, we found that M. notabilis is a species with polycentric chromosomes and the only reported polycentric chromosome species up to now. We propose a compelling model that explains the formation mechanism of new centromeres and addresses the unsolved scientific question of the chromosome fusion-fission cycle in mulberry species. Our study sheds light on the functional genomics, chromosome evolution, and genetic improvement of mulberry species.
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Affiliation(s)
- Bi Ma
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400715, China
| | - Honghong Wang
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400715, China
| | - Jingchun Liu
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400715, China
| | - Lin Chen
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400715, China
| | - Xiaoyu Xia
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400715, China
| | - Wuqi Wei
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400715, China
| | - Zhen Yang
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400715, China
| | - Jianglian Yuan
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400715, China
| | - Yiwei Luo
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400715, China
| | - Ningjia He
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400715, China
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23
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Passa K, Simal C, Tsormpatsidis E, Papasotiropoulos V, Lamari FN. Monitoring of Volatile Organic Compounds in Strawberry Genotypes over the Harvest Period. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091881. [PMID: 37176939 PMCID: PMC10181119 DOI: 10.3390/plants12091881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/02/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023]
Abstract
Volatile Organic Compounds (VOCs) over the harvest period have been assessed in twenty-five strawberry genotypes cultivated in western Greece. Using liquid-liquid extraction and gas chromatography-mass spectrometry (GC--MS), twenty-eight volatiles were monitored at early (T1) and mid-harvest (T3) time points to investigate the effect of the genotype and harvest time on strawberry volatilome. A quantitative impact of both harvest date and genotype on VOCs associated with aroma was demonstrated, with the most significant VOCs being terpenes, esters, and acids, followed by lactones and furanones. Harvest date was crucial for terpenoid and phenylpropanoid content, and important for esters, short-chain acids, and lactones. Six out of the twenty-five genotypes (four commercial varieties, including 'Rociera', 'Victory', 'Leyre', and 'Inspire', and two advanced selection genotypes (G2 and G8) were evaluated at two additional time points, covering the entire harvest season. The volatile levels were higher in fruits harvested at early stages (T1-T2) for most of the genotypes examined. The G2 genotype turned out to have a less ample but more stable volatile profile throughout harvesting, while 'Victory', 'Leyre', and 'Inspire' exhibited less abrupt changes than 'Rociera'. This study demonstrates that the determination of VOCs provides significant information regarding the differences in strawberry genotypes related to aroma and enables the selection of genotypes based on specific VOCs content and/or volatile stability over the harvest period. Furthermore, this study pinpoints that growers could opt for optimal harvest dates based on the genotypes and the VOC content.
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Affiliation(s)
- Kondylia Passa
- Laboratory of Agricultural Genetics & Plant Breeding, Department of Agriculture, University of Patras, 30200 Messolonghi, Greece
| | - Carmen Simal
- Laboratory of Pharmacognosy & Chemistry of Natural Products, Department of Pharmacy, University of Patras, 26504 Patras, Greece
| | | | - Vasileios Papasotiropoulos
- Laboratory of Agricultural Genetics & Plant Breeding, Department of Agriculture, University of Patras, 30200 Messolonghi, Greece
| | - Fotini N Lamari
- Laboratory of Pharmacognosy & Chemistry of Natural Products, Department of Pharmacy, University of Patras, 26504 Patras, Greece
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