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Huang W, Hu X, Ren Y, Song M, Ma C, Miao Z. IPOP: An Integrative Plant Multi-omics Platform for Cross-species Comparison and Evolutionary Study. Mol Biol Evol 2023; 40:msad248. [PMID: 37995323 PMCID: PMC10715199 DOI: 10.1093/molbev/msad248] [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: 08/20/2023] [Revised: 10/23/2023] [Accepted: 11/09/2023] [Indexed: 11/25/2023] Open
Abstract
The advent of high-throughput sequencing technologies has led to the production of a significant amount of omics data in plants, which serves as valuable assets for conducting cross-species multi-omics comparative analysis. Nevertheless, the current dearth of comprehensive platforms providing evolutionary annotation information and multi-species multi-omics data impedes users from systematically and efficiently performing evolutionary and functional analysis on specific genes. In order to establish an advanced plant multi-omics platform that provides timely, accurate, and high-caliber omics information, we collected 7 distinct types of omics data from 6 monocots, 6 dicots, and 1 moss, and reanalyzed these data using standardized pipelines. Additionally, we furnished homology information, duplication events, and phylostratigraphic stages of 13 species to facilitate evolutionary examination. Furthermore, the integrative plant omics platform (IPOP) is bundled with a variety of online analysis tools that aid users in conducting evolutionary and functional analysis. Specifically, the Multi-omics Integration Analysis tool is available to consolidate information from diverse omics sources, while the Transcriptome-wide Association Analysis tool facilitates the linkage of functional analysis with phenotype. To illustrate the application of IPOP, we conducted a case study on the YTH domain gene family, wherein we observed shared functionalities within orthologous groups and discerned variations in evolutionary patterns across these groups. To summarize, the IPOP platform offers valuable evolutionary insights and multi-omics data to the plant sciences community, effectively addressing the need for cross-species comparison and evolutionary research platforms. All data and modules within IPOP are freely accessible for academic purposes (http://omicstudio.cloud:4012/ipod/).
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Affiliation(s)
- Wenyue Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaona Hu
- College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yanlin Ren
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Minggui Song
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chuang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhenyan Miao
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
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Abdullah-Zawawi MR, Govender N, Harun S, Muhammad NAN, Zainal Z, Mohamed-Hussein ZA. Multi-Omics Approaches and Resources for Systems-Level Gene Function Prediction in the Plant Kingdom. PLANTS (BASEL, SWITZERLAND) 2022; 11:2614. [PMID: 36235479 PMCID: PMC9573505 DOI: 10.3390/plants11192614] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/05/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
In higher plants, the complexity of a system and the components within and among species are rapidly dissected by omics technologies. Multi-omics datasets are integrated to infer and enable a comprehensive understanding of the life processes of organisms of interest. Further, growing open-source datasets coupled with the emergence of high-performance computing and development of computational tools for biological sciences have assisted in silico functional prediction of unknown genes, proteins and metabolites, otherwise known as uncharacterized. The systems biology approach includes data collection and filtration, system modelling, experimentation and the establishment of new hypotheses for experimental validation. Informatics technologies add meaningful sense to the output generated by complex bioinformatics algorithms, which are now freely available in a user-friendly graphical user interface. These resources accentuate gene function prediction at a relatively minimal cost and effort. Herein, we present a comprehensive view of relevant approaches available for system-level gene function prediction in the plant kingdom. Together, the most recent applications and sought-after principles for gene mining are discussed to benefit the plant research community. A realistic tabulation of plant genomic resources is included for a less laborious and accurate candidate gene discovery in basic plant research and improvement strategies.
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Affiliation(s)
- Muhammad-Redha Abdullah-Zawawi
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia
- Institute of System Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Malaysia
| | - Nisha Govender
- Institute of System Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Malaysia
| | - Sarahani Harun
- Institute of System Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Malaysia
| | - Nor Azlan Nor Muhammad
- Institute of System Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Malaysia
| | - Zamri Zainal
- Institute of System Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Malaysia
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Malaysia
| | - Zeti-Azura Mohamed-Hussein
- Institute of System Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Malaysia
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Malaysia
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3
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Tan YC, Kumar AU, Wong YP, Ling APK. Bioinformatics approaches and applications in plant biotechnology. J Genet Eng Biotechnol 2022; 20:106. [PMID: 35838847 PMCID: PMC9287518 DOI: 10.1186/s43141-022-00394-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 07/05/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND In recent years, major advance in molecular biology and genomic technologies have led to an exponential growth in biological information. As the deluge of genomic information, there is a parallel growth in the demands of tools in the storage and management of data, and the development of software for analysis, visualization, modelling, and prediction of large data set. MAIN BODY Particularly in plant biotechnology, the amount of information has multiplied exponentially with a large number of databases available from many individual plant species. Efficient bioinformatics tools and methodologies are also developed to allow rapid genome sequence and the study of plant genome in the 'omics' approach. This review focuses on the various bioinformatic applications in plant biotechnology, and their advantages in improving the outcome in agriculture. The challenges or limitations faced in plant biotechnology in the aspect of bioinformatics approach that explained the low progression in plant genomics than in animal genomics are also reviewed and assessed. CONCLUSION There is a critical need for effective bioinformatic tools, which are able to provide longer reads with unbiased coverage in order to overcome the complexity of the plant's genome. The advancement in bioinformatics is not only beneficial to the field of plant biotechnology and agriculture sectors, but will also contribute enormously to the future of humanity.
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Affiliation(s)
- Yung Cheng Tan
- Division of Applied Biomedical Sciences and Biotechnology, School of Health Sciences, International Medical University, 126 Jalan Jalil Perkasa 19, Bukit Jalil, 57000, Kuala Lumpur, Malaysia
| | - Asqwin Uthaya Kumar
- Division of Applied Biomedical Sciences and Biotechnology, School of Health Sciences, International Medical University, 126 Jalan Jalil Perkasa 19, Bukit Jalil, 57000, Kuala Lumpur, Malaysia.,School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Malaysia
| | - Ying Pei Wong
- Division of Applied Biomedical Sciences and Biotechnology, School of Health Sciences, International Medical University, 126 Jalan Jalil Perkasa 19, Bukit Jalil, 57000, Kuala Lumpur, Malaysia
| | - Anna Pick Kiong Ling
- Division of Applied Biomedical Sciences and Biotechnology, School of Health Sciences, International Medical University, 126 Jalan Jalil Perkasa 19, Bukit Jalil, 57000, Kuala Lumpur, Malaysia.
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4
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Sampaio M, Rocha M, Dias O. Exploring synergies between plant metabolic modelling and machine learning. Comput Struct Biotechnol J 2022; 20:1885-1900. [PMID: 35521559 PMCID: PMC9052043 DOI: 10.1016/j.csbj.2022.04.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/08/2022] [Accepted: 04/11/2022] [Indexed: 11/03/2022] Open
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5
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Zhang P, Guo Z, Ullah S, Melagraki G, Afantitis A, Lynch I. Nanotechnology and artificial intelligence to enable sustainable and precision agriculture. NATURE PLANTS 2021; 7:864-876. [PMID: 34168318 DOI: 10.1038/s41477-021-00946-6] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 05/17/2021] [Indexed: 06/13/2023]
Abstract
Climate change, increasing populations, competing demands on land for production of biofuels and declining soil quality are challenging global food security. Finding sustainable solutions requires bold new approaches and integration of knowledge from diverse fields, such as materials science and informatics. The convergence of precision agriculture, in which farmers respond in real time to changes in crop growth with nanotechnology and artificial intelligence, offers exciting opportunities for sustainable food production. Coupling existing models for nutrient cycling and crop productivity with nanoinformatics approaches to optimize targeting, uptake, delivery, nutrient capture and long-term impacts on soil microbial communities will enable design of nanoscale agrochemicals that combine optimal safety and functionality profiles.
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Affiliation(s)
- Peng Zhang
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, UK.
