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Wang J, Song B, Yang M, Hu F, Qi H, Zhang H, Jia Y, Li Y, Wang Z, Wang X. Deciphering recursive polyploidization in Lamiales and reconstructing their chromosome evolutionary trajectories. PLANT PHYSIOLOGY 2024; 195:2143-2157. [PMID: 38482951 DOI: 10.1093/plphys/kiae151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 02/20/2024] [Indexed: 06/30/2024]
Abstract
Lamiales is an order of core eudicots with abundant diversity, and many Lamiales plants have important medicinal and ornamental values. Here, we comparatively reanalyzed 11 Lamiales species with well-assembled genome sequences and found evidence that Lamiales plants, in addition to a hexaploidization or whole-genome triplication (WGT) shared by core eudicots, experienced further polyploidization events, establishing new groups in the order. Notably, we identified a whole-genome duplication (WGD) occurred just before the split of Scrophulariaceae from the other Lamiales families, such as Acanthaceae, Bignoniaceae, and Lamiaceae, suggesting its likely being the causal reason for the establishment and fast divergence of these families. We also found that a WGT occurred ∼68 to 78 million years ago (Mya), near the split of Oleaceae from the other Lamiales families, implying that it may have caused their fast divergence and the establishment of the Oleaceae family. Then, by exploring and distinguishing intra- and intergenomic chromosomal homology due to recursive polyploidization and speciation, respectively, we inferred that the Lamiales ancestral cell karyotype had 11 proto-chromosomes. We reconstructed the evolutionary trajectories from these proto-chromosomes to form the extant chromosomes in each Lamiales plant under study. We must note that most of the inferred 11 proto-chromosomes, duplicated during a WGD thereafter, have been well preserved in jacaranda (Jacaranda mimosifolia) genome, showing the credibility of the present inference implementing a telomere-centric chromosome repatterning model. These efforts are important to understand genome repatterning after recursive polyploidization, especially shedding light on the origin of new plant groups and angiosperm cell karyotype evolution.
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Affiliation(s)
- Jiangli Wang
- School of Public Health, School of Life Science, and College of Mathematics and Sciences, North China University of Science and Technology, Tangshan 063210, China
| | - Bowen Song
- School of Public Health, School of Life Science, and College of Mathematics and Sciences, North China University of Science and Technology, Tangshan 063210, China
| | - Minran Yang
- School of Public Health, School of Life Science, and College of Mathematics and Sciences, North China University of Science and Technology, Tangshan 063210, China
| | - Fubo Hu
- School of Public Health, School of Life Science, and College of Mathematics and Sciences, North China University of Science and Technology, Tangshan 063210, China
| | - Huilong Qi
- School of Public Health, School of Life Science, and College of Mathematics and Sciences, North China University of Science and Technology, Tangshan 063210, China
| | - Huizhe Zhang
- School of Public Health, School of Life Science, and College of Mathematics and Sciences, North China University of Science and Technology, Tangshan 063210, China
| | - Yuelong Jia
- School of Public Health, School of Life Science, and College of Mathematics and Sciences, North China University of Science and Technology, Tangshan 063210, China
| | - Yingjie Li
- School of Public Health, School of Life Science, and College of Mathematics and Sciences, North China University of Science and Technology, Tangshan 063210, China
| | - Zhenyi Wang
- School of Public Health, School of Life Science, and College of Mathematics and Sciences, North China University of Science and Technology, Tangshan 063210, China
| | - Xiyin Wang
- School of Public Health, School of Life Science, and College of Mathematics and Sciences, North China University of Science and Technology, Tangshan 063210, China
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Chen L, Li C, Li B, Zhou X, Bai Y, Zou X, Zhou Z, He Q, Chen B, Wang M, Xue Y, Jiang Z, Feng J, Zhou T, Liu Z, Xu P. Evolutionary divergence of subgenomes in common carp provides insights into speciation and allopolyploid success. FUNDAMENTAL RESEARCH 2024; 4:589-602. [PMID: 38933191 PMCID: PMC11197550 DOI: 10.1016/j.fmre.2023.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 06/28/2024] Open
Abstract
Hybridization and polyploidization have made great contributions to speciation, heterosis, and agricultural production within plants, but there is still limited understanding and utilization in animals. Subgenome structure and expression reorganization and cooperation post hybridization and polyploidization are essential for speciation and allopolyploid success. However, the mechanisms have not yet been comprehensively assessed in animals. Here, we produced a high-fidelity reference genome sequence for common carp, a typical allotetraploid fish species cultured worldwide. This genome enabled in-depth analysis of the evolution of subgenome architecture and expression responses. Most genes were expressed with subgenome biases, with a trend of transition from the expression of subgenome A during the early stages to that of subgenome B during the late stages of embryonic development. While subgenome A evolved more rapidly, subgenome B contributed to a greater level of expression during development and under stressful conditions. Stable dominant patterns for homoeologous gene pairs both during development and under thermal stress suggest a potential fixed heterosis in the allotetraploid genome. Preferentially expressing either copy of a homoeologous gene at higher levels to confer development and response to stress indicates the dominant effect of heterosis. The plasticity of subgenomes and their shifting of dominant expression during early development, and in response to stressful conditions, provide novel insights into the molecular basis of the successful speciation, evolution, and heterosis of the allotetraploid common carp.
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Affiliation(s)
- Lin Chen
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Chengyu Li
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Bijun Li
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Xiaofan Zhou
- Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Yulin Bai
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Xiaoqing Zou
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Zhixiong Zhou
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Qian He
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Baohua Chen
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Mei Wang
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Yaguo Xue
- College of Fisheries, Henan Normal University, Xinxiang 453007, China
| | - Zhou Jiang
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Jianxin Feng
- Henan Academy of Fishery Science, Zhengzhou 450044, China
| | - Tao Zhou
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Zhanjiang Liu
- Department of Biology, College of Arts and Sciences, Syracuse University, Syracuse 13244, USA
| | - Peng Xu
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
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3
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Shi TL, Jia KH, Bao YT, Nie S, Tian XC, Yan XM, Chen ZY, Li ZC, Zhao SW, Ma HY, Zhao Y, Li X, Zhang RG, Guo J, Zhao W, El-Kassaby YA, Müller N, Van de Peer Y, Wang XR, Street NR, Porth I, An X, Mao JF. High-quality genome assembly enables prediction of allele-specific gene expression in hybrid poplar. PLANT PHYSIOLOGY 2024; 195:652-670. [PMID: 38412470 PMCID: PMC11060683 DOI: 10.1093/plphys/kiae078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 02/29/2024]
Abstract
Poplar (Populus) is a well-established model system for tree genomics and molecular breeding, and hybrid poplar is widely used in forest plantations. However, distinguishing its diploid homologous chromosomes is difficult, complicating advanced functional studies on specific alleles. In this study, we applied a trio-binning design and PacBio high-fidelity long-read sequencing to obtain haplotype-phased telomere-to-telomere genome assemblies for the 2 parents of the well-studied F1 hybrid "84K" (Populus alba × Populus tremula var. glandulosa). Almost all chromosomes, including the telomeres and centromeres, were completely assembled for each haplotype subgenome apart from 2 small gaps on one chromosome. By incorporating information from these haplotype assemblies and extensive RNA-seq data, we analyzed gene expression patterns between the 2 subgenomes and alleles. Transcription bias at the subgenome level was not uncovered, but extensive-expression differences were detected between alleles. We developed machine-learning (ML) models to predict allele-specific expression (ASE) with high accuracy and identified underlying genome features most highly influencing ASE. One of our models with 15 predictor variables achieved 77% accuracy on the training set and 74% accuracy on the testing set. ML models identified gene body CHG methylation, sequence divergence, and transposon occupancy both upstream and downstream of alleles as important factors for ASE. Our haplotype-phased genome assemblies and ML strategy highlight an avenue for functional studies in Populus and provide additional tools for studying ASE and heterosis in hybrids.
