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Jenny C, Guignon V, Manyer I Ballester F, Ruas M, Rouard M. Collecting and managing in situ banana genetic resources information (Musa spp.) using online resources and citizen science. Database (Oxford) 2024; 2024:baae036. [PMID: 38776381 PMCID: PMC11110932 DOI: 10.1093/database/baae036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/28/2024] [Accepted: 05/04/2024] [Indexed: 05/25/2024]
Abstract
The Musa Germplasm Information System (MGIS) stands as a pivotal database for managing global banana genetic resources information. In our latest effort, we have expanded MGIS to incorporate in situ observations. We thus incorporated more than 3000 in situ observations from 133 countries primarily sourced from iNaturalist, GBIF, Flickr, Pl@ntNet, Google Street view and expert curation of the literature. This addition provides a more comprehensive and detailed view of banana diversity and its distribution. Additional graphical interfaces, supported by new Drupal modules, were developed, allowing users to compare banana accessions and explore them based on various filters including taxonomy and geographic location. The integrated maps present a unified view, showcasing both in situ observations and the collecting locations of accessions held in germplasm collections. This enhancement not only broadens the scope of MGIS but also promotes a collaborative and open approach in documenting banana diversity, to allow more effective conservation and use of banana germplasm. Furthermore, this work documents a citizen-science approach that could be relevant for other communities. Database URL: https://www.crop-diversity.org/mgis/musa-in-situ.
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Affiliation(s)
- Christophe Jenny
- CIRAD, UMR AGAP Institut, University of Montpellier, F-34398, France
- UMR AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398, France
| | - Valentin Guignon
- UMR AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398, France
- Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier, France
| | - Felip Manyer I Ballester
- CIRAD, UMR AGAP Institut, University of Montpellier, F-34398, France
- UMR AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398, France
| | - Max Ruas
- UMR AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398, France
- Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier, France
| | - Mathieu Rouard
- UMR AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398, France
- Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier, France
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2
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Hu J, Huang B, Yin H, Qi K, Jia Y, Xie Z, Gao Y, Li H, Li Q, Wang Z, Zou Y, Zhang S, Qiao X. PearMODB: a multiomics database for pear (Pyrus) genomics, genetics and breeding study. Database (Oxford) 2023; 2023:baad050. [PMID: 37410918 PMCID: PMC10325485 DOI: 10.1093/database/baad050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 06/06/2023] [Accepted: 06/21/2023] [Indexed: 07/08/2023]
Abstract
Pear (Pyrus ssp.) belongs to Rosaceae and is an important fruit tree widely cultivated around the world. Currently, challenges to cope with the burgeoning sets of multiomics data are rapidly increasing. Here, we constructed the Pear Multiomics Database (PearMODB) by integrating genome, transcriptome, epigenome and population variation data, and aimed to provide a portal for accessing and analyzing pear multiomics data. A variety of online tools were built including gene search, BLAST, JBrowse, expression heatmap, synteny analysis and primer design. The information of DNA methylation sites and single-nucleotide polymorphisms can be retrieved through the custom JBrowse, providing an opportunity to explore the genetic polymorphisms linked to phenotype variation. Moreover, different gene families involving transcription factors, transcription regulators and disease resistance (nucleotide-binding site leucine-rich repeat) were identified and compiled for quick search. In particular, biosynthetic gene clusters (BGCs) were identified in pear genomes, and specialized webpages were set up to show detailed information of BGCs, laying a foundation for studying metabolic diversity among different pear varieties. Overall, PearMODB provides an important platform for pear genomics, genetics and breeding studies. Database URL http://pearomics.njau.edu.cn.
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Affiliation(s)
- Jian Hu
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China
- Jiangsu Engineering Research Center for Pear, Nanjing Agricultural University, Nanjing 210095, China
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Baisha Huang
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China
- Jiangsu Engineering Research Center for Pear, Nanjing Agricultural University, Nanjing 210095, China
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Hao Yin
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China
- Jiangsu Engineering Research Center for Pear, Nanjing Agricultural University, Nanjing 210095, China
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Kaijie Qi
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China
- Jiangsu Engineering Research Center for Pear, Nanjing Agricultural University, Nanjing 210095, China
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuanyuan Jia
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China
| | - Zhihua Xie
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China
- Jiangsu Engineering Research Center for Pear, Nanjing Agricultural University, Nanjing 210095, China
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuan Gao
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Hongxiang Li
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China
- Jiangsu Engineering Research Center for Pear, Nanjing Agricultural University, Nanjing 210095, China
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Qionghou Li
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China
- Jiangsu Engineering Research Center for Pear, Nanjing Agricultural University, Nanjing 210095, China
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zewen Wang
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China
- Jiangsu Engineering Research Center for Pear, Nanjing Agricultural University, Nanjing 210095, China
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ying Zou
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China
- Jiangsu Engineering Research Center for Pear, Nanjing Agricultural University, Nanjing 210095, China
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Shaoling Zhang
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China
- Jiangsu Engineering Research Center for Pear, Nanjing Agricultural University, Nanjing 210095, China
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xin Qiao
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China
- Jiangsu Engineering Research Center for Pear, Nanjing Agricultural University, Nanjing 210095, China
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
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3
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Droc G, Martin G, Guignon V, Summo M, Sempéré G, Durant E, Soriano A, Baurens FC, Cenci A, Breton C, Shah T, Aury JM, Ge XJ, Harrison PH, Yahiaoui N, D’Hont A, Rouard M. The banana genome hub: a community database for genomics in the Musaceae. HORTICULTURE RESEARCH 2022; 9:uhac221. [PMID: 36479579 PMCID: PMC9720444 DOI: 10.1093/hr/uhac221] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 09/22/2022] [Indexed: 06/17/2023]
Abstract
The Banana Genome Hub provides centralized access for genome assemblies, annotations, and the extensive related omics resources available for bananas and banana relatives. A series of tools and unique interfaces are implemented to harness the potential of genomics in bananas, leveraging the power of comparative analysis, while recognizing the differences between datasets. Besides effective genomic tools like BLAST and the JBrowse genome browser, additional interfaces enable advanced gene search and gene family analyses including multiple alignments and phylogenies. A synteny viewer enables the comparison of genome structures between chromosome-scale assemblies. Interfaces for differential expression analyses, metabolic pathways and GO enrichment were also added. A catalogue of variants spanning the banana diversity is made available for exploration, filtering, and export to a wide variety of software. Furthermore, we implemented new ways to graphically explore gene presence-absence in pangenomes as well as genome ancestry mosaics for cultivated bananas. Besides, to guide the community in future sequencing efforts, we provide recommendations for nomenclature of locus tags and a curated list of public genomic resources (assemblies, resequencing, high density genotyping) and upcoming resources-planned, ongoing or not yet public. The Banana Genome Hub aims at supporting the banana scientific community for basic, translational, and applied research and can be accessed at https://banana-genome-hub.southgreen.fr.
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Affiliation(s)
| | - Guillaume Martin
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
| | - Valentin Guignon
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier, France
| | - Marilyne Summo
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
| | - Guilhem Sempéré
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
- CIRAD, UMR INTERTRYP, F-34398 Montpellier, France
- INTERTRYP, Université de Montpellier, CIRAD, IRD, 34398 Montpellier, France
| | - Eloi Durant
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
- Syngenta Seeds SAS, Saint-Sauveur, 31790, France
- DIADE, Univ Montpellier, CIRAD, IRD, Montpellier, 34830, France
| | - Alexandre Soriano
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
| | - Franc-Christophe Baurens
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
| | - Alberto Cenci
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier, France
| | - Catherine Breton
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier, France
| | | | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510520, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510520, China
| | - Pat Heslop Harrison
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510520, China
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Nabila Yahiaoui
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
| | - Angélique D’Hont
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
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4
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Redsun S, Hokin S, Cameron CT, Cleary AM, Berendzen J, Dash S, Brown AV, Wilkey A, Campbell JD, Huang W, Kalberer SR, Weeks NT, Cannon SB, Farmer AD. Doing Genetic and Genomic Biology Using the Legume Information System and Associated Resources. Methods Mol Biol 2022; 2443:81-100. [PMID: 35037201 DOI: 10.1007/978-1-0716-2067-0_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
In this chapter, we introduce the main components of the Legume Information System ( https://legumeinfo.org ) and several associated resources. Additionally, we provide an example of their use by exploring a biological question: is there a common molecular basis, across legume species, that underlies the photoperiod-mediated transition from vegetative to reproductive development, that is, days to flowering? The Legume Information System (LIS) holds genetic and genomic data for a large number of crop and model legumes and provides a set of online bioinformatic tools designed to help biologists address questions and tasks related to legume biology. Such tasks include identifying the molecular basis of agronomic traits; identifying orthologs/syntelogs for known genes; determining gene expression patterns; accessing genomic datasets; identifying markers for breeding work; and identifying genetic similarities and differences among selected accessions. LIS integrates with other legume-focused informatics resources such as SoyBase ( https://soybase.org ), PeanutBase ( https://peanutbase.org ), and projects of the Legume Federation ( https://legumefederation.org ).
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Affiliation(s)
- Sven Redsun
- National Center for Genome Resources, Santa Fe, NM, USA
| | - Sam Hokin
- National Center for Genome Resources, Santa Fe, NM, USA
| | | | - Alan M Cleary
- National Center for Genome Resources, Santa Fe, NM, USA
| | | | - Sudhansu Dash
- National Center for Genome Resources, Santa Fe, NM, USA
| | - Anne V Brown
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA
| | - Andrew Wilkey
- ORISE, Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA
| | - Jacqueline D Campbell
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA
- Department of Computer Science, Iowa State University, Ames, IA, USA
| | - Wei Huang
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA
| | - Scott R Kalberer
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA
| | - Nathan T Weeks
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA
| | - Steven B Cannon
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA.
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5
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Yu J, Jung S, Cheng CH, Lee T, Zheng P, Buble K, Crabb J, Humann J, Hough H, Jones D, Campbell JT, Udall J, Main D. CottonGen: The Community Database for Cotton Genomics, Genetics, and Breeding Research. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10122805. [PMID: 34961276 PMCID: PMC8705096 DOI: 10.3390/plants10122805] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/11/2021] [Accepted: 12/12/2021] [Indexed: 05/12/2023]
Abstract
Over the last eight years, the volume of whole genome, gene expression, SNP genotyping, and phenotype data generated by the cotton research community has exponentially increased. The efficient utilization/re-utilization of these complex and large datasets for knowledge discovery, translation, and application in crop improvement requires them to be curated, integrated with other types of data, and made available for access and analysis through efficient online search tools. Initiated in 2012, CottonGen is an online community database providing access to integrated peer-reviewed cotton genomic, genetic, and breeding data, and analysis tools. Used by cotton researchers worldwide, and managed by experts with crop-specific knowledge, it continuous to be the logical choice to integrate new data and provide necessary interfaces for information retrieval. The repository in CottonGen contains colleague, gene, genome, genotype, germplasm, map, marker, metabolite, phenotype, publication, QTL, species, transcriptome, and trait data curated by the CottonGen team. The number of data entries housed in CottonGen has increased dramatically, for example, since 2014 there has been an 18-fold increase in genes/mRNAs, a 23-fold increase in whole genomes, and a 372-fold increase in genotype data. New tools include a genetic map viewer, a genome browser, a synteny viewer, a metabolite pathways browser, sequence retrieval, BLAST, and a breeding information management system (BIMS), as well as various search pages for new data types. CottonGen serves as the home to the International Cotton Genome Initiative, managing its elections and serving as a communication and coordination hub for the community. With its extensive curation and integration of data and online tools, CottonGen will continue to facilitate utilization of its critical resources to empower research for cotton crop improvement.