| | - Zhiling Guo
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, UK
| | - Sami Ullah
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, UK
| | - Georgia Melagraki
- Division of Physical Sciences and Applications, Hellenic Military Academy, Vari, Greece
| | | | - Iseult Lynch
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, UK
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Khan DA, Hamdani SDA, Iftikhar S, Malik SZ, Zaidi NUSS, Gul A, Babar MM, Ozturk M, Turkyilmaz Unal B, Gonenc T. Pharmacoinformatics approaches in the discovery of drug-like antimicrobials of plant origin. J Biomol Struct Dyn 2021; 40:7612-7628. [PMID: 33663347 DOI: 10.1080/07391102.2021.1894982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Medicinal plants have served as an important source for addressing the ailments of humans and animals alike. The emergence of advanced technologies in the field of drug discovery and development has helped in isolating various bioactive phytochemicals and developing them as drugs. Owing to their significant pharmacological benefits and minimum adverse effects, they not only serve as good candidates for therapeutics themselves but also help in the identification and development of related drug like molecules against various metabolic and infectious diseases. The ever-increasing diversity, severity and incidence of infectious diseases has resulted in an exaggerated mortality and morbidity levels. Geno-proteomic mutations in microbes, irrational prescribing of antibiotics, antimicrobial resistance and human population explosion, all call for continuous efforts to discover and develop alternated therapeutic options against the microbes. This review article describes the pharmacoinformatics tools and methods which are currently used in the discovery of bioactive phytochemicals, thus making the process more efficient and effective. The pharmacological aspects of the drug discovery and development process have also been reviewed with reference to the in silico activities. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Duaa Ahmad Khan
- Shifa College of Pharmaceutical Sciences, Shifa Tameer-e-Millat University, Islamabad, Pakistan
| | - Syed Damin Abbas Hamdani
- Shifa College of Pharmaceutical Sciences, Shifa Tameer-e-Millat University, Islamabad, Pakistan.,Riphah Institute of Pharmaceutical Sciences, Riphah International University, Islamabad, Pakistan
| | - Sahar Iftikhar
- Shifa College of Pharmaceutical Sciences, Shifa Tameer-e-Millat University, Islamabad, Pakistan
| | - Sohaib Zafar Malik
- Riphah Institute of Pharmaceutical Sciences, Riphah International University, Islamabad, Pakistan
| | - Najam-Us-Sahar Sadaf Zaidi
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences & Technology, Islamabad, Pakistan
| | - Alvina Gul
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences & Technology, Islamabad, Pakistan
| | - Mustafeez Mujtaba Babar
- Shifa College of Pharmaceutical Sciences, Shifa Tameer-e-Millat University, Islamabad, Pakistan
| | - Munir Ozturk
- Botany Department and Centre for Environmental Studies, Ege University, Izmir, Turkey
| | - Bengu Turkyilmaz Unal
- Biotechnology Department, Arts & Sciences Faculty, Nigde Omer Halisdemir University, Nigde, Turkey
| | - Tuba Gonenc
- Department of Pharmacognosy, Faculty of Pharmacy, Izmir Katip Çelebi University, Izmir, Turkey
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7
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Chao H, Li T, Luo C, Huang H, Ruan Y, Li X, Niu Y, Fan Y, Sun W, Zhang K, Li J, Qu C, Lu K. BrassicaEDB: A Gene Expression Database for Brassica Crops. Int J Mol Sci 2020; 21:ijms21165831. [PMID: 32823802 PMCID: PMC7461608 DOI: 10.3390/ijms21165831] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 08/04/2020] [Accepted: 08/11/2020] [Indexed: 12/26/2022] Open
Abstract
The genus Brassica contains several economically important crops, including rapeseed (Brassica napus, 2n = 38, AACC), the second largest source of seed oil and protein meal worldwide. However, research in rapeseed is hampered because it is complicated and time-consuming for researchers to access different types of expression data. We therefore developed the Brassica Expression Database (BrassicaEDB) for the research community. In the current BrassicaEDB, we only focused on the transcriptome level in rapeseed. We conducted RNA sequencing (RNA-Seq) of 103 tissues from rapeseed cultivar ZhongShuang11 (ZS11) at seven developmental stages (seed germination, seedling, bolting, initial flowering, full-bloom, podding, and maturation). We determined the expression patterns of 101,040 genes via FPKM analysis and displayed the results using the eFP browser. We also analyzed transcriptome data for rapeseed from 70 BioProjects in the SRA database and obtained three types of expression level data (FPKM, TPM, and read counts). We used this information to develop the BrassicaEDB, including “eFP”, “Treatment”, “Coexpression”, and “SRA Project” modules based on gene expression profiles and “Gene Feature”, “qPCR Primer”, and “BLAST” modules based on gene sequences. The BrassicaEDB provides comprehensive gene expression profile information and a user-friendly visualization interface for rapeseed researchers. Using this database, researchers can quickly retrieve the expression level data for target genes in different tissues and in response to different treatments to elucidate gene functions and explore the biology of rapeseed at the transcriptome level.
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Affiliation(s)
- Haoyu Chao
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China; (H.C.); (C.L.); (X.L.); (Y.N.); (Y.F.); (W.S.); (K.Z.); (J.L.); (C.Q.)
- Institute of Innovation & Entrepreneurship, Southwest University, Beibei, Chongqing 400715, China
| | - Tian Li
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; (T.L.); (Y.R.)
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing 400715, China
| | - Chaoyu Luo
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China; (H.C.); (C.L.); (X.L.); (Y.N.); (Y.F.); (W.S.); (K.Z.); (J.L.); (C.Q.)
| | - Hualei Huang
- Institute of Characteristic Crop Research, Chongqing Academy of Agricultural Sciences, Chongqing 402160, China;
| | - Yingfei Ruan
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; (T.L.); (Y.R.)
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing 400715, China
| | - Xiaodong Li
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China; (H.C.); (C.L.); (X.L.); (Y.N.); (Y.F.); (W.S.); (K.Z.); (J.L.); (C.Q.)
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Yue Niu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China; (H.C.); (C.L.); (X.L.); (Y.N.); (Y.F.); (W.S.); (K.Z.); (J.L.); (C.Q.)
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Yonghai Fan
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China; (H.C.); (C.L.); (X.L.); (Y.N.); (Y.F.); (W.S.); (K.Z.); (J.L.); (C.Q.)
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Wei Sun
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China; (H.C.); (C.L.); (X.L.); (Y.N.); (Y.F.); (W.S.); (K.Z.); (J.L.); (C.Q.)
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Kai Zhang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China; (H.C.); (C.L.); (X.L.); (Y.N.); (Y.F.); (W.S.); (K.Z.); (J.L.); (C.Q.)
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China; (H.C.); (C.L.); (X.L.); (Y.N.); (Y.F.); (W.S.); (K.Z.); (J.L.); (C.Q.)
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Cunmin Qu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China; (H.C.); (C.L.); (X.L.); (Y.N.); (Y.F.); (W.S.); (K.Z.); (J.L.); (C.Q.)
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Kun Lu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China; (H.C.); (C.L.); (X.L.); (Y.N.); (Y.F.); (W.S.); (K.Z.); (J.L.); (C.Q.)
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
- Correspondence: ; Tel./Fax: +86-23-6825-1264
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8
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Wong DCJ. Network aggregation improves gene function prediction of grapevine gene co-expression networks. PLANT MOLECULAR BIOLOGY 2020; 103:425-441. [PMID: 32266646 DOI: 10.1007/s11103-020-01001-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 03/21/2020] [Indexed: 05/08/2023]
Abstract
Aggregation across multiple networks highlights robust co-expression interactions and improves the functional connectivity of grapevine gene co-expression networks. In recent years, the rapid accumulation of transcriptome datasets from diverse experimental conditions has enabled the widespread use of gene co-expression network (GCN) analysis in plants. In grapevine, GCN analysis has shown great promise for gene function prediction, however, measurable progress is currently lacking. Using accumulated microarray datasets from the grapevine whole-genome array (33 experiments, 1359 samples), we explored how meta-analysis through aggregation influences the functional connectivity (performance) of derived networks using guilt-by-association neighbor voting. Two annotation schemes, i.e. MapMan BIN and Pfam, at two sparsity thresholds, i.e. top 100 (stringent) and 300 (relaxed) ranked genes were evaluated. We observed that aggregating across multiple networks improves performance dramatically, with the aggregate outperforming the majority of functional terms across individual networks. Network sparsity and size (i.e. the number of samples and aggregates) were key factors influencing performance while the choice of annotation scheme had little. Systematic comparison with various state-of-the-art microarray and RNA-seq networks was also performed, however, none outperformed the aggregate microarray network despite having good predictive performance. Repeating these series of tests using a functional enrichment-based performance metric also showed remarkably consistent findings with guilt-by-association neighbor voting. To demonstrate its functionality, we explore the function and transcriptional regulation of grapevine EXPANSIN genes. We envisage that network aggregation will offer new and unique opportunities for gene function prediction in future grapevine functional genomics studies. To this end, we make the aggregate networks and associated metadata publicly available at VTC-Agg (https://sites.google.com/view/vtc-agg).
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Affiliation(s)
- Darren C J Wong
- Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT, 2601, Australia.
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9
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Yamazaki K, Ishimori M, Kajiya-Kanegae H, Takanashi H, Fujimoto M, Yoneda JI, Yano K, Koshiba T, Tanaka R, Iwata H, Tokunaga T, Tsutsumi N, Fujiwara T. Effect of salt tolerance on biomass production in a large population of sorghum accessions. BREEDING SCIENCE 2020; 70:167-175. [PMID: 32523398 PMCID: PMC7272242 DOI: 10.1270/jsbbs.19009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 10/01/2019] [Indexed: 05/08/2023]
Abstract
Salinity causes major reductions in cultivated land area, crop productivity, and crop quality, and salt-tolerant crops have been required to sustain agriculture in salinized areas. The annual C4 crop plant Sorghum bicolor (L.) Moench is salt tolerant, with large variation among accessions. Sorghum's salt tolerance is often evaluated during early growth, but such evaluations are weakly related to overall performance. Here, we evaluated salt tolerance of 415 sorghum accessions grown in saline soil (0, 50, 100, and 150 mM NaCl) for 3 months. Some accessions produced up to 400 g per plant of biomass and showed no growth inhibition at 50 mM NaCl. Our analysis indicated that the genetic factors that affected biomass production under 100 mM salt stress were more different from those without salt stress, comparing to the differences between those under 50 mM and 100 mM salt stress. A genome-wide association study for salt tolerance identified two single-nucleotide polymorphisms (SNPs) that were significantly associated with biomass production, only at 50 mM NaCl. Additionally, two SNPs were significantly associated with salt tolerance index as an indicator for growth response of each accession to salt stress. Our results offer candidate genetic resources and SNP markers for breeding salt-tolerant sorghum.
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Affiliation(s)
- Kiyoshi Yamazaki
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Motoyuki Ishimori
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Hiromi Kajiya-Kanegae
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Hideki Takanashi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Masaru Fujimoto
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Breeding Genomics, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Jun-ichi Yoneda
- Earthnote Co. Ltd., 1386 Sokei, Ginozason, Kunigami-gun, Okinawa 904-1303, Japan
| | - Kentaro Yano
- Department of Life Sciences, School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Kawasaki, Kanagawa 214-8571, Japan
| | - Taichi Koshiba
- Earthnote Co. Ltd., 1386 Sokei, Ginozason, Kunigami-gun, Okinawa 904-1303, Japan
| | - Ryokei Tanaka
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Hiroyoshi Iwata
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Tsuyoshi Tokunaga
- Earthnote Co. Ltd., 1386 Sokei, Ginozason, Kunigami-gun, Okinawa 904-1303, Japan
| | - Nobuhiro Tsutsumi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Toru Fujiwara
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Corresponding author (e-mail: )
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10
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TRANSNAP: a web database providing comprehensive information on Japanese pear transcriptome. Sci Rep 2019; 9:18922. [PMID: 31831861 PMCID: PMC6908688 DOI: 10.1038/s41598-019-55287-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 11/21/2019] [Indexed: 01/01/2023] Open
Abstract
Japanese pear (Pyrus pyrifolia) is a major fruit tree in the family Rosaceae and is bred for fruit production. To promote the development of breeding strategies and molecular research for Japanese pear, we sequenced the transcripts of Japanese pear variety 'Hosui'. To exhaustively collect information of total gene expression, RNA samples from various organs and stages of Japanese pear were sequenced by three technologies, single-molecule real-time (SMRT) sequencing, 454 pyrosequencing, and Sanger sequencing. Using all those reads, we determined comprehensive reference sequences of Japanese pear. Then, their protein sequences were predicted, and biological functional annotations were assigned. Finally, we developed a web database, TRANSNAP (http://plantomics.mind.meiji.ac.jp/nashi), which is the first web resource of Japanese pear omics information. This database provides highly reliable information via a user-friendly web interface: the reference sequences, gene functional annotations, and gene expression profiles from microarray experiments. In addition, based on sequence comparisons among Japanese, Chinese and European pears, similar protein sequences among the pears and species-specific proteins in Japanese pear can be quickly and efficiently identified. TRANSNAP will aid molecular research and breeding in Japanese pear, and its information is available for comparative analysis among other pear species and families.