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Affiliation(s)
- Tian-Le Shi
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Kai-Hua Jia
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Key Laboratory of Crop Genetic Improvement & Ecology and Physiology, Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Ji’nan 250100, China
| | - Yu-Tao Bao
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Shuai Nie
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
| | - Xue-Chan Tian
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Xue-Mei Yan
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Zhao-Yang Chen
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Zhi-Chao Li
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Shi-Wei Zhao
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Hai-Yao Ma
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Ye Zhao
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Xiang Li
- School of Agriculture, Ningxia University, Yinchuan 750021, China
| | - Ren-Gang Zhang
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
| | - Jing Guo
- College of Forestry, Shandong Agricultural University, Tai’an 271000, China
| | - Wei Zhao
- Umeå Plant Science Centre, Department of Ecology and Environmental Science, Umeå University, SE-901 87 Umeå, Sweden
| | - Yousry Aly El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, Bc, V6T 1Z4, Canada
| | - Niels Müller
- Thünen-Institute of Forest Genetics, 22927 Grosshansdorf, Germany
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiao-Ru Wang
- Umeå Plant Science Centre, Department of Ecology and Environmental Science, Umeå University, SE-901 87 Umeå, Sweden
| | - Nathaniel Robert Street
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden
| | - Ilga Porth
- Départment des Sciences du Bois et de la Forêt, Faculté de Foresterie, de Géographie et Géomatique, Université Laval, Québec, QC G1V 0A6, Canada
| | - Xinmin An
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Jian-Feng Mao
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden
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Gupta P, Geniza M, Elser J, Al-Bader N, Baschieri R, Phillips JL, Haq E, Preece J, Naithani S, Jaiswal P. Reference genome of the nutrition-rich orphan crop chia ( Salvia hispanica) and its implications for future breeding. FRONTIERS IN PLANT SCIENCE 2023; 14:1272966. [PMID: 38162307 PMCID: PMC10757625 DOI: 10.3389/fpls.2023.1272966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/23/2023] [Indexed: 01/03/2024]
Abstract
Chia (Salvia hispanica L.) is one of the most popular nutrition-rich foods and pseudocereal crops of the family Lamiaceae. Chia seeds are a rich source of proteins, polyunsaturated fatty acids (PUFAs), dietary fibers, and antioxidants. In this study, we present the assembly of the chia reference genome, which spans 303.6 Mb and encodes 48,090 annotated protein-coding genes. Our analysis revealed that ~42% of the chia genome harbors repetitive content, and identified ~3 million single nucleotide polymorphisms (SNPs) and 15,380 simple sequence repeat (SSR) marker sites. By investigating the chia transcriptome, we discovered that ~44% of the genes undergo alternative splicing with a higher frequency of intron retention events. Additionally, we identified chia genes associated with important nutrient content and quality traits, such as the biosynthesis of PUFAs and seed mucilage fiber (dietary fiber) polysaccharides. Notably, this is the first report of in-silico annotation of a plant genome for protein-derived small bioactive peptides (biopeptides) associated with improving human health. To facilitate further research and translational applications of this valuable orphan crop, we have developed the Salvia genomics database (SalviaGDB), accessible at https://salviagdb.org.
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Affiliation(s)
- Parul Gupta
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Matthew Geniza
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
- Molecular and Cellular Biology Graduate Program, Oregon State University, Corvallis, OR, United States
| | - Justin Elser
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Noor Al-Bader
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
- Molecular and Cellular Biology Graduate Program, Oregon State University, Corvallis, OR, United States
| | - Rachel Baschieri
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Jeremy Levi Phillips
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Ebaad Haq
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Justin Preece
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Sushma Naithani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
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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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6
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Park HS, Jo IH, Raveendar S, Kim NH, Gil J, Shim D, Kim C, Yu JK, So YS, Chung JW. A chromosome-level genome assembly of Korean mint (Agastache rugosa). Sci Data 2023; 10:792. [PMID: 37949898 PMCID: PMC10638305 DOI: 10.1038/s41597-023-02714-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 11/01/2023] [Indexed: 11/12/2023] Open
Abstract
Agastache rugosa, also known as Korean mint, is a perennial plant from the Lamiaceae family that is traditionally used for various ailments and contains antioxidant and antibacterial phenolic compounds. Molecular breeding of A. rugosa can enhance secondary metabolite production and improve agricultural traits, but progress in this field has been delayed due to the lack of chromosome-scale genome information. Herein, we constructed a chromosome-level reference genome using Nanopore sequencing and Hi-C technology, resulting in a final genome assembly with a scaffold N50 of 52.15 Mbp and a total size of 410.67 Mbp. Nine pseudochromosomes accounted for 89.1% of the predicted genome. The BUSCO analysis indicated a high level of completeness in the assembly. Repeat annotation revealed 561,061 repeat elements, accounting for 61.65% of the genome, with Copia and Gypsy long terminal repeats being the most abundant. A total of 26,430 protein-coding genes were predicted, with an average length of 1,184 bp. The availability of this chromosome-scale genome will advance our understanding of A. rugosa's genetic makeup and its potential applications in various industries.
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Affiliation(s)
- Hyun-Seung Park
- Department of Integrative Biological Sciences and Industry, Convergence Research Center for Natural Products, Sejong University, Seoul, 05006, Korea
| | - Ick Hyun Jo
- Department of Crop Science and Biotechnology, Dankook University, Cheonan, 31116, South Korea
| | - Sebastin Raveendar
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, South Korea
| | | | - Jinsu Gil
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, South Korea
| | - Donghwan Shim
- Department of Biological Sciences, Chungnam National University, Daejeon, South Korea
| | - Changsoo Kim
- Department of Crop Sciences, Chungnam National University, Daejeon, South Korea
| | - Ju-Kyung Yu
- Department of Crop Science, Chungbuk National University, Cheongju, South Korea
| | - Yoon-Sup So
- Department of Crop Science, Chungbuk National University, Cheongju, South Korea.
| | - Jong-Wook Chung
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, South Korea.
