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Someya W, Akutsu T, Nacher JC. Target control of linear directed networks based on the path cover problem. Sci Rep 2024; 14:16881. [PMID: 39043768 PMCID: PMC11266607 DOI: 10.1038/s41598-024-67442-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 07/11/2024] [Indexed: 07/25/2024] Open
Abstract
Securing complete control of complex systems comprised of tens of thousands of interconnected nodes holds immense significance across various fields, spanning from cell biology and brain science to human-engineered systems. However, depending on specific functional requirements, it can be more practical and efficient to focus on a pre-defined subset of nodes for control, a concept known as target control. While some methods have been proposed to find the smallest driver node set for target control, they either rely on heuristic approaches based on k-walk theory, lacking a guarantee of optimal solutions, or they are overly complex and challenging to implement in real-world networks. To address this challenge, we introduce a simple and elegant algorithm, inspired by the path cover problem, which efficiently identifies the nodes required to control a target node set within polynomial time. To practically apply the algorithm in real-world systems, we have selected several networks in which a specific set of nodes with functional significance can be designated as a target control set. The analysed systems include the complete connectome of the nematode worm C. elegans, the recently disclosed connectome of the Drosophila larval brain, as well as dozens of genome-wide metabolic networks spanning major plant lineages. The target control analysis shed light on distinctions between neural systems in nematode worms and larval brain insects, particularly concerning the number of nodes necessary to regulate specific functional systems. Furthermore, our analysis uncovers evolutionary trends within plant lineages, notably when examining the proportion of nodes required to control functional pathways.
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Affiliation(s)
- Wataru Someya
- Department of Information Science, Faculty of Science, Toho University, Funabashi, Chiba, 274-8510, Japan
| | - Tatsuya Akutsu
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto, Uji, 611-0011, Japan
| | - Jose C Nacher
- Department of Information Science, Faculty of Science, Toho University, Funabashi, Chiba, 274-8510, Japan.
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Zhang F, Wang J, Li X, Zhang J, Liu Y, Chen Y, Yu Q, Li N. Genome-wide identification and expression analyses of phenylalanine ammonia-lyase gene family members from tomato ( Solanum lycopersicum) reveal their role in root-knot nematode infection. FRONTIERS IN PLANT SCIENCE 2023; 14:1204990. [PMID: 37346127 PMCID: PMC10280380 DOI: 10.3389/fpls.2023.1204990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 05/10/2023] [Indexed: 06/23/2023]
Abstract
Phenylalanine ammonia-lyase (PAL) is a key enzyme and rate-limiting enzyme of phenylpropanoid metabolism, which is a very important pathway in plants, and the secondary products it produces play an important role in plant growth and development, disease resistance, and stress resistance responses. However, PALs still lack systematic characterization in tomato. Based on a bioinformatics methods, PAL family genes were identified and characterized from tomato. qRT-PCR was used to study the expression of PAL genes in cultivated tomato after root-knot nematode infection. In this study, 14 and 11 PAL genes were identified in cultivated and wild tomatoes, and phylogenetic analysis classified them into three subfamilies, with different subfamilies of PAL proteins evolving in different directions in monocotyledonous and dicotyledonous plants. The extensive presence of stress, growth, hormone, and light response elements in the promoter sequences of SlPAL (Solanum lycopersicum) and SpenPAL (Solanum pennellii) genes suggests that this family has a critical role in abiotic stress. Collinearity indicates that members of the tomato and Arabidopsis PAL genes family are from the same ancestor, and the SlPAL10 gene is directly homologous to monocotyledonous rice and maize, suggesting that the SlPAL10 gene was present before monocotyledonous differentiation. Two co-expressed gene modules containing PAL genes were screened by WGCNA, and the core genes in the network were mined and functionally annotated by calculating the connectivity of genes within the modules. In addition, the expression of some genes changed significantly after root-knot nematode infection, with up-regulation of 4 genes and down-regulation of 3 genes. This result provides a data reference for the study of PAL family gene functions in tomato, and also provides a potential application for the subsequent selection of PAL genes in tomato for root-knot nematode resistance.
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Affiliation(s)
- Fulin Zhang
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
- College of Horticulture, Xinjiang Agricultural University, Urumqi, China
| | - Juan Wang
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Xianguo Li
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
- College of Horticulture, Xinjiang Agricultural University, Urumqi, China
| | - Jun Zhang
- Comprehensive Proving Ground, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Yuxiang Liu
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
- College of Horticulture, Xinjiang Agricultural University, Urumqi, China
| | - Yijia Chen
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
- College of Horticulture, Xinjiang Agricultural University, Urumqi, China
| | - Qinghui Yu
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Ning Li
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
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Yu D, Huang R, Yu S, Liang Q, Wang Y, Dang H, Zhang Y. Construction of the first high-density genetic linkage map and QTL mapping of flavonoid and leaf-size related traits in Epimedium. BMC PLANT BIOLOGY 2023; 23:278. [PMID: 37231361 DOI: 10.1186/s12870-023-04257-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 04/28/2023] [Indexed: 05/27/2023]
Abstract
BACKGROUND Leaves are the main medicinal organ in Epimedium herbs, and leaf flavonoid content is an important criterion of Epimedium herbs. However, the underlying genes that regulate leaf size and flavonoid content are unclear, which limits the use of breeding for Epimedium development. This study focuses on QTL mapping of flavonoid and leaf-size related traits in Epimedium. RESULTS We constructed the first high-density genetic map (HDGM) using 109 F1 hybrids of Epimedium leptorrhizum and Epimedium sagittatum over three years (2019-2021). Using 5,271 single nucleotide polymorphism (SNP) markers, an HDGM with an overall distance of 2,366.07 cM and a mean gap of 0.612 cM was generated by utilizing genotyping by sequencing (GBS) technology. Every year for three years, 46 stable quantitative trait loci (QTLs) for leaf size and flavonoid contents were discovered, including 31 stable loci for Epimedin C (EC), one stable locus for total flavone content (TFC), 12 stable loci for leaf length (LL), and two stable loci for leaf area (LA). For flavonoid content and leaf size, the phenotypic variance explained for these loci varied between 4.00 and 16.80% and 14.95 and 17.34%, respectively. CONCLUSIONS Forty-six stable QTLs for leaf size and flavonoid content traits were repeatedly detected over three years. The HDGM and stable QTLs are laying the basis for breeding and gene investigation in Epimedium and will contribute to accelerating the identification of desirable genotypes for Epimedium breeding.
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Affiliation(s)
- Dongyue Yu
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, P.R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P.R. China
| | - Ruoqi Huang
- University of Chinese Academy of Sciences, Beijing, 100049, P.R. China
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, P. R. China
| | - Shuxia Yu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, P. R. China
| | - Qiong Liang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, P. R. China
| | - Ying Wang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, P.R. China
| | - Haishan Dang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, P.R. China.
| | - Yanjun Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, P. R. China.
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Chen H, Guo M, Dong S, Wu X, Zhang G, He L, Jiao Y, Chen S, Li L, Luo H. A chromosome-scale genome assembly of Artemisia argyi reveals unbiased subgenome evolution and key contributions of gene duplication to volatile terpenoid diversity. PLANT COMMUNICATIONS 2023; 4:100516. [PMID: 36597358 DOI: 10.1016/j.xplc.2023.100516] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 12/14/2022] [Accepted: 12/31/2022] [Indexed: 05/11/2023]
Abstract
Artemisia argyi Lévl. et Vant., a perennial Artemisia herb with an intense fragrance, is widely used in traditional medicine in China and many other Asian countries. Here, we present a chromosome-scale genome assembly of A. argyi comprising 3.89 Gb assembled into 17 pseudochromosomes. Phylogenetic and comparative genomic analyses revealed that A. argyi underwent a recent lineage-specific whole-genome duplication (WGD) event after divergence from Artemisia annua, resulting in two subgenomes. We deciphered the diploid ancestral genome of A. argyi, and unbiased subgenome evolution was observed. The recent WGD led to a large number of duplicated genes in the A. argyi genome. Expansion of the terpene synthase (TPS) gene family through various types of gene duplication may have greatly contributed to the diversity of volatile terpenoids in A. argyi. In particular, we identified a typical germacrene D synthase gene cluster within the expanded TPS gene family. The entire biosynthetic pathways of germacrenes, (+)-borneol, and (+)-camphor were elucidated in A. argyi. In addition, partial deletion of the amorpha-4,11-diene synthase (ADS) gene and loss of function of ADS homologs may have resulted in the lack of artemisinin production in A. argyi. Our study provides new insights into the genome evolution of Artemisia and lays a foundation for further improvement of the quality of this important medicinal plant.
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Affiliation(s)
- Hongyu Chen
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Miaoxian Guo
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Shuting Dong
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Xinling Wu
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China; Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Guobin Zhang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian 271018, China; College of Agronomy, Shandong Agricultural University, Taian 271018, China
| | - Liu He
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Yuannian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Shilin Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
| | - Li Li
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA; Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
| | - Hongmei Luo
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China.
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Shirazi Z, Khakdan F, Rafiei F, Balalami MY, Ranjbar M. Genome-wide identification and expression profile analysis of metal tolerance protein gene family in Eucalyptus grandis under metal stresses. BMC PLANT BIOLOGY 2023; 23:240. [PMID: 37149585 PMCID: PMC10163719 DOI: 10.1186/s12870-023-04240-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 04/21/2023] [Indexed: 05/08/2023]
Abstract
Metal tolerance proteins (MTPs) as Me2+/H+(K+) antiporters participate in the transport of divalent cations, leading to heavy metal stress resistance and mineral utilization in plants. In the present study, to obtain better knowledge of the biological functions of the MTPs family, 20 potential EgMTPs genes were identified in Eucalyptus grandis and classified into seven groups belonging to three cation diffusion facilitator groups (Mn-CDFs, Zn/Fe-CDFs, and Zn-CDFs) and seven groups. EgMTP-encoded amino acids ranged from 315 to 884, and most of them contained 4-6 recognized transmembrane domains and were clearly prognosticated to localize into the cell vacuole. Almost all EgMTP genes experienced gene duplication events, in which some might be uniformly distributed in the genome. The numbers of cation efflux and the zinc transporter dimerization domain were highest in EgMTP proteins. The promoter regions of EgMTP genes have different cis-regulatory elements, indicating that the transcription rate of EgMTP genes can be a controlled response to different stimuli in multiple pathways. Our findings provide accurate perception on the role of the predicted miRNAs and the presence of SSR marker in the Eucalyptus genome and clarify their functions in metal tolerance regulation and marker-assisted selection, respectively. Gene expression profiling based on previous RNA-seq data indicates a probable function for EgMTP genes during development and responses to biotic stress. Additionally, the upregulation of EgMTP6, EgMTP5, and EgMTP11.1 to excess Cd2+ and Cu2+ exposure might be responsible for metal translocation from roots to leaves.
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Affiliation(s)
- Zahra Shirazi
- Department of Biotechnology Research, Research Institute of Forests and Rangelands, Agricultural Research, Education and Extension Organization (AREEO), National Botanical Garden, Tehran Karaj Freeway, P.O. Box 13185-116, Tehran, Iran.
| | | | - Fariba Rafiei
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
| | - Mahdi Yahyazadeh Balalami
- Department of Medicinal Plant Research, Research Institute of Forests and Rangelands, Agricultural Research, Education and Extension Organization (AREEO), National Botanical Garden, Tehran Karaj Freeway, P.O. Box 13185-116, Tehran, Iran
| | - Mojtaba Ranjbar
- Microbial Biotechnology Department, College of Biotechnology, University of Special Modern Technologies, Amol, Iran
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Menconi J, Perata P, Gonzali S. Novel R2R3 MYB transcription factors regulate anthocyanin synthesis in Aubergine tomato plants. BMC PLANT BIOLOGY 2023; 23:148. [PMID: 36935480 PMCID: PMC10026432 DOI: 10.1186/s12870-023-04153-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 03/01/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND A high content in anthocyanins, for their health beneficial properties, represents an added value for fruits and vegetables. Tomato (Solanum lycopersicum) is one of the most consumed vegetables worldwide and is rich in vitamins and carotenoids. In recent years, purple-skinned tomatoes, enriched of anthocyanins, were produced recovering allelic variants from wild Solanum species. The molecular basis of the Anthocyanin fruit (Aft) locus, exploited by breeders to activate the anthocyanin synthesis in tomato epicarp, has been recently identified in the correct splicing of the R2R3 MYB gene AN2like. Aubergine (Abg) is a tomato accession which introgressed from Solanum lycopersicoides a locus activating the synthesis of anthocyanins in the fruit. The Abg locus was mapped in the region of chromosome 10 containing Aft and the possibility that Abg and Aft represented alleles of the same gene was hypothesized. RESULTS We dissected the R2R3 MYB gene cluster located in the Abg genomic introgression and demonstrated that AN2like is correctly spliced in Abg plants and is expressed in the fruit epicarp. Moreover, its silencing specifically inhibits the anthocyanin synthesis. The Abg allele of AN2like undergoes alternative splicing and produces two proteins with different activities. Furthermore, in Abg the master regulator of the anthocyanin synthesis in tomato vegetative tissues, AN2, is very poorly expressed. Finally, a novel R2R3 MYB gene was identified: it encodes another positive regulator of the pathway, whose activity was lost in tomato and in its closest relatives. CONCLUSION In this study, we propose that AN2like is responsible of the anthocyanin production in Abg fruits. Unlike wild type tomato, the Abg allele of AN2like is active and able to regulate its targets. Furthermore, in Abg alternative splicing leads to two forms of AN2like with different activities, likely representing a novel type of regulation of anthocyanin synthesis in tomato.
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Affiliation(s)
- Jacopo Menconi
- PlantLab, Center of Plant Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, Pisa, 56127, Italy
| | - Pierdomenico Perata
- PlantLab, Center of Plant Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, Pisa, 56127, Italy
| | - Silvia Gonzali
- PlantLab, Center of Plant Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, Pisa, 56127, Italy.