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11
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Sakamoto L, Kajiya-Kanegae H, Noshita K, Takanashi H, Kobayashi M, Kudo T, Yano K, Tokunaga T, Tsutsumi N, Iwata H. Comparison of shape quantification methods for genomic prediction, and genome-wide association study of sorghum seed morphology. PLoS One 2019; 14:e0224695. [PMID: 31751371 PMCID: PMC6872133 DOI: 10.1371/journal.pone.0224695] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 10/18/2019] [Indexed: 11/19/2022] Open
Abstract
Seed shape is an important agronomic trait with continuous variation among genotypes. Therefore, the quantitative evaluation of this variation is highly important. Among geometric morphometrics methods, elliptic Fourier analysis and semi-landmark analysis are often used for the quantification of biological shape variations. Elliptic Fourier analysis is an approximation method to treat contours as a waveform. Semi-landmark analysis is a method of superimposed points in which the differences of multiple contour positions are minimized. However, no detailed comparison of these methods has been undertaken. Moreover, these shape descriptors vary when the scale and direction of the contour and the starting point of the contour trace change. Thus, these methods should be compared with respect to the standardization of the scale and direction of the contour and the starting point of the contour trace. In the present study, we evaluated seed shape variations in a sorghum (Sorghum bicolor Moench) germplasm collection to analyze the association between shape variations and genome-wide single-nucleotide polymorphisms by genomic prediction (GP) and genome-wide association studies (GWAS). In our analysis, we used all possible combinations of three shape description methods and eight standardization procedures for the scale and direction of the contour as well as the starting point of the contour trace; these combinations were compared in terms of GP accuracy and the GWAS results. We compared the shape description methods (elliptic Fourier descriptors and the coordinates of superposed pseudo-landmark points) and found that principal component analysis of their quantitative descriptors yielded similar results. Different scaling and direction standardization procedures caused differences in the principal component scores, average shape, and the results of GP and GWAS.
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Affiliation(s)
- Lisa Sakamoto
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
- JSPS Research Fellow, Tokyo, Japan
| | | | - Koji Noshita
- Department of Biology, Kyushu University, Fukuoka, Japan
- PRESTO, JST, Saitama, Japan
| | - Hideki Takanashi
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | | | - Toru Kudo
- Faculty of Agriculture, Meiji University, Kanagawa, Japan
| | - Kentaro Yano
- Faculty of Agriculture, Meiji University, Kanagawa, Japan
| | | | - Nobuhiro Tsutsumi
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Hiroyoshi Iwata
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
- * E-mail:
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12
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Complete chloroplast genome sequence and phylogenetic analysis of wasabi (Eutrema japonicum) and its relatives. Sci Rep 2019; 9:14377. [PMID: 31591417 PMCID: PMC6779752 DOI: 10.1038/s41598-019-49667-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 08/29/2019] [Indexed: 12/18/2022] Open
Abstract
In Japan, two Eutrema species, wasabi (Eutrema japonicum, the important traditional Japanese condiment) and yuriwasabi (E. tenue), have been recognized as endemic species. We sequenced complete chloroplast (cp) genomes of seven wasabi and yuriwasabi accessions from Japan to study their phylogeny and evolution, using molecular dating of species divergence. Phylogenetic analyses of the complete cp DNA of these two Japanese species and five other Eurasian Eutrema species revealed that wasabi and yuriwasabi did not form a monophyletic group. One yuriwasabi accession (Gifu) formed a clade with E. yunnanense from China, indicating that this accession should be considered as a different species from the other yuriwasabi accessions. We reveal that Japanese Eutrema species diverged from the ‘E. yunnanense–yuriwasabi (Gifu)’ clade approximately 1.3 million years ago (Mya), suggesting that the connection between Japan and the Eurasian continent has existed more recently than the Quaternary period. The abundance of cp sequence data in this study also allowed the detection of genetic differentiation among wasabi cultivars. The two polymorphic sites detected between ‘Fujidaruma’ and ‘Shimane No.3’ were used to develop genotyping markers. The cp genome information provided here will thus inform the evolutionary histories of Japanese Eutrema species and help in genotyping wasabi cultivars.
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13
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Vu NT, Kamiya K, Fukushima A, Hao S, Ning W, Ariizumi T, Ezura H, Kusano M. Comparative co-expression network analysis extracts the SlHSP70 gene affecting to shoot elongation of tomato. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2019; 36:143-153. [PMID: 31768116 PMCID: PMC6854337 DOI: 10.5511/plantbiotechnology.19.0603a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Tomato is one of vegetables crops that has the highest value in the world. Thus, researchers are continually improving the agronomical traits of tomato fruits. Auxins and gibberellins regulate plant growth and development. Aux/indole-3-acetic acid 9 (SlIAA9) and the gene encoding the DELLA protein (SlDELLA) are well-known genes that regulate plant growth and development, including fruit set and enlargement by cell division and cell expansion. The absence of tomato SlIAA9 and SlDELLA results in abnormal shoot growth and leaf shape and giving rise to parthenocarpy. To investigate the key regulators that exist up- or downstream of SlIAA9 and SlDELLA signaling pathways for tomato growth and development, we performed gene co-expression network analysis by using publicly available microarray data to extract genes that are directly connected to the SlIAA9 and SlDELLA nodes, respectively. Consequently, we chose a gene in the group of heat-shock protein (HSP)70s that was connected with the SlIAA9 node and SlDELLA node in each co-expression network. To validate the extent of effect of SlHSP70-1 on tomato growth and development, overexpressing lines of the target gene were generated. We found that overexpression of the targeted SlHSP70-1 resulted in internode elongation, but the overexpressing lines did not show abnormal leaf shape, fruit set, or fruit size when compared with that of the wild type. Our study suggests that the targeted SlHSP70-1 is likely to function in shoot growth, like SlIAA9 and SlDELLA, but it does not contribute to parthenocarpy as well as fruit set. Our study also shows that only a single SlHSP70 out of 25 homologous genes could change the shoot length.
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Affiliation(s)
- Nam Tuan Vu
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Ken Kamiya
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Atsushi Fukushima
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
| | - Shuhei Hao
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Wang Ning
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
- Graduate School of Life and Environmental Science, Tsukuba-Plant Innovation Research Center (T-PIRC), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Tohru Ariizumi
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
- Graduate School of Life and Environmental Science, Tsukuba-Plant Innovation Research Center (T-PIRC), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Hiroshi Ezura
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
- Graduate School of Life and Environmental Science, Tsukuba-Plant Innovation Research Center (T-PIRC), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Miyako Kusano
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
- Graduate School of Life and Environmental Science, Tsukuba-Plant Innovation Research Center (T-PIRC), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
- E-mail: Tel & Fax: +81-29-853-4809
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14
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Takano T, Yamamoto N, Suzuki T, Dohra H, Choi JH, Terashima Y, Yokoyama K, Kawagishi H, Yano K. Genome sequence analysis of the fairy ring-forming fungus Lepista sordida and gene candidates for interaction with plants. Sci Rep 2019; 9:5888. [PMID: 30971747 PMCID: PMC6458111 DOI: 10.1038/s41598-019-42231-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 03/21/2019] [Indexed: 12/21/2022] Open
Abstract
Circular patterns called "fairy rings" in fields are a natural phenomenon that arises through the interaction between basidiomycete fungi and plants. Acceleration or inhibition of plant vegetative growth and the formation of mushroom fruiting bodies are both commonly observed when fairy rings form. The gene of an enzyme involved in the biosynthesis of these regulators was recently isolated in the fairy ring-forming fungus, Lepista sordida. To identify other genes involved in L. sordida fairy ring formation, we used previously generated sequence data to produce a more complete draft genome sequence for this species. Finally, we predicted the metabolic pathways of the plant growth regulators and 29 candidate enzyme-coding genes involved in fairy-ring formation based on gene annotations. Comparisons of protein coding genes among basidiomycete fungi revealed two nitric oxide synthase gene candidates that were uniquely encoded in genomes of fairy ring-forming fungi. These results provide a basis for the discovery of genes involved in fairy ring formation and for understanding the mechanisms involved in the interaction between fungi and plants. We also constructed a new web database F-RINGS ( http://bioinf.mind.meiji.ac.jp/f-rings/ ) to provide the comprehensive genomic information for L. sordida.
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Affiliation(s)
- Tomoyuki Takano
- Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Kawasaki, 214-8571, Japan
| | - Naoki Yamamoto
- Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Kawasaki, 214-8571, Japan
- Rice Research Institute, Sichuan Agricultural University, 211 Huiminglu, Wenjiang, Chengdu, China
| | - Tomohiro Suzuki
- Center for Bioscience Research and Education, Utsunomiya University, 350 Mine-machi, Utsunomiya, Tochigi, 321-8505, Japan
| | - Hideo Dohra
- Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Jae-Hoon Choi
- Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Yurika Terashima
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Koji Yokoyama
- Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Kawasaki, 214-8571, Japan
| | - Hirokazu Kawagishi
- Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan.