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Li J, Li H, Wang Y, Zhang W, Wang D, Dong Y, Ling Z, Bai H, Jin X, Hu X, Shi L. Decoupling subgenomes within hybrid lavandin provide new insights into speciation and monoterpenoid diversification of Lavandula. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:2084-2099. [PMID: 37399213 PMCID: PMC10502749 DOI: 10.1111/pbi.14115] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 05/17/2023] [Accepted: 06/17/2023] [Indexed: 07/05/2023]
Abstract
Polyploidization and transposon elements contribute to shape plant genome diversity and secondary metabolic variation in some edible crops. However, the specific contribution of these variations to the chemo-diversity of Lamiaceae, particularly in economic shrubs, is still poorly documented. The rich essential oils (EOs) of Lavandula plants are distinguished by monoterpenoids among the main EO-producing species, L. angustifolia (LA), L. × intermedia (LX) and L. latifolia (LL). Herein, the first allele-aware chromosome-level genome was assembled using a lavandin cultivar 'Super' and its hybrid origin was verified by two complete subgenomes (LX-LA and LX-LL). Genome-wide phylogenetics confirmed that LL, like LA, underwent two lineage-specific WGDs after the γ triplication event, and their speciation occurred after the last WGD. Chloroplast phylogenetic analysis indicated LA was the maternal source of 'Super', which produced premium EO (higher linalyl/lavandulyl acetate and lower 1,8-cineole and camphor) close to LA. Gene expression, especially the monoterpenoid biosynthetic genes, showed bias to LX-LA alleles. Asymmetric transposon insertions in two decoupling 'Super' subgenomes were responsible for speciation and monoterpenoid divergence of the progenitors. Both hybrid and parental evolutionary analysis revealed that LTR (long terminal repeat) retrotransposon associated with AAT gene loss cause no linalyl/lavandulyl acetate production in LL, and multi-BDH copies retained by tandem duplication and DNA transposon resulted in higher camphor accumulation of LL. Advances in allelic variations of monoterpenoids have the potential to revolutionize future lavandin breeding and EO production.
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Affiliation(s)
- Jingrui Li
- Key Laboratory of Plant ResourcesInstitute of Botany, Chinese Academy of SciencesBeijingChina
- China National Botanical GardenBeijingChina
| | - Hui Li
- Key Laboratory of Plant ResourcesInstitute of Botany, Chinese Academy of SciencesBeijingChina
- China National Botanical GardenBeijingChina
| | - Yiming Wang
- Novogene Bioinformatics InstituteBeijingChina
| | - Wenying Zhang
- Key Laboratory of Plant ResourcesInstitute of Botany, Chinese Academy of SciencesBeijingChina
- China National Botanical GardenBeijingChina
| | - Di Wang
- Key Laboratory of Plant ResourcesInstitute of Botany, Chinese Academy of SciencesBeijingChina
- China National Botanical GardenBeijingChina
| | - Yanmei Dong
- Key Laboratory of Plant ResourcesInstitute of Botany, Chinese Academy of SciencesBeijingChina
- China National Botanical GardenBeijingChina
| | - Zhengyi Ling
- Key Laboratory of Plant ResourcesInstitute of Botany, Chinese Academy of SciencesBeijingChina
- China National Botanical GardenBeijingChina
| | - Hongtong Bai
- Key Laboratory of Plant ResourcesInstitute of Botany, Chinese Academy of SciencesBeijingChina
- China National Botanical GardenBeijingChina
| | - Xiaohua Jin
- China National Botanical GardenBeijingChina
- State Key Laboratory of Systematic and Evolutionary BotanyInstitute of Botany, Chinese Academy of SciencesBeijingChina
| | - Xiaodi Hu
- Novogene Bioinformatics InstituteBeijingChina
| | - Lei Shi
- Key Laboratory of Plant ResourcesInstitute of Botany, Chinese Academy of SciencesBeijingChina
- China National Botanical GardenBeijingChina
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8
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Shelake RM, Jadhav AM, Bhosale PB, Kim JY. Unlocking secrets of nature's chemists: Potential of CRISPR/Cas-based tools in plant metabolic engineering for customized nutraceutical and medicinal profiles. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108070. [PMID: 37816270 DOI: 10.1016/j.plaphy.2023.108070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/12/2023]
Abstract
Plant species have evolved diverse metabolic pathways to effectively respond to internal and external signals throughout their life cycle, allowing adaptation to their sessile and phototropic nature. These pathways selectively activate specific metabolic processes, producing plant secondary metabolites (PSMs) governed by genetic and environmental factors. Humans have utilized PSM-enriched plant sources for millennia in medicine and nutraceuticals. Recent technological advances have significantly contributed to discovering metabolic pathways and related genes involved in the biosynthesis of specific PSM in different food crops and medicinal plants. Consequently, there is a growing demand for plant materials rich in nutrients and bioactive compounds, marketed as "superfoods". To meet the industrial demand for superfoods and therapeutic PSMs, modern methods such as system biology, omics, synthetic biology, and genome editing (GE) play a crucial role in identifying the molecular players, limiting steps, and regulatory circuitry involved in PSM production. Among these methods, clustered regularly interspaced short palindromic repeats-CRISPR associated protein (CRISPR/Cas) is the most widely used system for plant GE due to its simple design, flexibility, precision, and multiplexing capabilities. Utilizing the CRISPR-based toolbox for metabolic engineering (ME) offers an ideal solution for developing plants with tailored preventive (nutraceuticals) and curative (therapeutic) metabolic profiles in an ecofriendly way. This review discusses recent advances in understanding the multifactorial regulation of metabolic pathways, the application of CRISPR-based tools for plant ME, and the potential research areas for enhancing plant metabolic profiles.
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Affiliation(s)
- Rahul Mahadev Shelake
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Republic of Korea.
| | - Amol Maruti Jadhav
- Research Institute of Green Energy Convergence Technology (RIGET), Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Pritam Bhagwan Bhosale
- Department of Veterinary Medicine, Research Institute of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Republic of Korea; Division of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea; Nulla Bio Inc, 501 Jinju-daero, Jinju, 52828, Republic of Korea.
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9
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Giuseppe A, Raffaella EM. The First Genome-Wide Mildew Locus O Genes Characterization in the Lamiaceae Plant Family. Int J Mol Sci 2023; 24:13627. [PMID: 37686433 PMCID: PMC10487521 DOI: 10.3390/ijms241713627] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
Powdery mildew (PM) is a widespread plant disease that causes significant economic losses in thousands crops of temperate climates, including Lamiaceae species. Multiple scientific studies describe a peculiar form of PM-resistance associated at the inactivation of specific members of the Mildew Locus O (MLO) gene family, referred to as mlo-resistance. The characterization of Lamiaceae MLO genes, at the genomic level, would be a first step toward their potential use in breeding programs. We carried out a genome-wide characterization of the MLO gene family in 11 Lamiaceae species, providing a manual curated catalog of 324 MLO proteins. Evolutionary history and phylogenetic relationships were studied through maximum likelihood analysis and motif patter reconstruction. Our approach highlighted seven different clades diversified starting from an ancestral MLO domain pattern organized in 18 highly conserved motifs. In addition, 74 Lamiaceae putative PM susceptibility genes, clustering in clade V, were identified. Finally, we performed a codon-based evolutionary analysis, revealing a general high level of purifying selection in the eleven Lamiaceae MLO gene families, and the occurrence of few regions under diversifying selection in candidate susceptibility factors. The results of this work may help to address further biological questions concerning MLOs involved in PM susceptibility. In follow-up studies, it could be investigated whether the silencing or loss-of-function mutations in one or more of these candidate genes may lead to PM resistance.