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Yang Z, Li X, Yang L, Peng S, Song W, Lin Y, Xiang G, Li Y, Ye S, Ma C, Miao J, Zhang G, Chen W, Yang S, Dong Y. Comparative genomics reveals the diversification of triterpenoid biosynthesis and origin of ocotillol-type triterpenes in Panax. PLANT COMMUNICATIONS 2023:100591. [PMID: 36926697 PMCID: PMC10363511 DOI: 10.1016/j.xplc.2023.100591] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 01/14/2023] [Accepted: 03/13/2023] [Indexed: 06/18/2023]
Abstract
Gene duplication is assumed to be the major force driving the evolution of metabolite biosynthesis in plants. Freed from functional burdens, duplicated genes can mutate toward novelties until fixed due to selective fitness. However, the extent to which this mechanism has driven the diversification of metabolite biosynthesis remains to be tested. Here we performed comparative genomics analysis and functional characterization to evaluate the impact of gene duplication on the evolution of triterpenoid biosynthesis using Panax species as models. We found that whole-genome duplications (WGDs) occurred independently in Araliaceae and Apiaceae lineages. Comparative genomics revealed the evolutionary trajectories of triterpenoid biosynthesis in plants, which was mainly promoted by WGDs and tandem duplication. Lanosterol synthase (LAS) was likely derived from a tandem duplicate of cycloartenol synthase that predated the emergence of Nymphaeales. Under episodic diversifying selection, the LAS gene duplicates produced by γ whole-genome triplication have given rise to triterpene biosynthesis in core eudicots through neofunctionalization. Moreover, functional characterization revealed that oxidosqualene cyclases (OSCs) responsible for synthesizing dammarane-type triterpenes in Panax species were also capable of producing ocotillol-type triterpenes. Genomic and biochemical evidence suggested that Panax genes encoding the above OSCs originated from the specialization of one OSC gene duplicate produced from a recent WGD shared by Araliaceae (Pg-β). Our results reveal the crucial role of gene duplication in diversification of triterpenoid biosynthesis in plants and provide insight into the origin of ocotillol-type triterpenes in Panax species.
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Affiliation(s)
- Zijiang Yang
- National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China; The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, China
| | - Xiaobo Li
- National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China; The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, China
| | - Ling Yang
- National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China; College of Food Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Sufang Peng
- National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China; The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, China
| | - Wanling Song
- National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China; The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, China
| | - Yuan Lin
- National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China; The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, China
| | - Guisheng Xiang
- National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China; The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, China
| | - Ying Li
- National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China; The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, China
| | - Shuang Ye
- National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China; The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, China
| | - Chunhua Ma
- National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China; The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, China
| | - Jianhua Miao
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Guanghui Zhang
- National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China; The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, China
| | - Wei Chen
- National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China; Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China; Yunnan Plateau Characteristic Agriculture Industry Research Institute, Kunming, China
| | - Shengchao Yang
- National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China; The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, China.
| | - Yang Dong
- National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China; Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China; Yunnan Plateau Characteristic Agriculture Industry Research Institute, Kunming, China.
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Genome-wide identification and expression analysis of metal tolerance protein (MTP) gene family in soybean (Glycine max) under heavy metal stress. Mol Biol Rep 2023; 50:2975-2990. [PMID: 36653731 DOI: 10.1007/s11033-022-08100-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 11/08/2022] [Indexed: 01/19/2023]
Abstract
AIM Plant metal tolerance proteins (MTPs) are plant membrane divalent cation transporters that specifically contribute to heavy metal stress resistance and mineral uptake. However, little is known about this family's molecular behaviors and biological activities in soybean. METHODS AND RESULTS A total of 20 potential MTP candidate genes were identified and studied in the soybean genome for phylogenetic relationships, chromosomal distributions, gene structures, gene ontology, cis-elements, and previous gene expression. Furthermore, the expression of MTPs has been investigated under different heavy metals treatments. All identified soybean MTPs (GmaMTPs) contain a cation efflux domain or a ZT dimer and are further divided into three primary cation diffusion facilitator (CDF) groups: Mn-CDFs, Zn-CDFs, and Fe/Zn-CDFs. The developmental analysis reveals that segmental duplication contributes to the GmaMTP family's expansion. Tissue-specific expression profiling revealed comparative expression profiling in similar groups, although gene expression differed between groups. GmaMTP genes displayed biased responses in either plant leaves or roots when treated with heavy metal. In the leaves and roots, nine and ten GmaMTPs responded to at least one metal ion treatment. Furthermore, in most heavy metal treatments, GmaMTP1.1, GmaMTP1.2, GmaMTP3.1, GmaMTP3.2, GmaMTP4.1, and GmaMTP4.3 exhibited significant expression responses. CONCLUSION Our findings provided insight into the evolution of MTPs in soybean. Overall, our findings shed light on the evolution of the MTP gene family in soybean and pave the path for further functional characterization of this gene family.
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Mottiar Y, Smith RA, Karlen SD, Ralph J, Mansfield SD. Evolution of p-coumaroylated lignin in eudicots provides new tools for cell wall engineering. THE NEW PHYTOLOGIST 2023; 237:251-264. [PMID: 36196006 PMCID: PMC10099755 DOI: 10.1111/nph.18518] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
Ester-linked p-coumarate (pCA) is a hallmark feature of the secondary cell walls in commelinid monocot plants. It has been shown that pCA groups arise during lignin polymerisation from the participation of monolignol conjugates assembled by p-coumaroyl-CoA:monolignol transferase (PMT) enzymes, members of the BAHD superfamily of acyltransferases. Herein, we report that a eudicot species, kenaf (Hibiscus cannabinus), naturally contains p-coumaroylated lignin in the core tissues of the stems but not in the bast fibres. Moreover, we identified a novel acyltransferase, HcPMT, that shares <30% amino acid identity with known monocot PMT sequences. Recombinant HcPMT showed a preference in enzyme assays for p-coumaroyl-CoA and benzoyl-CoA as acyl donor substrates and sinapyl alcohol as an acyl acceptor. Heterologous expression of HcPMT in hybrid poplar trees led to the incorporation of pCA in lignin, but no improvement in the saccharification potential of the wood. This work illustrates the value in mining diverse plant taxa for new monolignol acyltransferases. Furthermore, the occurrence of pCA outside monocot lineages may represent another example of convergent evolution in lignin structure. This discovery expands textbook views on cell wall biochemistry and provides a new molecular tool for engineering the lignin of biomass feedstock plants.
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Affiliation(s)
- Yaseen Mottiar
- Department of Wood ScienceUniversity of British Columbia2424 Main MallVancouverBCV6T 1Z4Canada
- Department of Energy Great Lakes Bioenergy Research CenterUniversity of Wisconsin1552 University AvenueMadisonWI53726USA
| | - Rebecca A. Smith
- Department of Energy Great Lakes Bioenergy Research CenterUniversity of Wisconsin1552 University AvenueMadisonWI53726USA
- Department of BiochemistryUniversity of Wisconsin433 Babcock DriveMadisonWI53706USA
| | - Steven D. Karlen
- Department of Energy Great Lakes Bioenergy Research CenterUniversity of Wisconsin1552 University AvenueMadisonWI53726USA
- Department of BiochemistryUniversity of Wisconsin433 Babcock DriveMadisonWI53706USA
| | - John Ralph
- Department of Energy Great Lakes Bioenergy Research CenterUniversity of Wisconsin1552 University AvenueMadisonWI53726USA
- Department of BiochemistryUniversity of Wisconsin433 Babcock DriveMadisonWI53706USA
| | - Shawn D. Mansfield
- Department of Wood ScienceUniversity of British Columbia2424 Main MallVancouverBCV6T 1Z4Canada
- Department of Energy Great Lakes Bioenergy Research CenterUniversity of Wisconsin1552 University AvenueMadisonWI53726USA
- Department of BotanyUniversity of British Columbia6270 University BoulevardVancouverBCV6T 1Z4Canada
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10
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Sun C, Xie YH, Li Z, Liu YJ, Sun XM, Li JJ, Quan WP, Zeng QY, Van de Peer Y, Zhang SG. The Larix kaempferi genome reveals new insights into wood properties. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:1364-1373. [PMID: 35442564 DOI: 10.1111/jipb.13265] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 04/18/2022] [Indexed: 06/14/2023]
Abstract
Here, through single-molecule real-time sequencing, we present a high-quality genome sequence of the Japanese larch (Larix kaempferi), a conifer species with great value for wood production and ecological afforestation. The assembled genome is 10.97 Gb in size, harboring 45,828 protein-coding genes. Of the genome, 66.8% consists of repeat sequences, of which long terminal repeat retrotransposons are dominant and make up 69.86%. We find that tandem duplications have been responsible for the expansion of genes involved in transcriptional regulation and stress responses, unveiling their crucial roles in adaptive evolution. Population transcriptome analysis reveals that lignin content in L. kaempferi is mainly determined by the process of monolignol polymerization. The expression values of six genes (LkCOMT7, LkCOMT8, LkLAC23, LkLAC102, LkPRX148, and LkPRX166) have significantly positive correlations with lignin content. These results indicated that the increased expression of these six genes might be responsible for the high lignin content of the larches' wood. Overall, this study provides new genome resources for investigating the evolution and biological function of conifer trees, and also offers new insights into wood properties of larches.
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Affiliation(s)
- Chao Sun
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Yun-Hui Xie
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, B-9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, B-9052, Belgium
| | - Yan-Jing Liu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
| | - Xiao-Mei Sun
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Jing-Jing Li
- Nextomics Biosciences Co., Ltd, Wuhan, 430073, China
| | - Wei-Peng Quan
- Nextomics Biosciences Co., Ltd, Wuhan, 430073, China
| | - Qing-Yin Zeng
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, B-9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, B-9052, Belgium
- Department of Biochemistry, Genetics and Microbiology, Pretoria, South Africa
| | - Shou-Gong Zhang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
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11
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Zhou X, Liu Z. Unlocking plant metabolic diversity: A (pan)-genomic view. PLANT COMMUNICATIONS 2022; 3:100300. [PMID: 35529944 PMCID: PMC9073316 DOI: 10.1016/j.xplc.2022.100300] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/12/2021] [Accepted: 01/13/2022] [Indexed: 05/28/2023]
Abstract
Plants produce a remarkable diversity of structurally and functionally diverse natural chemicals that serve as adaptive compounds throughout their life cycles. However, unlocking this metabolic diversity is significantly impeded by the size, complexity, and abundant repetitive elements of typical plant genomes. As genome sequencing becomes routine, we anticipate that links between metabolic diversity and genetic variation will be strengthened. In addition, an ever-increasing number of plant genomes have revealed that biosynthetic gene clusters are not only a hallmark of microbes and fungi; gene clusters for various classes of compounds have also been found in plants, and many are associated with important agronomic traits. We present recent examples of plant metabolic diversification that have been discovered through the exploration and exploitation of various genomic and pan-genomic data. We also draw attention to the fundamental genomic and pan-genomic basis of plant chemodiversity and discuss challenges and future perspectives for investigating metabolic diversity in the coming pan-genomics era.
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Affiliation(s)
- Xuan Zhou
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhenhua Liu
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
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12
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Abdullaeva Y, Ratering S, Ambika Manirajan B, Rosado-Porto D, Schnell S, Cardinale M. Domestication Impacts the Wheat-Associated Microbiota and the Rhizosphere Colonization by Seed- and Soil-Originated Microbiomes, Across Different Fields. FRONTIERS IN PLANT SCIENCE 2022; 12:806915. [PMID: 35095978 PMCID: PMC8789879 DOI: 10.3389/fpls.2021.806915] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 12/13/2021] [Indexed: 05/17/2023]
Abstract
The seed-transmitted microorganisms and the microbiome of the soil in which the plant grows are major drivers of the rhizosphere microbiome, a crucial component of the plant holobiont. The seed-borne microbiome can be even coevolved with the host plant as a result of adaptation and vertical transmission over generations. The reduced genome diversity and crossing events during domestication might have influenced plant traits that are important for root colonization by seed-borne microbes and also rhizosphere recruitment of microbes from the bulk soil. However, the impact of the breeding on seed-transmitted microbiome composition and the plant ability of microbiome selection from the soil remain unknown. Here, we analyzed both endorhiza and rhizosphere microbiome of two couples of genetically related wild and cultivated wheat species (Aegilops tauschii/Triticum aestivum and T. dicoccoides/T. durum) grown in three locations, using 16S rRNA gene and ITS2 metabarcoding, to assess the relative contribution of seed-borne and soil-derived microbes to the assemblage of the rhizosphere microbiome. We found that more bacterial and fungal ASVs are transmitted from seed to the endosphere of all species compared with the rhizosphere, and these transmitted ASVs were species-specific regardless of location. Only in one location, more microbial seed transmission occurred also in the rhizosphere of A. tauschii compared with other species. Concerning soil-derived microbiome, the most distinct microbial genera occurred in the rhizosphere of A. tauschii compared with other species in all locations. The rhizosphere of genetically connected wheat species was enriched with similar taxa, differently between locations. Our results demonstrate that host plant criteria for soil bank's and seed-originated microbiome recruitment depend on both plants' genotype and availability of microorganisms in a particular environment. This study also provides indications of coevolution between the host plant and its associated microbiome resulting from the vertical transmission of seed-originated taxa.