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Affiliation(s)
- Jing Yu
- Department of Horticulture, Washington State University, Pullman, WA 99164, USA; (J.Y.); (S.J.); (C.-H.C.); (T.L.); (P.Z.); (K.B.); (J.C.); (J.H.); (H.H.)
| | - Sook Jung
- Department of Horticulture, Washington State University, Pullman, WA 99164, USA; (J.Y.); (S.J.); (C.-H.C.); (T.L.); (P.Z.); (K.B.); (J.C.); (J.H.); (H.H.)
| | - Chun-Huai Cheng
- Department of Horticulture, Washington State University, Pullman, WA 99164, USA; (J.Y.); (S.J.); (C.-H.C.); (T.L.); (P.Z.); (K.B.); (J.C.); (J.H.); (H.H.)
| | - Taein Lee
- Department of Horticulture, Washington State University, Pullman, WA 99164, USA; (J.Y.); (S.J.); (C.-H.C.); (T.L.); (P.Z.); (K.B.); (J.C.); (J.H.); (H.H.)
| | - Ping Zheng
- Department of Horticulture, Washington State University, Pullman, WA 99164, USA; (J.Y.); (S.J.); (C.-H.C.); (T.L.); (P.Z.); (K.B.); (J.C.); (J.H.); (H.H.)
| | - Katheryn Buble
- Department of Horticulture, Washington State University, Pullman, WA 99164, USA; (J.Y.); (S.J.); (C.-H.C.); (T.L.); (P.Z.); (K.B.); (J.C.); (J.H.); (H.H.)
| | - James Crabb
- Department of Horticulture, Washington State University, Pullman, WA 99164, USA; (J.Y.); (S.J.); (C.-H.C.); (T.L.); (P.Z.); (K.B.); (J.C.); (J.H.); (H.H.)
| | - Jodi Humann
- Department of Horticulture, Washington State University, Pullman, WA 99164, USA; (J.Y.); (S.J.); (C.-H.C.); (T.L.); (P.Z.); (K.B.); (J.C.); (J.H.); (H.H.)
| | - Heidi Hough
- Department of Horticulture, Washington State University, Pullman, WA 99164, USA; (J.Y.); (S.J.); (C.-H.C.); (T.L.); (P.Z.); (K.B.); (J.C.); (J.H.); (H.H.)
| | - Don Jones
- Cotton Incorporated, Cary, NC 27513, USA;
| | - J. Todd Campbell
- The Agricultural Research Service of U.S. Department of Agriculture, Florence, SC 29501, USA;
| | - Josh Udall
- The Agricultural Research Service of U.S. Department of Agriculture, College Station, TX 77845, USA;
| | - Dorrie Main
- Department of Horticulture, Washington State University, Pullman, WA 99164, USA; (J.Y.); (S.J.); (C.-H.C.); (T.L.); (P.Z.); (K.B.); (J.C.); (J.H.); (H.H.)
- Correspondence: ; Tel.: +1-509-335-2774
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6
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Anderson TK, Inderski B, Diel DG, Hause BM, Porter EG, Clement T, Nelson EA, Bai J, Christopher-Hennings J, Gauger PC, Zhang J, Harmon KM, Main R, Lager KM, Faaberg KS. The United States Swine Pathogen Database: integrating veterinary diagnostic laboratory sequence data to monitor emerging pathogens of swine. Database (Oxford) 2021; 2021:6462938. [PMID: 35165687 PMCID: PMC8903347 DOI: 10.1093/database/baab078] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 11/04/2021] [Accepted: 11/29/2021] [Indexed: 11/12/2022]
Abstract
Veterinary diagnostic laboratories derive thousands of nucleotide sequences from clinical samples of swine pathogens such as porcine reproductive and respiratory syndrome virus (PRRSV), Senecavirus A and swine enteric coronaviruses. In addition, next generation sequencing has resulted in the rapid production of full-length genomes. Presently, sequence data are released to diagnostic clients but are not publicly available as data may be associated with sensitive information. However, these data can be used for field-relevant vaccines; determining where and when pathogens are spreading; have relevance to research in molecular and comparative virology; and are a component in pandemic preparedness efforts. We have developed a centralized sequence database that integrates private clinical data using PRRSV data as an exemplar, alongside publicly available genomic information. We implemented the Tripal toolkit, a collection of Drupal modules that are used to manage, visualize and disseminate biological data stored within the Chado database schema. New sequences sourced from diagnostic laboratories contain: genomic information; date of collection; collection location; and a unique identifier. Users can download annotated genomic sequences using a customized search interface that incorporates data mined from published literature; search for similar sequences using BLAST-based tools; and explore annotated reference genomes. Additionally, custom annotation pipelines have determined species, the location of open reading frames and nonstructural proteins and the occurrence of putative frame shifts. Eighteen swine pathogens have been curated. The database provides researchers access to sequences discovered by veterinary diagnosticians, allowing for epidemiological and comparative virology studies. The result will be a better understanding on the emergence of novel swine viruses and how these novel strains are disseminated in the USA and abroad. Database URLhttps://swinepathogendb.org.
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Affiliation(s)
- Tavis K Anderson
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, 1920 Dayton Avenue, Ames, IA 50010, USA
| | - Blake Inderski
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, 1920 Dayton Avenue, Ames, IA 50010, USA
| | - Diego G Diel
- Department of Veterinary & Biomedical Sciences, South Dakota State University, 1155 North Campus Drive, Brookings, SD 57007, USA.,South Dakota Animal Disease Research & Diagnostic Laboratory, South Dakota State University, 1155 North Campus Drive, Brookings, SD 57007, USA.,Diego G. Diel, Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Benjamin M Hause
- Department of Veterinary & Biomedical Sciences, South Dakota State University, 1155 North Campus Drive, Brookings, SD 57007, USA.,South Dakota Animal Disease Research & Diagnostic Laboratory, South Dakota State University, 1155 North Campus Drive, Brookings, SD 57007, USA
| | - Elizabeth G Porter
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, 1800 Denison Avenue, Manhattan, KS 66506, USA.,Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, 1800 Denison Avenue, Manhattan, KS 66506, USA
| | - Travis Clement
- Department of Veterinary & Biomedical Sciences, South Dakota State University, 1155 North Campus Drive, Brookings, SD 57007, USA.,South Dakota Animal Disease Research & Diagnostic Laboratory, South Dakota State University, 1155 North Campus Drive, Brookings, SD 57007, USA
| | - Eric A Nelson
- Department of Veterinary & Biomedical Sciences, South Dakota State University, 1155 North Campus Drive, Brookings, SD 57007, USA.,South Dakota Animal Disease Research & Diagnostic Laboratory, South Dakota State University, 1155 North Campus Drive, Brookings, SD 57007, USA
| | - Jianfa Bai
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, 1800 Denison Avenue, Manhattan, KS 66506, USA.,Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, 1800 Denison Avenue, Manhattan, KS 66506, USA
| | - Jane Christopher-Hennings
- Department of Veterinary & Biomedical Sciences, South Dakota State University, 1155 North Campus Drive, Brookings, SD 57007, USA.,South Dakota Animal Disease Research & Diagnostic Laboratory, South Dakota State University, 1155 North Campus Drive, Brookings, SD 57007, USA
| | - Phillip C Gauger
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA.,Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA
| | - Jianqiang Zhang
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA.,Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA
| | - Karen M Harmon
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA.,Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA
| | - Rodger Main
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA.,Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA
| | - Kelly M Lager
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, 1920 Dayton Avenue, Ames, IA 50010, USA
| | - Kay S Faaberg
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, 1920 Dayton Avenue, Ames, IA 50010, USA
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7
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Bellucci E, Mario Aguilar O, Alseekh S, Bett K, Brezeanu C, Cook D, De la Rosa L, Delledonne M, Dostatny DF, Ferreira JJ, Geffroy V, Ghitarrini S, Kroc M, Kumar Agrawal S, Logozzo G, Marino M, Mary‐Huard T, McClean P, Meglič V, Messer T, Muel F, Nanni L, Neumann K, Servalli F, Străjeru S, Varshney RK, Vasconcelos MW, Zaccardelli M, Zavarzin A, Bitocchi E, Frontoni E, Fernie AR, Gioia T, Graner A, Guasch L, Prochnow L, Oppermann M, Susek K, Tenaillon M, Papa R. The INCREASE project: Intelligent Collections of food-legume genetic resources for European agrofood systems. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:646-660. [PMID: 34427014 PMCID: PMC9293105 DOI: 10.1111/tpj.15472] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/11/2021] [Accepted: 08/17/2021] [Indexed: 05/14/2023]
Abstract
Food legumes are crucial for all agriculture-related societal challenges, including climate change mitigation, agrobiodiversity conservation, sustainable agriculture, food security and human health. The transition to plant-based diets, largely based on food legumes, could present major opportunities for adaptation and mitigation, generating significant co-benefits for human health. The characterization, maintenance and exploitation of food-legume genetic resources, to date largely unexploited, form the core development of both sustainable agriculture and a healthy food system. INCREASE will implement, on chickpea (Cicer arietinum), common bean (Phaseolus vulgaris), lentil (Lens culinaris) and lupin (Lupinus albus and L. mutabilis), a new approach to conserve, manage and characterize genetic resources. Intelligent Collections, consisting of nested core collections composed of single-seed descent-purified accessions (i.e., inbred lines), will be developed, exploiting germplasm available both from genebanks and on-farm and subjected to different levels of genotypic and phenotypic characterization. Phenotyping and gene discovery activities will meet, via a participatory approach, the needs of various actors, including breeders, scientists, farmers and agri-food and non-food industries, exploiting also the power of massive metabolomics and transcriptomics and of artificial intelligence and smart tools. Moreover, INCREASE will test, with a citizen science experiment, an innovative system of conservation and use of genetic resources based on a decentralized approach for data management and dynamic conservation. By promoting the use of food legumes, improving their quality, adaptation and yield and boosting the competitiveness of the agriculture and food sector, the INCREASE strategy will have a major impact on economy and society and represents a case study of integrative and participatory approaches towards conservation and exploitation of crop genetic resources.
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Affiliation(s)
- Elisa Bellucci
- Department of Agricultural, Food and Environmental SciencesPolytechnic University of Marchevia Brecce BiancheAncona60131Italy
| | - Orlando Mario Aguilar
- Instituto de Biotecnología y Biología MolecularUNLP‐CONICETCCT La PlataLa PlataArgentina
| | - Saleh Alseekh
- Max‐Planck‐Institute of Molecular Plant PhysiologyAm MüePotsdam‐Golm14476Germany
- Centre of Plant Systems Biology and BiotechnologyPlovdiv4000Bulgaria
| | - Kirstin Bett
- Department of Plant SciencesUniversity of Saskatchewan51 Campus DriveSaskatoonSKS7N 5A8Canada
| | - Creola Brezeanu
- Staţiunea de Cercetare Dezvoltare Pentru LegumiculturăBacău600388Romania
| | - Douglas Cook
- Department of Plant PathologyUniversity of California DavisDavisCA95616‐8680USA
| | - Lucía De la Rosa
- Spanish Plant Genetic Resources National Center (INIA, CRF)National Institute for Agricultural and Food Research and TechnologyAlcalá de HenaresMadrid28800Spain
| | - Massimo Delledonne
- Department of BiotechnologyUniversity of VeronaStrada Le Grazie 15Verona37134Italy
| | - Denise F. Dostatny
- National Centre for Plant Genetic Resources, Plant Breeding and Acclimatization Institute‐NRIRadzikówBłonie05‐870Poland
| | - Juan J. Ferreira
- Regional Service for Agrofood Research and Development (SERIDA)Ctra AS‐267, PK 19VillaviciosaAsturias33300Spain
| | - Valérie Geffroy
- CNRSINRAEInstitute of Plant Sciences Paris‐Saclay (IPS2)Univ EvryUniversité Paris‐SaclayOrsay91405France
- CNRSINRAEInstitute of Plant Sciences Paris Saclay (IPS2)Université de ParisOrsay91405France
| | | | - Magdalena Kroc
- Legume Genomics TeamInstitute of Plant GeneticsPolish Academy of SciencesStrzeszynska 34Poznan60‐479Poland
| | - Shiv Kumar Agrawal
- Genetic Resources SectionInternational Center for Agricultural Research in the Dry AreasICARDAAgdal RabatMorocco
| | - Giuseppina Logozzo
- School of Agricultural, Forestry, Food and Environmental SciencesUniversity of BasilicataPotenza85100Italy
| | - Mario Marino
- International Treaty on Plant Genetic Resources for Food and Agriculture (ITPGRFA)Food and Agriculture Organization of the United Nations (FAO)Viale delle Terme di CaracallaRome00153Italy
| | - Tristan Mary‐Huard
- INRAECNRSAgroParisTechGénétique Quantitative et Evolution ‐ Le MoulonUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - Phil McClean
- Department of Plant Sciences, Genomics and Bioinformatics ProgramNorth Dakota State UniversityFargoND58108USA
| | - Vladimir Meglič
- Crop Science DepartmentAgricultural Institute of SloveniaHacquetova ulica 17Ljubljana1000Slovenia
| | - Tamara Messer
- EURICE ‐ European Research and Project Office GmbHHeinrich‐Hertz‐Allee 1St. Ingbert66386Germany
| | - Frédéric Muel
- Terres InoviaInstitut Technique des oléagineux, des protéagineux eu du chanvren1 Av L. BrétignièresThiverval-Grignon78850France