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Affiliation(s)
- Andolfo Giuseppe
- Department of Agricultural Sciences, University of Naples “Federico II”, Via Università 100, Portici, 80055 Naples, Italy
| | - Ercolano Maria Raffaella
- Department of Agricultural Sciences, University of Naples “Federico II”, Via Università 100, Portici, 80055 Naples, Italy
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10
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Hu J, Qiu S, Wang F, Li Q, Xiang CL, Di P, Wu Z, Jiang R, Li J, Zeng Z, Wang J, Wang X, Zhang Y, Fang S, Qiao Y, Ding J, Jiang Y, Xu Z, Chen J, Chen W. Functional divergence of CYP76AKs shapes the chemodiversity of abietane-type diterpenoids in genus Salvia. Nat Commun 2023; 14:4696. [PMID: 37542034 PMCID: PMC10403556 DOI: 10.1038/s41467-023-40401-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 07/26/2023] [Indexed: 08/06/2023] Open
Abstract
The genus Salvia L. (Lamiaceae) comprises myriad distinct medicinal herbs, with terpenoids as one of their major active chemical groups. Abietane-type diterpenoids (ATDs), such as tanshinones and carnosic acids, are specific to Salvia and exhibit taxonomic chemical diversity among lineages. To elucidate how ATD chemical diversity evolved, we carried out large-scale metabolic and phylogenetic analyses of 71 Salvia species, combined with enzyme function, ancestral sequence and chemical trait reconstruction, and comparative genomics experiments. This integrated approach showed that the lineage-wide ATD diversities in Salvia were induced by differences in the oxidation of the terpenoid skeleton at C-20, which was caused by the functional divergence of the cytochrome P450 subfamily CYP76AK. These findings present a unique pattern of chemical diversity in plants that was shaped by the loss of enzyme activity and associated catalytic pathways.
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Affiliation(s)
- Jiadong Hu
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
- Department of Pharmacy, Second Affiliated Hospital of Navy Medical University, Shanghai, 200003, China
| | - Shi Qiu
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
| | - Feiyan Wang
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Qing Li
- Department of Pharmacy, Second Affiliated Hospital of Navy Medical University, Shanghai, 200003, China
| | - Chun-Lei Xiang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Peng Di
- State Local Joint Engineering Research Center of Ginseng Breeding and Application, College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, 130118, China
| | - Ziding Wu
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Rui Jiang
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Jinxing Li
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Zhen Zeng
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Jing Wang
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Xingxing Wang
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Yuchen Zhang
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Shiyuan Fang
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Yuqi Qiao
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Jie Ding
- Urban Horticulture Research and Extension Center, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Yun Jiang
- Urban Horticulture Research and Extension Center, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Zhichao Xu
- College of Life Sciences, Northeast Forestry University, Harbin, 150040, China.
| | - Junfeng Chen
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
| | - Wansheng Chen
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
- Department of Pharmacy, Second Affiliated Hospital of Navy Medical University, Shanghai, 200003, China.
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11
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Bălășoiu RM, Biță A, Stănciulescu EC, Bălășoiu M, Bejenaru C, Bejenaru LE, Pisoschi CG. In vitro Antimicrobial Activity of Some Extracts of Salvia spp Harvested from the Oltenia Flora Using Different Solvents. CURRENT HEALTH SCIENCES JOURNAL 2023; 49:397-402. [PMID: 38314220 PMCID: PMC10832872 DOI: 10.12865/chsj.49.03.12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 08/20/2023] [Indexed: 02/06/2024]
Abstract
In this study, the antimicrobial activity of three Salvia spp. (S. glutinosa, S. splendens, S. verticillata) extracts prepared with different solvents was assessed using the diffusion method and the quantification of the minimum inhibitory concentration for each extract on S. aureus, E. coli and C. albicans standard strains. The results showed that the extracts of the three Salvia spp. are suppressing the growth of the bacteria tested with variable potency. Among the different solvent extracts, n-butanolic extracts of all the three species of Salvia spp. revealed the most important antibacterial activity against S. aureus and E. coli. S. splendens extracts proved to be the most efficient on C. albicans regardless of the solvent used.
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Affiliation(s)
- Roxana Maria Bălășoiu
- PhD Student, Doctoral School, University of Medicine and Pharmacy of Craiova
- Department of Pharmaceutical Biochemistry, University of Medicine and Pharmacy of Craiova
| | - Andrei Biță
- Department of Pharmacognosy & Phytotherapy, University of Medicine and Pharmacy of Craiova
| | | | - Maria Bălășoiu
- Department of Microbiology, University of Medicine and Pharmacy of Craiova
| | - Cornelia Bejenaru
- Department of Pharmaceutical Botany, University of Medicine and Pharmacy of Craiova
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12
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Li L, Song J, Zhang M, Iqbal S, Li Y, Zhang H, Zhang H. A near complete genome assembly of chia assists in identification of key fatty acid desaturases in developing seeds. FRONTIERS IN PLANT SCIENCE 2023; 14:1102715. [PMID: 37021303 PMCID: PMC10067618 DOI: 10.3389/fpls.2023.1102715] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 03/06/2023] [Indexed: 06/19/2023]
Abstract
Chia is an annual crop whose seeds have the highest content of α-linolenic acid (ALA) of any plant known to date. We generated a high-quality assembly of the chia genome using circular consensus sequencing (CCS) of PacBio. The assembled six chromosomes are composed of 21 contigs and have a total length of 361.7 Mb. Genome annotation revealed a 53.5% repeat content and 35,850 protein-coding genes. Chia shared a common ancestor with Salvia splendens ~6.1 million years ago. Utilizing the reference genome and two transcriptome datasets, we identified candidate fatty acid desaturases responsible for ALA biosynthesis during chia seed development. Because the seed of S. splendens contains significantly lower proportion of ALA but similar total contents of unsaturated fatty acids, we suggest that strong expression of two ShFAD3 genes are critical for the high ALA content of chia seeds. This genome assembly will serve as a valuable resource for breeding, comparative genomics, and functional genomics studies of chia.