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan.
- Graduate School of Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan.
| | - Kentaro Yano
- Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Kawasaki, 214-8571, Japan.
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15
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Rahman MH, Toda E, Kobayashi M, Kudo T, Koshimizu S, Takahara M, Iwami M, Watanabe Y, Sekimoto H, Yano K, Okamoto T. Expression of Genes from Paternal Alleles in Rice Zygotes and Involvement of OsASGR-BBML1 in Initiation of Zygotic Development. PLANT & CELL PHYSIOLOGY 2019; 60:725-737. [PMID: 30801122 DOI: 10.1093/pcp/pcz030] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 02/07/2019] [Indexed: 05/11/2023]
Abstract
Upon fertilization in angiosperms, one sperm cell fuses with the egg cell to produce a zygote, and, via karyogamy, the parental genetic information is combined to form the diploid zygotic genome. Recently, analyses with parentally imbalanced rice zygotes indicated that parental genomes are utilized synergistically in zygotes with different functions, and that genes transcribed from the paternal or maternal allele might play important roles in zygotic development. Herein, we first conducted single nucleotide polymorphism-based mRNA-sequencing using intersubspecific rice zygotes. Twenty-three genes, with paternal allele-specific expression in zygotes, were identified, and, surprisingly, their allele dependencies in the globular-like embryo tended to be biallelic. This suggests that the paternal-dependent expression of these genes is temporary, occurring during the early stages of zygote development. Of the 23 genes, we focused on Oryza sativa Apospory-specific Genome Region (ASGR)-BABY-BOOM LIKE (BBML) 1 (OsASGR-BBML1), presumed to encode an AP2-transcription factor, due to its reported role in zygotic development. Interestingly, ectopic expression of OsASGR-BBML1 in egg cells induced nuclear and cell divisions, indicating that exogenously expressed OsASGR-BBML1 converts the proliferation status of the egg cell from quiescent to active. In addition, the suppression of the function of OsASGR-BBML1 and its homologs in zygotes resulted in the developmental arrest, suggesting that OsASGR-BBML1 possesses an important role in initiating zygotic development. Monoallelic or preferential gene expression from the paternal genome in the zygote might be a safety mechanism allowing egg cells to suppress the gene expression cascade toward early embryogenesis that is normally triggered by fusion with a sperm cell.
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Affiliation(s)
- Md Hassanur Rahman
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan
| | - Erika Toda
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan
| | | | - Toru Kudo
- Department of Life Sciences, Meiji University, Kanagawa, Japan
| | | | - Mirei Takahara
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan
| | - Momoka Iwami
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan
| | - Yoriko Watanabe
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan
| | - Hiroyuki Sekimoto
- Department of Chemical and Biological Sciences, Japan Women's University, Tokyo, Japan
| | - Kentaro Yano
- Department of Life Sciences, Meiji University, Kanagawa, Japan
| | - Takashi Okamoto
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan
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16
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Ando T, Matsuda T, Goto K, Hara K, Ito A, Hirata J, Yatomi J, Kajitani R, Okuno M, Yamaguchi K, Kobayashi M, Takano T, Minakuchi Y, Seki M, Suzuki Y, Yano K, Itoh T, Shigenobu S, Toyoda A, Niimi T. Repeated inversions within a pannier intron drive diversification of intraspecific colour patterns of ladybird beetles. Nat Commun 2018; 9:3843. [PMID: 30242156 PMCID: PMC6155092 DOI: 10.1038/s41467-018-06116-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 08/15/2018] [Indexed: 11/16/2022] Open
Abstract
How genetic information is modified to generate phenotypic variation within a species is one of the central questions in evolutionary biology. Here we focus on the striking intraspecific diversity of >200 aposematic elytral (forewing) colour patterns of the multicoloured Asian ladybird beetle, Harmonia axyridis, which is regulated by a tightly linked genetic locus h. Our loss-of-function analyses, genetic association studies, de novo genome assemblies, and gene expression data reveal that the GATA transcription factor gene pannier is the major regulatory gene located at the h locus, and suggest that repeated inversions and cis-regulatory modifications at pannier led to the expansion of colour pattern variation in H. axyridis. Moreover, we show that the colour-patterning function of pannier is conserved in the seven-spotted ladybird beetle, Coccinella septempunctata, suggesting that H. axyridis’ extraordinary intraspecific variation may have arisen from ancient modifications in conserved elytral colour-patterning mechanisms in ladybird beetles. The harlequin ladybird beetle, Harmonia axyridis, has remarkable phenotypic diversity, with over 200 colour patterns. Here, Ando et al. show that this patterning is regulated by the transcription factor gene pannier and has diversified by repeated inversions and cis-regulatory modifications of pannier.
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Affiliation(s)
- Toshiya Ando
- Division of Evolutionary Developmental Biology, National Institute for Basic Biology, Okazaki, Aichi, 444-8585, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, 444-8585, Japan
| | - Takeshi Matsuda
- Laboratory of Sericulture and Entomoresources, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | - Kumiko Goto
- Laboratory of Sericulture and Entomoresources, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | - Kimiko Hara
- Laboratory of Sericulture and Entomoresources, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | - Akinori Ito
- Laboratory of Sericulture and Entomoresources, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | - Junya Hirata
- Laboratory of Sericulture and Entomoresources, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | - Joichiro Yatomi
- Laboratory of Sericulture and Entomoresources, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | - Rei Kajitani
- Department of Biological Information, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
| | - Miki Okuno
- Department of Biological Information, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
| | - Katsushi Yamaguchi
- NIBB Core Research Facilities, National Institute for Basic Biology, Okazaki, Aichi, 444-8585, Japan
| | - Masaaki Kobayashi
- Bioinformatics Laboratory, Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa, 214-8571, Japan
| | - Tomoyuki Takano
- Bioinformatics Laboratory, Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa, 214-8571, Japan
| | - Yohei Minakuchi
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Masahide Seki
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Yutaka Suzuki
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Kentaro Yano
- Bioinformatics Laboratory, Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa, 214-8571, Japan
| | - Takehiko Itoh
- Department of Biological Information, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
| | - Shuji Shigenobu
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, 444-8585, Japan.,NIBB Core Research Facilities, National Institute for Basic Biology, Okazaki, Aichi, 444-8585, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan.,Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Teruyuki Niimi
- Division of Evolutionary Developmental Biology, National Institute for Basic Biology, Okazaki, Aichi, 444-8585, Japan. .,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, 444-8585, Japan. .,Laboratory of Sericulture and Entomoresources, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan.
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17
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Hansen BO, Meyer EH, Ferrari C, Vaid N, Movahedi S, Vandepoele K, Nikoloski Z, Mutwil M. Ensemble gene function prediction database reveals genes important for complex I formation in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2018; 217:1521-1534. [PMID: 29205376 DOI: 10.1111/nph.14921] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 10/24/2017] [Indexed: 05/25/2023]
Abstract
Recent advances in gene function prediction rely on ensemble approaches that integrate results from multiple inference methods to produce superior predictions. Yet, these developments remain largely unexplored in plants. We have explored and compared two methods to integrate 10 gene co-function networks for Arabidopsis thaliana and demonstrate how the integration of these networks produces more accurate gene function predictions for a larger fraction of genes with unknown function. These predictions were used to identify genes involved in mitochondrial complex I formation, and for five of them, we confirmed the predictions experimentally. The ensemble predictions are provided as a user-friendly online database, EnsembleNet. The methods presented here demonstrate that ensemble gene function prediction is a powerful method to boost prediction performance, whereas the EnsembleNet database provides a cutting-edge community tool to guide experimentalists.
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Affiliation(s)
- Bjoern Oest Hansen
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, Potsdam, 14476, Germany
- Institut für Medizinische Informatik, Universitätsmedizin Göttingen, Robert-Koch-Str. 40, Göttingen, 37075, Germany
| | - Etienne H Meyer
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, Potsdam, 14476, Germany
| | - Camilla Ferrari
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, Potsdam, 14476, Germany
| | - Neha Vaid
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, Potsdam, 14476, Germany
| | - Sara Movahedi
- Department of Plant Biotechnology and Bioinformatics, VIB Center for Plant Systems Biology, Ghent University, Technologiepark 927, Gent, B-9052, Belgium
- Rijk Zwaan Breeding BV, Burgemeester Crezéelaan 40, PO Box 40, De Lier, 2678 ZG, the Netherlands
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, VIB Center for Plant Systems Biology, Ghent University, Technologiepark 927, Gent, B-9052, Belgium
| | - Zoran Nikoloski
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, Potsdam, 14476, Germany
- Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, Potsdam-Golm, 14476, Germany
| | - Marek Mutwil
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, Potsdam, 14476, Germany
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
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18
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Kobayashi M, Ohyanagi H, Takanashi H, Asano S, Kudo T, Kajiya-Kanegae H, Nagano AJ, Tainaka H, Tokunaga T, Sazuka T, Iwata H, Tsutsumi N, Yano K. Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput sequencing data. DNA Res 2017; 24:397-405. [PMID: 28498906 PMCID: PMC5737671 DOI: 10.1093/dnares/dsx012] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 04/20/2017] [Indexed: 12/30/2022] Open
Abstract
Recent availability of large-scale genomic resources enables us to conduct so called genome-wide association studies (GWAS) and genomic prediction (GP) studies, particularly with next-generation sequencing (NGS) data. The effectiveness of GWAS and GP depends on not only their mathematical models, but the quality and quantity of variants employed in the analysis. In NGS single nucleotide polymorphism (SNP) calling, conventional tools ideally require more reads for higher SNP sensitivity and accuracy. In this study, we aimed to develop a tool, Heap, that enables robustly sensitive and accurate calling of SNPs, particularly with a low coverage NGS data, which must be aligned to the reference genome sequences in advance. To reduce false positive SNPs, Heap determines genotypes and calls SNPs at each site except for sites at the both ends of reads or containing a minor allele supported by only one read. Performance comparison with existing tools showed that Heap achieved the highest F-scores with low coverage (7X) restriction-site associated DNA sequencing reads of sorghum and rice individuals. This will facilitate cost-effective GWAS and GP studies in this NGS era. Code and documentation of Heap are freely available from https://github.com/meiji-bioinf/heap (29 March 2017, date last accessed) and our web site (http://bioinf.mind.meiji.ac.jp/lab/en/tools.html (29 March 2017, date last accessed)).