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Affiliation(s)
| | - Stefan Ratering
- Institute of Applied Microbiology, Justus-Liebig-University, Giessen, Germany
| | | | - David Rosado-Porto
- Institute of Applied Microbiology, Justus-Liebig-University, Giessen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, Justus-Liebig-University, Giessen, Germany
| | - Massimiliano Cardinale
- Institute of Applied Microbiology, Justus-Liebig-University, Giessen, Germany
- Department of Biological and Environmental Sciences and Technologies – DiSTeBA, University of Salento, Lecce, Italy
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13
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El- Sappah AH, Elrys AS, Desoky ESM, Zhao X, Bingwen W, El-Sappah HH, Zhu Y, Zhou W, Zhao X, Li J. Comprehensive genome wide identification and expression analysis of MTP gene family in tomato ( Solanum lycopersicum) under multiple heavy metal stress. Saudi J Biol Sci 2021; 28:6946-6956. [PMID: 34866994 PMCID: PMC8626246 DOI: 10.1016/j.sjbs.2021.07.073] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 06/22/2021] [Accepted: 07/26/2021] [Indexed: 11/24/2022] Open
Abstract
Plant metal tolerance proteins (MTPs) play major roles in enhancing resistance to heavy metal tolerance and homeostasis. However, the role of MTPs genes in tomato, which is one of the most popular crops, is still largely limited. Hence, we investigated genome-wide study of tomato MTPs, including phylogenetic, duplication, gene structure, gene ontology and previous transcriptomic data analysis. Moreover, the MTPs expression behaviour under various heavy metals stress has rarely been investigated. In the current study, eleven MTP candidate genes were genome-wide identified and classified into three major groups; Mn-cation diffusion facilitators (CDFs), Fe/Zn-CDFs, and Zn-CDFs based on the phylogeny. Structural analysis of SlMTPs showed high gene similarity within the same group with cation_efflux or ZT_dimerdomains. Evolutionary analysis revealed that segmental duplication contributed to the expansion of the SlMTP family. Gene ontology further showed the vital roles of MTPs in metal-related processes. Tissue-specific expression profiling exhibited similar expression patterns in the same group, whereas gene expression varied among groups. The MTPs expression was evaluated after tomato treatments by five divalent heavy metals (Cd2+, Co2+, Mn2+, Zn2+, and Fe2+). SlMTP genes displayed differential responses in either plant leaves or roots under heavy metals treatments. Nine and ten SlMTPs responded to at least one metal ion treatment in leaves and roots, respectively. In addition SlMTP1, SlMTP3, SlMTP4, SlMTP8, SlMTP10 and SlMTP11 exhibited the highest expression responses in most of heavy metals treatments. Overall, our findings presented a standpoint on the evolution of MTPs and their evolution in tomato and paved the way for additional functional characterization under heavy metal toxicity.
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Affiliation(s)
- Ahmed H. El- Sappah
- School of Agriculture, Forestry, and Food Engineering, Yibin University, Yibin 644000, Sichuan, China
- Genetics Department, Faculty of Agriculture, Zagazig University, 44511 Zagazig, Egypt
| | - Ahmed S. Elrys
- Soil Science Department, Faculty of Agriculture, Zagazig University, 44511 Zagazig, Egypt
| | - El-Sayed M. Desoky
- Botany Department, Faculty of Agriculture, Zagazig University, 44511 Zagazig, Egypt
| | - Xia Zhao
- School of Agriculture, Forestry, and Food Engineering, Yibin University, Yibin 644000, Sichuan, China
| | - Wang Bingwen
- School of Agriculture, Forestry, and Food Engineering, Yibin University, Yibin 644000, Sichuan, China
| | | | - Yumin Zhu
- School of Agriculture, Forestry, and Food Engineering, Yibin University, Yibin 644000, Sichuan, China
| | - Wanhai Zhou
- School of Agriculture, Forestry, and Food Engineering, Yibin University, Yibin 644000, Sichuan, China
| | - Xianming Zhao
- School of Agriculture, Forestry, and Food Engineering, Yibin University, Yibin 644000, Sichuan, China
| | - Jia Li
- School of Agriculture, Forestry, and Food Engineering, Yibin University, Yibin 644000, Sichuan, China
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14
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El-Sappah AH, Elbaiomy RG, Elrys AS, Wang Y, Zhu Y, Huang Q, Yan K, Xianming Z, Abbas M, El-Tarabily KA, Li J. Genome-Wide Identification and Expression Analysis of Metal Tolerance Protein Gene Family in Medicago truncatula Under a Broad Range of Heavy Metal Stress. Front Genet 2021; 12:713224. [PMID: 34603378 PMCID: PMC8482800 DOI: 10.3389/fgene.2021.713224] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 06/30/2021] [Indexed: 01/02/2023] Open
Abstract
Metal tolerance proteins (MTPs) encompass plant membrane divalent cation transporters to specifically participate in heavy metal stress resistance and mineral acquisition. However, the molecular behaviors and biological functions of this family in Medicago truncatula are scarcely known. A total of 12 potential MTP candidate genes in the M. truncatula genome were successfully identified and analyzed for a phylogenetic relationship, chromosomal distributions, gene structures, docking analysis, gene ontology, and previous gene expression. M. truncatula MTPs (MtMTPs) were further classified into three major cation diffusion facilitator (CDFs) groups: Mn-CDFs, Zn-CDFs, and Fe/Zn-CDFs. The structural analysis of MtMTPs displayed high gene similarity within the same group where all of them have cation_efflux domain or ZT_dimer. Cis-acting element analysis suggested that various abiotic stresses and phytohormones could induce the most MtMTP gene transcripts. Among all MTPs, PF16916 is the specific domain, whereas GLY, ILE, LEU, MET, ALA, SER, THR, VAL, ASN, and PHE amino acids were predicted to be the binding residues in the ligand-binding site of all these proteins. RNA-seq and gene ontology analysis revealed the significant role of MTP genes in the growth and development of M. truncatula. MtMTP genes displayed differential responses in plant leaves, stems, and roots under five divalent heavy metals (Cd2+, Co2+, Mn2+, Zn2+, and Fe2+). Ten, seven, and nine MtMTPs responded to at least one metal ion treatment in the leaves, stems, and roots, respectively. Additionally, MtMTP1.1, MtMTP1.2, and MtMTP4 exhibited the highest expression responses in most heavy metal treatments. Our results presented a standpoint on the evolution of MTPs in M. truncatula. Overall, our study provides a novel insight into the evolution of the MTP gene family in M. truncatula and paves the way for additional functional characterization of this gene family.
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Affiliation(s)
- Ahmed H El-Sappah
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China.,Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | | | - Ahmed S Elrys
- Soil Science Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Yu Wang
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Yumin Zhu
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Qiulan Huang
- College of Tea Science, Yibin University, Yibin, China
| | - Kuan Yan
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Zhao Xianming
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Manzar Abbas
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Khaled A El-Tarabily
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, United Arab Emirates.,Harry Butler Institute, Murdoch University, Murdoch, WA, Australia
| | - Jia Li
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
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15
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Neuronal odor coding in the larval sensory cone of Anopheles coluzzii: Complex responses from a simple system. Cell Rep 2021; 36:109555. [PMID: 34407405 PMCID: PMC8420959 DOI: 10.1016/j.celrep.2021.109555] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 05/18/2021] [Accepted: 07/28/2021] [Indexed: 11/20/2022] Open
Abstract
Anopheles mosquitoes are the sole vectors of malaria. Although adult females are directly responsible for disease transmission and accordingly have been extensively studied, the survival of pre-adult larval stages is vital. Mosquito larvae utilize a spectrum of chemosensory and other cues to navigate their aquatic habitats to avoid predators and search for food. Here we examine larval olfactory responses, in which the peripheral components are associated with the antennal sensory cone. Larval behavior and sensory cone responses to volatile stimuli in Anopheles coluzzii demonstrate the sensory cone is particularly tuned to alcohols, thiazoles, and heterocyclics, and these responses can be assigned to discrete groups of sensory cone neurons with distinctive profiles. These studies reveal that the anopheline larvae actively sample volatile odors above their aquatic habitats via a highly sophisticated olfactory system that is sensitive to a broad range of compounds with significant behavioral relevance. Sun et al. investigate larval sensory cone and behavioral responses to volatile stimuli in Anopheles coluzzii. They find that malaria mosquito larvae actively sample volatile odors above their aquatic habitats via a highly sophisticated olfactory system that is sensitive to a broad range of compounds with significant behavioral relevance.
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16
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Gene Expression and Isoform Identification of PacBio Full-Length cDNA Sequences for Berberine Biosynthesis in Berberis koreana. PLANTS 2021; 10:plants10071314. [PMID: 34203474 PMCID: PMC8308982 DOI: 10.3390/plants10071314] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/18/2021] [Accepted: 06/25/2021] [Indexed: 12/13/2022]
Abstract
Berberis koreana is a medicinal plant containing berberine, which is a bioactive compound of the benzylisoquinoline alkaloid (BIA) class. BIA is widely used in the food and drug industry for its health benefits. To investigate the berberine biosynthesis pathway, gene expression analysis was performed in leaves, flowers, and fruits at different stages of growth. This was followed by full-length cDNA sequencing analysis using the PacBio sequencer platform to determine the number of isoforms of those expressed genes. We identified 23,246 full-length unigenes, among which 8479 had more than one isoform. The number of isoforms ranged between two to thirty-one among all genes. Complete isoform analysis was carried out on the unigenes encoding BIA synthesis. Thirteen of the sixteen genes encoding enzymes for berberine synthesis were present in more than one copy. This demonstrates that gene duplication and translation into isoforms may contribute to the functional specificity of the duplicated genes and isoforms in plant alkaloid synthesis. Our study also demonstrated the streamlining of berberine biosynthesis via the absence of genes for enzymes of other BIAs, but the presence of all the genes for berberine biosynthesize in B. koreana. In addition to genes encoding enzymes for the berberine biosynthesis pathway, the genes encoding enzymes for other BIAs were not present in our dataset except for those encoding corytuberine synthase (CTS) and berbamunine synthase (BS). Therefore, this explains how B. koreana produces berberine by blocking the pathways leading to other BIAs, effectively only allowing the pathway to lead to berberine synthesis.
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17
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Zhang Y, Deng T, Sun L, Landis JB, Moore MJ, Wang H, Wang Y, Hao X, Chen J, Li S, Xu M, Puno PT, Raven PH, Sun H. Phylogenetic patterns suggest frequent multiple origins of secondary metabolites across the seed-plant 'tree of life'. Natl Sci Rev 2021; 8:nwaa105. [PMID: 34691607 PMCID: PMC8288438 DOI: 10.1093/nsr/nwaa105] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 04/04/2020] [Indexed: 11/13/2022] Open
Abstract
To evaluate the phylogenetic patterns of the distribution and evolution of plant secondary metabolites (PSMs), we selected 8 classes of PSMs and mapped them onto an updated phylogenetic tree including 437 families of seed plants. A significant phylogenetic signal was detected in 17 of the 18 tested seed-plant clades for at least 1 of the 8 PSM classes using the D statistic. The phylogenetic signal, nevertheless, indicated weak clustering of PSMs compared to a random distribution across all seed plants. The observed signal suggests strong diversifying selection during seed-plant evolution and/or relatively weak evolutionary constraints on the evolution of PSMs. In the survey of the current phylogenetic distributions of PSMs, we found that multiple origins of PSM biosynthesis due to external selective forces for diverse genetic pathways may have played important roles. In contrast, a single origin of PSMs seems rather uncommon. The distribution patterns for PSMs observed in this study may also be useful in the search for natural compounds for medicinal purposes.
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Affiliation(s)
- Yongzeng Zhang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Tao Deng
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Lu Sun
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Jacob B Landis
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY 14853, USA
| | - Michael J Moore
- Department of Biology, Oberlin College, Oberlin, OH 44074, USA
| | - Hengchang Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Chinese Academy of Sciences, Wuhan 430074, China
| | - Yuehua Wang
- School of Life Science, Yunnan University, Kunming 650091, China
| | - Xiaojiang Hao
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Jijun Chen
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Shenghong Li
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Maonian Xu
- Pharmaceutical Sciences, University of Iceland, 107 Reykjavik, Iceland
| | - Pema-Tenzin Puno
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | | | - Hang Sun
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
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18
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Jacoby RP, Koprivova A, Kopriva S. Pinpointing secondary metabolites that shape the composition and function of the plant microbiome. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:57-69. [PMID: 32995888 PMCID: PMC7816845 DOI: 10.1093/jxb/eraa424] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 09/10/2020] [Indexed: 05/02/2023]
Abstract
One of the major questions in contemporary plant science involves determining the functional mechanisms that plants use to shape their microbiome. Plants produce a plethora of chemically diverse secondary metabolites, many of which exert bioactive effects on microorganisms. Several recent publications have unequivocally shown that plant secondary metabolites affect microbiome composition and function. These studies have pinpointed that the microbiome can be influenced by a diverse set of molecules, including: coumarins, glucosinolates, benzoxazinoids, camalexin, and triterpenes. In this review, we summarize the role of secondary metabolites in shaping the plant microbiome, highlighting recent literature. A body of knowledge is now emerging that links specific plant metabolites with distinct microbial responses, mediated via defined biochemical mechanisms. There is significant potential to boost agricultural sustainability via the targeted enhancement of beneficial microbial traits, and here we argue that the newly discovered links between root chemistry and microbiome composition could provide a new set of tools for rationally manipulating the plant microbiome.
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Affiliation(s)
- Richard P Jacoby
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Anna Koprivova
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Stanislav Kopriva
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
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19
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Penin AA, Kasianov AS, Klepikova AV, Kirov IV, Gerasimov ES, Fesenko AN, Logacheva MD. High-Resolution Transcriptome Atlas and Improved Genome Assembly of Common Buckwheat, Fagopyrum esculentum. FRONTIERS IN PLANT SCIENCE 2021; 12:612382. [PMID: 33815435 PMCID: PMC8010679 DOI: 10.3389/fpls.2021.612382] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 02/03/2021] [Indexed: 05/06/2023]
Abstract
Common buckwheat (Fagopyrum esculentum) is an important non-cereal grain crop and a prospective component of functional food. Despite this, the genomic resources for this species and for the whole family Polygonaceae, to which it belongs, are scarce. Here, we report the assembly of the buckwheat genome using long-read technology and a high-resolution expression atlas including 46 organs and developmental stages. We found that the buckwheat genome has an extremely high content of transposable elements, including several classes of recently (0.5-1 Mya) multiplied TEs ("transposon burst") and gradually accumulated TEs. The difference in TE content is a major factor contributing to the three-fold increase in the genome size of F. esculentum compared with its sister species F. tataricum. Moreover, we detected the differences in TE content between the wild ancestral subspecies F. esculentum ssp. ancestrale and buckwheat cultivars, suggesting that TE activity accompanied buckwheat domestication. Expression profiling allowed us to test a hypothesis about the genetic control of petaloidy of tepals in buckwheat. We showed that it is not mediated by B-class gene activity, in contrast to the prediction from the ABC model. Based on a survey of expression profiles and phylogenetic analysis, we identified the MYB family transcription factor gene tr_18111 as a potential candidate for the determination of conical cells in buckwheat petaloid tepals. The information on expression patterns has been integrated into the publicly available database TraVA: http://travadb.org/browse/Species=Fesc/. The improved genome assembly and transcriptomic resources will enable research on buckwheat, including practical applications.