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Affiliation(s)
- Leiting Li
- National Key Laboratory of Molecular Plant Genetics, Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jingjing Song
- National Key Laboratory of Molecular Plant Genetics, Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Meiling Zhang
- Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, Chinese Academy of Sciences, Shanghai, China
| | - Shahid Iqbal
- Institute of Plant Breeding and Biotechnology, Muhammad Nawaz Shareef University of Agriculture, Multan, Pakistan
| | - Yuanyuan Li
- Centre for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Heng Zhang
- National Key Laboratory of Molecular Plant Genetics, Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Hui Zhang
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, Shandong, China
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13
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Sun Y, Shao J, Liu H, Wang H, Wang G, Li J, Mao Y, Chen Z, Ma K, Xu L, Wang Y. A chromosome-level genome assembly reveals that tandem-duplicated CYP706V oxidase genes control oridonin biosynthesis in the shoot apex of Isodon rubescens. MOLECULAR PLANT 2023; 16:517-532. [PMID: 36518072 DOI: 10.1016/j.molp.2022.12.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 11/17/2022] [Accepted: 12/08/2022] [Indexed: 06/09/2023]
Abstract
The ent-kaurenoids (e.g., oridonin and enmein) from the Isodon genus (Lamiaceae) are one class of diterpenoids with rich structural diversity and intriguing pharmaceutical activity. In contrast to the well-established gibberellin pathway, oxidative modifications diversifying the ent-kaurene skeleton in Isodon have remained undetermined for half a century. Here we report a chromosome-level genome assembly of I. rubescens, a well-recognized oridonin producer long favored by Asian people as a traditional herb with antitumor effects. The shoot apex was confirmed to be the actual region actively producing ent-kaurene diterpenoids. Through comparative genomics and phylogenetic analyses, we discovered a cluster of tandem-duplicated CYP706V oxygenase-encoding genes located on an ancient genomic block widely distributed in eudicots, whereas almost exclusively emerged in Isodon plants. In the shoot apex, IrCYP706V2 and IrCYP706V7 oxidized the ent-kaurene core in the initial stage of oridonin biosynthesis. Loss of CYP706Vs in other Lamiaceae plants offered an explanation for the specific kaurenoid production in Isodon plants. Moreover, we found that the Isodon genomes encode multiple diterpenoid synthases that are potentially involved in generating diterpenoid diversity. These findings provided new insights into the evolution of the lineage-specific diterpenoid pathway and laid a foundation for improving production of bioactive ent-kaurene-type diterpenoids by molecular breeding and synthetic biology approaches.
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Affiliation(s)
- Yuwei Sun
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jie Shao
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Haili Liu
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Hua Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Guangyi Wang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Jianhua Li
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yaping Mao
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Zhuo Chen
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Ke Ma
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yong Wang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
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14
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Han D, Li W, Hou Z, Lin C, Xie Y, Zhou X, Gao Y, Huang J, Lai J, Wang L, Zhang L, Yang C. The chromosome-scale assembly of the Salvia rosmarinus genome provides insight into carnosic acid biosynthesis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:819-832. [PMID: 36579923 DOI: 10.1111/tpj.16087] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 12/16/2022] [Accepted: 12/26/2022] [Indexed: 06/17/2023]
Abstract
Rosemary (Salvia rosmarinus) is considered a sacred plant because of its special fragrance and is commonly used in cooking and traditional medicine. Here, we report a high-quality chromosome-level assembly of the S. rosmarinus genome of 1.11 Gb in size; the genome has a scaffold N50 value of 95.5 Mb and contains 40 701 protein-coding genes. In contrast to other diploid Labiataceae, an independent whole-genome duplication event occurred in S. rosmarinus at approximately 15 million years ago. Transcriptomic comparison of two S. rosmarinus cultivars with contrasting carnosic acid (CA) content revealed 842 genes significantly positively associated with CA biosynthesis in S. rosmarinus. Many of these genes have been reported to be involved in CA biosynthesis previously, such as genes involved in the mevalonate/methylerythritol phosphate pathways and CYP71-coding genes. Based on the genomes and these genes, we propose a model of CA biosynthesis in S. rosmarinus. Further, comparative genome analysis of the congeneric species revealed the species-specific evolution of CA biosynthesis genes. The genes encoding diterpene synthase and the cytochrome P450 (CYP450) family of CA synthesis-associated genes form a biosynthetic gene cluster (CPSs-KSLs-CYP76AHs) responsible for the synthesis of leaf and root diterpenoids, which are located on S. rosmarinus chromosomes 1 and 2, respectively. Such clustering is also observed in other sage (Salvia) plants, thus suggesting that genes involved in diterpenoid synthesis are conserved in the Labiataceae family. These findings provide new insights into the synthesis of aromatic terpenoids and their regulation.
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Affiliation(s)
- Danlu Han
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, 510631, Guangzhou, China
| | - Wenliang Li
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, 510631, Guangzhou, China
| | - Zhuangwei Hou
- Shenzhen Branch Guangdong Laboratory for Lingnan Modern Agriculture/Genome Analysis Laboratory of the Ministry of Agriculture/Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Chufang Lin
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, 510631, Guangzhou, China
| | - Yun Xie
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, 510631, Guangzhou, China
| | - Xiaofang Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, 510642, Guangzhou, China
| | - Yuan Gao
- Shenzhen Branch, Guangdong Laboratory of 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, China
| | - Junwen Huang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, 510631, Guangzhou, China
| | - Jianbin Lai
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, 510631, Guangzhou, China
| | - Li Wang
- Shenzhen Branch Guangdong Laboratory for Lingnan Modern Agriculture/Genome Analysis Laboratory of the Ministry of Agriculture/Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Liangsheng Zhang
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Chengwei Yang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, 510631, Guangzhou, China
- SCNU Qingyuan Institute of Science and Technology Innovation Co., Ltd., Qingyuan, 511517, China
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15
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Ritz M, Ahmad N, Brueck T, Mehlmer N. Comparative Genome-Wide Analysis of Two Caryopteris x Clandonensis Cultivars: Insights on the Biosynthesis of Volatile Terpenoids. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12030632. [PMID: 36771729 PMCID: PMC9921992 DOI: 10.3390/plants12030632] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/25/2023] [Accepted: 01/27/2023] [Indexed: 05/31/2023]
Abstract
Caryopteris x Clandonensis, also known as bluebeard, is an ornamental plant containing a large variety of terpenes and terpene-like compounds. Four different cultivars were subjected to a principal component analysis to elucidate variations in terpenoid-biosynthesis and consequently, two representative cultivars were sequenced on a genomic level. Functional annotation of genes as well as comparative genome analysis on long read datasets enabled the identification of cultivar-specific terpene synthase and cytochrome p450 enzyme sequences. This enables new insights, especially since terpenoids in research and industry are gaining increasing interest due to their importance in areas such as food preservation, fragrances, or as active ingredients in pharmaceutical formulations. According to BUSCO assessments, the presented genomes have an average size of 355 Mb and about 96.8% completeness. An average of 52,090 genes could be annotated as putative proteins, whereas about 42 were associated with terpene synthases and about 1340 with cytochrome p450 enzymes.