| | - Laura Nanni
- Department of Agricultural, Food and Environmental SciencesPolytechnic University of Marchevia Brecce BiancheAncona60131Italy
| | - Kerstin Neumann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeeland06466Germany
| | - Filippo Servalli
- Comunità del Mais Spinato di Gandino (MASP)Via XX Settembre, 5GandinoBergamo24024Italy
| | - Silvia Străjeru
- Suceava Genebank (BRGV)Bdul 1 Mai, nr. 17Suceava720224Romania
| | - Rajeev K. Varshney
- Center of Excellence in Genomics and Systems Biology (CEGSB)International Crops Research Institute for the Semi- Arid Tropics (ICRISAT)PatancheruIndia
- State Agricultural Biotechnology CentreCentre for Crop and Food InnovationFood Futures InstituteMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Marta W. Vasconcelos
- CBQF – Centro de Biotecnologia e Química Fina – Laboratório AssociadoEscola Superior de BiotecnologiaUniversidade Católica PortuguesaRua Diogo Botelho 1327Porto4169-005Portugal
| | - Massimo Zaccardelli
- Council for Agricultural Research and EconomicsResearch Centre for Vegetable and Ornamental CropsVia Cavalleggeri 25Pontecagnano‐FaianoSA84098Italy
| | - Aleksei Zavarzin
- Federal Research CenterThe N.I. Vavilov All‐Russian Institute of Plant Genetic ResourcesSt. Petersburg190031Russia
| | - Elena Bitocchi
- Department of Agricultural, Food and Environmental SciencesPolytechnic University of Marchevia Brecce BiancheAncona60131Italy
| | - Emanuele Frontoni
- Department of Information EngineeringPolytechnic University of Marchevia Brecce BiancheAncona60131Italy
| | - Alisdair R. Fernie
- Max‐Planck‐Institute of Molecular Plant PhysiologyAm MüePotsdam‐Golm14476Germany
- Centre of Plant Systems Biology and BiotechnologyPlovdiv4000Bulgaria
| | - Tania Gioia
- School of Agricultural, Forestry, Food and Environmental SciencesUniversity of BasilicataPotenza85100Italy
| | - Andreas Graner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeeland06466Germany
| | - Luis Guasch
- Spanish Plant Genetic Resources National Center (INIA, CRF)National Institute for Agricultural and Food Research and TechnologyAlcalá de HenaresMadrid28800Spain
| | - Lena Prochnow
- EURICE ‐ European Research and Project Office GmbHHeinrich‐Hertz‐Allee 1St. Ingbert66386Germany
| | - Markus Oppermann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeeland06466Germany
| | - Karolina Susek
- Legume Genomics TeamInstitute of Plant GeneticsPolish Academy of SciencesStrzeszynska 34Poznan60‐479Poland
| | - Maud Tenaillon
- INRAECNRSAgroParisTechGénétique Quantitative et Evolution ‐ Le MoulonUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - Roberto Papa
- Department of Agricultural, Food and Environmental SciencesPolytechnic University of Marchevia Brecce BiancheAncona60131Italy
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8
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Staton M, Cannon E, Sanderson LA, Wegrzyn J, Anderson T, Buehler S, Cobo-Simón I, Faaberg K, Grau E, Guignon V, Gunoskey J, Inderski B, Jung S, Lager K, Main D, Poelchau M, Ramnath R, Richter P, West J, Ficklin S. Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases. Brief Bioinform 2021; 22:6318561. [PMID: 34251419 PMCID: PMC8574961 DOI: 10.1093/bib/bbab238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/28/2021] [Accepted: 06/01/2021] [Indexed: 12/01/2022] Open
Abstract
Online, open access databases for biological knowledge serve as central repositories for research communities to store, find and analyze integrated, multi-disciplinary datasets. With increasing volumes, complexity and the need to integrate genomic, transcriptomic, metabolomic, proteomic, phenomic and environmental data, community databases face tremendous challenges in ongoing maintenance, expansion and upgrades. A common infrastructure framework using community standards shared by many databases can reduce development burden, provide interoperability, ensure use of common standards and support long-term sustainability. Tripal is a mature, open source platform built to meet this need. With ongoing improvement since its first release in 2009, Tripal provides full functionality for searching, browsing, loading and curating numerous types of data and is a primary technology powering at least 31 publicly available databases spanning plants, animals and human data, primarily storing genomics, genetics and breeding data. Tripal software development is managed by a shared, inclusive governance structure including both project management and advisory teams. Here, we report on the most important and innovative aspects of Tripal after 11 years development, including integration of diverse types of biological data, successful collaborative projects across member databases, and support for implementing FAIR principles.
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Affiliation(s)
| | - Ethalinda Cannon
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA USA
| | | | | | | | | | | | - Kay Faaberg
- USDA-ARS, National Animal Disease Center, Ames, IA, USA
| | - Emily Grau
- University of Connecticut, Storrs, CT USA
| | | | | | | | - Sook Jung
- Washington State University, Pullman, WA USA
| | - Kelly Lager
- USDA-ARS, National Animal Disease Center, Ames, IA, USA
| | - Dorrie Main
- Washington State University, Pullman, WA USA
| | - Monica Poelchau
- USDA-ARS, National Agricultural Library, Beltsville, MD, USA
| | | | | | - Joe West
- University of Tennessee, Knoxville, TN USA
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9
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Spoor S, Wytko C, Soto B, Chen M, Almsaeed A, Condon B, Herndon N, Hough H, Jung S, Staton M, Wegrzyn J, Main D, Feltus FA, Ficklin SP. Tripal and Galaxy: supporting reproducible scientific workflows for community biological databases. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2021; 2020:5866148. [PMID: 32621602 PMCID: PMC7334887 DOI: 10.1093/database/baaa032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 02/25/2020] [Accepted: 03/31/2020] [Indexed: 12/12/2022]
Abstract
Online biological databases housing genomics, genetic and breeding data can be constructed using the Tripal toolkit. Tripal is an open-source, internationally developed framework that implements FAIR data principles and is meant to ease the burden of constructing such websites for research communities. Use of a common, open framework improves the sustainability and manageability of such as site. Site developers can create extensions for their site and in turn share those extensions with others. One challenge that community databases often face is the need to provide tools for their users that analyze increasingly larger datasets using multiple software tools strung together in a scientific workflow on complicated computational resources. The Tripal Galaxy module, a ‘plug-in’ for Tripal, meets this need through integration of Tripal with the Galaxy Project workflow management system. Site developers can create workflows appropriate to the needs of their community using Galaxy and then share those for execution on their Tripal sites via automatically constructed, but configurable, web forms or using an application programming interface to power web-based analytical applications. The Tripal Galaxy module helps reduce duplication of effort by allowing site developers to spend time constructing workflows and building their applications rather than rebuilding infrastructure for job management of multi-step applications.
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Affiliation(s)
- Shawna Spoor
- Dept of Horticulture, Washington State University, 149 Johnson Hall 646414, Pullman, WA 99164-6414, USA
| | - Connor Wytko
- Dept of Horticulture, Washington State University, 149 Johnson Hall 646414, Pullman, WA 99164-6414, USA
| | - Brian Soto
- Dept of Horticulture, Washington State University, 149 Johnson Hall 646414, Pullman, WA 99164-6414, USA
| | - Ming Chen
- Entomology and Plant Pathology, University of Tennessee, 2505, 370 E J. Chapman Dr Plant Biotechnology Building, Knoxville, TN 37996, USA
| | - Abdullah Almsaeed
- Entomology and Plant Pathology, University of Tennessee, 2505, 370 E J. Chapman Dr Plant Biotechnology Building, Knoxville, TN 37996, USA
| | - Bradford Condon
- Entomology and Plant Pathology, University of Tennessee, 2505, 370 E J. Chapman Dr Plant Biotechnology Building, Knoxville, TN 37996, USA
| | - Nic Herndon
- Dept of Computer Science, East Carolina University, College of Engineering and Technology East 5th Street Greenville, NC 27858-4353, USA
| | - Heidi Hough
- Dept of Horticulture, Washington State University, 149 Johnson Hall 646414, Pullman, WA 99164-6414, USA
| | - Sook Jung
- Dept of Horticulture, Washington State University, 149 Johnson Hall 646414, Pullman, WA 99164-6414, USA
| | - Meg Staton
- Entomology and Plant Pathology, University of Tennessee, 2505, 370 E J. Chapman Dr Plant Biotechnology Building, Knoxville, TN 37996, USA
| | - Jill Wegrzyn
- Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, Unit 3043 Storrs, CT 06269-3043, USA
| | - Dorrie Main
- Dept of Horticulture, Washington State University, 149 Johnson Hall 646414, Pullman, WA 99164-6414, USA
| | - F Alex Feltus
- Dept of Genetics and Biochemistry, Clemson University, 154 Poole Agricultural Center Clemson, SC 29634, USA
| | - Stephen P Ficklin
- Dept of Horticulture, Washington State University, 149 Johnson Hall 646414, Pullman, WA 99164-6414, USA
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Jung S, Cheng CH, Buble K, Lee T, Humann J, Yu J, Crabb J, Hough H, Main D. Tripal MegaSearch: a tool for interactive and customizable query and download of big data. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2021; 2021:6253732. [PMID: 33900378 PMCID: PMC8074878 DOI: 10.1093/database/baab023] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/01/2021] [Accepted: 04/16/2021] [Indexed: 11/14/2022]
Abstract
Tripal MegaSearch is a Tripal module for querying and downloading biological data stored in Chado. This module allows site users to select data types, restrict the dataset by applying various filters and then customizing fields to view and download through a single interface. Set by site administrators, example data types include gene, germplasm, marker, map, QTL, genotype, phenotype and expression data. When querying for genes, users can restrict the gene dataset using various filters such as name, chromosome position and functional annotation. They can then customize fields to download, such as name, organism, type, chromosome position, various functional annotations such as BLAST, KEGG, InterPro and GO term. FASTA files can also be downloaded for the sequence data. Site administrators can choose from two different data sources to serve data: Tripal MegaSearch materialized views or Chado tables. If neither data source is desired, administrators may also create their own materialized views and serve them through the flexible dynamic Tripal MegaSearch query form. Tripal MegaSearch is currently implemented in several databases including the Genome Database for Rosaceae www.rosaceae.org and TreeGenes www.https://treegenesdb.org/.
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Affiliation(s)
- Sook Jung
- Department of Horticulture, Washington State University, 45 Johnson Hall, Pullman, WA 99164, USA
| | - Chun-Huai Cheng
- Department of Horticulture, Washington State University, 45 Johnson Hall, Pullman, WA 99164, USA
| | - Katheryn Buble
- Department of Horticulture, Washington State University, 45 Johnson Hall, Pullman, WA 99164, USA
| | - Taein Lee
- Department of Horticulture, Washington State University, 45 Johnson Hall, Pullman, WA 99164, USA
| | - Jodi Humann
- Department of Horticulture, Washington State University, 45 Johnson Hall, Pullman, WA 99164, USA
| | - Jing Yu
- Department of Horticulture, Washington State University, 45 Johnson Hall, Pullman, WA 99164, USA
| | - James Crabb
- Department of Horticulture, Washington State University, 45 Johnson Hall, Pullman, WA 99164, USA
| | - Heidi Hough
- Department of Horticulture, Washington State University, 45 Johnson Hall, Pullman, WA 99164, USA
| | - Dorrie Main
- Department of Horticulture, Washington State University, 45 Johnson Hall, Pullman, WA 99164, USA
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Gomez-Cano F, Carey L, Lucas K, García Navarrete T, Mukundi E, Lundback S, Schnell D, Grotewold E. CamRegBase: a gene regulation database for the biofuel crop, Camelina sativa. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2020:6031001. [PMID: 33306801 PMCID: PMC7731927 DOI: 10.1093/database/baaa075] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 08/07/2020] [Accepted: 08/11/2020] [Indexed: 12/03/2022]
Abstract
Camelina is an annual oilseed plant from the Brassicaceae family that is gaining momentum as a biofuel winter cover crop. However, a significant limitation in further enhancing its utility as a producer of oils that can be used as biofuels, jet fuels or bio-based products is the absence of a repository for all the gene expression and regulatory information that is being rapidly generated by the community. Here, we provide CamRegBase (https://camregbase.org/) as a one-stop resource to access Camelina information on gene expression and co-expression, transcription factors, lipid associated genes and genome-wide orthologs in the close-relative reference plant Arabidopsis. We envision this as a resource of curated information for users, as well as a repository of new gene regulation information.