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Affiliation(s)
- Aleksey A. Penin
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Artem S. Kasianov
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Anna V. Klepikova
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Ilya V. Kirov
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
| | | | | | - Maria D. Logacheva
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
- Skolkovo Institute of Science and Technology, Moscow, Russia
- *Correspondence: Maria D. Logacheva,
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20
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Li H, Jiang S, Li C, Liu L, Lin Z, He H, Deng XW, Zhang Z, Wang X. The hybrid protein interactome contributes to rice heterosis as epistatic effects. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:116-128. [PMID: 31736145 DOI: 10.1111/tpj.14616] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 10/27/2019] [Accepted: 11/01/2019] [Indexed: 05/15/2023]
Abstract
Heterosis is the phenomenon in which hybrid progeny exhibits superior traits in comparison with those of their parents. Genomic variations between the two parental genomes may generate epistasis interactions, which is one of the genetic hypotheses explaining heterosis. We postulate that protein-protein interactions specific to F1 hybrids (F1 -specific PPIs) may occur when two parental genomes combine, as the proteome of each parent may supply novel interacting partners. To test our assumption, an inter-subspecies hybrid interactome was simulated by in silico PPI prediction between rice japonica (cultivar Nipponbare) and indica (cultivar 9311). Four-thousand, six-hundred and twelve F1 -specific PPIs accounting for 20.5% of total PPIs in the hybrid interactome were found. Genes participating in F1 -specific PPIs tend to encode metabolic enzymes and are generally localized in genomic regions harboring metabolic gene clusters. To test the genetic effect of F1 -specific PPIs in heterosis, genomic selection analysis was performed for trait prediction with additive, dominant and epistatic effects separately considered in the model. We found that the removal of single nucleotide polymorphisms associated with F1 -specific PPIs reduced prediction accuracy when epistatic effects were considered in the model, but no significant changes were observed when additive or dominant effects were considered. In summary, genomic divergence widely dispersed between japonica and indica rice may generate F1 -specific PPIs, part of which may accumulatively contribute to heterosis according to our computational analysis. These candidate F1 -specific PPIs, especially for those involved in metabolic biosynthesis pathways, are worthy of experimental validation when large-scale protein interactome datasets are generated in hybrid rice in the future.
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Affiliation(s)
- Hong Li
- National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, 570228, China
| | - Shuqin Jiang
- National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Chen Li
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Lei Liu
- Beijing Key Laboratory of Plant Resources Research and Development, School of Sciences, Beijing Technology and Business University, Beijing, 100048, China
| | - Zechuan Lin
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Hang He
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Xing-Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Ziding Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xiangfeng Wang
- National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
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21
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Krishnamurthy P, Tsukamoto C, Ishimoto M. Reconstruction of the Evolutionary Histories of UGT Gene Superfamily in Legumes Clarifies the Functional Divergence of Duplicates in Specialized Metabolism. Int J Mol Sci 2020; 21:E1855. [PMID: 32182686 PMCID: PMC7084467 DOI: 10.3390/ijms21051855] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 03/03/2020] [Accepted: 03/05/2020] [Indexed: 01/08/2023] Open
Abstract
Plant uridine 5'-diphosphate glycosyltransferases (UGTs) influence the physiochemical properties of several classes of specialized metabolites including triterpenoids via glycosylation. To uncover the evolutionary past of UGTs of soyasaponins (a group of beneficial triterpene glycosides widespread among Leguminosae), the UGT gene superfamily in Medicago truncatula, Glycine max, Phaseolus vulgaris, Lotus japonicus, and Trifolium pratense genomes were systematically mined. A total of 834 nonredundant UGTs were identified and categorized into 98 putative orthologous loci (POLs) using tree-based and graph-based methods. Major key findings in this study were of, (i) 17 POLs represent potential catalysts for triterpene glycosylation in legumes, (ii) UGTs responsible for the addition of second (UGT73P2: galactosyltransferase and UGT73P10: arabinosyltransferase) and third (UGT91H4: rhamnosyltransferase and UGT91H9: glucosyltransferase) sugars of the C-3 sugar chain of soyasaponins were resulted from duplication events occurred before and after the hologalegina-millettoid split, respectively, and followed neofunctionalization in species-/ lineage-specific manner, and (iii) UGTs responsible for the C-22-O glycosylation of group A (arabinosyltransferase) and DDMP saponins (DDMPtransferase) and the second sugar of C-22 sugar chain of group A saponins (UGT73F2: glucosyltransferase) may all share a common ancestor. Our findings showed a way to trace the evolutionary history of UGTs involved in specialized metabolism.
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Affiliation(s)
| | - Chigen Tsukamoto
- Faculty of Agriculture, Iwate University, Morioka 020-8550, Japan
| | - Masao Ishimoto
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba 305-8518, Japan
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22
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Labarrere B, Prinzing A, Dorey T, Chesneau E, Hennion F. Variations of Secondary Metabolites among Natural Populations of Sub-Antarctic Ranunculus Species Suggest Functional Redundancy and Versatility. PLANTS (BASEL, SWITZERLAND) 2019; 8:E234. [PMID: 31331007 PMCID: PMC6681328 DOI: 10.3390/plants8070234] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 06/28/2019] [Accepted: 07/16/2019] [Indexed: 11/25/2022]
Abstract
Plants produce a high diversity of metabolites which help them sustain environmental stresses and are involved in local adaptation. However, shaped by both the genome and the environment, the patterns of variation of the metabolome in nature are difficult to decipher. Few studies have explored the relative parts of geographical region versus environment or phenotype in metabolomic variability within species and none have discussed a possible effect of the region on the correlations between metabolites and environments or phenotypes. In three sub-Antarctic Ranunculus species, we examined the role of region in metabolite differences and in the relationship between individual compounds and environmental conditions or phenotypic traits. Populations of three Ranunculus species were sampled across similar environmental gradients in two distinct geographical regions in îles Kerguelen. Two metabolite classes were studied, amines (quantified by high-performance liquid chromatography and fluorescence spectrophotometry) and flavonols (quantified by ultra-high-performance liquid chromatography with triple quadrupole mass spectrometry). Depending on regions, the same environment or the same trait may be related to different metabolites, suggesting metabolite redundancy within species. In several cases, a given metabolite showed different or even opposite relations with the same environmental condition or the same trait across the two regions, suggesting metabolite versatility within species. Our results suggest that metabolites may be functionally redundant and versatile within species, both in their response to environments and in their relation with the phenotype. These findings open new perspectives for understanding evolutionary responses of plants to environmental changes.
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Affiliation(s)
- Bastien Labarrere
- UMR 6553 ECOBIO, Université de Rennes 1, OSUR, CNRS, Av du Général Leclerc, F-35042 Rennes, France
| | - Andreas Prinzing
- UMR 6553 ECOBIO, Université de Rennes 1, OSUR, CNRS, Av du Général Leclerc, F-35042 Rennes, France
| | - Thomas Dorey
- Institut für Systematische und Evolutionäre Botanik, Zollikerstrasse 107, 8008 Zürich, Switzerland
| | - Emeline Chesneau
- UMR 6553 ECOBIO, Université de Rennes 1, OSUR, CNRS, Av du Général Leclerc, F-35042 Rennes, France
| | - Françoise Hennion
- UMR 6553 ECOBIO, Université de Rennes 1, OSUR, CNRS, Av du Général Leclerc, F-35042 Rennes, France.
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23
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Colle M, Leisner CP, Wai CM, Ou S, Bird KA, Wang J, Wisecaver JH, Yocca AE, Alger EI, Tang H, Xiong Z, Callow P, Ben-Zvi G, Brodt A, Baruch K, Swale T, Shiue L, Song GQ, Childs KL, Schilmiller A, Vorsa N, Buell CR, VanBuren R, Jiang N, Edger PP. Haplotype-phased genome and evolution of phytonutrient pathways of tetraploid blueberry. Gigascience 2019; 8:5304886. [PMID: 30715294 PMCID: PMC6423372 DOI: 10.1093/gigascience/giz012] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 12/18/2018] [Accepted: 01/18/2019] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Highbush blueberry (Vaccinium corymbosum) has long been consumed for its unique flavor and composition of health-promoting phytonutrients. However, breeding efforts to improve fruit quality in blueberry have been greatly hampered by the lack of adequate genomic resources and a limited understanding of the underlying genetics encoding key traits. The genome of highbush blueberry has been particularly challenging to assemble due, in large part, to its polyploid nature and genome size. FINDINGS Here, we present a chromosome-scale and haplotype-phased genome assembly of the cultivar "Draper," which has the highest antioxidant levels among a diversity panel of 71 cultivars and 13 wild Vaccinium species. We leveraged this genome, combined with gene expression and metabolite data measured across fruit development, to identify candidate genes involved in the biosynthesis of important phytonutrients among other metabolites associated with superior fruit quality. Genome-wide analyses revealed that both polyploidy and tandem gene duplications modified various pathways involved in the biosynthesis of key phytonutrients. Furthermore, gene expression analyses hint at the presence of a spatial-temporal specific dominantly expressed subgenome including during fruit development. CONCLUSIONS These findings and the reference genome will serve as a valuable resource to guide future genome-enabled breeding of important agronomic traits in highbush blueberry.
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Affiliation(s)
- Marivi Colle
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI, 48824, USA.,MSU AgBioResearch, Michigan State University, 446 West Circle Drive, East Lansing, MI, 48824, USA
| | - Courtney P Leisner
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824 USA
| | - Ching Man Wai
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI, 48824, USA
| | - Shujun Ou
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI, 48824, USA.,Ecology, Evolutionary Biology and Behavior, Michigan State University, 293 Farm Lane, East Lansing, MI, 48824, USA
| | - Kevin A Bird
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI, 48824, USA.,Ecology, Evolutionary Biology and Behavior, Michigan State University, 293 Farm Lane, East Lansing, MI, 48824, USA
| | - Jie Wang
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824 USA.,Center for Genomics Enabled Plant Science, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824, USA
| | - Jennifer H Wisecaver
- Department of Biochemistry, Purdue University, 175 South University Street, West Lafayette, IN, 47907, USA.,Purdue Center for Plant Biology, Purdue University, 610 Purdue Mall, West Lafayette, IN, 47907, USA
| | - Alan E Yocca
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI, 48824, USA.,Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824 USA
| | - Elizabeth I Alger
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI, 48824, USA
| | - Haibao Tang
- Human Longevity Inc., 4570 Executive Drive, San Diego, CA 92121, USA
| | - Zhiyong Xiong
- Key Laboratory of Herbage and Endemic Crop Biotechnology, School of Life Sciences, Inner Mongolia University, 221 Aimin Road, Hohhot, 010070, China
| | - Pete Callow
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI, 48824, USA
| | - Gil Ben-Zvi
- NRGene, 5 Golda Meir Street, Ness Ziona, 7403648, Israel
| | - Avital Brodt
- NRGene, 5 Golda Meir Street, Ness Ziona, 7403648, Israel
| | - Kobi Baruch
- NRGene, 5 Golda Meir Street, Ness Ziona, 7403648, Israel
| | - Thomas Swale
- Dovetail Genomics, 100 Enterprise Way, Scotts Valley, CA, 95066, USA
| | - Lily Shiue
- Dovetail Genomics, 100 Enterprise Way, Scotts Valley, CA, 95066, USA
| | - Guo-Qing Song
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI, 48824, USA
| | - Kevin L Childs
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824 USA.,Center for Genomics Enabled Plant Science, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824, USA
| | - Anthony Schilmiller
- Mass Spectrometry & Metabolomics Core Facility, Michigan State University, 603 Wilson Road, East Lansing, MI, 48824, USA
| | - Nicholi Vorsa
- Department of Plant Biology, Rutgers University, 59 Dudley Road, New Brunswick, NJ, 08901, USA.,Philip E. Marucci Center for Blueberry and Cranberry Research and Extension, Rutgers University, 125A Lake Oswego Road, Chatsworth, NJ, 08019, USA
| | - C Robin Buell
- MSU AgBioResearch, Michigan State University, 446 West Circle Drive, East Lansing, MI, 48824, USA.,Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824 USA.,Plant Resilience Institute, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824 USA
| | - Robert VanBuren
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI, 48824, USA.,Plant Resilience Institute, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824 USA
| | - Ning Jiang
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI, 48824, USA.,Ecology, Evolutionary Biology and Behavior, Michigan State University, 293 Farm Lane, East Lansing, MI, 48824, USA
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI, 48824, USA.,MSU AgBioResearch, Michigan State University, 446 West Circle Drive, East Lansing, MI, 48824, USA.,Ecology, Evolutionary Biology and Behavior, Michigan State University, 293 Farm Lane, East Lansing, MI, 48824, USA
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24
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Wang S, Alseekh S, Fernie AR, Luo J. The Structure and Function of Major Plant Metabolite Modifications. MOLECULAR PLANT 2019; 12:899-919. [PMID: 31200079 DOI: 10.1016/j.molp.2019.06.001] [Citation(s) in RCA: 191] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/27/2019] [Accepted: 06/04/2019] [Indexed: 05/23/2023]
Abstract
Plants produce a myriad of structurally and functionally diverse metabolites that play many different roles in plant growth and development and in plant response to continually changing environmental conditions as well as abiotic and biotic stresses. This metabolic diversity is, to a large extent, due to chemical modification of the basic skeletons of metabolites. Here, we review the major known plant metabolite modifications and summarize the progress that has been achieved and the challenges we are facing in the field. We focus on discussing both technical and functional aspects in studying the influences that various modifications have on biosynthesis, degradation, transport, and storage of metabolites, as well as their bioactivity and toxicity. Finally, we discuss some emerging insights into the evolution of metabolic pathways and metabolite functionality.