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16
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Tamura K, Sakamoto M, Tanizawa Y, Mochizuki T, Matsushita S, Kato Y, Ishikawa T, Okuhara K, Nakamura Y, Bono H. A highly contiguous genome assembly of red perilla (Perilla frutescens) domesticated in Japan. DNA Res 2023; 30:dsac044. [PMID: 36383440 PMCID: PMC9835750 DOI: 10.1093/dnares/dsac044] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 11/17/2022] Open
Abstract
Perilla frutescens (Lamiaceae) is an important herbal plant with hundreds of bioactive chemicals, among which perillaldehyde and rosmarinic acid are the two major bioactive compounds in the plant. The leaves of red perilla are used as traditional Kampo medicine or food ingredients. However, the medicinal and nutritional uses of this plant could be improved by enhancing the production of valuable metabolites through the manipulation of key enzymes or regulatory genes using genome editing technology. Here, we generated a high-quality genome assembly of red perilla domesticated in Japan. A near-complete chromosome-level assembly of P. frutescens was generated contigs with N50 of 41.5 Mb from PacBio HiFi reads. 99.2% of the assembly was anchored into 20 pseudochromosomes, among which seven pseudochromosomes consisted of one contig, while the rest consisted of less than six contigs. Gene annotation and prediction of the sequences successfully predicted 86,258 gene models, including 76,825 protein-coding genes. Further analysis showed that potential targets of genome editing for the engineering of anthocyanin pathways in P. frutescens are located on the late-stage pathways. Overall, our genome assembly could serve as a valuable reference for selecting target genes for genome editing of P. frutescens.
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Affiliation(s)
- Keita Tamura
- Laboratory of Genome Informatics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-0046, Japan
- Laboratory of BioDX, Genome Editing Innovation Center, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-0046, Japan
| | - Mika Sakamoto
- Genome Informatics Laboratory, Department of Informatics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Yasuhiro Tanizawa
- Genome Informatics Laboratory, Department of Informatics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Takako Mochizuki
- Genome Informatics Laboratory, Department of Informatics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Shuji Matsushita
- Agricultural Technology Research Center, Hiroshima Prefectural Technology Research Institute, Higashi-Hiroshima, Hiroshima 739-0151, Japan
| | - Yoshihiro Kato
- Mishima Foods Co., Ltd., Hiroshima City, Hiroshima 733-0036, Japan
| | - Takeshi Ishikawa
- Mishima Foods Co., Ltd., Hiroshima City, Hiroshima 733-0036, Japan
| | - Keisuke Okuhara
- Laboratory of Genome Informatics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-0046, Japan
- PtBio Inc., Higashi-Hiroshima, Hiroshima 739-0046, Japan
| | - Yasukazu Nakamura
- Genome Informatics Laboratory, Department of Informatics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Hidemasa Bono
- Laboratory of Genome Informatics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-0046, Japan
- Laboratory of BioDX, Genome Editing Innovation Center, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-0046, Japan
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17
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Zhou T, Bai G, Hu Y, Ruhsam M, Yang Y, Zhao Y. De novo genome assembly of the medicinal plant Gentiana macrophylla provides insights into the genomic evolution and biosynthesis of iridoids. DNA Res 2022; 29:6748869. [PMID: 36197098 PMCID: PMC9724787 DOI: 10.1093/dnares/dsac034] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 08/24/2022] [Accepted: 09/12/2022] [Indexed: 12/13/2022] Open
Abstract
Gentiana macrophylla is a perennial herb in the Gentianaceae family, whose dried roots are used in traditional Chinese medicine. Here, we assembled a chromosome-level genome of G. macrophylla using a combination of Nanopore, Illumina, and Hi-C scaffolding approaches. The final genome size was ~1.79 Gb (contig N50 = 720.804 kb), and 98.89% of the genome sequences were anchored on 13 pseudochromosomes (scaffold N50 = 122.73 Mb). The genome contained 55,337 protein-coding genes, and 73.47% of the assemblies were repetitive sequences. Genome evolution analysis indicated that G. macrophylla underwent two rounds of whole-genome duplication after the core eudicot γ genome triplication event. We further identified candidate genes related to the biosynthesis of iridoids, and the corresponding gene families mostly expanded in G. macrophylla. In addition, we found that root-specific genes are enriched in pathways involved in defense responses, which may greatly improve the biological adaptability of G. macrophylla. Phylogenomic analyses showed a sister relationship of asterids and rosids, and all Gentianales species formed a monophyletic group. Our study contributes to the understanding of genome evolution and active component biosynthesis in G. macrophylla and provides important genomic resource for the genetic improvement and breeding of G. macrophylla.
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Affiliation(s)
- Tao Zhou
- Corresponding author: Tel. +86 29 8265 5424. (T.Z.); (Y.Z.)
| | | | | | - Markus Ruhsam
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK
| | - Yanci Yang
- School of Biological Science and Technology, Baotou Teachers’ College, Baotou, China
| | - Yuemei Zhao
- Corresponding author: Tel. +86 29 8265 5424. (T.Z.); (Y.Z.)
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18
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Guo L, Yao H, Chen W, Wang X, Ye P, Xu Z, Zhang S, Wu H. Natural products of medicinal plants: biosynthesis and bioengineering in post-genomic era. HORTICULTURE RESEARCH 2022; 9:uhac223. [PMID: 36479585 PMCID: PMC9720450 DOI: 10.1093/hr/uhac223] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 09/22/2022] [Indexed: 06/01/2023]
Abstract
Globally, medicinal plant natural products (PNPs) are a major source of substances used in traditional and modern medicine. As we human race face the tremendous public health challenge posed by emerging infectious diseases, antibiotic resistance and surging drug prices etc., harnessing the healing power of medicinal plants gifted from mother nature is more urgent than ever in helping us survive future challenge in a sustainable way. PNP research efforts in the pre-genomic era focus on discovering bioactive molecules with pharmaceutical activities, and identifying individual genes responsible for biosynthesis. Critically, systemic biological, multi- and inter-disciplinary approaches integrating and interrogating all accessible data from genomics, metabolomics, structural biology, and chemical informatics are necessary to accelerate the full characterization of biosynthetic and regulatory circuitry for producing PNPs in medicinal plants. In this review, we attempt to provide a brief update on the current research of PNPs in medicinal plants by focusing on how different state-of-the-art biotechnologies facilitate their discovery, the molecular basis of their biosynthesis, as well as synthetic biology. Finally, we humbly provide a foresight of the research trend for understanding the biology of medicinal plants in the coming decades.