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Affiliation(s)
- Fabio Gomez-Cano
- Department of Biochemistry and Molecular Biology, 603 Wilson Road, Room 212, Biochemistry Building, East Lansing, MI 48824-6473, USA
| | - Lisa Carey
- Department of Plant Biology, Michigan State University, 612 Wilson Road, Room 166, East Lansing, MI 48824-1312, USA
| | - Kevin Lucas
- Department of Biochemistry and Molecular Biology, 603 Wilson Road, Room 212, Biochemistry Building, East Lansing, MI 48824-6473, USA
| | - Tatiana García Navarrete
- Department of Biochemistry and Molecular Biology, 603 Wilson Road, Room 212, Biochemistry Building, East Lansing, MI 48824-6473, USA
| | - Eric Mukundi
- Department of Biochemistry and Molecular Biology, 603 Wilson Road, Room 212, Biochemistry Building, East Lansing, MI 48824-6473, USA
| | - Steve Lundback
- Department of Biochemistry and Molecular Biology, 603 Wilson Road, Room 212, Biochemistry Building, East Lansing, MI 48824-6473, USA
| | - Danny Schnell
- Department of Plant Biology, Michigan State University, 612 Wilson Road, Room 166, East Lansing, MI 48824-1312, USA
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, 603 Wilson Road, Room 212, Biochemistry Building, East Lansing, MI 48824-6473, USA
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Yue J, Liu J, Tang W, Wu YQ, Tang X, Li W, Yang Y, Wang L, Huang S, Fang C, Zhao K, Fei Z, Liu Y, Zheng Y. Kiwifruit Genome Database (KGD): a comprehensive resource for kiwifruit genomics. HORTICULTURE RESEARCH 2020; 7:117. [PMID: 32821400 PMCID: PMC7395147 DOI: 10.1038/s41438-020-0338-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 04/12/2020] [Accepted: 05/01/2020] [Indexed: 05/25/2023]
Abstract
Kiwifruit (Actinidia spp.) plants produce economically important fruits containing abundant, balanced phytonutrients with extraordinarily high vitamin C contents. Since the release of the first kiwifruit reference genome sequence in 2013, large volumes of genome and transcriptome data have been rapidly accumulated for a handful of kiwifruit species. To efficiently store, analyze, integrate, and disseminate these large-scale datasets to the research community, we constructed the Kiwifruit Genome Database (KGD; http://kiwifruitgenome.org/). The database currently contains all publicly available genome and gene sequences, gene annotations, biochemical pathways, transcriptome profiles derived from public RNA-Seq datasets, and comparative genomic analysis results such as syntenic blocks and homologous gene pairs between different kiwifruit genome assemblies. A set of user-friendly query interfaces, analysis tools and visualization modules have been implemented in KGD to facilitate translational and applied research in kiwifruit, which include JBrowse, a popular genome browser, and the NCBI BLAST sequence search tool. Other notable tools developed within KGD include a genome synteny viewer and tools for differential gene expression analysis as well as gene ontology (GO) term and pathway enrichment analysis.
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Affiliation(s)
- Junyang Yue
- School of Horticulture, Anhui Agricultural University, Hefei, 230036 China
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009 China
| | - Jiacheng Liu
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853 USA
| | - Wei Tang
- School of Horticulture, Anhui Agricultural University, Hefei, 230036 China
| | - Ya Qing Wu
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853 USA
| | - Xiaofeng Tang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009 China
| | - Wei Li
- School of Horticulture, Anhui Agricultural University, Hefei, 230036 China
| | - Ying Yang
- School of Horticulture, Anhui Agricultural University, Hefei, 230036 China
| | - Lihuan Wang
- School of Horticulture, Anhui Agricultural University, Hefei, 230036 China
| | - Shengxiong Huang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009 China
| | - Congbing Fang
- School of Horticulture, Anhui Agricultural University, Hefei, 230036 China
| | - Kun Zhao
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853 USA
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853 USA
- USDA-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853 USA
| | - Yongsheng Liu
- School of Horticulture, Anhui Agricultural University, Hefei, 230036 China
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009 China
- Ministry of Education Key Laboratory for Bio-resource and Eco-environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610064 China
| | - Yi Zheng
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853 USA
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, 102206 China
- Plant Science and Technology College, Beijing University of Agriculture, Beijing, 102206 China
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13
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Rispe C, Legeai F, Nabity PD, Fernández R, Arora AK, Baa-Puyoulet P, Banfill CR, Bao L, Barberà M, Bouallègue M, Bretaudeau A, Brisson JA, Calevro F, Capy P, Catrice O, Chertemps T, Couture C, Delière L, Douglas AE, Dufault-Thompson K, Escuer P, Feng H, Forneck A, Gabaldón T, Guigó R, Hilliou F, Hinojosa-Alvarez S, Hsiao YM, Hudaverdian S, Jacquin-Joly E, James EB, Johnston S, Joubard B, Le Goff G, Le Trionnaire G, Librado P, Liu S, Lombaert E, Lu HL, Maïbèche M, Makni M, Marcet-Houben M, Martínez-Torres D, Meslin C, Montagné N, Moran NA, Papura D, Parisot N, Rahbé Y, Lopes MR, Ripoll-Cladellas A, Robin S, Roques C, Roux P, Rozas J, Sánchez-Gracia A, Sánchez-Herrero JF, Santesmasses D, Scatoni I, Serre RF, Tang M, Tian W, Umina PA, van Munster M, Vincent-Monégat C, Wemmer J, Wilson ACC, Zhang Y, Zhao C, Zhao J, Zhao S, Zhou X, Delmotte F, Tagu D. The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest. BMC Biol 2020; 18:90. [PMID: 32698880 PMCID: PMC7376646 DOI: 10.1186/s12915-020-00820-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 06/22/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Although native to North America, the invasion of the aphid-like grape phylloxera Daktulosphaira vitifoliae across the globe altered the course of grape cultivation. For the past 150 years, viticulture relied on grafting-resistant North American Vitis species as rootstocks, thereby limiting genetic stocks tolerant to other stressors such as pathogens and climate change. Limited understanding of the insect genetics resulted in successive outbreaks across the globe when rootstocks failed. Here we report the 294-Mb genome of D. vitifoliae as a basic tool to understand host plant manipulation, nutritional endosymbiosis, and enhance global viticulture. RESULTS Using a combination of genome, RNA, and population resequencing, we found grape phylloxera showed high duplication rates since its common ancestor with aphids, but similarity in most metabolic genes, despite lacking obligate nutritional symbioses and feeding from parenchyma. Similarly, no enrichment occurred in development genes in relation to viviparity. However, phylloxera evolved > 2700 unique genes that resemble putative effectors and are active during feeding. Population sequencing revealed the global invasion began from the upper Mississippi River in North America, spread to Europe and from there to the rest of the world. CONCLUSIONS The grape phylloxera genome reveals genetic architecture relative to the evolution of nutritional endosymbiosis, viviparity, and herbivory. The extraordinary expansion in effector genes also suggests novel adaptations to plant feeding and how insects induce complex plant phenotypes, for instance galls. Finally, our understanding of the origin of this invasive species and its genome provide genetics resources to alleviate rootstock bottlenecks restricting the advancement of viticulture.
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Affiliation(s)
| | - Fabrice Legeai
- BIPAA, IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650 Le Rheu, France
| | - Paul D. Nabity
- Department of Botany and Plant Sciences, University of California, Riverside, USA
| | - Rosa Fernández
- Bioinformatics and Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader, 88, 08003 Barcelona, Spain
- Present address: Institute of Evolutionary Biology (CSIC-UPF), Passeig marítim de la Barceloneta 37-49, 08003 Barcelona, Spain
| | - Arinder K. Arora
- Department of Entomology, Cornell University, Ithaca, NY 14853 USA
| | | | | | | | - Miquel Barberà
- Institut de Biologia Integrativa de Sistemes, Parc Cientific Universitat de Valencia, C/ Catedrático José Beltrán n° 2, 46980 Paterna, València Spain
| | - Maryem Bouallègue
- Université de Tunis El Manar, Faculté des Sciences de Tunis, LR01ES05 Biochimie et Biotechnologie, 2092 Tunis, Tunisia
| | - Anthony Bretaudeau
- BIPAA, IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650 Le Rheu, France
| | | | - Federica Calevro
- Univ Lyon, INSA-Lyon, INRAE, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Pierre Capy
- Laboratoire Evolution, Génomes, Comportement, Ecologie CNRS, Univ. Paris-Sud, IRD, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Olivier Catrice
- LIPM, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Thomas Chertemps
- Sorbonne Université, UPEC, Université Paris 7, INRAE, CNRS, IRD, Institute of Ecology and Environmental Sciences, Paris, France
| | - Carole Couture
- SAVE, INRAE, Bordeaux Sciences Agro, Villenave d’Ornon, France
| | - Laurent Delière
- SAVE, INRAE, Bordeaux Sciences Agro, Villenave d’Ornon, France
| | - Angela E. Douglas
- Department of Entomology, Cornell University, Ithaca, NY 14853 USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853 USA
| | - Keith Dufault-Thompson
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, RI USA
| | - Paula Escuer
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Honglin Feng
- Department of Biology, University of Miami, Coral Gables, USA
- Current affiliation: Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, USA
| | | | - Toni Gabaldón
- Bioinformatics and Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader, 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Frédérique Hilliou
- Université Côte d’Azur, INRAE, CNRS, Institut Sophia Agrobiotech, Sophia-Antipolis, France
| | - Silvia Hinojosa-Alvarez
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Yi-min Hsiao
- Institute of Biotechnology and Department of Entomology, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
- Present affiliation: Bone and Joint Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Sylvie Hudaverdian
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650 Le Rheu, France
| | | | - Edward B. James
- Department of Biology, University of Miami, Coral Gables, FL 33146 USA
| | - Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX 77843 USA
| | | | - Gaëlle Le Goff
- Université Côte d’Azur, INRAE, CNRS, Institut Sophia Agrobiotech, Sophia-Antipolis, France
| | - Gaël Le Trionnaire
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650 Le Rheu, France
| | - Pablo Librado
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Shanlin Liu
- China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, 518083 Guangdong Province People’s Republic of China
- BGI-Shenzhen, Shenzhen, 518083 Guangdong Province People’s Republic of China
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, 100193 People’s Republic of China
| | - Eric Lombaert
- Université Côte d’Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Hsiao-ling Lu
- Department of Post-Modern Agriculture, MingDao University, Changhua, Taiwan
| | - Martine Maïbèche
- Sorbonne Université, UPEC, Université Paris 7, INRAE, CNRS, IRD, Institute of Ecology and Environmental Sciences, Paris, France
| | - Mohamed Makni
- Université de Tunis El Manar, Faculté des Sciences de Tunis, LR01ES05 Biochimie et Biotechnologie, 2092 Tunis, Tunisia
| | - Marina Marcet-Houben
- Bioinformatics and Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader, 88, 08003 Barcelona, Spain
| | - David Martínez-Torres
- Institut de Biologia Integrativa de Sistemes, Parc Cientific Universitat de Valencia, C/ Catedrático José Beltrán n° 2, 46980 Paterna, València Spain
| | - Camille Meslin
- INRAE, Institute of Ecology and Environmental Sciences, Versailles, France
| | - Nicolas Montagné
- Sorbonne Université, Institute of Ecology and Environmental Sciences, Paris, France
| | - Nancy A. Moran
- Department of Integrative Biology, University of Texas at Austin, Austin, USA
| | - Daciana Papura
- SAVE, INRAE, Bordeaux Sciences Agro, Villenave d’Ornon, France
| | - Nicolas Parisot
- Univ Lyon, INSA-Lyon, INRAE, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Yvan Rahbé
- Univ Lyon, INRAE, INSA-Lyon, CNRS, UCBL, UMR5240 MAP, F-69622 Villeurbanne, France
| | | | - Aida Ripoll-Cladellas
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Stéphanie Robin
- BIPAA IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650 Le Rheu, France
| | - Céline Roques
- Plateforme Génomique GeT-PlaGe, Centre INRAE de Toulouse Midi-Pyrénées, 24 Chemin de Borde Rouge, Auzeville, CS 52627, 31326 Castanet-Tolosan Cedex, France
| | - Pascale Roux
- SAVE, INRAE, Bordeaux Sciences Agro, Villenave d’Ornon, France
| | - Julio Rozas
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Alejandro Sánchez-Gracia
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Jose F. Sánchez-Herrero
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Didac Santesmasses
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 USA
| | | | - Rémy-Félix Serre
- Plateforme Génomique GeT-PlaGe, Centre INRAE de Toulouse Midi-Pyrénées, 24 Chemin de Borde Rouge, Auzeville, CS 52627, 31326 Castanet-Tolosan Cedex, France
| | - Ming Tang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, 100193 People’s Republic of China
| | - Wenhua Tian
- Department of Botany and Plant Sciences, University of California, Riverside, USA
| | - Paul A. Umina
- School of BioSciences, The University of Melbourne, Parkville, VIC Australia
| | - Manuella van Munster
- BGPI, Université Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | | | - Joshua Wemmer
- Department of Botany and Plant Sciences, University of California, Riverside, USA
| | - Alex C. C. Wilson
- Department of Biology, University of Miami, Coral Gables, FL 33146 USA
| | - Ying Zhang
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, RI USA
| | - Chaoyang Zhao
- Department of Botany and Plant Sciences, University of California, Riverside, USA
| | - Jing Zhao
- China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, 518083 Guangdong Province People’s Republic of China
- BGI-Shenzhen, Shenzhen, 518083 Guangdong Province People’s Republic of China
| | - Serena Zhao
- Department of Integrative Biology, University of Texas at Austin, Austin, USA
| | - Xin Zhou
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, 100193 People’s Republic of China
| | | | - Denis Tagu
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650 Le Rheu, France
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14
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Zheng Y, Wu S, Bai Y, Sun H, Jiao C, Guo S, Zhao K, Blanca J, Zhang Z, Huang S, Xu Y, Weng Y, Mazourek M, K Reddy U, Ando K, McCreight JD, Schaffer AA, Burger J, Tadmor Y, Katzir N, Tang X, Liu Y, Giovannoni JJ, Ling KS, Wechter WP, Levi A, Garcia-Mas J, Grumet R, Fei Z. Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops. Nucleic Acids Res 2020; 47:D1128-D1136. [PMID: 30321383 PMCID: PMC6324010 DOI: 10.1093/nar/gky944] [Citation(s) in RCA: 111] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 10/04/2018] [Indexed: 11/17/2022] Open
Abstract
The Cucurbitaceae family (cucurbit) includes several economically important crops, such as melon, cucumber, watermelon, pumpkin, squash and gourds. During the past several years, genomic and genetic data have been rapidly accumulated for cucurbits. To store, mine, analyze, integrate and disseminate these large-scale datasets and to provide a central portal for the cucurbit research and breeding community, we have developed the Cucurbit Genomics Database (CuGenDB; http://cucurbitgenomics.org) using the Tripal toolkit. The database currently contains all available genome and expressed sequence tag (EST) sequences, genetic maps, and transcriptome profiles for cucurbit species, as well as sequence annotations, biochemical pathways and comparative genomic analysis results such as synteny blocks and homologous gene pairs between different cucurbit species. A set of analysis and visualization tools and user-friendly query interfaces have been implemented in the database to facilitate the usage of these large-scale data by the community. In particular, two new tools have been developed in the database, a ‘SyntenyViewer’ to view genome synteny between different cucurbit species and an ‘RNA-Seq’ module to analyze and visualize gene expression profiles. Both tools have been packed as Tripal extension modules that can be adopted in other genomics databases developed using the Tripal system.