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Affiliation(s)
- Shouchuang Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou 572208, China
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany; Centre of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany; Centre of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria.
| | - Jie Luo
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou 572208, China; National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
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25
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Yang Z, Yang L, Liu C, Qin X, Liu H, Chen J, Ji Y. Transcriptome analyses of Paris polyphylla var. chinensis, Ypsilandra thibetica, and Polygonatum kingianum characterize their steroidal saponin biosynthesis pathway. Fitoterapia 2019; 135:52-63. [PMID: 30999023 DOI: 10.1016/j.fitote.2019.04.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 04/01/2019] [Accepted: 04/13/2019] [Indexed: 10/27/2022]
Abstract
Steroidal saponins, one of the most diverse groups of plant-derived natural products, elicit biological and pharmacological activities; however, the genes involved in their biosynthesis and the corresponding biosynthetic pathway in monocotyledon plants remain unclear. This study aimed to identify genes involved in the biosynthesis of steroidal saponins by performing a comparative analysis among transcriptomes of Paris polyphylla var. chinensis (PPC), Ypsilandra thibetica (YT), and Polygonatum kingianum (PK). De novo transcriptome assemblies generated 57,537, 140,420, and 151,773 unigenes from PPC, YT, and PK, respectively, of which 56.54, 47.81, and 44.30% were successfully annotated, respectively. Among the transcriptomes for PPC, YT, and PK, we identified 194, 169, and 131; 17, 14, and 26; and, 80, 122, and 113 unigenes corresponding to terpenoid backbone biosynthesis; sesquiterpenoid and triterpenoid biosynthesis; and, steroid biosynthesis pathways, respectively. These genes are putatively involved in the biosynthesis of cholesterol that is the primary precursor of steroidal saponins. Phylogenetic analyses indicated that lanosterol synthase may be exclusive to dicotyledon plant species, and the cytochrome P450 unigenes were closely related to clusters CYP90B1 and CYP734A1, which are UDP-glycosyltransferases unigenes homologous with the UGT73 family. Thus, unigenes of β-glucosidase may be candidate genes for catalysis of later period modifications of the steroidal saponin skeleton. Our data provide evidence to support the hypothesis that monocotyledons biosynthesize steroidal saponins from cholesterol via the cycloartenol pathway.
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Affiliation(s)
- Zhenyan Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, PR China; Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Population, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, PR China
| | - Lifang Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, PR China; School of Life Science, Yunnan University, Kunming 650201, Yunnan, PR China
| | - Changkun Liu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, PR China; Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Population, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, PR China
| | - Xujie Qin
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, PR China
| | - Haiyang Liu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, PR China
| | - Jiahui Chen
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, PR China.
| | - Yunheng Ji
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, PR China; Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Population, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, PR China.
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26
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Kreis W, Munkert J. Exploiting enzyme promiscuity to shape plant specialized metabolism. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1435-1445. [PMID: 30715457 DOI: 10.1093/jxb/erz025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 12/11/2018] [Accepted: 01/11/2019] [Indexed: 05/23/2023]
Abstract
The amazing variability of plant metabolism and its rapid divergence during evolution pose fundamental questions as to the driving forces, mechanisms, and players in metabolic differentiation. This review examines concepts that help us understand adaptive pathway evolution, with a particular emphasis on plant specialized metabolism, previously often termed secondary metabolism. Following a general introduction to pathway and metabolite evolution, the focus is directed to enzyme promiscuity and its classification. Promiscuous enzymes (or substrates), 'silent' elements of the metabolome, and the 'underground metabolism' may be used and combined to evolve 'new' metabolic pathways. It appears that new pathways rarely appear from scratch, but instead emerge from 'floppy' enzymes and elements of a 'messy' metabolism, and in this way a range of metabolites is generated, some of which may provide benefits to the plant.
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Affiliation(s)
| | - Jennifer Munkert
- Friedrich-Alexander University Erlangen-Nürnberg, Department of Biology, Division of Pharmaceutical Biology, Erlangen, Germany
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27
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Ruel DM, Yakir E, Bohbot JD. Supersensitive Odorant Receptor Underscores Pleiotropic Roles of Indoles in Mosquito Ecology. Front Cell Neurosci 2019; 12:533. [PMID: 30733668 PMCID: PMC6353850 DOI: 10.3389/fncel.2018.00533] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 12/31/2018] [Indexed: 11/13/2022] Open
Abstract
Mosquitoes exhibit highly diverse and fast evolving odorant receptors (ORs). The indole-sensitive OR gene clade, comprised of Or2 and Or10 is a notable exception on account of its conservation in both mosquito subfamilies. This group of paralogous genes exhibits a complex developmental expression pattern in Aedes aegypti: AaegOr2 is expressed in both adults and larvae, AaegOr10 is adult-specific and a third member named AaegOr9 is larva-specific. OR2 and OR10 have been deorphanized and are selectively activated by indole and skatole, respectively. Using the two-electrode voltage clamp of Xenopus oocytes expressing Ae. aegypti ORs, we show that AaegOR9 is supersensitive and narrowly tuned to skatole. Our findings suggest that Ae. aegypti has evolved two distinct molecular strategies to detect skatole in aquatic and terrestrial environments, highlighting the central ecological roles of indolic compounds in the evolutionary and life histories of these insects.
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Affiliation(s)
| | | | - Jonathan D. Bohbot
- Department of Entomology, The Hebrew University of Jerusalem, Rehovot, Israel
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28
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Yan F, Li H, Zhao P. Genome-Wide Identification and Transcriptional Expression of the PAL Gene Family in Common Walnut ( Juglans Regia L.). Genes (Basel) 2019; 10:E46. [PMID: 30650597 PMCID: PMC6357058 DOI: 10.3390/genes10010046] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 01/10/2019] [Accepted: 01/10/2019] [Indexed: 12/19/2022] Open
Abstract
Juglans regia L. is an economically important crop cultivated worldwide for its high quality and quantity of wood and nuts. Phenylalanine ammonia-lyase (PAL) is the first enzyme in the phenylpropanoid pathway that plays a critical role in plant growth, development, and adaptation, but there have been few reports of the PAL gene family in common walnut. Here, we report a genome-wide study of J. regiaPAL genes and analyze their phylogeny, duplication, microRNA, and transcriptional expression. A total of 12 PAL genes were identified in the common walnut and clustered into two subfamilies based on phylogenetic analysis. These common walnut PALs are distributed on eight different pseudo-chromosomes. Seven of the 12 PALs (JrPAL2-3, JrPAL4-2, JrPAL2-1, JrPAL4-1, JrPAL8, JrPAL9, and JrPAL6) were specific found in J. regia, and JrPAL3, JrPAL5, JrPAL1-2, JrPAL7, and JrPAL2-2 were found to be closely associated with the woody plant Populus trichocarpa. Additionally, the expression patterns of JrPAL3, JrPAL7, JrPAL9, and JrPAL2-1 showed that they had high expression in female and male flowers. The miRNA ath-miR830-5p regulates two genes, JrPAL5 and JrPAL1, such that they have low expression in the male and female flowers of the common walnut. Our research provides useful information for further research into the function of PAL genes in common walnut and Juglans.
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Affiliation(s)
- Feng Yan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China.
| | - Huaizhu Li
- School of Chemistry and Chemical Engineering, Xianyang Normal University, Xianyang 712000, China.
| | - Peng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China.
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Kuo YT, Chao YT, Chen WC, Shih MC, Chang SB. Segmental and tandem chromosome duplications led to divergent evolution of the chalcone synthase gene family in Phalaenopsis orchids. ANNALS OF BOTANY 2019; 123:69-77. [PMID: 30113635 PMCID: PMC6344096 DOI: 10.1093/aob/mcy136] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 07/22/2018] [Indexed: 05/13/2023]
Abstract
BACKGROUND AND AIMS Orchidaceae is a large plant family, and its extraordinary adaptations may have guaranteed its evolutionary success. Flavonoids are a group of secondary metabolites that mediate plant acclimation to challenge environments. Chalcone synthase (CHS) catalyses the initial step in the flavonoid biosynthetic pathway. This is the first chromosome-level investigation of the CHS gene family in Phalaenopsis aphrodite and was conducted to elucidate if divergence of this gene family is associated with chromosome evolution. METHODS Complete CHS genes were identified from our whole-genome sequencing data sets and their gene expression profiles were obtained from our transcriptomic data sets. Fluorescence in situ hybridization (FISH) was conducted to position five CHS genes to high-resolution pachytene chromosomes. KEY RESULTS The five Phalaenopsis CHS genes can be classified into three groups, PaCHS1, PaCHS2 and the tandemly arrayed three-gene cluster, which diverged earlier than those of the orchid genera and species. Additionally, pachytene chromosome-based FISH mapping showed that the three groups of CHS genes are localized on three distinct chromosomes. Moreover, an expression analysis of RNA sequencing revealed that the five CHS genes had highly differentiated expression patterns and its expression pattern-based clustering showed high correlations between sequence divergences and chromosomal localizations of the CHS gene family in P. aphrodite. CONCLUSIONS Based on their phylogenetic relationships, expression clustering analysis and chromosomal distributions of the five paralogous PaCHS genes, we proposed that expansion of this gene family in P. aphrodite occurred through segmental duplications, followed by tandem duplications. These findings provide information for further studies of CHS functions and regulations, and shed light on the divergence of an important gene family in orchids.
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Affiliation(s)
- Yi-Tzu Kuo
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Ya-Ting Chao
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Wan-Chieh Chen
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Ming-Che Shih
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Song-Bin Chang
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
- For correspondence. E-mail:
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30
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Feng G, Xu L, Wang J, Nie G, Bushman BS, Xie W, Yan H, Yang Z, Guan H, Huang L, Zhang X. Integration of small RNAs and transcriptome sequencing uncovers a complex regulatory network during vernalization and heading stages of orchardgrass (Dactylis glomerata L.). BMC Genomics 2018; 19:727. [PMID: 30285619 PMCID: PMC6171228 DOI: 10.1186/s12864-018-5104-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 09/21/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Flowering is a critical reproductive process in higher plants. Timing of optimal flowering depends upon the coordination among seasonal environmental cues. For cool season grasses, such as Dactylis glomerata, vernalization induced by low temperature provides competence to initiate flowering after prolonged cold. We combined analyses of the transcriptome and microRNAs (miRNAs) to generate a comprehensive resource for regulatory miRNAs and their target circuits during vernalization and heading stages. RESULTS A total of 3,846 differentially expressed genes (DEGs) and 69 differentially expressed miRNAs were identified across five flowering stages. The expression of miR395, miR530, miR167, miR396, miR528, novel_42, novel_72, novel_107, and novel_123 demonstrated significant variations during vernalization. These miRNA targeted genes were involved in phytohormones, transmembrane transport, and plant morphogenesis in response to vernalization. The expression patterns of DEGs related to plant hormones, stress responses, energy metabolism, and signal transduction changed significantly in the transition from vegetative to reproductive phases. CONCLUSIONS Five hub genes, c136110_g1 (BRI1), c131375_g1 (BZR1), c133350_g1 (VRN1), c139830_g1 (VIN3), and c125792_g2 (FT), might play central roles in vernalization response. Our comprehensive analyses have provided a useful platform for investigating consecutive transcriptional and post-transcriptional regulation of critical phases in D. glomerata and provided insights into the genetic engineering of flowering-control in cereal crops.
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Affiliation(s)
- Guangyan Feng
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 Sichuan Province China
| | - Lei Xu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 Sichuan Province China
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL 32611 USA
| | - Gang Nie
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 Sichuan Province China
| | | | - Wengang Xie
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020 Gansu Province China
| | - Haidong Yan
- Department of Horticulture, Virginia Tech, Blacksburg, VA 24061 USA
| | - Zhongfu Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 Sichuan Province China
| | - Hao Guan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 Sichuan Province China
| | - Linkai Huang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 Sichuan Province China
| | - Xinquan Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 Sichuan Province China
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31
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Shirai K, Matsuda F, Nakabayashi R, Okamoto M, Tanaka M, Fujimoto A, Shimizu M, Shinozaki K, Seki M, Saito K, Hanada K. A Highly Specific Genome-Wide Association Study Integrated with Transcriptome Data Reveals the Contribution of Copy Number Variations to Specialized Metabolites in Arabidopsis thaliana Accessions. Mol Biol Evol 2018; 34:3111-3122. [PMID: 28961930 DOI: 10.1093/molbev/msx234] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Lineage-specific gene duplications contribute to a large variation in specialized metabolites among different plant species. There is also considerable variability in the specialized metabolites within a single plant species. However, it is unclear whether copy number variations (CNVs) derived from gene duplication events contribute to the diversity of specialized metabolites within species. We identified metabolome quantitative trait genes (mQTGs) associated with quantitative metabolite variations and examined the relationship between mQTGs and CNVs. We obtained 1,335 specialized metabolite signals from 53 worldwide A. thaliana accessions using liquid chromatography-quadrupole time-of-flight mass spectrometry. In this study, genes associated with specialized metabolites were inferred by either a generally authorized genome-wide association study (GWAS) approach or a novel analysis of the association between gene expression and metabolite accumulation. Genes qualified by both analyses are defined to be mQTGs. The integrated method enabled us to detect mQTGs with a low false positive rate (=5.71 × 10-4). We also identified 5,654 genes associated with 1,335 specialized metabolites. Of these genes, 4.4% were affected by CNVs, which was more than expected (χ2 test: P < 0.01). This result suggests that CNVs contribute to variations in specialized metabolites within a species. To assess the contribution of CNVs to adaptive evolution in A. thaliana, we examined the selective sweeps around the mQTGs. We observed that the mQTGs with CNVs tended to undergo selective sweeps. These observations imply that variations in specialized metabolites caused by CNVs contribute to the adaptive evolution of A. thaliana.