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Affiliation(s)
- Masaaki Kobayashi
- Bioinformatics Laboratory, Department of Life Sciences, School of Agriculture, Meiji University, Kanagawa 214-8571, Japan
| | - Hajime Ohyanagi
- Bioinformatics Laboratory, Department of Life Sciences, School of Agriculture, Meiji University, Kanagawa 214-8571, Japan.,King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Hideki Takanashi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Satomi Asano
- Bioinformatics Laboratory, Department of Life Sciences, School of Agriculture, Meiji University, Kanagawa 214-8571, Japan
| | - Toru Kudo
- Bioinformatics Laboratory, Department of Life Sciences, School of Agriculture, Meiji University, Kanagawa 214-8571, Japan
| | - Hiromi Kajiya-Kanegae
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Shiga 520-2194, Japan.,PRESTO, Japan Science and Technology Agency, Japan.,Center for Ecological Research, Kyoto University, Shiga 520-2113, Japan
| | - Hitoshi Tainaka
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | | | - Takashi Sazuka
- Bioscience and Biotechnology Center, Nagoya University, Aichi 464-8601, Japan
| | - Hiroyoshi Iwata
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Nobuhiro Tsutsumi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Kentaro Yano
- Bioinformatics Laboratory, Department of Life Sciences, School of Agriculture, Meiji University, Kanagawa 214-8571, Japan
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19
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Jokipii‐Lukkari S, Sundell D, Nilsson O, Hvidsten TR, Street NR, Tuominen H. NorWood: a gene expression resource for evo-devo studies of conifer wood development. THE NEW PHYTOLOGIST 2017; 216:482-494. [PMID: 28186632 PMCID: PMC6079643 DOI: 10.1111/nph.14458] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 12/22/2016] [Indexed: 05/04/2023]
Abstract
The secondary xylem of conifers is composed mainly of tracheids that differ anatomically and chemically from angiosperm xylem cells. There is currently no high-spatial-resolution data available profiling gene expression during wood formation for any coniferous species, which limits insight into tracheid development. RNA-sequencing data from replicated, high-spatial-resolution section series throughout the cambial and woody tissues of Picea abies were used to generate the NorWood.conGenIE.org web resource, which facilitates exploration of the associated gene expression profiles and co-expression networks. Integration within PlantGenIE.org enabled a comparative regulomics analysis, revealing divergent co-expression networks between P. abies and the two angiosperm species Arabidopsis thaliana and Populus tremula for the secondary cell wall (SCW) master regulator NAC Class IIB transcription factors. The SCW cellulose synthase genes (CesAs) were located in the neighbourhoods of the NAC factors in A. thaliana and P. tremula, but not in P. abies. The NorWood co-expression network enabled identification of potential SCW CesA regulators in P. abies. The NorWood web resource represents a powerful community tool for generating evo-devo insights into the divergence of wood formation between angiosperms and gymnosperms and for advancing understanding of the regulation of wood development in P. abies.
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Affiliation(s)
- Soile Jokipii‐Lukkari
- Umeå Plant Science CentreDepartment of Plant PhysiologyUmeå UniversitySE‐901 87UmeåSweden
- Umeå Plant Science CentreDepartment of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesSE‐901 84UmeåSweden
| | - David Sundell
- Umeå Plant Science CentreDepartment of Plant PhysiologyUmeå UniversitySE‐901 87UmeåSweden
| | - Ove Nilsson
- Umeå Plant Science CentreDepartment of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesSE‐901 84UmeåSweden
| | - Torgeir R. Hvidsten
- Umeå Plant Science CentreDepartment of Plant PhysiologyUmeå UniversitySE‐901 87UmeåSweden
- Department of Chemistry, Biotechnology and Food ScienceNorwegian University of Life Sciences1430ÅsNorway
| | - Nathaniel R. Street
- Umeå Plant Science CentreDepartment of Plant PhysiologyUmeå UniversitySE‐901 87UmeåSweden
| | - Hannele Tuominen
- Umeå Plant Science CentreDepartment of Plant PhysiologyUmeå UniversitySE‐901 87UmeåSweden
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Salhi A, Negrão S, Essack M, Morton MJL, Bougouffa S, Razali R, Radovanovic A, Marchand B, Kulmanov M, Hoehndorf R, Tester M, Bajic VB. DES-TOMATO: A Knowledge Exploration System Focused On Tomato Species. Sci Rep 2017; 7:5968. [PMID: 28729549 PMCID: PMC5519719 DOI: 10.1038/s41598-017-05448-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 05/25/2017] [Indexed: 12/29/2022] Open
Abstract
Tomato is the most economically important horticultural crop used as a model to study plant biology and particularly fruit development. Knowledge obtained from tomato research initiated improvements in tomato and, being transferrable to other such economically important crops, has led to a surge of tomato-related research and published literature. We developed DES-TOMATO knowledgebase (KB) for exploration of information related to tomato. Information exploration is enabled through terms from 26 dictionaries and combination of these terms. To illustrate the utility of DES-TOMATO, we provide several examples how one can efficiently use this KB to retrieve known or potentially novel information. DES-TOMATO is free for academic and nonprofit users and can be accessed at http://cbrc.kaust.edu.sa/des_tomato/, using any of the mainstream web browsers, including Firefox, Safari and Chrome.
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Affiliation(s)
- Adil Salhi
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955-6900, Saudi Arabia
| | - Sónia Negrão
- King Abdullah University of Science and Technology (KAUST), Division of Biological and Environmental Sciences and Engineering, Thuwal, 23955-6900, Saudi Arabia
| | - Magbubah Essack
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955-6900, Saudi Arabia
| | - Mitchell J L Morton
- King Abdullah University of Science and Technology (KAUST), Division of Biological and Environmental Sciences and Engineering, Thuwal, 23955-6900, Saudi Arabia
| | - Salim Bougouffa
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955-6900, Saudi Arabia
| | - Rozaimi Razali
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955-6900, Saudi Arabia
| | - Aleksandar Radovanovic
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955-6900, Saudi Arabia
| | | | - Maxat Kulmanov
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955-6900, Saudi Arabia
| | - Robert Hoehndorf
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955-6900, Saudi Arabia
- King Abdullah University of Science and Technology (KAUST), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Thuwal, 23955-6900, Saudi Arabia
| | - Mark Tester
- King Abdullah University of Science and Technology (KAUST), Division of Biological and Environmental Sciences and Engineering, Thuwal, 23955-6900, Saudi Arabia
| | - Vladimir B Bajic
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955-6900, Saudi Arabia.
- King Abdullah University of Science and Technology (KAUST), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Thuwal, 23955-6900, Saudi Arabia.
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Narise T, Sakurai N, Obayashi T, Ohta H, Shibata D. Co-expressed Pathways DataBase for Tomato: a database to predict pathways relevant to a query gene. BMC Genomics 2017; 18:437. [PMID: 28583129 PMCID: PMC5460524 DOI: 10.1186/s12864-017-3786-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 05/10/2017] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Gene co-expression, the similarity of gene expression profiles under various experimental conditions, has been used as an indicator of functional relationships between genes, and many co-expression databases have been developed for predicting gene functions. These databases usually provide users with a co-expression network and a list of strongly co-expressed genes for a query gene. Several of these databases also provide functional information on a set of strongly co-expressed genes (i.e., provide biological processes and pathways that are enriched in these strongly co-expressed genes), which is generally analyzed via over-representation analysis (ORA). A limitation of this approach may be that users can predict gene functions only based on the strongly co-expressed genes. RESULTS In this study, we developed a new co-expression database that enables users to predict the function of tomato genes from the results of functional enrichment analyses of co-expressed genes while considering the genes that are not strongly co-expressed. To achieve this, we used the ORA approach with several thresholds to select co-expressed genes, and performed gene set enrichment analysis (GSEA) applied to a ranked list of genes ordered by the co-expression degree. We found that internal correlation in pathways affected the significance levels of the enrichment analyses. Therefore, we introduced a new measure for evaluating the relationship between the gene and pathway, termed the percentile (p)-score, which enables users to predict functionally relevant pathways without being affected by the internal correlation in pathways. In addition, we evaluated our approaches using receiver operating characteristic curves, which concluded that the p-score could improve the performance of the ORA. CONCLUSIONS We developed a new database, named Co-expressed Pathways DataBase for Tomato, which is available at http://cox-path-db.kazusa.or.jp/tomato . The database allows users to predict pathways that are relevant to a query gene, which would help to infer gene functions.
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Affiliation(s)
- Takafumi Narise
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818 Japan
| | - Nozomu Sakurai
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818 Japan
| | - Takeshi Obayashi
- Graduate School of Information Sciences, Tohoku University, 6-3-09 Aramaki-Aza-Aoba, Aoba-ku, Sendai, Miyagi, 980-8579 Japan
| | - Hiroyuki Ohta
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259-B-65 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8501 Japan
| | - Daisuke Shibata
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818 Japan
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Rai A, Saito K, Yamazaki M. Integrated omics analysis of specialized metabolism in medicinal plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:764-787. [PMID: 28109168 DOI: 10.1111/tpj.13485] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 01/10/2017] [Accepted: 01/11/2017] [Indexed: 05/19/2023]
Abstract
Medicinal plants are a rich source of highly diverse specialized metabolites with important pharmacological properties. Until recently, plant biologists were limited in their ability to explore the biosynthetic pathways of these metabolites, mainly due to the scarcity of plant genomics resources. However, recent advances in high-throughput large-scale analytical methods have enabled plant biologists to discover biosynthetic pathways for important plant-based medicinal metabolites. The reduced cost of generating omics datasets and the development of computational tools for their analysis and integration have led to the elucidation of biosynthetic pathways of several bioactive metabolites of plant origin. These discoveries have inspired synthetic biology approaches to develop microbial systems to produce bioactive metabolites originating from plants, an alternative sustainable source of medicinally important chemicals. Since the demand for medicinal compounds are increasing with the world's population, understanding the complete biosynthesis of specialized metabolites becomes important to identify or develop reliable sources in the future. Here, we review the contributions of major omics approaches and their integration to our understanding of the biosynthetic pathways of bioactive metabolites. We briefly discuss different approaches for integrating omics datasets to extract biologically relevant knowledge and the application of omics datasets in the construction and reconstruction of metabolic models.