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Affiliation(s)
- Yi Zheng
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Shan Wu
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Yang Bai
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Honghe Sun
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA.,National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Chen Jiao
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Shaogui Guo
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA.,National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Kun Zhao
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Jose Blanca
- Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV-UPV), Universitat Politècnica de València, Valencia 46022, Spain
| | - Zhonghua Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Sanwen Huang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.,Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, China
| | - Yong Xu
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Yiqun Weng
- U.S. Department of Agriculture-Agricultural Research Service, Vegetable Crops Research Unit, Madison, WI 53706, USA.,Department of Horticulture, University of Wisconsin, Madison, WI 53706, USA
| | - Michael Mazourek
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Umesh K Reddy
- Department of Biology, West Virginia State University, Institute, WV 25112, USA
| | - Kaori Ando
- U.S. Department of Agriculture-Agricultural Research Service, Crop Improvement and Protection Research Unit, Salinas, CA 93905, USA
| | - James D McCreight
- U.S. Department of Agriculture-Agricultural Research Service, Crop Improvement and Protection Research Unit, Salinas, CA 93905, USA
| | - Arthur A Schaffer
- Plant Science Institute, Agricultural Research Organization, The Volcani Center, P.O.B. 6, Bet-Dagan 50250, Israel
| | - Joseph Burger
- Plant Science Institute, Agricultural Research Organization, Newe Yaar Research Center, Ramat Yishai 30095, Israel
| | - Yaakov Tadmor
- Plant Science Institute, Agricultural Research Organization, Newe Yaar Research Center, Ramat Yishai 30095, Israel
| | - Nurit Katzir
- Plant Science Institute, Agricultural Research Organization, Newe Yaar Research Center, Ramat Yishai 30095, Israel
| | - Xuemei Tang
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Yang Liu
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA.,Horticulture Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - James J Giovannoni
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA.,U.S. Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
| | - Kai-Shu Ling
- U.S. Department of Agriculture-Agricultural Research Service, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC 29414, USA
| | - W Patrick Wechter
- U.S. Department of Agriculture-Agricultural Research Service, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC 29414, USA
| | - Amnon Levi
- U.S. Department of Agriculture-Agricultural Research Service, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC 29414, USA
| | - Jordi Garcia-Mas
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Barcelona 08193, Spain.,Institut de Recerca i Tecnologia Agroalimentàries, Barcelona 08193, Spain
| | - Rebecca Grumet
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA.,U.S. Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
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15
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Collins K, Zhao K, Jiao C, Xu C, Cai X, Wang X, Ge C, Dai S, Wang Q, Wang Q, Fei Z, Zheng Y. SpinachBase: a central portal for spinach genomics. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2019:5519838. [PMID: 31211398 PMCID: PMC6580994 DOI: 10.1093/database/baz072] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 04/30/2019] [Accepted: 05/07/2019] [Indexed: 12/13/2022]
Abstract
Spinach (Spinacia oleracea L.) is a nutritious vegetable enriched with many essential minerals and vitamins. A reference spinach genome has been recently released, and additional spinach genomic resources are being rapidly developed. Therefore, there is an urgent need of a central database to store, query, analyze and integrate various resources of spinach genomic data. To this end, we developed SpinachBase (http://spinachbase.org), which provides centralized public accesses to genomic data as well as analytical tools to assist research and breeding in spinach. The database currently stores the spinach reference genome sequence, and sequences and comprehensive functional annotations of protein-coding genes predicted from the genome. The database also contains gene expression profiles derived from RNA-Seq experiments as well as highly co-expressed genes and genetic variants called from transcriptome sequences of 120 cultivated and wild Spinacia accessions. Biochemical pathways have been predicted from spinach protein-coding genes and are available through a pathway database (SpinachCyc) within SpinachBase. SpinachBase provides a suite of analysis and visualization tools including a genome browser, sequence similarity searches with BLAST, functional enrichment and functional classification analyses and functions to query and retrieve gene sequences and annotations.
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Affiliation(s)
- Keeley Collins
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA
| | - Kun Zhao
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA
| | - Chen Jiao
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA
| | - Chenxi Xu
- Development and Collaborative Innovation Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Xiaofeng Cai
- Development and Collaborative Innovation Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Xiaoli Wang
- Development and Collaborative Innovation Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Chenhui Ge
- Development and Collaborative Innovation Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Shaojun Dai
- Development and Collaborative Innovation Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Quanxi Wang
- Development and Collaborative Innovation Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Quanhua Wang
- Development and Collaborative Innovation Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA.,Development and Collaborative Innovation Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China.,USDA-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
| | - Yi Zheng
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA
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16
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Spoor S, Cheng CH, Sanderson LA, Condon B, Almsaeed A, Chen M, Bretaudeau A, Rasche H, Jung S, Main D, Bett K, Staton M, Wegrzyn JL, Feltus FA, Ficklin SP. Tripal v3: an ontology-based toolkit for construction of FAIR biological community databases. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2019:5532788. [PMID: 31328773 PMCID: PMC6643302 DOI: 10.1093/database/baz077] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 05/12/2019] [Accepted: 05/22/2019] [Indexed: 12/20/2022]
Abstract
Community biological databases provide an important online resource for both public and private data, analysis tools and community engagement. These sites house genomic, transcriptomic, genetic, breeding and ancillary data for specific species, families or clades. Due to the complexity and increasing quantities of these data, construction of online resources is increasingly difficult especially with limited funding and access to technical expertise. Furthermore, online repositories are expected to promote FAIR data principles (findable, accessible, interoperable and reusable) that presents additional challenges. The open-source Tripal database toolkit seeks to mitigate these challenges by creating both the software and an interactive community of developers for construction of online community databases. Additionally, through coordinated, distributed co-development, Tripal sites encourage community-wide sustainability. Here, we report the release of Tripal version 3 that improves data accessibility and data sharing through systematic use of controlled vocabularies (CVs). Tripal uses the community-developed Chado database as a default data store, but now provides tools to support other data stores, while ensuring that CVs remain the central organizational structure for the data. A new site developer can use Tripal to develop a basic site with little to no programming, with the ability to integrate other data types using extension modules and the Tripal application programming interface. A thorough online User’s Guide and Developer’s Handbook are available at http://tripal.info, providing download, installation and step-by-step setup instructions.
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Affiliation(s)
- Shawna Spoor
- Department of Horticulture, Washington State University, Pullman, WA, USA
| | - Chun-Huai Cheng
- Department of Horticulture, Washington State University, Pullman, WA, USA
| | | | - Bradford Condon
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA
| | - Abdullah Almsaeed
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA
| | - Ming Chen
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA
| | - Anthony Bretaudeau
- INRA, UMR IGEPP, BIPAA/GenOuest, INRIA/Irisa - Campus de Beaulieu, Rennes Cedex, France
| | - Helena Rasche
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg im Breisgau, Germany
| | - Sook Jung
- Department of Horticulture, Washington State University, Pullman, WA, USA
| | - Dorrie Main
- Department of Horticulture, Washington State University, Pullman, WA, USA
| | - Kirstin Bett
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Margaret Staton
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA.,Computational Biology Core, Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
| | - F Alex Feltus
- Dept. of Genetics and Biochemistry, Clemson University, Clemson, USA
| | - Stephen P Ficklin
- Department of Horticulture, Washington State University, Pullman, WA, USA
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17
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Wegrzyn JL, Falk T, Grau E, Buehler S, Ramnath R, Herndon N. Cyberinfrastructure and resources to enable an integrative approach to studying forest trees. Evol Appl 2020; 13:228-241. [PMID: 31892954 PMCID: PMC6935593 DOI: 10.1111/eva.12860] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 08/11/2019] [Accepted: 08/14/2019] [Indexed: 12/19/2022] Open
Abstract
Sequencing technologies and bioinformatic approaches are now available to resolve the challenges associated with complex and heterozygous genomes. Increased access to less expensive and more effective instrumentation will contribute to a wealth of high-quality plant genomes in the next few years. In the meantime, more than 370 tree species are associated with public projects in primary repositories that are interrogating expression profiles, identifying variants, or analyzing targeted capture without a high-quality reference genome. Genomic data from these projects generates sequences that represent intermediate assemblies for transcriptomes and genomes. These data contribute to forest tree biology, but the associated sequence remains trapped in supplemental files that are poorly integrated in plant community databases and comparative genomic platforms. Successful implementation of life science cyberinfrastructure is improving data standards, ontologies, analytic workflows, and integrated database platforms for both model and non-model plant species. Unique to forest trees with large populations that are long-lived, outcrossing, and genetically diverse, the phenotypic and environmental metrics associated with georeferenced populations are just as important as the genomic data sampled for each individual. To address questions related to forest health and productivity, cyberinfrastructure must keep pace with the magnitude of genomic and phenomic sampling of larger populations. This review examines the current landscape of cyberinfrastructure, with an emphasis on best practices and resources to align community data with the Findable, Accessible, Interoperable, and Reusable (FAIR) guidelines.
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Affiliation(s)
- Jill L. Wegrzyn
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticut
| | - Taylor Falk
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticut
| | - Emily Grau
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticut
| | - Sean Buehler
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticut
| | - Risharde Ramnath
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticut
| | - Nic Herndon
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticut
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18
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Lu K, Li T, He J, Chang W, Zhang R, Liu M, Yu M, Fan Y, Ma J, Sun W, Qu C, Liu L, Li N, Liang Y, Wang R, Qian W, Tang Z, Xu X, Lei B, Zhang K, Li J. qPrimerDB: a thermodynamics-based gene-specific qPCR primer database for 147 organisms. Nucleic Acids Res 2019; 46:D1229-D1236. [PMID: 28977518 PMCID: PMC5753361 DOI: 10.1093/nar/gkx725] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 08/08/2017] [Indexed: 01/09/2023] Open
Abstract
Real-time quantitative polymerase chain reaction (qPCR) is one of the most important methods for analyzing the expression patterns of target genes. However, successful qPCR experiments rely heavily on the use of high-quality primers. Various qPCR primer databases have been developed to address this issue, but these databases target only a few important organisms. Here, we developed the qPrimerDB database, founded on an automatic gene-specific qPCR primer design and thermodynamics-based validation workflow. The qPrimerDB database is the most comprehensive qPCR primer database available to date, with a web front-end providing gene-specific and pre-computed primer pairs across 147 important organisms, including human, mouse, zebrafish, yeast, thale cress, rice and maize. In this database, we provide 3331426 of the best primer pairs for each gene, based on primer pair coverage, as well as 47760359 alternative gene-specific primer pairs, which can be conveniently batch downloaded. The specificity and efficiency was validated for qPCR primer pairs for 66 randomly selected genes, in six different organisms, through qPCR assays and gel electrophoresis. The qPrimerDB database represents a valuable, timesaving resource for gene expression analysis. This resource, which will be routinely updated, is publically accessible at http://biodb.swu.edu.cn/qprimerdb.