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Affiliation(s)
- Li Guo
- Corresponding authors. E-mails: ;
| | | | | | - Xumei Wang
- School of Pharmacy, Xi’an Jiaotong University, Xi’an 710061, China
| | - Peng Ye
- State Key laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory For Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Zhichao Xu
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Sisheng Zhang
- State Key laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory For Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Hong Wu
- Corresponding authors. E-mails: ;
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19
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Integration of Repeatomic and Cytogenetic Data on Satellite DNA for the Genome Analysis in the Genus Salvia (Lamiaceae). PLANTS 2022; 11:plants11172244. [PMID: 36079625 PMCID: PMC9460151 DOI: 10.3390/plants11172244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/25/2022] [Accepted: 08/25/2022] [Indexed: 11/17/2022]
Abstract
Within the complicated and controversial taxonomy of cosmopolitan genus Salvia L. (Lamiaceae) are valuable species Salvia officinalis L. and Salvia sclarea L., which are important for the pharmaceutical, ornamental horticulture, food, and perfume industries. Genome organization and chromosome structure of these essential oil species remain insufficiently studied. For the first time, the comparative repeatome analysis of S. officinalis and S. sclarea was performed using the obtained NGS data, RepeatExplorer/TAREAN pipelines and FISH-based chromosome mapping of the revealed satellite DNA families (satDNAs). In repeatomes of these species, LTR retrotransposons made up the majority of their repetitive DNA. Interspecific variations in genome abundance of Class I and Class II transposable elements, ribosomal DNA, and satellite DNA were revealed. Four (S. sclarea) and twelve (S. officinalis) putative satDNAs were identified. Based on patterns of chromosomal distribution of 45S rDNA; 5S rDNA and the revealed satDNAs, karyograms of S. officinalis and S. sclarea were constructed. Promising satDNAs which can be further used as chromosome markers to assess inter- and intraspecific chromosome variability in Salvia karyotypes were determined. The specific localization of homologous satDNA and 45S rDNA on chromosomes of the studied Salvia species confirmed their common origin, which is consistent with previously reported molecular phylogenetic data.
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20
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Wang L, Lee M, Sun F, Song Z, Yang Z, Yue GH. A chromosome-level genome assembly of chia provides insights into high omega-3 content and coat color variation of its seeds. PLANT COMMUNICATIONS 2022; 3:100326. [PMID: 35605203 PMCID: PMC9284293 DOI: 10.1016/j.xplc.2022.100326] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 03/14/2022] [Accepted: 04/11/2022] [Indexed: 05/26/2023]
Abstract
Chia (Salvia hispanica) is a functional food crop for humans. Although its seeds contain high omega-3 fatty acids, the seed yield of chia is still low. Genomic resources available for this plant are limited. We report the first high-quality chromosome-level genome sequence of chia. The assembled genome size was 347.6 Mb and covered 98.1% of the estimated genome size. A total of 31 069 protein-coding genes were predicted. The absence of recent whole-genome duplication and the relatively low intensity of transposable element expansion in chia compared to its sister species contribute to its small genome size. Transcriptome sequencing and gene duplication analysis reveal that the expansion of the fab2 gene family is likely to be related to the high content of omega-3 in seeds. The white seed coat color is determined by a single locus on chromosome 4. This study provides novel insights into the evolution of Salvia species and high omega-3 content, as well as valuable genomic resources for genetic improvement of important commercial traits of chia and its related species.
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Affiliation(s)
- Le Wang
- Temasek Life Sciences Laboratory, Singapore 117604, Singapore
| | - May Lee
- Temasek Life Sciences Laboratory, Singapore 117604, Singapore
| | - Fei Sun
- Temasek Life Sciences Laboratory, Singapore 117604, Singapore
| | - Zhuojun Song
- Temasek Life Sciences Laboratory, Singapore 117604, Singapore
| | - Zituo Yang
- Temasek Life Sciences Laboratory, Singapore 117604, Singapore
| | - Gen Hua Yue
- Temasek Life Sciences Laboratory, Singapore 117604, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore.
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21
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Jia KH, Wang ZX, Wang L, Li GY, Zhang W, Wang XL, Xu FJ, Jiao SQ, Zhou SS, Liu H, Ma Y, Bi G, Zhao W, El-Kassaby YA, Porth I, Li G, Zhang RG, Mao JF. SubPhaser: a robust allopolyploid subgenome phasing method based on subgenome-specific k-mers. THE NEW PHYTOLOGIST 2022; 235:801-809. [PMID: 35460274 DOI: 10.1111/nph.18173] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 04/04/2022] [Indexed: 05/02/2023]
Abstract
With advanced sequencing technology, dozens of complex polyploid plant genomes have been characterized. However, for many polyploid species, their diploid ancestors are unknown or extinct, making it impossible to unravel the subgenomes and genome evolution directly. We developed a novel subgenome-phasing algorithm, SubPhaser, specifically designed for a neoallopolyploid or a homoploid hybrid. SubPhaser first searches for the subgenome-specific sequence (k-mer), then assigns homoeologous chromosomes into subgenomes, and further provides tools to annotate and investigate specific sequences. SubPhaser works well on neoallopolyploids and homoploid hybrids containing subgenome-specific sequences like wheat, but fails on autopolyploids lacking subgenome-specific sequences like alfalfa, indicating that SubPhaser can phase neoallopolyploid/homoploid hybrids with high accuracy, sensitivity and performance. This highly accurate, highly sensitive, ancestral data free chromosome phasing algorithm, SubPhaser, offers significant application value for subgenome phasing in neoallopolyploids and homoploid hybrids, and for the subsequent exploration of genome evolution and related genetic/epigenetic mechanisms.