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Affiliation(s)
- Amit Rai
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8675, Japan
| | - Kazuki Saito
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8675, Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Mami Yamazaki
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8675, Japan
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Mochizuki T, Tanizawa Y, Fujisawa T, Ohta T, Nikoh N, Shimizu T, Toyoda A, Fujiyama A, Kurata N, Nagasaki H, Kaminuma E, Nakamura Y. DNApod: DNA polymorphism annotation database from next-generation sequence read archives. PLoS One 2017; 12:e0172269. [PMID: 28234924 PMCID: PMC5325239 DOI: 10.1371/journal.pone.0172269] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 02/02/2017] [Indexed: 01/18/2023] Open
Abstract
With the rapid advances in next-generation sequencing (NGS), datasets for DNA polymorphisms among various species and strains have been produced, stored, and distributed. However, reliability varies among these datasets because the experimental and analytical conditions used differ among assays. Furthermore, such datasets have been frequently distributed from the websites of individual sequencing projects. It is desirable to integrate DNA polymorphism data into one database featuring uniform quality control that is distributed from a single platform at a single place. DNA polymorphism annotation database (DNApod; http://tga.nig.ac.jp/dnapod/) is an integrated database that stores genome-wide DNA polymorphism datasets acquired under uniform analytical conditions, and this includes uniformity in the quality of the raw data, the reference genome version, and evaluation algorithms. DNApod genotypic data are re-analyzed whole-genome shotgun datasets extracted from sequence read archives, and DNApod distributes genome-wide DNA polymorphism datasets and known-gene annotations for each DNA polymorphism. This new database was developed for storing genome-wide DNA polymorphism datasets of plants, with crops being the first priority. Here, we describe our analyzed data for 679, 404, and 66 strains of rice, maize, and sorghum, respectively. The analytical methods are available as a DNApod workflow in an NGS annotation system of the DNA Data Bank of Japan and a virtual machine image. Furthermore, DNApod provides tables of links of identifiers between DNApod genotypic data and public phenotypic data. To advance the sharing of organism knowledge, DNApod offers basic and ubiquitous functions for multiple alignment and phylogenetic tree construction by using orthologous gene information.
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Affiliation(s)
- Takako Mochizuki
- Genome Informatics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Yasuhiro Tanizawa
- Genome Informatics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Takatomo Fujisawa
- Genome Informatics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Tazro Ohta
- Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Mishima, Shizuoka, Japan
| | - Naruo Nikoh
- Department of Liberal Arts, The Open University of Japan, Chiba, Chiba, Japan
| | - Tokurou Shimizu
- Division of Citrus Research, Institute of Fruit Tree and Tea Science, NARO, Shimizu, Shizuoka, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Asao Fujiyama
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Nori Kurata
- Plant Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Hideki Nagasaki
- Genome Informatics Group, Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
| | - Eli Kaminuma
- Genome Informatics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
- * E-mail:
| | - Yasukazu Nakamura
- Genome Informatics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
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Kudo T, Kobayashi M, Terashima S, Katayama M, Ozaki S, Kanno M, Saito M, Yokoyama K, Ohyanagi H, Aoki K, Kubo Y, Yano K. TOMATOMICS: A Web Database for Integrated Omics Information in Tomato. PLANT & CELL PHYSIOLOGY 2017; 58:e8. [PMID: 28111364 PMCID: PMC5444566 DOI: 10.1093/pcp/pcw207] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 11/16/2016] [Indexed: 05/23/2023]
Abstract
Solanum lycopersicum (tomato) is an important agronomic crop and a major model fruit-producing plant. To facilitate basic and applied research, comprehensive experimental resources and omics information on tomato are available following their development. Mutant lines and cDNA clones from a dwarf cultivar, Micro-Tom, are two of these genetic resources. Large-scale sequencing data for ESTs and full-length cDNAs from Micro-Tom continue to be gathered. In conjunction with information on the reference genome sequence of another cultivar, Heinz 1706, the Micro-Tom experimental resources have facilitated comprehensive functional analyses. To enhance the efficiency of acquiring omics information for tomato biology, we have integrated the information on the Micro-Tom experimental resources and the Heinz 1706 genome sequence. We have also inferred gene structure by comparison of sequences between the genome of Heinz 1706 and the transcriptome, which are comprised of Micro-Tom full-length cDNAs and Heinz 1706 RNA-seq data stored in the KaFTom and Sequence Read Archive databases. In order to provide large-scale omics information with streamlined connectivity we have developed and maintain a web database TOMATOMICS (http://bioinf.mind.meiji.ac.jp/tomatomics/). In TOMATOMICS, access to the information on the cDNA clone resources, full-length mRNA sequences, gene structures, expression profiles and functional annotations of genes is available through search functions and the genome browser, which has an intuitive graphical interface.
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Affiliation(s)
- Toru Kudo
- Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - Masaaki Kobayashi
- Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - Shin Terashima
- Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - Minami Katayama
- Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - Soichi Ozaki
- Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - Maasa Kanno
- Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - Misa Saito
- Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - Koji Yokoyama
- Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - Hajime Ohyanagi
- Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Koh Aoki
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, 599-8531 Japan
| | - Yasutaka Kubo
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530 Japan
| | - Kentaro Yano
- Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
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Practical Utilization of OryzaExpress and Plant Omics Data Center Databases to Explore Gene Expression Networks in Oryza Sativa and Other Plant Species. Methods Mol Biol 2017; 1533:229-240. [PMID: 27987174 DOI: 10.1007/978-1-4939-6658-5_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Analysis of a gene expression network (GEN), which is constructed based on similarity of gene expression profiles, is a widely used approach to gain clues for new biological insights. The recent abundant availability of transcriptome data in public databases is enabling GEN analysis under various experimental conditions, and even comparative GEN analysis across species. To provide a platform to gain biological insights from public transcriptome data, valuable databases have been created and maintained. This chapter introduces the web database OryzaExpress, providing omics information on Oryza sativa (rice). The integrated database Plant Omics Data Center, supporting a wide variety of plant species, is also described to compare omics information among multiple plant species.
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Nakamura Y, Kudo T, Terashima S, Saito M, Nambara E, Yano K. CATchUP: A Web Database for Spatiotemporally Regulated Genes. PLANT & CELL PHYSIOLOGY 2017; 58:e3. [PMID: 28013273 DOI: 10.1093/pcp/pcw199] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Accepted: 11/06/2016] [Indexed: 06/06/2023]
Abstract
For proper control of biological activity, some key genes are highly expressed in a particular spatiotemporal domain. Mining of such spatiotemporally expressed genes using large-scale gene expression data derived from a broad range of experimental sources facilitates our understanding of genome-scale functional gene networks. However, comprehensive information on spatiotemporally expressed genes is lacking in plants. To collect such information, we devised a new index, Δdmax, which is the maximum difference in relative gene expression levels between sample runs which are neighboring when sorted by the levels. Employing this index, we comprehensively evaluated transcripts using large-scale RNA sequencing (RNA-Seq) data stored in the Sequence Read Archive for eight plant species: Arabidopsis thaliana (Arabidopsis), Solanum lycopersicum (tomato), Solanum tuberosum (potato), Oryza sativa (rice), Sorghum bicolor (sorghum), Vitis vinifera (grape), Medicago truncatula (Medicago), and Glycine max (soybean). Based on the frequency distribution of the Δdmax values, approximately 70,000 transcripts showing 0.3 or larger Δdmax values were extracted for the eight species. Information on these genes including the Δdmax values, functional annotations, conservation among species, and experimental conditions where the genes show high expression levels is provided in a new database, CATchUP (http://plantomics.mind.meiji.ac.jp/CATchUP). The CATchUP database assists in identifying genes specifically expressed under particular conditions with powerful search functions and an intuitive graphical user interface.
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Affiliation(s)
- Yukino Nakamura
- Bioinformatics Laboratory, School of Agriculture, Meiji University, Higashi-mita, Tama-ku, Kawasaki, Kanagawa, Japan
| | - Toru Kudo
- Bioinformatics Laboratory, School of Agriculture, Meiji University, Higashi-mita, Tama-ku, Kawasaki, Kanagawa, Japan
| | - Shin Terashima
- Bioinformatics Laboratory, School of Agriculture, Meiji University, Higashi-mita, Tama-ku, Kawasaki, Kanagawa, Japan
| | - Misa Saito
- Bioinformatics Laboratory, School of Agriculture, Meiji University, Higashi-mita, Tama-ku, Kawasaki, Kanagawa, Japan
| | - Eiji Nambara
- Department of Cell & Systems Biology, University of Toronto, Willcocks Street, Toronto, Ontario, Canada
| | - Kentaro Yano
- Bioinformatics Laboratory, School of Agriculture, Meiji University, Higashi-mita, Tama-ku, Kawasaki, Kanagawa, Japan
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Kudo T, Terashima S, Takaki Y, Tomita K, Saito M, Kanno M, Yokoyama K, Yano K. PlantExpress: A Database Integrating OryzaExpress and ArthaExpress for Single-species and Cross-species Gene Expression Network Analyses with Microarray-Based Transcriptome Data. PLANT & CELL PHYSIOLOGY 2017; 58:e1. [PMID: 28158643 DOI: 10.1093/pcp/pcw208] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/19/2016] [Indexed: 06/06/2023]
Abstract
Publicly available microarray-based transcriptome data on plants are remarkably valuable in terms of abundance and variation of samples, particularly for Oryza sativa (rice) and Arabidopsis thaliana (Arabidopsis). Here, we introduce the web database PlantExpress (http://plantomics.mind.meiji.ac.jp/PlantExpress/) as a platform for gene expression network (GEN) analysis with the public microarray data of rice and Arabidopsis. PlantExpress has two functional modes. The single-species mode is specialized for GEN analysis within one of the species, while the cross-species mode is optimized for comparative GEN analysis between the species. The single-species mode for rice is the new version of OryzaExpress, which we have maintained since 2006. The single-species mode for Arabidopsis, named ArthaExpress, was newly developed. PlantExpress stores data obtained from three microarrays, the Affymetrix Rice Genome Array, the Agilent Rice Gene Expression 4x44K Microarray, and the Affymetrix Arabidopsis ATH1 Genome Array, with respective totals of 2,678, 1,206, and 10,940 samples. This database employs a ‘MyList’ function with which users may save lists of arbitrary genes and samples (experimental conditions) to use in analyses. In cross-species mode, the MyList function allows performing comparative GEN analysis between rice and Arabidopsis. In addition, the gene lists saved in MyList can be directly exported to the PODC database, which provides information and a platform for comparative GEN analysis based on RNA-seq data and knowledge-based functional annotation of plant genes. PlantExpress will facilitate understanding the biological functions of plant genes.