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Affiliation(s)
- Kun Lu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China.,Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Tian Li
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China
| | - Jian He
- Shennong Class, Southwest University, Beibei, Chongqing 400715, China.,College of Resources and Environment, Southwest University, Chongqing 400715, China
| | - Wei Chang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China.,Shennong Class, Southwest University, Beibei, Chongqing 400715, China
| | - Rui Zhang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China
| | - Miao Liu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China
| | - Mengna Yu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China
| | - Yonghai Fan
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China
| | - Jinqi Ma
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China.,Shennong Class, Southwest University, Beibei, Chongqing 400715, China
| | - Wei Sun
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China
| | - Cunmin Qu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China.,Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Liezhao Liu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China.,Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Nannan Li
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China.,College of Resources and Environment, Southwest University, Chongqing 400715, China
| | - Ying Liang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China.,Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Rui Wang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China.,Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Wei Qian
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China
| | - Zhanglin Tang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China
| | - Xinfu Xu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China.,Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Bo Lei
- Key Laboratory of Molecular Genetics, China National Tobacco Corporation, Guizhou Academy of Tobacco Science, Guiyang 550081, China.,Upland Flue-Cured Tobacco Quality and Ecology Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang 550081, China
| | - Kai Zhang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China.,Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
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19
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Sanderson LA, Caron CT, Tan R, Shen Y, Liu R, Bett KE. KnowPulse: A Web-Resource Focused on Diversity Data for Pulse Crop Improvement. FRONTIERS IN PLANT SCIENCE 2019; 10:965. [PMID: 31428111 PMCID: PMC6690010 DOI: 10.3389/fpls.2019.00965] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 07/10/2019] [Indexed: 05/25/2023]
Abstract
KnowPulse (https://knowpulse.usask.ca) is a breeder-focused web portal for pulse breeders and geneticists. With a focus on diversity data, KnowPulse provides information on genetic markers, sequence variants, phenotypic traits and germplasm for chickpea, common bean, field pea, faba bean, and lentil. Genotypic data is accessible through the genotype matrix tool, displayed as a marker-by-germplasm table of genotype calls specific to germplasm chosen by the researcher. It is also summarized on genetic marker and sequence variant pages. Phenotypic data is visualized in trait distribution plots: violin plots for quantitative data and histograms for qualitative data. These plots are accessible through trait, germplasm, and experiment pages, as well as through a single page search tool. KnowPulse is built using the open-source Tripal toolkit and utilizes open-source tools including, but not limited to, species-specific JBrowse instances, a BLAST interface, and whole-genome CViTjs visualizations. KnowPulse is constantly evolving with data and tools added as they become available. Full integration of genetic maps and quantitative trait loci is imminent, and development of tools exploring structural variation is being explored.
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Affiliation(s)
| | | | | | | | | | - Kirstin E. Bett
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
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20
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Wegrzyn JL, Staton MA, Street NR, Main D, Grau E, Herndon N, Buehler S, Falk T, Zaman S, Ramnath R, Richter P, Sun L, Condon B, Almsaeed A, Chen M, Mannapperuma C, Jung S, Ficklin S. Cyberinfrastructure to Improve Forest Health and Productivity: The Role of Tree Databases in Connecting Genomes, Phenomes, and the Environment. FRONTIERS IN PLANT SCIENCE 2019; 10:813. [PMID: 31293610 PMCID: PMC6603172 DOI: 10.3389/fpls.2019.00813] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 06/05/2019] [Indexed: 05/11/2023]
Abstract
Despite tremendous advancements in high throughput sequencing, the vast majority of tree genomes, and in particular, forest trees, remain elusive. Although primary databases store genetic resources for just over 2,000 forest tree species, these are largely focused on sequence storage, basic genome assemblies, and functional assignment through existing pipelines. The tree databases reviewed here serve as secondary repositories for community data. They vary in their focal species, the data they curate, and the analytics provided, but they are united in moving toward a goal of centralizing both data access and analysis. They provide frameworks to view and update annotations for complex genomes, interrogate systems level expression profiles, curate data for comparative genomics, and perform real-time analysis with genotype and phenotype data. The organism databases of today are no longer simply catalogs or containers of genetic information. These repositories represent integrated cyberinfrastructure that support cross-site queries and analysis in web-based environments. These resources are striving to integrate across diverse experimental designs, sequence types, and related measures through ontologies, community standards, and web services. Efficient, simple, and robust platforms that enhance the data generated by the research community, contribute to improving forest health and productivity.
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Affiliation(s)
- Jill L. Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, United States
| | - Margaret A. Staton
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Nathaniel R. Street
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Dorrie Main
- Department of Horticulture, Washington State University, Pullman, WA, United States
| | - Emily Grau
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, United States
| | - Nic Herndon
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, United States
| | - Sean Buehler
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, United States
| | - Taylor Falk
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, United States
| | - Sumaira Zaman
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, United States
| | - Risharde Ramnath
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, United States
| | - Peter Richter
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, United States
| | - Lang Sun
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, United States
| | - Bradford Condon
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Abdullah Almsaeed
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Ming Chen
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Chanaka Mannapperuma
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Sook Jung
- Department of Horticulture, Washington State University, Pullman, WA, United States
| | - Stephen Ficklin
- Department of Horticulture, Washington State University, Pullman, WA, United States
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21
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Peace CP, Bianco L, Troggio M, van de Weg E, Howard NP, Cornille A, Durel CE, Myles S, Migicovsky Z, Schaffer RJ, Costes E, Fazio G, Yamane H, van Nocker S, Gottschalk C, Costa F, Chagné D, Zhang X, Patocchi A, Gardiner SE, Hardner C, Kumar S, Laurens F, Bucher E, Main D, Jung S, Vanderzande S. Apple whole genome sequences: recent advances and new prospects. HORTICULTURE RESEARCH 2019; 6:59. [PMID: 30962944 PMCID: PMC6450873 DOI: 10.1038/s41438-019-0141-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 03/15/2019] [Accepted: 03/15/2019] [Indexed: 05/19/2023]
Abstract
In 2010, a major scientific milestone was achieved for tree fruit crops: publication of the first draft whole genome sequence (WGS) for apple (Malus domestica). This WGS, v1.0, was valuable as the initial reference for sequence information, fine mapping, gene discovery, variant discovery, and tool development. A new, high quality apple WGS, GDDH13 v1.1, was released in 2017 and now serves as the reference genome for apple. Over the past decade, these apple WGSs have had an enormous impact on our understanding of apple biological functioning, trait physiology and inheritance, leading to practical applications for improving this highly valued crop. Causal gene identities for phenotypes of fundamental and practical interest can today be discovered much more rapidly. Genome-wide polymorphisms at high genetic resolution are screened efficiently over hundreds to thousands of individuals with new insights into genetic relationships and pedigrees. High-density genetic maps are constructed efficiently and quantitative trait loci for valuable traits are readily associated with positional candidate genes and/or converted into diagnostic tests for breeders. We understand the species, geographical, and genomic origins of domesticated apple more precisely, as well as its relationship to wild relatives. The WGS has turbo-charged application of these classical research steps to crop improvement and drives innovative methods to achieve more durable, environmentally sound, productive, and consumer-desirable apple production. This review includes examples of basic and practical breakthroughs and challenges in using the apple WGSs. Recommendations for "what's next" focus on necessary upgrades to the genome sequence data pool, as well as for use of the data, to reach new frontiers in genomics-based scientific understanding of apple.
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Affiliation(s)
- Cameron P. Peace
- Department of Horticulture, Washington State University, Pullman, WA 99164 USA
| | - Luca Bianco
- Computational Biology, Fondazione Edmund Mach, San Michele all’Adige, TN 38010 Italy
| | - Michela Troggio
- Department of Genomics and Biology of Fruit Crops, Fondazione Edmund Mach, San Michele all’Adige, TN 38010 Italy
| | - Eric van de Weg
- Plant Breeding, Wageningen University and Research, Wageningen, 6708PB The Netherlands
| | - Nicholas P. Howard
- Department of Horticultural Science, University of Minnesota, St. Paul, MN 55108 USA
- Institut für Biologie und Umweltwissenschaften, Carl von Ossietzky Universität, 26129 Oldenburg, Germany
| | - Amandine Cornille
- GQE – Le Moulon, Institut National de la Recherche Agronomique, University of Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Charles-Eric Durel
- Institut National de la Recherche Agronomique, Institut de Recherche en Horticulture et Semences, UMR 1345, 49071 Beaucouzé, France
| | - Sean Myles
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 5E3 Canada
| | - Zoë Migicovsky
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 5E3 Canada
| | - Robert J. Schaffer
- The New Zealand Institute for Plant and Food Research Ltd, Motueka, 7198 New Zealand
- School of Biological Sciences, University of Auckland, Auckland, 1142 New Zealand
| | - Evelyne Costes
- AGAP, INRA, CIRAD, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Gennaro Fazio
- Plant Genetic Resources Unit, USDA ARS, Geneva, NY 14456 USA
| | - Hisayo Yamane
- Laboratory of Pomology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502 Japan
| | - Steve van Nocker
- Department of Horticulture, Michigan State University, East Lansing, MI 48824 USA
| | - Chris Gottschalk
- Department of Horticulture, Michigan State University, East Lansing, MI 48824 USA
| | - Fabrizio Costa
- Department of Genomics and Biology of Fruit Crops, Fondazione Edmund Mach, San Michele all’Adige, TN 38010 Italy
| | - David Chagné
- The New Zealand Institute for Plant and Food Research Ltd (Plant & Food Research), Palmerston North Research Centre, Palmerston North, 4474 New Zealand
| | - Xinzhong Zhang
- College of Horticulture, China Agricultural University, 100193 Beijing, China
| | | | - Susan E. Gardiner
- The New Zealand Institute for Plant and Food Research Ltd (Plant & Food Research), Palmerston North Research Centre, Palmerston North, 4474 New Zealand
| | - Craig Hardner
- Queensland Alliance of Agriculture and Food Innovation, University of Queensland, St Lucia, 4072 Australia
| | - Satish Kumar
- New Cultivar Innovation, Plant and Food Research, Havelock North, 4130 New Zealand
| | - Francois Laurens
- Institut National de la Recherche Agronomique, Institut de Recherche en Horticulture et Semences, UMR 1345, 49071 Beaucouzé, France
| | - Etienne Bucher
- Institut National de la Recherche Agronomique, Institut de Recherche en Horticulture et Semences, UMR 1345, 49071 Beaucouzé, France
- Agroscope, 1260 Changins, Switzerland
| | - Dorrie Main
- Department of Horticulture, Washington State University, Pullman, WA 99164 USA
| | - Sook Jung
- Department of Horticulture, Washington State University, Pullman, WA 99164 USA
| | - Stijn Vanderzande
- Department of Horticulture, Washington State University, Pullman, WA 99164 USA
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22
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Zheng Y, Wu S, Bai Y, Sun H, Jiao C, Guo S, Zhao K, Blanca J, Zhang Z, Huang S, Xu Y, Weng Y, Mazourek M, K Reddy U, Ando K, McCreight JD, Schaffer AA, Burger J, Tadmor Y, Katzir N, Tang X, Liu Y, Giovannoni JJ, Ling KS, Wechter WP, Levi A, Garcia-Mas J, Grumet R, Fei Z. Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops. Nucleic Acids Res 2019; 47:D1128-D1136. [PMID: 30321383 DOI: 10.1093/nar/gky944s] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 10/04/2018] [Indexed: 05/20/2023] Open
Abstract
The Cucurbitaceae family (cucurbit) includes several economically important crops, such as melon, cucumber, watermelon, pumpkin, squash and gourds. During the past several years, genomic and genetic data have been rapidly accumulated for cucurbits. To store, mine, analyze, integrate and disseminate these large-scale datasets and to provide a central portal for the cucurbit research and breeding community, we have developed the Cucurbit Genomics Database (CuGenDB; http://cucurbitgenomics.org) using the Tripal toolkit. The database currently contains all available genome and expressed sequence tag (EST) sequences, genetic maps, and transcriptome profiles for cucurbit species, as well as sequence annotations, biochemical pathways and comparative genomic analysis results such as synteny blocks and homologous gene pairs between different cucurbit species. A set of analysis and visualization tools and user-friendly query interfaces have been implemented in the database to facilitate the usage of these large-scale data by the community. In particular, two new tools have been developed in the database, a 'SyntenyViewer' to view genome synteny between different cucurbit species and an 'RNA-Seq' module to analyze and visualize gene expression profiles. Both tools have been packed as Tripal extension modules that can be adopted in other genomics databases developed using the Tripal system.