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Affiliation(s)
- Kai-Hua Jia
- Key Laboratory of Crop Genetic Improvement & Ecology and Physiology, Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Ji'nan, 250100, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Research Center of Tree Breeding and Ecological Restoration, Ministry of Education, Beijing Forestry University, Beijing, 100083, China
| | - Zhao-Xuan Wang
- Shijiazhuang People's Medical College, Shijiazhuang, 050091, China
| | - Longxin Wang
- School of Biological Science and Technology, University of Jinan, Ji'nan, 250022, China
| | - Guang-Yuan Li
- Department of Bioinformatics, Ori (Shandong) Gene Science and Technology Co. Ltd, Weifang, 261322, China
| | - Wei Zhang
- Department of Bioinformatics, Ori (Shandong) Gene Science and Technology Co. Ltd, Weifang, 261322, China
| | - Xiao-Ling Wang
- BGI Shenzhen, Shenzhen, 518083, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
| | - Fang-Ji Xu
- Key Laboratory of Crop Genetic Improvement & Ecology and Physiology, Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Ji'nan, 250100, China
| | - Si-Qian Jiao
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Research Center of Tree Breeding and Ecological Restoration, Ministry of Education, Beijing Forestry University, Beijing, 100083, China
| | - Shan-Shan Zhou
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Research Center of Tree Breeding and Ecological Restoration, Ministry of Education, Beijing Forestry University, Beijing, 100083, China
| | - Hui Liu
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Research Center of Tree Breeding and Ecological Restoration, Ministry of Education, Beijing Forestry University, Beijing, 100083, China
| | - Yongpeng Ma
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Guiqi Bi
- 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
| | - Wei Zhao
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Research Center of Tree Breeding and Ecological Restoration, Ministry of Education, Beijing Forestry University, Beijing, 100083, China
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Ilga Porth
- Départment des Sciences du Bois et de la Forêt, Faculté de Foresterie, de Géographie et Géomatique, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Guowei Li
- Key Laboratory of Crop Genetic Improvement & Ecology and Physiology, Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Ji'nan, 250100, China
| | - Ren-Gang Zhang
- Department of Bioinformatics, Ori (Shandong) Gene Science and Technology Co. Ltd, Weifang, 261322, China
| | - Jian-Feng Mao
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Research Center of Tree Breeding and Ecological Restoration, Ministry of Education, Beijing Forestry University, Beijing, 100083, China
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22
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Hu J, Wang F, Liang F, Wu Z, Jiang R, Li J, Chen J, Qiu S, Wang J, Zhang Y, Li Q, Chen W. Identification of Abietane-Type Diterpenoids and Phenolic Acids Biosynthesis Genes in Salvia apiana Jepson Through Full-Length Transcriptomic and Metabolomic Profiling. FRONTIERS IN PLANT SCIENCE 2022; 13:919025. [PMID: 35755672 PMCID: PMC9213684 DOI: 10.3389/fpls.2022.919025] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 04/28/2022] [Indexed: 06/15/2023]
Abstract
Salvia apiana (S. apiana) Jepson is a medicinal plant that is frequently used by the Chumash Indians in southern California as a diaphoretic, calmative, diuretic, or antimicrobial agent. Abietane-type diterpenoids (ATDs) and phenolic acids (PAs) are the main bioactive ingredients in S. apiana. However, few studies have looked into the biosynthesis of ATDs and PAs in S. apiana. In this study, using metabolic profiling focused on the ATDs and PAs in the roots and leaves of S. apiana, we found a distinctive metabolic feature with all-around accumulation of ATDs, but absence of salvianolic acid B. To identify the candidate genes involved in these biosynthesis pathways, full-length transcriptome was performed by PacBio single-molecule real-time (SMRT) sequencing. A total of 50 and 40 unigenes were predicted to be involved in ATDs and PAs biosynthesis, respectively. Further transcriptional profile using Illumina HiSeq sequencing showed that the transcriptional variations of these pathways were consistent with the accumulation patterns of corresponding metabolites. A plant kingdom-wide phylogenetic analysis of cytochromes (CYPs) identified two CYP76AK and two CYP76AH subfamily genes that might contribute for the specific ATDs biosynthesis in S. apiana. We also noticed that the clade VII laccase gene family was significantly expanded in Salvia miltiorrhiza compared with that of S. apiana, indicating their involvements in the formation of salvianolic acid B. In conclusion, our results will enable the further understanding of ATDs and PAs biosynthesis in S. apiana and Salvia genus.
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Affiliation(s)
- Jiadong Hu
- Center of Chinese Traditional Medicine Resources and Biotechnology, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Feiyan Wang
- Center of Chinese Traditional Medicine Resources and Biotechnology, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Fengying Liang
- Department of Pharmacy, Second Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Ziding Wu
- Center of Chinese Traditional Medicine Resources and Biotechnology, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Rui Jiang
- Center of Chinese Traditional Medicine Resources and Biotechnology, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jinxing Li
- Center of Chinese Traditional Medicine Resources and Biotechnology, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Junfeng Chen
- Center of Chinese Traditional Medicine Resources and Biotechnology, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Shi Qiu
- Center of Chinese Traditional Medicine Resources and Biotechnology, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jing Wang
- Center of Chinese Traditional Medicine Resources and Biotechnology, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yuchen Zhang
- Center of Chinese Traditional Medicine Resources and Biotechnology, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Qing Li
- Department of Pharmacy, Second Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Wansheng Chen
- Center of Chinese Traditional Medicine Resources and Biotechnology, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Department of Pharmacy, Second Affiliated Hospital of Naval Medical University, Shanghai, China
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23
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Islam AKMM, Suttiyut T, Anwar MP, Juraimi AS, Kato-Noguchi H. Allelopathic Properties of Lamiaceae Species: Prospects and Challenges to Use in Agriculture. PLANTS 2022; 11:plants11111478. [PMID: 35684250 PMCID: PMC9182988 DOI: 10.3390/plants11111478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 05/29/2022] [Accepted: 05/30/2022] [Indexed: 11/16/2022]
Abstract
Herbicide resistance due to the increasing reliance on herbicides is a near-term challenge for the world’s agriculture. This has led to a desire to develop new herbicides with a novel mode of action, to address resistance in weed species. Lamiaceae, a large dicotyledonous plant family, is very well known for the multitudinous pharmacological and toxicological properties of its member species. Moreover, many species of this family are significant for their allelopathic activity in natural and laboratory settings. Thus, plants in Lamiaceae have the potential to be sources of alternative herbicides. However, gaps in our knowledge need to be addressed prior to adopting these allelopathic activities in agriculture. Therefore, we review the existing state of knowledge about the Lamiaceae family, the reported allelopathic properties of plant extracts, and their isolated allelochemicals under laboratory, greenhouse, and field conditions. In addition, we offer a perspective on existing challenges and future opportunities for adopting the allelopathic properties of Lamiaceae plant species for green agriculture.
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Affiliation(s)
- A. K. M. Mominul Islam
- Department of Agronomy, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh;
- Correspondence: ; Tel.: +880-1718-512082
| | - Thiti Suttiyut
- Department of Horticulture and Landscape Architecture, Purdue University, 625 Agriculture Mall Dr, West Lafayette, IN 47907, USA;
- Purdue Center of Plant Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Md. Parvez Anwar
- Department of Agronomy, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh;
| | - Abdul Shukor Juraimi
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia;
| | - Hisashi Kato-Noguchi
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, Miki 761-0795, Japan;
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24
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Wang Z, Peters RJ. Tanshinones: Leading the way into Lamiaceae labdane-related diterpenoid biosynthesis. CURRENT OPINION IN PLANT BIOLOGY 2022; 66:102189. [PMID: 35196638 PMCID: PMC8940693 DOI: 10.1016/j.pbi.2022.102189] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 01/06/2022] [Accepted: 01/14/2022] [Indexed: 05/06/2023]
Abstract
Tanshinones are the bioactive diterpenoid constituents of the traditional Chinese medicinal herb Danshen (Salvia miltiorrhiza), and are examples of the phenolic abietanes widely found within the Lamiaceae plant family. Due to the significant interest in these labdane-related diterpenoid natural products, their biosynthesis has been intensively investigated. In addition to providing the basis for metabolic engineering efforts, this work further yielded pioneering insights into labdane-related diterpenoid biosynthesis in the Lamiaceae more broadly. This includes stereochemical foreshadowing of aromatization, with novel protein domain loss in the relevant diterpene synthase, as well as broader phylogenetic conservation of the relevant enzymes. Beyond such summary of more widespread metabolism, formation of the furan ring that characterizes the tanshinones also has been recently elucidated. Nevertheless, the biocatalysts for the pair of demethylations remain unknown, and the intriguing potential connection of these reactions to the further aromatization observed in the tanshinones are speculated upon here.
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Affiliation(s)
- Zhibiao Wang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 100029, China; Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Reuben J Peters
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011, USA.
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