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Affiliation(s)
- Toru Kudo
- Bioinformatics Laboratory, School of Agriculture, Meiji University, Higashi-mita, Tama-ku, Kawasaki, Kanagawa, Japan
| | - Shin Terashima
- Bioinformatics Laboratory, School of Agriculture, Meiji University, Higashi-mita, Tama-ku, Kawasaki, Kanagawa, Japan
| | - Yuno Takaki
- Bioinformatics Laboratory, School of Agriculture, Meiji University, Higashi-mita, Tama-ku, Kawasaki, Kanagawa, Japan
| | - Ken Tomita
- Bioinformatics Laboratory, School of Agriculture, Meiji University, Higashi-mita, Tama-ku, Kawasaki, Kanagawa, Japan
| | - Misa Saito
- Bioinformatics Laboratory, School of Agriculture, Meiji University, Higashi-mita, Tama-ku, Kawasaki, Kanagawa, Japan
| | - Maasa Kanno
- Bioinformatics Laboratory, School of Agriculture, Meiji University, Higashi-mita, Tama-ku, Kawasaki, Kanagawa, Japan
| | - Koji Yokoyama
- Bioinformatics Laboratory, School of Agriculture, Meiji University, Higashi-mita, Tama-ku, Kawasaki, Kanagawa, Japan
| | - Kentaro Yano
- Bioinformatics Laboratory, School of Agriculture, Meiji University, Higashi-mita, Tama-ku, Kawasaki, Kanagawa, Japan
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Kudo T, Sasaki Y, Terashima S, Matsuda-Imai N, Takano T, Saito M, Kanno M, Ozaki S, Suwabe K, Suzuki G, Watanabe M, Matsuoka M, Takayama S, Yano K. Identification of reference genes for quantitative expression analysis using large-scale RNA-seq data of Arabidopsis thaliana and model crop plants. Genes Genet Syst 2016; 91:111-125. [PMID: 27040147 DOI: 10.1266/ggs.15-00065] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
In quantitative gene expression analysis, normalization using a reference gene as an internal control is frequently performed for appropriate interpretation of the results. Efforts have been devoted to exploring superior novel reference genes using microarray transcriptomic data and to evaluating commonly used reference genes by targeting analysis. However, because the number of specifically detectable genes is totally dependent on probe design in the microarray analysis, exploration using microarray data may miss some of the best choices for the reference genes. Recently emerging RNA sequencing (RNA-seq) provides an ideal resource for comprehensive exploration of reference genes since this method is capable of detecting all expressed genes, in principle including even unknown genes. We report the results of a comprehensive exploration of reference genes using public RNA-seq data from plants such as Arabidopsis thaliana (Arabidopsis), Glycine max (soybean), Solanum lycopersicum (tomato) and Oryza sativa (rice). To select reference genes suitable for the broadest experimental conditions possible, candidates were surveyed by the following four steps: (1) evaluation of the basal expression level of each gene in each experiment; (2) evaluation of the expression stability of each gene in each experiment; (3) evaluation of the expression stability of each gene across the experiments; and (4) selection of top-ranked genes, after ranking according to the number of experiments in which the gene was expressed stably. Employing this procedure, 13, 10, 12 and 21 top candidates for reference genes were proposed in Arabidopsis, soybean, tomato and rice, respectively. Microarray expression data confirmed that the expression of the proposed reference genes under broad experimental conditions was more stable than that of commonly used reference genes. These novel reference genes will be useful for analyzing gene expression profiles across experiments carried out under various experimental conditions.
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Affiliation(s)
- Toru Kudo
- School of Agriculture, Meiji University
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Ingvarsson PK, Hvidsten TR, Street NR. Towards integration of population and comparative genomics in forest trees. THE NEW PHYTOLOGIST 2016; 212:338-44. [PMID: 27575589 DOI: 10.1111/nph.14153] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 06/27/2016] [Indexed: 05/08/2023]
Abstract
Contents 338 I. 338 II. 339 III. 340 IV. 342 343 References 343 SUMMARY: The past decade saw the initiation of an ongoing revolution in sequencing technologies that is transforming all fields of biology. This has been driven by the advent and widespread availability of high-throughput, massively parallel short-read sequencing (MPS) platforms. These technologies have enabled previously unimaginable studies, including draft assemblies of the massive genomes of coniferous species and population-scale resequencing. Transcriptomics studies have likewise been transformed, with RNA-sequencing enabling studies in nonmodel organisms, the discovery of previously unannotated genes (novel transcripts), entirely new classes of RNAs and previously unknown regulatory mechanisms. Here we touch upon current developments in the areas of genome assembly, comparative regulomics and population genetics as they relate to studies of forest tree species.
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Affiliation(s)
- Pär K Ingvarsson
- Umeå Plant Science Centre, Department of Ecology and Environmental Science, Umeå University, 901 87, Umeå, Sweden
| | - Torgeir R Hvidsten
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432, Ås, Norway
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87, Umeå, Sweden
| | - Nathaniel R Street
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87, Umeå, Sweden.
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Proost S, Mutwil M. Tools of the trade: studying molecular networks in plants. CURRENT OPINION IN PLANT BIOLOGY 2016; 30:143-150. [PMID: 26990519 DOI: 10.1016/j.pbi.2016.02.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 02/23/2016] [Accepted: 02/29/2016] [Indexed: 06/05/2023]
Abstract
Driven by recent technological improvements, genes can be now studied in a larger biological context. Genes and their protein products rarely operate as a single entity and large-scale mapping by protein-protein interactions can unveil the molecular complexes that form in the cell to carry out various functions. Expression analysis under multiple conditions, supplemented with protein-DNA binding data can highlight when genes are active and how they are regulated. Representing these data in networks and finding strongly connected sub-graphs has proven to be a powerful tool to predict the function of unknown genes. As such networks are gradually becoming available for various plant species, it becomes possible to study how networks evolve. This review summarizes currently available network data and related tools for plants. Furthermore we aim to provide an outlook of future analyses that can be done in plants based on work done in other fields.
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Affiliation(s)
- Sebastian Proost
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Marek Mutwil
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
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Tzfadia O, Diels T, De Meyer S, Vandepoele K, Aharoni A, Van de Peer Y. CoExpNetViz: Comparative Co-Expression Networks Construction and Visualization Tool. FRONTIERS IN PLANT SCIENCE 2016; 6:1194. [PMID: 26779228 PMCID: PMC4700130 DOI: 10.3389/fpls.2015.01194] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 12/11/2015] [Indexed: 05/23/2023]
Abstract
MOTIVATION Comparative transcriptomics is a common approach in functional gene discovery efforts. It allows for finding conserved co-expression patterns between orthologous genes in closely related plant species, suggesting that these genes potentially share similar function and regulation. Several efficient co-expression-based tools have been commonly used in plant research but most of these pipelines are limited to data from model systems, which greatly limit their utility. Moreover, in addition, none of the existing pipelines allow plant researchers to make use of their own unpublished gene expression data for performing a comparative co-expression analysis and generate multi-species co-expression networks. RESULTS We introduce CoExpNetViz, a computational tool that uses a set of query or "bait" genes as an input (chosen by the user) and a minimum of one pre-processed gene expression dataset. The CoExpNetViz algorithm proceeds in three main steps; (i) for every bait gene submitted, co-expression values are calculated using mutual information and Pearson correlation coefficients, (ii) non-bait (or target) genes are grouped based on cross-species orthology, and (iii) output files are generated and results can be visualized as network graphs in Cytoscape. AVAILABILITY The CoExpNetViz tool is freely available both as a PHP web server (link: http://bioinformatics.psb.ugent.be/webtools/coexpr/) (implemented in C++) and as a Cytoscape plugin (implemented in Java). Both versions of the CoExpNetViz tool support LINUX and Windows platforms.