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Affiliation(s)
- Yi Zheng
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Shan Wu
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Yang Bai
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Honghe Sun
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Chen Jiao
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Shaogui Guo
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Kun Zhao
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Jose Blanca
- Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV-UPV), Universitat Politècnica de València, Valencia 46022, Spain
| | - Zhonghua Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Sanwen Huang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, China
| | - Yong Xu
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Yiqun Weng
- U.S. Department of Agriculture-Agricultural Research Service, Vegetable Crops Research Unit, Madison, WI 53706, USA
- Department of Horticulture, University of Wisconsin, Madison, WI 53706, USA
| | - Michael Mazourek
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Umesh K Reddy
- Department of Biology, West Virginia State University, Institute, WV 25112, USA
| | - Kaori Ando
- U.S. Department of Agriculture-Agricultural Research Service, Crop Improvement and Protection Research Unit, Salinas, CA 93905, USA
| | - James D McCreight
- U.S. Department of Agriculture-Agricultural Research Service, Crop Improvement and Protection Research Unit, Salinas, CA 93905, USA
| | - Arthur A Schaffer
- Plant Science Institute, Agricultural Research Organization, The Volcani Center, P.O.B. 6, Bet-Dagan 50250, Israel
| | - Joseph Burger
- Plant Science Institute, Agricultural Research Organization, Newe Yaar Research Center, Ramat Yishai 30095, Israel
| | - Yaakov Tadmor
- Plant Science Institute, Agricultural Research Organization, Newe Yaar Research Center, Ramat Yishai 30095, Israel
| | - Nurit Katzir
- Plant Science Institute, Agricultural Research Organization, Newe Yaar Research Center, Ramat Yishai 30095, Israel
| | - Xuemei Tang
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Yang Liu
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
- Horticulture Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - James J Giovannoni
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
- U.S. Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
| | - Kai-Shu Ling
- U.S. Department of Agriculture-Agricultural Research Service, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC 29414, USA
| | - W Patrick Wechter
- U.S. Department of Agriculture-Agricultural Research Service, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC 29414, USA
| | - Amnon Levi
- U.S. Department of Agriculture-Agricultural Research Service, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC 29414, USA
| | - Jordi Garcia-Mas
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Barcelona 08193, Spain
- Institut de Recerca i Tecnologia Agroalimentàries, Barcelona 08193, Spain
| | - Rebecca Grumet
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
- U.S. Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
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23
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Jung S, Lee T, Cheng CH, Buble K, Zheng P, Yu J, Humann J, Ficklin SP, Gasic K, Scott K, Frank M, Ru S, Hough H, Evans K, Peace C, Olmstead M, DeVetter LW, McFerson J, Coe M, Wegrzyn JL, Staton ME, Abbott AG, Main D. 15 years of GDR: New data and functionality in the Genome Database for Rosaceae. Nucleic Acids Res 2019; 47:D1137-D1145. [PMID: 30357347 PMCID: PMC6324069 DOI: 10.1093/nar/gky1000] [Citation(s) in RCA: 191] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 10/09/2018] [Indexed: 12/13/2022] Open
Abstract
The Genome Database for Rosaceae (GDR, https://www.rosaceae.org) is an integrated web-based community database resource providing access to publicly available genomics, genetics and breeding data and data-mining tools to facilitate basic, translational and applied research in Rosaceae. The volume of data in GDR has increased greatly over the last 5 years. The GDR now houses multiple versions of whole genome assembly and annotation data from 14 species, made available by recent advances in sequencing technology. Annotated and searchable reference transcriptomes, RefTrans, combining peer-reviewed published RNA-Seq as well as EST datasets, are newly available for major crop species. Significantly more quantitative trait loci, genetic maps and markers are available in MapViewer, a new visualization tool that better integrates with other pages in GDR. Pathways can be accessed through the new GDR Cyc Pathways databases, and synteny among the newest genome assemblies from eight species can be viewed through the new synteny browser, SynView. Collated single-nucleotide polymorphism diversity data and phenotypic data from publicly available breeding datasets are integrated with other relevant data. Also, the new Breeding Information Management System allows breeders to upload, manage and analyze their private breeding data within the secure GDR server with an option to release data publicly.
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Affiliation(s)
- Sook Jung
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Taein Lee
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Chun-Huai Cheng
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Katheryn Buble
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Ping Zheng
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Jing Yu
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Jodi Humann
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Stephen P Ficklin
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Ksenija Gasic
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634-0310, USA
| | - Kristin Scott
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Morgan Frank
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Sushan Ru
- Department of Agronomy and Plant Genetics, University of Minnesota, St Paul, MN 55108, USA
| | - Heidi Hough
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Kate Evans
- Department of Horticulture, Washington State University Tree Fruit Research and Extension Center, Wenatchee, WA 98801, USA
| | - Cameron Peace
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Mercy Olmstead
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Lisa W DeVetter
- Department of Horticulture, Washington State University, Northwestern Washington Research and Extension Center, Mount Vernon, WA 98273, USA
| | - James McFerson
- Department of Horticulture, Washington State University Tree Fruit Research and Extension Center, Wenatchee, WA 98801, USA
| | - Michael Coe
- Cedar Lake Research Group, LLC, Portland, OR 97293, USA
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Margaret E Staton
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA
| | - Albert G Abbott
- Forest Health Research and Extension Center, University of Kentucky, Lexington, KY 40546-0091, USA
| | - Dorrie Main
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
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24
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Buble K, Jung S, Humann JL, Yu J, Cheng CH, Lee T, Ficklin SP, Hough H, Condon B, Staton ME, Wegrzyn JL, Main D. Tripal MapViewer: A tool for interactive visualization and comparison of genetic maps. Database (Oxford) 2019; 2019:baz100. [PMID: 31688940 PMCID: PMC6829499 DOI: 10.1093/database/baz100] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 06/09/2019] [Accepted: 07/16/2019] [Indexed: 11/14/2022]
Abstract
Tripal is an open-source, resource-efficient toolkit for construction of genomic, genetic and breeding databases. It facilitates development of biological websites by providing tools to integrate and display biological data using the generic database schema, Chado, together with Drupal, a popular website creation and content management system. Tripal MapViewer is a new interactive tool for visualizing genetic map data. Developed as a Tripal replacement for Comparative Map Viewer (CMap), it enables visualization of entire maps or linkage groups and features such as molecular markers, quantitative trait loci (QTLs) and heritable phenotypic markers. It also provides graphical comparison of maps sharing the same markers as well as dot plot and correspondence matrices. MapViewer integrates directly with the Tripal application programming interface framework, improving data searching capability and providing a more seamless experience for site visitors. The Tripal MapViewer interface can be integrated in any Tripal map page and linked from any Tripal page for markers, QTLs, heritable morphological markers or genes. Configuration of the display is available through a control panel and the administration interface. The administration interface also allows configuration of the custom database query for building materialized views, providing better performance and flexibility in the way data is stored in the Chado database schema. MapViewer is implemented with the D3.js technology and is currently being used at the Genome Database for Rosaceae (https://www.rosaceae.org), CottonGen (https://www.cottongen.org), Citrus Genome Database (https://citrusgenomedb.org), Vaccinium Genome Database (https://www.vaccinium.org) and Cool Season Food Legume Database (https://www.coolseasonfoodlegume.org). It is also currently in development on the Hardwood Genomics Web (https://hardwoodgenomics.org) and TreeGenes (https://treegenesdb.org). Database URL: https://gitlab.com/mainlabwsu/tripal_map.
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Affiliation(s)
- Katheryn Buble
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Sook Jung
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Jodi L Humann
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Jing Yu
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Chun-Huai Cheng
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Taein Lee
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Stephen P Ficklin
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Heidi Hough
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Bradford Condon
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA
| | - Margaret E Staton
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Dorrie Main
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
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25
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Chen M, Henry N, Almsaeed A, Zhou X, Wegrzyn J, Ficklin S, Staton M. New extension software modules to enhance searching and display of transcriptome data in Tripal databases. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2017:4049442. [PMID: 29220446 PMCID: PMC5532966 DOI: 10.1093/database/bax052] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 06/20/2017] [Indexed: 01/16/2023]
Abstract
Tripal is an open source software package for developing biological databases with a focus on genetic and genomic data. It consists of a set of core modules that deliver essential functions for loading and displaying data records and associated attributes including organisms, sequence features and genetic markers. Beyond the core modules, community members are encouraged to contribute extension modules to build on the Tripal core and to customize Tripal for individual community needs. To expand the utility of the Tripal software system, particularly for RNASeq data, we developed two new extension modules. Tripal Elasticsearch enables fast, scalable searching of the entire content of a Tripal site as well as the construction of customized advanced searches of specific data types. We demonstrate the use of this module for searching assembled transcripts by functional annotation. A second module, Tripal Analysis Expression, houses and displays records from gene expression assays such as RNA sequencing. This includes biological source materials (biomaterials), gene expression values and protocols used to generate the data. In the case of an RNASeq experiment, this would reflect the individual organisms and tissues used to produce sequencing libraries, the normalized gene expression values derived from the RNASeq data analysis and a description of the software or code used to generate the expression values. The module will load data from common flat file formats including standard NCBI Biosample XML. Data loading, display options and other configurations can be controlled by authorized users in the Drupal administrative backend. Both modules are open source, include usage documentation, and can be found in the Tripal organization’s GitHub repository. Database URL: Tripal Elasticsearch module:https://github.com/tripal/tripal_elasticsearch Tripal Analysis Expression module:https://github.com/tripal/tripal_analysis_expression
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Affiliation(s)
- Ming Chen
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA.,Department of Genome Science and Technology, University of Tennessee, Knoxville, TN, USA
| | - Nathan Henry
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA
| | - Abdullah Almsaeed
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA
| | - Xiao Zhou
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA
| | - Jill Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Stephen Ficklin
- Department of Horticulture, Washington State University, Pullman, WA, USA
| | - Margaret Staton
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA
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26
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Ruas M, Guignon V, Sempere G, Sardos J, Hueber Y, Duvergey H, Andrieu A, Chase R, Jenny C, Hazekamp T, Irish B, Jelali K, Adeka J, Ayala-Silva T, Chao CP, Daniells J, Dowiya B, Effa Effa B, Gueco L, Herradura L, Ibobondji L, Kempenaers E, Kilangi J, Muhangi S, Ngo Xuan P, Paofa J, Pavis C, Thiemele D, Tossou C, Sandoval J, Sutanto A, Vangu Paka G, Yi G, Van den Houwe I, Roux N, Rouard M. MGIS: managing banana (Musa spp.) genetic resources information and high-throughput genotyping data. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2017:3866796. [PMID: 29220435 PMCID: PMC5502358 DOI: 10.1093/database/bax046] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 05/12/2017] [Indexed: 12/22/2022]
Abstract
Unraveling the genetic diversity held in genebanks on a large scale is underway, due to advances in Next-generation sequence (NGS) based technologies that produce high-density genetic markers for a large number of samples at low cost. Genebank users should be in a position to identify and select germplasm from the global genepool based on a combination of passport, genotypic and phenotypic data. To facilitate this, a new generation of information systems is being designed to efficiently handle data and link it with other external resources such as genome or breeding databases. The Musa Germplasm Information System (MGIS), the database for global ex situ-held banana genetic resources, has been developed to address those needs in a user-friendly way. In developing MGIS, we selected a generic database schema (Chado), the robust content management system Drupal for the user interface, and Tripal, a set of Drupal modules which links the Chado schema to Drupal. MGIS allows germplasm collection examination, accession browsing, advanced search functions, and germplasm orders. Additionally, we developed unique graphical interfaces to compare accessions and to explore them based on their taxonomic information. Accession-based data has been enriched with publications, genotyping studies and associated genotyping datasets reporting on germplasm use. Finally, an interoperability layer has been implemented to facilitate the link with complementary databases like the Banana Genome Hub and the MusaBase breeding database. Database URL:https://www.crop-diversity.org/mgis/
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Affiliation(s)
- Max Ruas
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - V Guignon
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France.,South Green Bioinformatics Platform, Montpellier, France