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Affiliation(s)
- Kazumasa Shirai
- Frontier Research Academy for Young Researchers, Kyushu Institute of Technology, Fukuoka, Japan
| | - Fumio Matsuda
- Center for Sustainable Resource Science, RIKEN, Kanagawa, Japan.,Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
| | - Ryo Nakabayashi
- Center for Sustainable Resource Science, RIKEN, Kanagawa, Japan
| | - Masanori Okamoto
- Center for Sustainable Resource Science, RIKEN, Kanagawa, Japan.,Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, Japan
| | - Maho Tanaka
- Center for Sustainable Resource Science, RIKEN, Kanagawa, Japan
| | - Akihiro Fujimoto
- Department of Drug Discovery Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Center for Integrative Medical Sciences, RIKEN, Kanagawa, Japan
| | - Minami Shimizu
- Center for Sustainable Resource Science, RIKEN, Kanagawa, Japan
| | - Kazuo Shinozaki
- Center for Sustainable Resource Science, RIKEN, Kanagawa, Japan
| | - Motoaki Seki
- Center for Sustainable Resource Science, RIKEN, Kanagawa, Japan
| | - Kazuki Saito
- Center for Sustainable Resource Science, RIKEN, Kanagawa, Japan.,Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Kousuke Hanada
- Frontier Research Academy for Young Researchers, Kyushu Institute of Technology, Fukuoka, Japan.,Center for Sustainable Resource Science, RIKEN, Kanagawa, Japan
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Priya P, Yadav A, Chand J, Yadav G. Terzyme: a tool for identification and analysis of the plant terpenome. PLANT METHODS 2018; 14:4. [PMID: 29339971 PMCID: PMC5761147 DOI: 10.1186/s13007-017-0269-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 12/19/2017] [Indexed: 05/13/2023]
Abstract
BACKGROUND Terpenoid hydrocarbons represent the largest and most ancient group of phytochemicals, such that the entire chemical library of a plant is often referred to as its 'terpenome'. Besides having numerous pharmacological properties, terpenes contribute to the scent of the rose, the flavors of cinnamon and the yellow of sunflowers. Rapidly increasing -omics datasets provide an unprecedented opportunity for terpenome detection, paving the way for automated web resources dedicated to phytochemical predictions in genomic data. RESULTS We have developed Terzyme, a predictive algorithm for identification, classification and assignment of broad substrate unit to terpene synthase (TPS) and prenyl transferase (PT) enzymes, known to generate the enormous structural and functional diversity of terpenoid compounds across the plant kingdom. Terzyme uses sequence information, plant taxonomy and machine learning methods for predicting TPSs and PTs in genome and proteome datasets. We demonstrate a significant enrichment of the currently identified terpenome by running Terzyme on more than 40 plants. CONCLUSIONS Terzyme is the result of a rigorous analysis of evolutionary relationships between hundreds of characterized sequences of TPSs and PTs with known specificities, followed by analysis of genome-wide gene distribution patterns, ontology based clustering and optimization of various parameters for building accurate profile Hidden Markov Models. The predictive webserver and database is freely available at http://nipgr.res.in/terzyme.html and would serve as a useful tool for deciphering the species-specific phytochemical potential of plant genomes.
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Affiliation(s)
- Piyush Priya
- Computational Biology Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Archana Yadav
- Computational Biology Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Jyoti Chand
- Computational Biology Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Gitanjali Yadav
- Computational Biology Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067 India
- Department of Plant Sciences, University of Cambridge, Downing Site, Cambridge, CB2 3EA UK
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Deng X, Zhao L, Fang T, Xiong Y, Ogutu C, Yang D, Vimolmangkang S, Liu Y, Han Y. Investigation of benzylisoquinoline alkaloid biosynthetic pathway and its transcriptional regulation in lotus. HORTICULTURE RESEARCH 2018; 5:29. [PMID: 29872534 PMCID: PMC5981371 DOI: 10.1038/s41438-018-0035-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 03/11/2018] [Accepted: 03/12/2018] [Indexed: 05/10/2023]
Abstract
Lotus predominantly accumulates benzylisoquinoline alkaloids (BIAs), but their biosynthesis and regulation remain unclear. Here, we investigated structural and regulatory genes involved in BIA accumulation in lotus. Two clustered CYP80 genes were identified to be responsible for the biosynthesis of bis-BIAs and aporphine-type BIAs, respectively, and their tissue-specific expression causes divergence in alkaloid component between leaf and embryo. In contrast with the common (S)-reticuline precursor for most BIAs, aporphine alkaloids in lotus leaf may result from the (S)-N-methylcoclaurine precursor. Structural diversity of BIA alkaloids in the leaf is attributed to enzymatic modifications, including intramolecular C-C phenol coupling on ring A and methylation and demethylation at certain positions. Additionally, most BIA biosynthetic pathway genes show higher levels of expression in the leaf of high-BIA cultivar compared with low-BIA cultivar, suggesting transcriptional regulation of BIA accumulation in lotus. Five transcription factors, including three MYBs, one ethylene-responsive factor, and one basic helix-loop-helix (bHLH), were identified to be candidate regulators of BIA biosynthesis in lotus. Our study reveals a BIA biosynthetic pathway and its transcriptional regulation in lotus, which will enable a deeper understanding of BIA biosynthesis in plants.
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Affiliation(s)
- Xianbao Deng
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074 China
| | - Li Zhao
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074 China
- Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049 China
| | - Ting Fang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074 China
- Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049 China
| | - Yaqian Xiong
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074 China
| | - Collins Ogutu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074 China
- Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049 China
| | - Dong Yang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074 China
| | - Sornkanok Vimolmangkang
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, 10330 Thailand
| | - Yanling Liu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074 China
| | - Yuepeng Han
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074 China
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074 China
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Boehm MMA, Ojeda DI, Cronk QCB. Dissecting the 'bacon and eggs' phenotype: transcriptomics of post-anthesis colour change in Lotus. ANNALS OF BOTANY 2017; 120:563-575. [PMID: 28981620 PMCID: PMC5737274 DOI: 10.1093/aob/mcx090] [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: 12/12/2016] [Accepted: 06/07/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND AND AIMS Post-anthesis colour change (PACC) is widely thought to be an adaptation to signal floral suitability to pollinators. Lotus filicaulis and Lotus sessilifolius are insect-pollinated herbaceous legumes with flowers that open yellow, shift to orange and finally red. This study examines the molecular basis for floral colour change in these Lotus species. METHODS Lotus filicaulis was cultivated in a glasshouse from which pollinating insects (bees) were excluded, and the rate of colour change was recorded in both unpollinated and manually pollinated flowers. Unpollinated flowers from both the yellow stage and the red stage were sampled for sequencing. The transcriptomes of L. filicaulis and L. sessilifolius of both colour stages were analysed for differentially expressed genes and enriched ontologies. KEY RESULTS The rate of progression through PACC doubled when L. filicaulis was hand-pollinated. De novo assembly of RNA-Seq reads from non-model Lotus species outperformed heterologous alignment of reads to the L. japonicus genome. Differential expression analysis suggested that the carotenoid biosynthetic pathway is upregulated at anthesis while the flavonoid biosynthetic pathway is upregulated with the onset of PACC in L. filicaulis and L. sessilifolius . CONCLUSION Pollination significantly accelerates PACC in L. filicaulis , consistent with the hypothesis that PACC increases pollination efficiency by directing pollinators to unpollinated flowers. RNA-Seq results show the synchronized upregulation of the entire cyanidin biosynthesis pathway in the red stage of PACC in L. filicaulis and L. sessilifolius . The genes implicated offer the basis for further investigations into how gene families, transcription factors and related pathways are likely to be involved in PACC.
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Affiliation(s)
- Mannfred M A Boehm
- Biodiversity Research Centre and Department of Botany, University of British Columbia, 6804 SW Marine Drive, Vancouver V6T 1Z4, Canada
| | - Dario I Ojeda
- Department of Evolutionary Biology and Ecology, Université Libre de Bruxelles, Av. F.D. Roosevelt, 50, CP 160/12, B-1050 Brussels, Belgium
| | - Quentin C B Cronk
- Biodiversity Research Centre and Department of Botany, University of British Columbia, 6804 SW Marine Drive, Vancouver V6T 1Z4, Canada
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Dezfulian MH, Foreman C, Jalili E, Pal M, Dhaliwal RK, Roberto DKA, Imre KM, Kohalmi SE, Crosby WL. Acetolactate synthase regulatory subunits play divergent and overlapping roles in branched-chain amino acid synthesis and Arabidopsis development. BMC PLANT BIOLOGY 2017; 17:71. [PMID: 28388946 PMCID: PMC5384131 DOI: 10.1186/s12870-017-1022-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 03/30/2017] [Indexed: 05/16/2023]
Abstract
BACKGROUND Branched-chain amino acids (BCAAs) are synthesized by plants, fungi, bacteria, and archaea with plants being the major source of these amino acids in animal diets. Acetolactate synthase (ALS) is the first enzyme in the BCAA synthesis pathway. Although the functional contribution of ALS to BCAA biosynthesis has been extensively characterized, a comprehensive understanding of the regulation of this pathway at the molecular level is still lacking. RESULTS To characterize the regulatory processes governing ALS activity we utilized several complementary approaches. Using the ALS catalytic protein subunit as bait we performed a yeast two-hybrid (Y2H) screen which resulted in the identification of a set of interacting proteins, two of which (denoted as ALS-INTERACTING PROTEIN1 and 3 [AIP1 and AIP3, respectively]) were found to be evolutionarily conserved orthologues of bacterial feedback-regulatory proteins and therefore implicated in the regulation of ALS activity. To investigate the molecular role AIPs might play in BCAA synthesis in Arabidopsis thaliana, we examined the functional contribution of aip1 and aip3 knockout alleles to plant patterning and development and BCAA synthesis under various growth conditions. Loss-of-function genetic backgrounds involving these two genes exhibited differential aberrant growth responses in valine-, isoleucine-, and sodium chloride-supplemented media. While BCAA synthesis is believed to be localized to the chloroplast, both AIP1 and AIP3 were found to localize to the peroxisome in addition to the chloroplast. Analysis of free amino acid pools in the mutant backgrounds revealed that they differ in the absolute amount of individual BCAAs accumulated and exhibit elevated levels of BCAAs in leaf tissues. Despite the phenotypic differences observed in aip1 and aip3 backgrounds, functional redundancy between these loci was suggested by the finding that aip1/aip3 double knockout mutants are severely developmentally compromised. CONCLUSIONS Taken together the data suggests that the two regulatory proteins, in conjunction with ALS, have overlapping but distinct functions in BCAA synthesis, and also play a role in pathways unrelated to BCAA synthesis such as sodium-ion homeostasis, extending to broader aspects of patterning and development.
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Affiliation(s)
- Mohammad H. Dezfulian
- Department of Biological Sciences, University of Windsor, Windsor, ON Canada
- Present address: Department of Genetics, Harvard Medical School, Boston, MA 02115 USA
| | - Curtis Foreman
- Department of Biological Sciences, University of Windsor, Windsor, ON Canada
| | - Espanta Jalili
- Department of Biological Sciences, University of Windsor, Windsor, ON Canada
| | - Mrinal Pal
- Department of Biological Sciences, University of Windsor, Windsor, ON Canada
| | - Rajdeep K. Dhaliwal
- Department of Biological Sciences, University of Windsor, Windsor, ON Canada
| | - Don Karl A. Roberto
- Department of Biological Sciences, University of Windsor, Windsor, ON Canada
| | - Kathleen M. Imre
- Department of Biochemistry and Molecular Biology, Michigan State University, Lansing, MI USA
| | | | - William L. Crosby
- Department of Biological Sciences, University of Windsor, Windsor, ON Canada
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Misra RC, Sharma S, Garg A, Chanotiya CS, Ghosh S. Two CYP716A subfamily cytochrome P450 monooxygenases of sweet basil play similar but nonredundant roles in ursane- and oleanane-type pentacyclic triterpene biosynthesis. THE NEW PHYTOLOGIST 2017; 214:706-720. [PMID: 28967669 DOI: 10.1111/nph.14412] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 11/23/2016] [Indexed: 05/23/2023]
Abstract
The medicinal plant sweet basil (Ocimum basilicum) accumulates bioactive ursane- and oleanane-type pentacyclic triterpenes (PCTs), ursolic acid and oleanolic acid, respectively, in a spatio-temporal manner; however, the biosynthetic enzymes and their contributions towards PCT biosynthesis remain to be elucidated. Two CYP716A subfamily cytochrome P450 monooxygenases (CYP716A252 and CYP716A253) are identified from a methyl jasmonate-responsive expression sequence tag collection and functionally characterized, employing yeast (Saccharomyces cerevisiae) expression platform and adapting virus-induced gene silencing (VIGS) in sweet basil. CYP716A252 and CYP716A253 catalyzed sequential three-step oxidation at the C-28 position of α-amyrin and β-amyrin to produce ursolic acid and oleanolic acid, respectively. Although CYP716A253 was more efficient than CYP716A252 for amyrin C-28 oxidation in yeast, VIGS revealed essential roles for both of these CYP716As in constitutive biosynthesis of ursolic acid and oleanolic acid in sweet basil leaves. However, CYP716A253 played a major role in elicitor-induced biosynthesis of ursolic acid and oleanolic acid. Overall, the results suggest similar as well as distinct roles of CYP716A252 and CYP716A253 for the spatio-temporal biosynthesis of PCTs. CYP716A252 and CYP716A253 might be useful for the alternative and sustainable production of PCTs in microbial host, besides increasing plant metabolite content through genetic modification.
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Affiliation(s)
- Rajesh Chandra Misra
- Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India
| | - Shubha Sharma
- Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India
- Academy of Scientific and Innovative Research, New Delhi, India
| | - Anchal Garg
- Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India
| | - Chandan Singh Chanotiya
- Analytical Chemistry Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India
| | - Sumit Ghosh
- Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India
- Academy of Scientific and Innovative Research, New Delhi, India
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Nomura T. Function and application of a non-ester-hydrolyzing carboxylesterase discovered in tulip. Biosci Biotechnol Biochem 2017; 81:81-94. [DOI: 10.1080/09168451.2016.1240608] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Abstract
Plants have evolved secondary metabolite biosynthetic pathways of immense rich diversity. The genes encoding enzymes for secondary metabolite biosynthesis have evolved through gene duplication followed by neofunctionalization, thereby generating functional diversity. Emerging evidence demonstrates that some of those enzymes catalyze reactions entirely different from those usually catalyzed by other members of the same family; e.g. transacylation catalyzed by an enzyme similar to a hydrolytic enzyme. Tuliposide-converting enzyme (TCE), which we recently discovered from tulip, catalyzes the conversion of major defensive secondary metabolites, tuliposides, to antimicrobial tulipalins. The TCEs belong to the carboxylesterase family in the α/β-hydrolase fold superfamily, and specifically catalyze intramolecular transesterification, but not hydrolysis. This non-ester-hydrolyzing carboxylesterase is an example of an enzyme showing catalytic properties that are unpredictable from its primary structure. This review describes the biochemical and physiological aspects of tulipalin biogenesis, and the diverse functions of plant carboxylesterases in the α/β-hydrolase fold superfamily.