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Affiliation(s)
- Oren Tzfadia
- Department of Plant Systems Biology, Vlaams Instituut voor BiotechnologieGhent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent UniversityGhent, Belgium
- Bioinformatics Institute Ghent, Ghent UniversityGhent, Belgium
| | - Tim Diels
- Department of Plant Systems Biology, Vlaams Instituut voor BiotechnologieGhent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent UniversityGhent, Belgium
- Bioinformatics Institute Ghent, Ghent UniversityGhent, Belgium
| | - Sam De Meyer
- Department of Plant Systems Biology, Vlaams Instituut voor BiotechnologieGhent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent UniversityGhent, Belgium
| | - Klaas Vandepoele
- Department of Plant Systems Biology, Vlaams Instituut voor BiotechnologieGhent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent UniversityGhent, Belgium
- Bioinformatics Institute Ghent, Ghent UniversityGhent, Belgium
| | - Asaph Aharoni
- Department of Plant Sciences and the Environment, Weizmann Institute of ScienceRehovot, Israel
| | - Yves Van de Peer
- Department of Plant Systems Biology, Vlaams Instituut voor BiotechnologieGhent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent UniversityGhent, Belgium
- Bioinformatics Institute Ghent, Ghent UniversityGhent, Belgium
- Genomics Research Institute, University of PretoriaPretoria, South Africa
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Ohyanagi H, Ebata T, Huang X, Gong H, Fujita M, Mochizuki T, Toyoda A, Fujiyama A, Kaminuma E, Nakamura Y, Feng Q, Wang ZX, Han B, Kurata N. OryzaGenome: Genome Diversity Database of Wild Oryza Species. PLANT & CELL PHYSIOLOGY 2016; 57:e1. [PMID: 26578696 PMCID: PMC4722174 DOI: 10.1093/pcp/pcv171] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 10/26/2015] [Indexed: 05/18/2023]
Abstract
The species in the genus Oryza, encompassing nine genome types and 23 species, are a rich genetic resource and may have applications in deeper genomic analyses aiming to understand the evolution of plant genomes. With the advancement of next-generation sequencing (NGS) technology, a flood of Oryza species reference genomes and genomic variation information has become available in recent years. This genomic information, combined with the comprehensive phenotypic information that we are accumulating in our Oryzabase, can serve as an excellent genotype-phenotype association resource for analyzing rice functional and structural evolution, and the associated diversity of the Oryza genus. Here we integrate our previous and future phenotypic/habitat information and newly determined genotype information into a united repository, named OryzaGenome, providing the variant information with hyperlinks to Oryzabase. The current version of OryzaGenome includes genotype information of 446 O. rufipogon accessions derived by imputation and of 17 accessions derived by imputation-free deep sequencing. Two variant viewers are implemented: SNP Viewer as a conventional genome browser interface and Variant Table as a text-based browser for precise inspection of each variant one by one. Portable VCF (variant call format) file or tab-delimited file download is also available. Following these SNP (single nucleotide polymorphism) data, reference pseudomolecules/scaffolds/contigs and genome-wide variation information for almost all of the closely and distantly related wild Oryza species from the NIG Wild Rice Collection will be available in future releases. All of the resources can be accessed through http://viewer.shigen.info/oryzagenome/.
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Affiliation(s)
- Hajime Ohyanagi
- Plant Genetics Laboratory, National Institute of Genetics, Mishima, Japan Bioinformatics Laboratory, Meiji University, Kawasaki, Japan Tsukuba Division, Mitsubishi Space Software Co., Ltd., Tsukuba, Japan Present address: Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | | | - Xuehui Huang
- National Center for Gene Research, Chinese Academy of Sciences, Shanghai, PR China
| | - Hao Gong
- National Center for Gene Research, Chinese Academy of Sciences, Shanghai, PR China
| | - Masahiro Fujita
- Plant Genetics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Takako Mochizuki
- Genome Informatics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Asao Fujiyama
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Japan Department of Genetics, School of Life Science, Graduate University for Advanced Studies, Mishima, Japan
| | - Eli Kaminuma
- Genome Informatics Laboratory, National Institute of Genetics, Mishima, Japan Department of Genetics, School of Life Science, Graduate University for Advanced Studies, Mishima, Japan
| | - Yasukazu Nakamura
- Genome Informatics Laboratory, National Institute of Genetics, Mishima, Japan Department of Genetics, School of Life Science, Graduate University for Advanced Studies, Mishima, Japan
| | - Qi Feng
- National Center for Gene Research, Chinese Academy of Sciences, Shanghai, PR China
| | - Zi-Xuan Wang
- Plant Genetics Laboratory, National Institute of Genetics, Mishima, Japan National Center for Gene Research, Chinese Academy of Sciences, Shanghai, PR China
| | - Bin Han
- National Center for Gene Research, Chinese Academy of Sciences, Shanghai, PR China
| | - Nori Kurata
- Plant Genetics Laboratory, National Institute of Genetics, Mishima, Japan Department of Genetics, School of Life Science, Graduate University for Advanced Studies, Mishima, Japan
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Aoki Y, Okamura Y, Ohta H, Kinoshita K, Obayashi T. ALCOdb: Gene Coexpression Database for Microalgae. PLANT & CELL PHYSIOLOGY 2016; 57:e3. [PMID: 26644461 PMCID: PMC4722175 DOI: 10.1093/pcp/pcv190] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 11/24/2015] [Indexed: 05/21/2023]
Abstract
In the era of energy and food shortage, microalgae have gained much attention as promising sources of biofuels and food ingredients. However, only a small fraction of microalgal genes have been functionally characterized. Here, we have developed the Algae Gene Coexpression database (ALCOdb; http://alcodb.jp), which provides gene coexpression information to survey gene modules for a function of interest. ALCOdb currently supports two model algae: the green alga Chlamydomonas reinhardtii and the red alga Cyanidioschyzon merolae. Users can retrieve coexpression information for genes of interest through three unique data pages: (i) Coexpressed Gene List; (ii) Gene Information; and (iii) Coexpressed Gene Network. In addition to the basal coexpression information, ALCOdb also provides several advanced functionalities such as an expression profile viewer and a differentially expressed gene search tool. Using these user interfaces, we demonstrated that our gene coexpression data have the potential to detect functionally related genes and are useful in extrapolating the biological roles of uncharacterized genes. ALCOdb will facilitate molecular and biochemical studies of microalgal biological phenomena, such as lipid metabolism and organelle development, and promote the evolutionary understanding of plant cellular systems.
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Affiliation(s)
- Yuichi Aoki
- Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki-Aza-Aoba, Aoba-ku, Sendai, 980-8579 Japan Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Kawaguchi, Saitama, Japan
| | - Yasunobu Okamura
- Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki-Aza-Aoba, Aoba-ku, Sendai, 980-8579 Japan
| | - Hiroyuki Ohta
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Kawaguchi, Saitama, Japan Department of Biological Sciences, Tokyo Institute of Technology, Yokohama, Kanagawa, 226-8501 Japan Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8551 Japan
| | - Kengo Kinoshita
- Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki-Aza-Aoba, Aoba-ku, Sendai, 980-8579 Japan Institute of Development, Aging, and Cancer, Tohoku University, Sendai, 980-8575 Japan Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8573 Japan
| | - Takeshi Obayashi
- Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki-Aza-Aoba, Aoba-ku, Sendai, 980-8579 Japan Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Kawaguchi, Saitama, Japan
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Yamamoto N, Kudo T, Fujiwara S, Takatsuka Y, Hirokawa Y, Tsuzuki M, Takano T, Kobayashi M, Suda K, Asamizu E, Yokoyama K, Shibata D, Tabata S, Yano K. Pleurochrysome: A Web Database of Pleurochrysis Transcripts and Orthologs Among Heterogeneous Algae. PLANT & CELL PHYSIOLOGY 2016; 57:e6. [PMID: 26746174 PMCID: PMC4722176 DOI: 10.1093/pcp/pcv195] [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: 09/01/2015] [Accepted: 11/27/2015] [Indexed: 05/04/2023]
Abstract
Pleurochrysis is a coccolithophorid genus, which belongs to the Coccolithales in the Haptophyta. The genus has been used extensively for biological research, together with Emiliania in the Isochrysidales, to understand distinctive features between the two coccolithophorid-including orders. However, molecular biological research on Pleurochrysis such as elucidation of the molecular mechanism behind coccolith formation has not made great progress at least in part because of lack of comprehensive gene information. To provide such information to the research community, we built an open web database, the Pleurochrysome (http://bioinf.mind.meiji.ac.jp/phapt/), which currently stores 9,023 unique gene sequences (designated as UNIGENEs) assembled from expressed sequence tag sequences of P. haptonemofera as core information. The UNIGENEs were annotated with gene sequences sharing significant homology, conserved domains, Gene Ontology, KEGG Orthology, predicted subcellular localization, open reading frames and orthologous relationship with genes of 10 other algal species, a cyanobacterium and the yeast Saccharomyces cerevisiae. This sequence and annotation information can be easily accessed via several search functions. Besides fundamental functions such as BLAST and keyword searches, this database also offers search functions to explore orthologous genes in the 12 organisms and to seek novel genes. The Pleurochrysome will promote molecular biological and phylogenetic research on coccolithophorids and other haptophytes by helping scientists mine data from the primary transcriptome of P. haptonemofera.
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Affiliation(s)
- Naoki Yamamoto
- Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa, 214-8571 Japan These authors contributed equally to this work. Present address: International Rice Research Institute, DAPO 7777, Metro Manila 1301, Philippines.
| | - Toru Kudo
- Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa, 214-8571 Japan These authors contributed equally to this work.
| | - Shoko Fujiwara
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392 Japan, CREST, Japan These authors contributed equally to this work.
| | - Yukiko Takatsuka
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392 Japan, CREST, Japan
| | - Yasutaka Hirokawa
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392 Japan, CREST, Japan
| | - Mikio Tsuzuki
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392 Japan, CREST, Japan
| | - Tomoyuki Takano
- Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa, 214-8571 Japan
| | - Masaaki Kobayashi
- Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa, 214-8571 Japan
| | - Kunihiro Suda
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818 Japan
| | - Erika Asamizu
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818 Japan
| | - Koji Yokoyama
- Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa, 214-8571 Japan
| | - Daisuke Shibata
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818 Japan
| | - Satoshi Tabata
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818 Japan
| | - Kentaro Yano
- Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa, 214-8571 Japan
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Kobayashi M, Ohyanagi H, Yano K. Databases for Solanaceae and Cucurbitaceae Research. BIOTECHNOLOGY IN AGRICULTURE AND FORESTRY 2016. [DOI: 10.1007/978-3-662-48535-4_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Ohyanagi H, Obayashi T, Yano K. Editorial: Plant and Cell Physiology's 2015 database issue. PLANT & CELL PHYSIOLOGY 2015; 56:4-6. [PMID: 25756138 DOI: 10.1093/pcp/pcu206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
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