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Rai A, Hirakawa H, Rai M, Shimizu Y, Shirasawa K, Kikuchi S, Seki H, Yamazaki M, Toyoda A, Isobe S, Muranaka T, Saito K. Chromosome-scale genome assembly of Glycyrrhiza uralensis revealed metabolic gene cluster centred specialized metabolites biosynthesis. DNA Res 2022; 29:6916896. [PMID: 36535891 PMCID: PMC9763095 DOI: 10.1093/dnares/dsac043] [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: 09/07/2022] [Accepted: 11/21/2022] [Indexed: 12/24/2022] Open
Abstract
A high-quality genome assembly is imperative to explore the evolutionary basis of characteristic attributes that define chemotype and provide essential resources for a molecular breeding strategy for enhanced production of medicinal metabolites. Here, using single-molecule high-fidelity (HiFi) sequencing reads, we report chromosome-scale genome assembly for Chinese licorice (Glycyrrhiza uralensis), a widely used herbal and natural medicine. The entire genome assembly was achieved in eight chromosomes, with contig and scaffold N50 as 36.02 and 60.2 Mb, respectively. With only 17 assembly gaps and half of the chromosomes having no or one assembly gap, the presented genome assembly is among the best plant genomes to date. Our results showed an advantage of using highly accurate long-read HiFi sequencing data for assembling a highly heterozygous genome including its complexed repeat content. Additionally, our analysis revealed that G. uralensis experienced a recent whole-genome duplication at approximately 59.02 million years ago post a gamma (γ) whole-genome triplication event, which contributed to its present chemotype features. The metabolic gene cluster analysis identified 355 gene clusters, which included the entire biosynthesis pathway of glycyrrhizin. The genome assembly and its annotations provide an essential resource for licorice improvement through molecular breeding and the discovery of valuable genes for engineering bioactive components and understanding the evolution of specialized metabolites biosynthesis.
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Affiliation(s)
- Amit Rai
- To whom correspondence should be addressed. Tel. +81 045 503 9489; Fax: +81-(0)45-503-9489. ;
| | | | - Megha Rai
- Plant Molecular Science Center, Chiba University, Chiba, Japan,Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan,Institute of Advance Academic Research, Chiba University, Chiba, Japan
| | - Yohei Shimizu
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | | | - Shinji Kikuchi
- Plant Molecular Science Center, Chiba University, Chiba, Japan,Graduate School of Horticulture, Chiba University, Chiba, Japan
| | - Hikaru Seki
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan,Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Japan
| | - Mami Yamazaki
- Plant Molecular Science Center, Chiba University, Chiba, Japan,Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Sachiko Isobe
- Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
| | - Toshiya Muranaka
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan,Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan,Plant Molecular Science Center, Chiba University, Chiba, Japan
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Zhang H, Mascher M, Abbo S, Jayakodi M. Advancing Grain Legumes Domestication and Evolution Studies with Genomics. PLANT & CELL PHYSIOLOGY 2022; 63:1540-1553. [PMID: 35534441 PMCID: PMC9680859 DOI: 10.1093/pcp/pcac062] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 05/03/2022] [Accepted: 05/09/2022] [Indexed: 06/14/2023]
Abstract
Grain legumes were domesticated in parallel with cereals in several regions of the world and formed the economic basis of early farming cultures. Since then, legumes have played a vital role in human and animal diets and in fostering agrobiodiversity. Increasing grain legume cultivation will be crucial to safeguard nutritional security and the resilience of agricultural ecosystems across the globe. A better understanding of the molecular underpinnings of domestication and crop evolution of grain legumes may be translated into practical approaches in modern breeding programs to stabilize yield, which is threatened by evolving pathogens and changing climates. During recent decades, domestication research in all crops has greatly benefited from the fast progress in genomic technologies. Yet still, many questions surrounding the domestication and diversification of legumes remain unanswered. In this review, we assess the potential of genomic approaches in grain legume research. We describe the centers of origin and the crucial domestication traits of grain legumes. In addition, we survey the effect of domestication on both above-ground and below-ground traits that have economic importance. Finally, we discuss open questions in grain legume domestication and diversification and outline how to bridge the gap between the preservation of historic crop diversity and their utilization in modern plant breeding.
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Affiliation(s)
- Hailin Zhang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, Gatersleben, Seeland 06466, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, Gatersleben, Seeland 06466, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, Leipzig 04103, Germany
| | - Shahal Abbo
- The Levi Eshkol School of Agriculture, The Hebrew University of Jerusalem, POB 12, Rehovot 7610001, Israel
| | - Murukarthick Jayakodi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, Gatersleben, Seeland 06466, Germany
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You MP, Akhatar J, Mittal M, Barbetti MJ, Maina S, Banga SS. Comparative analysis of draft genome assemblies developed from whole genome sequences of two Hyaloperonospora brassicae isolate samples differing in field virulence on Brassica napus. BIOTECHNOLOGY REPORTS 2021; 31:e00653. [PMID: 34258242 PMCID: PMC8254085 DOI: 10.1016/j.btre.2021.e00653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 05/28/2021] [Accepted: 06/16/2021] [Indexed: 11/25/2022]
Abstract
We report first draft genome assemblies for two isolates Hyaloperonospora brassicae, differing for their virulence. These revealed genome sizes of genome sizes of 72.762 and 76.950Mb and 6,438 and 6,470 scaffolds respectively. In silico annotation allowed understanding of the genome architecture of H. brassicae in terms of genes for pathogenicity and virulence. The observed reduction in virulence or loss of pathogenicity in a larger number of genes in the sample with low virulence in comparison to sample with high virulence may reflect differential rates of mutation and selection during host–parasite co‐evolution. Genomic resources develop will aid in monitoring field prevalence of H. brassicae pathotypes and to detect early any virulence changes within pathogen populations.
Hyaloperonospora brassicae causes downy mildew, a major disease of Brassicaceae species. We sequenced the genomes of two H. brassicae isolates of high (Sample B) and low (Sample C) virulence. Sequencing reads were first assembled de novo with software's SOAPdenovo2, ABySS V2.1 and Velvet V1.1 and later combined to create meta-assemblies with genome sizes of 72.762 and 76.950Mb and predicted gene densities of 1628 and 1644 /Mb, respectively. We could annotate 12.255 and 13,030 genes with high proportions (91-92%) of complete BUSCOs for Sample B and C, respectively. Comparative analysis revealed conserved and varied molecular machinery underlying the physiological specialisation and infection capabilities. BLAST analysis against PHI gene database suggested a relatively higher loss of genes for virulence and pathogenicity in Sample C compared to Sample B, reflecting pathogen evolution through differential rates of mutation and selection. These studies will enable identification and monitoring of H. brassicae virulence factors prevailing in-field.
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