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Affiliation(s)
- Taiji Nomura
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Imizu, Japan
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Mochida K, Sakurai T, Seki H, Yoshida T, Takahagi K, Sawai S, Uchiyama H, Muranaka T, Saito K. Draft genome assembly and annotation of Glycyrrhiza uralensis, a medicinal legume. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:181-194. [PMID: 27775193 DOI: 10.1111/tpj.13385] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 09/08/2016] [Accepted: 09/26/2016] [Indexed: 05/21/2023]
Abstract
Chinese liquorice/licorice (Glycyrrhiza uralensis) is a leguminous plant species whose roots and rhizomes have been widely used as a herbal medicine and natural sweetener. Whole-genome sequencing is essential for gene discovery studies and molecular breeding in liquorice. Here, we report a draft assembly of the approximately 379-Mb whole-genome sequence of strain 308-19 of G. uralensis; this assembly contains 34 445 predicted protein-coding genes. Comparative analyses suggested well-conserved genomic components and collinearity of gene loci (synteny) between the genome of liquorice and those of other legumes such as Medicago and chickpea. We observed that three genes involved in isoflavonoid biosynthesis, namely, 2-hydroxyisoflavanone synthase (CYP93C), 2,7,4'-trihydroxyisoflavanone 4'-O-methyltransferase/isoflavone 4'-O-methyltransferase (HI4OMT) and isoflavone-7-O-methyltransferase (7-IOMT) formed a cluster on the scaffold of the liquorice genome and showed conserved microsynteny with Medicago and chickpea. Based on the liquorice genome annotation, we predicted genes in the P450 and UDP-dependent glycosyltransferase (UGT) superfamilies, some of which are involved in triterpenoid saponin biosynthesis, and characterised their gene expression with the reference genome sequence. The genome sequencing and its annotations provide an essential resource for liquorice improvement through molecular breeding and the discovery of useful genes for engineering bioactive components through synthetic biology approaches.
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Affiliation(s)
- Keiichi Mochida
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki, Okayama, 710-0046, Japan
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa, 244-0813, Japan
| | - Tetsuya Sakurai
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- Research and Education Faculty, Multidisciplinary Science Cluster, Interdisciplinary Science Unit, Kochi University, 200 Otsu, Monobe, Nankoku, Kochi, 783-8502, Japan
| | - Hikaru Seki
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Takuhiro Yoshida
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Kotaro Takahagi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa, 244-0813, Japan
| | - Satoru Sawai
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Hiroshi Uchiyama
- Department of Applied Biological Science, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, Japan
| | - Toshiya Muranaka
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8675, Japan
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Huang BH, Chen YW, Huang CL, Gao J, Liao PC. Imbalanced positive selection maintains the functional divergence of duplicated DIHYDROKAEMPFEROL 4-REDUCTASE genes. Sci Rep 2016; 6:39031. [PMID: 27966614 PMCID: PMC5155217 DOI: 10.1038/srep39031] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 11/16/2016] [Indexed: 01/19/2023] Open
Abstract
Gene duplication could be beneficial by functional division but might increase the risk of genetic load. The dynamics of duplicated paralogs number could involve recombination, positive selection, and functional divergence. Duplication of DIHYDROFLAVONOL 4-REDUCTASE (DFR) has been reported in several organisms and may have been retained by escape from adaptive conflict (EAC). In this study, we screened the angiosperm DFR gene focusing on a diversified genus Scutellaria to investigate how these duplicated genes are retained. We deduced that gene duplication involved multiple independent events in angiosperms, but the duplication of DFR was before the divergence of Scutellaria. Asymmetric positive selective pressures resulted in different evolutionary rates between the duplicates. Different numbers of regulatory elements, differential codon usages, radical amino acid changes, and differential gene expressions provide evidences of functional divergence between the two DFR duplicates in Scutellaria, implying adaptive subfunctionalization between duplicates. The discovery of pseudogenes accompanying a reduced replacement rate in one DFR paralogous gene suggested possibly leading to “loss of function” due to dosage imbalance after the transient adaptive subfunctionalization in the early stage of duplication. Notwithstanding, episodic gene duplication and functional divergence may be relevant to the diversification of ecological function of DFR gene in Scutellaria.
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Affiliation(s)
- Bing-Hong Huang
- Department of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan
| | - Yi-Wen Chen
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan
| | - Chia-Lung Huang
- Department of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan
| | - Jian Gao
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Pei-Chun Liao
- Department of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan
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Yoneyama K, Akashi T, Aoki T. Molecular Characterization of Soybean Pterocarpan 2-Dimethylallyltransferase in Glyceollin Biosynthesis: Local Gene and Whole-Genome Duplications of Prenyltransferase Genes Led to the Structural Diversity of Soybean Prenylated Isoflavonoids. PLANT & CELL PHYSIOLOGY 2016; 57:2497-2509. [PMID: 27986914 PMCID: PMC5159607 DOI: 10.1093/pcp/pcw178] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 10/15/2016] [Indexed: 05/19/2023]
Abstract
Soybean (Glycine max) accumulates several prenylated isoflavonoid phytoalexins, collectively referred to as glyceollins. Glyceollins (I, II, III, IV and V) possess modified pterocarpan skeletons with C5 moieties from dimethylallyl diphosphate, and they are commonly produced from (6aS, 11aS)-3,9,6a-trihydroxypterocarpan [(-)-glycinol]. The metabolic fate of (-)-glycinol is determined by the enzymatic introduction of a dimethylallyl group into C-4 or C-2, which is reportedly catalyzed by regiospecific prenyltransferases (PTs). 4-Dimethylallyl (-)-glycinol and 2-dimethylallyl (-)-glycinol are precursors of glyceollin I and other glyceollins, respectively. Although multiple genes encoding (-)-glycinol biosynthetic enzymes have been identified, those involved in the later steps of glyceollin formation mostly remain unidentified, except for (-)-glycinol 4-dimethylallyltransferase (G4DT), which is involved in glyceollin I biosynthesis. In this study, we identified four genes that encode isoflavonoid PTs, including (-)-glycinol 2-dimethylallyltransferase (G2DT), using homology-based in silico screening and biochemical characterization in yeast expression systems. Transcript analyses illustrated that changes in G2DT gene expression were correlated with the induction of glyceollins II, III, IV and V in elicitor-treated soybean cells and leaves, suggesting its involvement in glyceollin biosynthesis. Moreover, the genomic signatures of these PT genes revealed that G4DT and G2DT are paralogs derived from whole-genome duplications of the soybean genome, whereas other PT genes [isoflavone dimethylallyltransferase 1 (IDT1) and IDT2] were derived via local gene duplication on soybean chromosome 11.
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Affiliation(s)
- Keisuke Yoneyama
- Department of Applied Biological Sciences, Nihon University, Fujisawa, Kanagawa, 252-0880 Japan
| | - Tomoyoshi Akashi
- Department of Applied Biological Sciences, Nihon University, Fujisawa, Kanagawa, 252-0880 Japan
| | - Toshio Aoki
- Department of Applied Biological Sciences, Nihon University, Fujisawa, Kanagawa, 252-0880 Japan
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Evolutionary origin of the NCSI gene subfamily encoding norcoclaurine synthase is associated with the biosynthesis of benzylisoquinoline alkaloids in plants. Sci Rep 2016; 6:26323. [PMID: 27189519 PMCID: PMC4870700 DOI: 10.1038/srep26323] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 05/03/2016] [Indexed: 11/08/2022] Open
Abstract
Sacred lotus is rich in biologically active compounds, particularly benzylisoquinoline alkaloids (BIAs). Here, we report on isolation of genes encoding (S)-norcoclaurine synthase (NCS) in sacred lotus, which is a key entry-enzyme in BIA biosynthesis. Seven NCS genes, designated NnNCS1 through NnNCS7, were identified in the sacred lotus genome, and five are located next to each other within a 83 kb region on scaffold 8. The NCS genes are divided into two subfamilies, designated NCSI and NCSII. The NCSII genes are universal in plants, while the NCSI genes are only identified in a limited number of dicotyledonous taxa that produce BIAs. In sacred lotus, only NnNCS4 belongs to the NCSII subfamily, whilst the rest NCS genes within the NCSI subfamily. Overall, the NnNCS7 gene was predominantly expressed in all tested tissues, and its expression is significantly correlated with alkaloid content in leaf. In contrast, the NnNCS4 expression shows no significant correlation with alkaloid accumulation in leaf, and its lack of expression cannot inhibit alkaloid accumulation. Taken together, these results suggest that the NCSI subfamily is crucial for BIA biosynthesis, and its origin may represent an important evolutionary event that allows certain plant taxa to produce BIAs.
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Lee SG, Nwumeh R, Jez JM. Structure and Mechanism of Isopropylmalate Dehydrogenase from Arabidopsis thaliana: INSIGHTS ON LEUCINE AND ALIPHATIC GLUCOSINOLATE BIOSYNTHESIS. J Biol Chem 2016; 291:13421-30. [PMID: 27137927 DOI: 10.1074/jbc.m116.730358] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Indexed: 11/06/2022] Open
Abstract
Isopropylmalate dehydrogenase (IPMDH) and 3-(2'-methylthio)ethylmalate dehydrogenase catalyze the oxidative decarboxylation of different β-hydroxyacids in the leucine- and methionine-derived glucosinolate biosynthesis pathways, respectively, in plants. Evolution of the glucosinolate biosynthetic enzyme from IPMDH results from a single amino acid substitution that alters substrate specificity. Here, we present the x-ray crystal structures of Arabidopsis thaliana IPMDH2 (AtIPMDH2) in complex with either isopropylmalate and Mg(2+) or NAD(+) These structures reveal conformational changes that occur upon ligand binding and provide insight on the active site of the enzyme. The x-ray structures and kinetic analysis of site-directed mutants are consistent with a chemical mechanism in which Lys-232 activates a water molecule for catalysis. Structural analysis of the AtIPMDH2 K232M mutant and isothermal titration calorimetry supports a key role of Lys-232 in the reaction mechanism. This study suggests that IPMDH-like enzymes in both leucine and glucosinolate biosynthesis pathways use a common mechanism and that members of the β-hydroxyacid reductive decarboxylase family employ different active site features for similar reactions.
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Affiliation(s)
- Soon Goo Lee
- From the Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Ronald Nwumeh
- From the Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Joseph M Jez
- From the Department of Biology, Washington University, St. Louis, Missouri 63130
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Speed MP, Fenton A, Jones MG, Ruxton GD, Brockhurst MA. Coevolution can explain defensive secondary metabolite diversity in plants. THE NEW PHYTOLOGIST 2015; 208:1251-63. [PMID: 26243527 DOI: 10.1111/nph.13560] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 06/03/2015] [Indexed: 05/18/2023]
Abstract
Many plant species produce defensive compounds that are often highly diverse within and between populations. The genetic and cellular mechanisms by which metabolite diversity is produced are increasingly understood, but the evolutionary explanations for persistent diversification in plant secondary metabolites have received less attention. Here we consider the role of plant-herbivore coevolution in the maintenance and characteristics of diversity in plant secondary metabolites. We present a simple model in which plants can evolve to invest in a range of defensive toxins, and herbivores can evolve resistance to these toxins. We allow either single-species evolution or reciprocal coevolution. Our model shows that coevolution maintains toxin diversity within populations. Furthermore, there is a fundamental coevolutionary asymmetry between plants and their herbivores, because herbivores must resist all plant toxins, whereas plants need to challenge and nullify only one resistance trait. As a consequence, average plant fitness increases and insect fitness decreases as number of toxins increases. When costs apply, the model showed both arms race escalation and strong coevolutionary fluctuation in toxin concentrations across time. We discuss the results in the context of other evolutionary explanations for secondary metabolite diversification.
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Affiliation(s)
- Michael P Speed
- Department of Evolution, Ecology and Behaviour, Institute of Integrative Biology, Faculty of Health & Life Sciences, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Andy Fenton
- Department of Evolution, Ecology and Behaviour, Institute of Integrative Biology, Faculty of Health & Life Sciences, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Meriel G Jones
- Functional and Comparative Genomics, Institute of Integrative Biology, Faculty of Health & Life Sciences, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Graeme D Ruxton
- School of Biology, University of St Andrews, St Andrews, KY16 9TH, UK
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44
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Huang Y, Wang X, Ge S, Rao GY. Divergence and adaptive evolution of the gibberellin oxidase genes in plants. BMC Evol Biol 2015; 15:207. [PMID: 26416509 PMCID: PMC4587577 DOI: 10.1186/s12862-015-0490-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 09/17/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The important phytohormone gibberellins (GAs) play key roles in various developmental processes. GA oxidases (GAoxs) are critical enzymes in GA synthesis pathway, but their classification, evolutionary history and the forces driving the evolution of plant GAox genes remain poorly understood. RESULTS This study provides the first large-scale evolutionary analysis of GAox genes in plants by using an extensive whole-genome dataset of 41 species, representing green algae, bryophytes, pteridophyte, and seed plants. We defined eight subfamilies under the GAox family, namely C19-GA2ox, C20-GA2ox, GA20ox,GA3ox, GAox-A, GAox-B, GAox-C and GAox-D. Of these, subfamilies GAox-A, GAox-B, GAox-C and GAox-D are described for the first time. On the basis of phylogenetic analyses and characteristic motifs of GAox genes, we demonstrated a rapid expansion and functional divergence of the GAox genes during the diversification of land plants. We also detected the subfamily-specific motifs and potential sites of some GAox genes, which might have evolved under positive selection. CONCLUSIONS GAox genes originated very early-before the divergence of bryophytes and the vascular plants and the diversification of GAox genes is associated with the functional divergence and could be driven by positive selection. Our study not only provides information on the classification of GAox genes, but also facilitates the further functional characterization and analysis of GA oxidases.
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Affiliation(s)
- Yuan Huang
- College of Life Sciences, Peking University, Beijing, 100871, China.
| | - Xi Wang
- College of Life Sciences, Peking University, Beijing, 100871, China.
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Guang-Yuan Rao
- College of Life Sciences, Peking University, Beijing, 100871, China.
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Sievert C, Beuerle T, Hollmann J, Ober D. Single cell subtractive transcriptomics for identification of cell-specifically expressed candidate genes of pyrrolizidine alkaloid biosynthesis. PHYTOCHEMISTRY 2015; 117:17-24. [PMID: 26057225 DOI: 10.1016/j.phytochem.2015.05.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 05/11/2015] [Accepted: 05/14/2015] [Indexed: 06/04/2023]
Abstract
Progress has recently been made in the elucidation of pathways of secondary metabolism. However, because of its diversity, genetic information concerning biosynthetic details is still missing for many natural products. This is also the case for the biosynthesis of pyrrolizidine alkaloids. To close this gap, we tested strategies using tissues that express this pathway in comparison to tissues in which this pathway is not expressed. As many pathways of secondary metabolism are known to be induced by jasmonates, the pyrrolizidine alkaloid-producing species Heliotropium indicum, Symphytum officinale, and Cynoglossum officinale of the Boraginales order were treated with methyl jasmonate. An effect on pyrrolizidine alkaloid levels and on transcript levels of homospermidine synthase, the first specific enzyme of pyrrolizidine alkaloid biosynthesis, was not detectable. Therefore, a method was developed by making use of the often observed cell-specific production of secondary compounds. H. indicum produces pyrrolizidine alkaloids exclusively in the shoot. Homospermidine synthase is expressed only in the cells of the lower leaf epidermis and the epidermis of the stem. Suggesting that the whole pathway of pyrrolizidine alkaloid biosynthesis might be localized in these cells, we have isolated single cells of the upper and lower epidermis by laser-capture microdissection. The resulting cDNA preparations have been used in a subtractive transcriptomic approach. Quantitative real-time polymerase chain reaction has shown that the resulting library is significantly enriched for homospermidine-synthase-coding transcripts providing a valuable source for the identification of further genes involved in pyrrolizidine alkaloid biosynthesis.
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Affiliation(s)
- Christian Sievert
- Botanical Institute and Botanical Garden, Christian-Albrechts University Kiel, Germany
| | - Till Beuerle
- Institute for Pharmaceutical Biology, TU Braunschweig, Mendelssohnstrasse 1, D-38106 Braunschweig, Germany
| | - Julien Hollmann
- Botanical Institute and Botanical Garden, Christian-Albrechts University Kiel, Germany
| | - Dietrich Ober
- Botanical Institute and Botanical Garden, Christian-Albrechts University Kiel, Germany.
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Chung HH, Schwinn KE, Ngo HM, Lewis DH, Massey B, Calcott KE, Crowhurst R, Joyce DC, Gould KS, Davies KM, Harrison DK. Characterisation of betalain biosynthesis in Parakeelya flowers identifies the key biosynthetic gene DOD as belonging to an expanded LigB gene family that is conserved in betalain-producing species. FRONTIERS IN PLANT SCIENCE 2015; 6:499. [PMID: 26217353 PMCID: PMC4493658 DOI: 10.3389/fpls.2015.00499] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 06/22/2015] [Indexed: 05/18/2023]
Abstract
Plant betalain pigments are intriguing because they are restricted to the Caryophyllales and are mutually exclusive with the more common anthocyanins. However, betalain biosynthesis is poorly understood compared to that of anthocyanins. In this study, betalain production and betalain-related genes were characterized in Parakeelya mirabilis (Montiaceae). RT-PCR and transcriptomics identified three sequences related to the key biosynthetic enzyme Dopa 4,5-dioxgenase (DOD). In addition to a LigB gene similar to that of non-Caryophyllales species (Class I genes), two other P. mirabilis LigB genes were found (DOD and DOD-like, termed Class II). PmDOD and PmDOD-like had 70% amino acid identity. Only PmDOD was implicated in betalain synthesis based on transient assays of enzyme activity and correlation of transcript abundance to spatio-temporal betalain accumulation. The role of PmDOD-like remains unknown. The striking pigment patterning of the flowers was due to distinct zones of red betacyanin and yellow betaxanthin production. The major betacyanin was the unglycosylated betanidin rather than the commonly found glycosides, an occurrence for which there are a few previous reports. The white petal zones lacked pigment but had DOD activity suggesting alternate regulation of the pathway in this tissue. DOD and DOD-like sequences were also identified in other betalain-producing species but not in examples of anthocyanin-producing Caryophyllales or non-Caryophyllales species. A Class I LigB sequence from the anthocyanin-producing Caryophyllaceae species Dianthus superbus and two DOD-like sequences from the Amaranthaceae species Beta vulgaris and Ptilotus spp. did not show DOD activity in the transient assay. The additional sequences suggests that DOD is part of a larger LigB gene family in betalain-producing Caryophyllales taxa, and the tandem genomic arrangement of two of the three B. vulgaris LigB genes suggests the involvement of duplication in the gene family evolution.
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Affiliation(s)
- Hsiao-Hang Chung
- Centre for Native Floriculture, School of Agriculture and Food Sciences, The University of Queensland, GattonQLD, Australia
| | - Kathy E. Schwinn
- New Zealand Institute for Plant & Food Research LimitedPalmerston North, New Zealand
| | - Hanh M. Ngo
- New Zealand Institute for Plant & Food Research LimitedPalmerston North, New Zealand
| | - David H. Lewis
- New Zealand Institute for Plant & Food Research LimitedPalmerston North, New Zealand
| | - Baxter Massey
- Centre for Native Floriculture, School of Agriculture and Food Sciences, The University of Queensland, GattonQLD, Australia
| | - Kate E. Calcott
- New Zealand Institute for Plant & Food Research LimitedPalmerston North, New Zealand
- Victoria University of WellingtonWellington, New Zealand
| | - Ross Crowhurst
- New Zealand Institute for Plant & Food Research LimitedAuckland, New Zealand
| | - Daryl C. Joyce
- Centre for Native Floriculture, School of Agriculture and Food Sciences, The University of Queensland, GattonQLD, Australia
| | - Kevin S. Gould
- Victoria University of WellingtonWellington, New Zealand
| | - Kevin M. Davies
- New Zealand Institute for Plant & Food Research LimitedPalmerston North, New Zealand
| | - Dion K. Harrison
- Centre for Native Floriculture, School of Agriculture and Food Sciences, The University of Queensland, GattonQLD, Australia
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Sulmon C, van Baaren J, Cabello-Hurtado F, Gouesbet G, Hennion F, Mony C, Renault D, Bormans M, El Amrani A, Wiegand C, Gérard C. Abiotic stressors and stress responses: What commonalities appear between species across biological organization levels? ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2015; 202:66-77. [PMID: 25813422 DOI: 10.1016/j.envpol.2015.03.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 03/12/2015] [Accepted: 03/13/2015] [Indexed: 05/07/2023]
Abstract
Organisms are regularly subjected to abiotic stressors related to increasing anthropogenic activities, including chemicals and climatic changes that induce major stresses. Based on various key taxa involved in ecosystem functioning (photosynthetic microorganisms, plants, invertebrates), we review how organisms respond and adapt to chemical- and temperature-induced stresses from molecular to population level. Using field-realistic studies, our integrative analysis aims to compare i) how molecular and physiological mechanisms related to protection, repair and energy allocation can impact life history traits of stressed organisms, and ii) to what extent trait responses influence individual and population responses. Common response mechanisms are evident at molecular and cellular scales but become rather difficult to define at higher levels due to evolutionary distance and environmental complexity. We provide new insights into the understanding of the impact of molecular and cellular responses on individual and population dynamics and assess the potential related effects on communities and ecosystem functioning.
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Affiliation(s)
- Cécile Sulmon
- UMR CNRS 6553 ECOBIO, Université de Rennes 1, 263 Avenue du Général Leclerc, 35042 Rennes Cedex, France.
| | - Joan van Baaren
- UMR CNRS 6553 ECOBIO, Université de Rennes 1, 263 Avenue du Général Leclerc, 35042 Rennes Cedex, France
| | - Francisco Cabello-Hurtado
- UMR CNRS 6553 ECOBIO, Université de Rennes 1, 263 Avenue du Général Leclerc, 35042 Rennes Cedex, France
| | - Gwenola Gouesbet
- UMR CNRS 6553 ECOBIO, Université de Rennes 1, 263 Avenue du Général Leclerc, 35042 Rennes Cedex, France
| | - Françoise Hennion
- UMR CNRS 6553 ECOBIO, Université de Rennes 1, 263 Avenue du Général Leclerc, 35042 Rennes Cedex, France
| | - Cendrine Mony
- UMR CNRS 6553 ECOBIO, Université de Rennes 1, 263 Avenue du Général Leclerc, 35042 Rennes Cedex, France
| | - David Renault
- UMR CNRS 6553 ECOBIO, Université de Rennes 1, 263 Avenue du Général Leclerc, 35042 Rennes Cedex, France
| | - Myriam Bormans
- UMR CNRS 6553 ECOBIO, Université de Rennes 1, 263 Avenue du Général Leclerc, 35042 Rennes Cedex, France
| | - Abdelhak El Amrani
- UMR CNRS 6553 ECOBIO, Université de Rennes 1, 263 Avenue du Général Leclerc, 35042 Rennes Cedex, France
| | - Claudia Wiegand
- UMR CNRS 6553 ECOBIO, Université de Rennes 1, 263 Avenue du Général Leclerc, 35042 Rennes Cedex, France; Biologisk Institut, Syddansk Universitet, Campusvej 55, 5230 Odense M, Denmark
| | - Claudia Gérard
- UMR CNRS 6553 ECOBIO, Université de Rennes 1, 263 Avenue du Général Leclerc, 35042 Rennes Cedex, France.
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Chamala S, Feng G, Chavarro C, Barbazuk WB. Genome-wide identification of evolutionarily conserved alternative splicing events in flowering plants. Front Bioeng Biotechnol 2015; 3:33. [PMID: 25859541 PMCID: PMC4374538 DOI: 10.3389/fbioe.2015.00033] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 03/02/2015] [Indexed: 11/13/2022] Open
Abstract
Alternative splicing (AS) plays important roles in many plant functions, but its conservation across the plant kingdom is not known. We describe a methodology to identify AS events and identify conserved AS events across large phylogenetic distances using RNA-Seq datasets. We applied this methodology to transcriptome data from nine angiosperms including Amborella, the single sister species to all other extant flowering plants. AS events within 40–70% of the expressed multi-exonic genes per species were found, 27,120 of which are conserved among two or more of the taxa studied. While many events are species specific, many others are shared across long evolutionary distances suggesting they have functional significance. Conservation of AS event data provides an estimate of the number of ancestral AS events present at each node of the tree representing the nine species studied. Furthermore, the presence or absence of AS isoforms between species with different whole genome duplication (WGD) histories provides the opportunity to examine the impact of WDG on AS potential. Examining AS in gene families identifies those with high rates of AS, and conservation can distinguish ancient events vs. recent or species specific adaptations. The MADS-box and SR protein families are found to represent families with low and high occurrences of AS, respectively, yet their AS events were likely present in the MRCA of angiosperms.
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Affiliation(s)
- Srikar Chamala
- Department of Biology, University of Florida , Gainesville, FL , USA
| | - Guanqiao Feng
- Graduate Program in Plant Molecular and Cellular Biology, University of Florida , Gainesville, FL , USA
| | - Carolina Chavarro
- Center for Applied Genetic Technologies, University of Georgia , Athens, GA , USA
| | - W Brad Barbazuk
- Department of Biology, University of Florida , Gainesville, FL , USA ; Genetics Institute, University of Florida , Gainesville, FL , USA
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Wang J, Chu S, Zhu Y, Cheng H, Yu D. Positive selection drives neofunctionalization of the UbiA prenyltransferase gene family. PLANT MOLECULAR BIOLOGY 2015; 87:383-94. [PMID: 25605655 DOI: 10.1007/s11103-015-0285-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 01/12/2015] [Indexed: 05/05/2023]
Abstract
Gene duplication provides the key materials for new genes and novel functions. However, the mechanism underlying functional innovation remains unknown. In this study, we revealed the evolutionary pattern of the prenyltransferases of the UbiA gene family in 15 higher plants. Prenyltransferases of the UbiA gene family are involved in many important biological processes of both primary and secondary metabolism. Based on the phylogenetic relationships of the UbiA genes, seven subfamilies are classified. Confirming this classification, genes within each subfamily are characterized by similar exon numbers, exon lengths and patterns of motif combinations. Similar numbers of UbiA genes are found in different species within each subfamily except for Subfamily I, in which a Phaseoleae-specific expansion is detected in clade I-A. Homologous genes in clade I-A evolve rapidly, exchange sequences frequently and experience positive selection. Genes in clade I-A function as flavonoid prenyltransferase synthesis secondary compounds, while other genes from Subfamily I encode homogentisate phytyltransferase, which plays a role in primary metabolism. Thus, our results suggest that the secondary metabolism genes acquire new functions from those of primary metabolism through gene duplication and neofunctionalization driven by positive selection.
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Affiliation(s)
- Jiao Wang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
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Yuan L, Grotewold E. Metabolic engineering to enhance the value of plants as green factories. Metab Eng 2014; 27:83-91. [PMID: 25461830 DOI: 10.1016/j.ymben.2014.11.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 11/08/2014] [Accepted: 11/11/2014] [Indexed: 12/21/2022]
Abstract
The promise of plants to serve as the green factories of the future is ever increasing. Plants have been used traditionally for construction, energy, food and feed. Bioactive compounds primarily derived from specialized plant metabolism continue to serve as important scaffold molecules for pharmaceutical drug production. Yet, the past few years have witnessed a growing interest on plants as the ultimate harvesters of carbon and energy from the sun, providing carbohydrate and lipid biofuels that would contribute to balancing atmospheric carbon. How can the metabolic output from plants be increased even further, and what are the bottlenecks? Here, we present what we perceive to be the main opportunities and challenges associated with increasing the efficiency of plants as chemical factories. We offer some perspectives on when it makes sense to use plants as production systems because the amount of biomass needed makes any other system unfeasible. However, there are other instances in which plants serve as great sources of biological catalysts, yet are not necessarily the best-suited systems for production. We also present emerging opportunities for manipulating plant genomes to make plant synthetic biology a reality.
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Affiliation(s)
- Ling Yuan
- Department of Plant and Soil Sciences, University of Kentucky, 1401 University Drive, Lexington, KY 40546, United States
| | - Erich Grotewold
- Center for Applied Plant Sciences (CAPS), Department of Molecular Genetics and Department of Horticulture and Crop Science, The Ohio State University, 012 Rightmire Hall, 1060 Carmack Rd, Columbus, OH 43210, United States.
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