| | - G Sempere
- South Green Bioinformatics Platform, Montpellier, France.,CIRAD, UMR AGAP 34398 Montpellier Cedex 5, France
| | - J Sardos
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - Y Hueber
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France.,South Green Bioinformatics Platform, Montpellier, France
| | - H Duvergey
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - A Andrieu
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - R Chase
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - C Jenny
- CIRAD, UMR AGAP 34398 Montpellier Cedex 5, France
| | - T Hazekamp
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - B Irish
- USDA-ARS-Tropical Agriculture Research Station, Mayaguez, Puerto Rico
| | - K Jelali
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - J Adeka
- University of Kisangani, Kisangani (UNIKIS), Democratic Republic of Congo
| | - T Ayala-Silva
- USDA-ARS-Tropical Agriculture Research Station, Mayaguez, Puerto Rico
| | - C P Chao
- Taiwan Banana Research Institute (TBRI), Chiuju, Pingtung, Taiwan, Republic of China
| | - J Daniells
- Department of Agriculture, Fisheries and Forestry, Queensland Government (DAFF South Johnstone), Brisbane, Australia
| | - B Dowiya
- Institut National pour l'Etude et la Recherche Agronomiques (INERA), Democratic Republic of Congo
| | - B Effa Effa
- Centre National de la Recherche Scientifique et Technologique (CENAREST), Libreville, Gabon
| | - L Gueco
- Institute of Plant Breeding (IPB), University of the Philippines (UPLB), Los Baños, Philippines
| | - L Herradura
- Bureau of Plant Industry (BPI) - Davao National Crop Research and Development Center, Davao City, Philippines
| | - L Ibobondji
- Centre Africain de Recherche sur Bananes et Plantains (CARBAP), Njombe, Cameroon
| | - E Kempenaers
- Bioversity International, International Musa Germplasm Transit Center (ITC), KULeuven, Leuven, Belgium
| | - J Kilangi
- Agricultural Research Institute (ARI) Maruku, Bukoba, Tanzania
| | - S Muhangi
- National Agricultural Research Organization (NARO), Mbarara, Uganda
| | - P Ngo Xuan
- Fruit and Vegetable Research Institute (FAVRI), Hanoi, Vietnam
| | - J Paofa
- National Agricultural Research Institute (NARI), Laloki Papua, New Guinea
| | - C Pavis
- CRB Plantes Tropicales, CIRAD INRA - Neufchâteau, Guadeloupe, France
| | - D Thiemele
- Centre National de Recherches Agronomiques (CNRA), Abidjan, Cote d'Ivoire
| | - C Tossou
- Institut National de Recherche Agronomique du Bénin (INRAB), Cotonou, Bénin
| | - J Sandoval
- Corporación Bananera Nacional S.A (CORBANA), San José, Costa Rica
| | - A Sutanto
- Indonesian Centre for Horticultural Research and Development (ICHORD), Bogor, Indonesia
| | - G Vangu Paka
- Institut National pour l'Etude et la Recherche Agronomiques (INERA), Democratic Republic of Congo
| | - G Yi
- Institute of Fruit Tree Research (IFTR), Guangdong Academy of Agricultural Sciences (GDAAS), Guangdong, China
| | - I Van den Houwe
- Bioversity International, International Musa Germplasm Transit Center (ITC), KULeuven, Leuven, Belgium
| | - N Roux
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France.,Bioversity International, International Musa Germplasm Transit Center (ITC), KULeuven, Leuven, Belgium
| | - M Rouard
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France.,South Green Bioinformatics Platform, Montpellier, France
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27
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Harper L, Campbell J, Cannon EKS, Jung S, Poelchau M, Walls R, Andorf C, Arnaud E, Berardini TZ, Birkett C, Cannon S, Carson J, Condon B, Cooper L, Dunn N, Elsik CG, Farmer A, Ficklin SP, Grant D, Grau E, Herndon N, Hu ZL, Humann J, Jaiswal P, Jonquet C, Laporte MA, Larmande P, Lazo G, McCarthy F, Menda N, Mungall CJ, Munoz-Torres MC, Naithani S, Nelson R, Nesdill D, Park C, Reecy J, Reiser L, Sanderson LA, Sen TZ, Staton M, Subramaniam S, Tello-Ruiz MK, Unda V, Unni D, Wang L, Ware D, Wegrzyn J, Williams J, Woodhouse M, Yu J, Main D. AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. Database (Oxford) 2018; 2018:5096675. [PMID: 30239679 PMCID: PMC6146126 DOI: 10.1093/database/bay088] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 07/19/2018] [Accepted: 07/30/2018] [Indexed: 01/07/2023]
Abstract
The future of agricultural research depends on data. The sheer volume of agricultural biological data being produced today makes excellent data management essential. Governmental agencies, publishers and science funders require data management plans for publicly funded research. Furthermore, the value of data increases exponentially when they are properly stored, described, integrated and shared, so that they can be easily utilized in future analyses. AgBioData (https://www.agbiodata.org) is a consortium of people working at agricultural biological databases, data archives and knowledgbases who strive to identify common issues in database development, curation and management, with the goal of creating database products that are more Findable, Accessible, Interoperable and Reusable. We strive to promote authentic, detailed, accurate and explicit communication between all parties involved in scientific data. As a step toward this goal, we present the current state of biocuration, ontologies, metadata and persistence, database platforms, programmatic (machine) access to data, communication and sustainability with regard to data curation. Each section describes challenges and opportunities for these topics, along with recommendations and best practices.
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Affiliation(s)
- Lisa Harper
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA
| | | | - Ethalinda K S Cannon
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA
- Computer Science, Iowa State University, Ames, IA, USA
| | - Sook Jung
- Horticulture, Washington State University, Pullman, WA, USA
| | - Monica Poelchau
- National Agricultural Library, USDA Agricultural Research Service, Beltsville, MD, USA
| | | | - Carson Andorf
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA
- Computer Science, Iowa State University, Ames, IA, USA
| | - Elizabeth Arnaud
- Bioversity International, Informatics Unit, Conservation and Availability Programme, Parc Scientifique Agropolis II, Montpellier, France
| | - Tanya Z Berardini
- The Arabidopsis Information Resource, Phoenix Bioinformatics, Fremont, CA, USA
| | | | - Steve Cannon
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA
| | - James Carson
- Texas Advanced Computing Center, The University of Texas at Austin, Austin, TX, USA
| | - Bradford Condon
- Entomology and Plant Pathology, University of Tennessee Knoxville, Knoxville, TN, USA
| | - Laurel Cooper
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Nathan Dunn
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Christine G Elsik
- Division of Animal Sciences and Division of Plant Sciences, University of Missouri, Columbia, MO, USA
| | - Andrew Farmer
- National Center for Genome Resources, Santa Fe, NM, USA
| | | | - David Grant
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA
| | - Emily Grau
- National Center for Genome Resources, Santa Fe, NM, USA
| | - Nic Herndon
- Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Zhi-Liang Hu
- Animal Science, Iowa State University, Ames, USA
| | - Jodi Humann
- Horticulture, Washington State University, Pullman, WA, USA
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Clement Jonquet
- Laboratory of Informatics, Robotics, Microelectronics of Montpellier, University of Montpellier & CNRS, Montpellier, France
| | - Marie-Angélique Laporte
- Bioversity International, Informatics Unit, Conservation and Availability Programme, Parc Scientifique Agropolis II, Montpellier, France
| | | | - Gerard Lazo
- Crop Improvement and Genetics Research Unit, USDA-ARS, Albany, CA, USA
| | - Fiona McCarthy
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, USA
| | | | | | | | - Sushma Naithani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Rex Nelson
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA
| | - Daureen Nesdill
- Marriott Library, University of Utah, Salt Lake City, UT, USA
| | - Carissa Park
- Animal Science, Iowa State University, Ames, USA
| | - James Reecy
- Animal Science, Iowa State University, Ames, USA
| | - Leonore Reiser
- The Arabidopsis Information Resource, Phoenix Bioinformatics, Fremont, CA, USA
| | | | - Taner Z Sen
- Crop Improvement and Genetics Research Unit, USDA-ARS, Albany, CA, USA
| | - Margaret Staton
- Entomology and Plant Pathology, University of Tennessee Knoxville, Knoxville, TN, USA
| | | | | | - Victor Unda
- Horticulture, Washington State University, Pullman, WA, USA
| | - Deepak Unni
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Liya Wang
- Plant Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Doreen Ware
- USDA, Plant, Soil and Nutrition Research, Ithaca, NY, USA
- Plant Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Jill Wegrzyn
- Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Jason Williams
- Cold Spring Harbor Laboratory, DNA Learning Center, Cold Spring Harbor, NY, USA
| | - Margaret Woodhouse
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Jing Yu
- Horticulture, Washington State University, Pullman, WA, USA
| | - Doreen Main
- Horticulture, Washington State University, Pullman, WA, USA
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28
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Condon B, Almsaeed A, Chen M, West J, Staton M. Tripal Developer Toolkit. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2018:5103920. [PMID: 30295719 PMCID: PMC6147213 DOI: 10.1093/database/bay099] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 08/27/2018] [Indexed: 11/28/2022]
Abstract
Tripal community database construction toolkit utilizing the content management system Drupal. Tripal is used to make biological, genetic and genomic data more discoverable, shareable, searchable and standardized. As funding for community-level genomics databases declines, Tripal’s open-source codebase provides a means for sites to be built and maintained with a minimal investment in staff and new development. Tripal is ultimately as strong as the community of sites and developers that use it. We present a set of developer tools that will make building and maintaining Tripal 3 sites easier for new and returning users. These tools break down barriers to entry such as setting up developer and testing environments, acquiring and loading test datasets, working with controlled vocabulary terms and writing new Drupal classes.
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Affiliation(s)
- Bradford Condon
- Department of Entomology and Plant Pathology, University of Tennessee Institute of Agriculture, E.J. Chapman Blvd, 370 Plant Biotechnology Building, Knoxville, TN
| | - Abdullah Almsaeed
- Department of Entomology and Plant Pathology, University of Tennessee Institute of Agriculture, E.J. Chapman Blvd, 370 Plant Biotechnology Building, Knoxville, TN
| | - Ming Chen
- Department of Entomology and Plant Pathology, University of Tennessee Institute of Agriculture, E.J. Chapman Blvd, 370 Plant Biotechnology Building, Knoxville, TN.,Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, M411 Walters Life Science, Knoxville, TN
| | - Joe West
- Department of Entomology and Plant Pathology, University of Tennessee Institute of Agriculture, E.J. Chapman Blvd, 370 Plant Biotechnology Building, Knoxville, TN
| | - Margaret Staton
- Department of Entomology and Plant Pathology, University of Tennessee Institute of Agriculture, E.J. Chapman Blvd, 370 Plant Biotechnology Building, Knoxville, TN
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29
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Falk T, Herndon N, Grau E, Buehler S, Richter P, Zaman S, Baker EM, Ramnath R, Ficklin S, Staton M, Feltus FA, Jung S, Main D, Wegrzyn JL. Growing and cultivating the forest genomics database, TreeGenes. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2018:1-11. [PMID: 30239664 PMCID: PMC6146132 DOI: 10.1093/database/bay084] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 07/20/2018] [Indexed: 11/15/2022]
Abstract
Forest trees are valued sources of pulp, timber and biofuels, and serve a role in carbon sequestration, biodiversity maintenance and watershed stability. Examining the relationships among genetic, phenotypic and environmental factors for these species provides insight on the areas of concern for breeders and researchers alike. The TreeGenes database is a web-based repository that is home to 1790 tree species and over 1500 registered users. The database provides a curated archive for high-throughput genomics, including reference genomes, transcriptomes, genetic maps and variant data. These resources are paired with extensive phenotypic information and environmental layers. TreeGenes recently migrated to Tripal, an integrated and open-source database schema and content management system. This migration enabled developments focused on data exchange, data transfer and improved analytical capacity, as well as providing TreeGenes the opportunity to communicate with the following partner databases: Hardwood Genomics Web, Genome Database for Rosaceae, and the Citrus Genome Database. Recent development in TreeGenes has focused on coordinating information for georeferenced accessions, including metadata acquisition and ontological frameworks, to improve integration across studies combining genetic, phenotypic and environmental data. This focus was paired with the development of tools to enable comparative genomics and data visualization. By combining advanced data importers, relevant metadata standards and integrated analytical frameworks, TreeGenes provides a platform for researchers to store, submit and analyze forest tree data.
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Affiliation(s)
- Taylor Falk
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Nic Herndon
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Emily Grau
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Sean Buehler
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Peter Richter
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Sumaira Zaman
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Eliza M Baker
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Risharde Ramnath
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Stephen Ficklin
- Department of Horticulture, Washington State University, Pullman, WA, USA
| | - Margaret Staton
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA
| | - Frank A Feltus
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA
| | - Sook Jung
- Department of Horticulture, Washington State University, Pullman, WA, USA
| | - Doreen Main
- Department of Horticulture, Washington State University, Pullman, WA, USA
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
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30
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Jung S, Lee T, Cheng CH, Ficklin S, Yu J, Humann J, Main D. Extension modules for storage, visualization and querying of genomic, genetic and breeding data in Tripal databases. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2017; 2017:4718480. [PMID: 31725859 PMCID: PMC5727400 DOI: 10.1093/database/bax092] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 11/11/2017] [Accepted: 11/16/2017] [Indexed: 01/15/2023]
Abstract
Tripal is an open-source database platform primarily used for development of genomic, genetic and breeding databases. We report here on the release of the Chado Loader, Chado Data Display and Chado Search modules to extend the functionality of the core Tripal modules. These new extension modules provide additional tools for (1) data loading, (2) customized visualization and (3) advanced search functions for supported data types such as organism, marker, QTL/Mendelian Trait Loci, germplasm, map, project, phenotype, genotype and their respective metadata. The Chado Loader module provides data collection templates in Excel with defined metadata and data loaders with front end forms. The Chado Data Display module contains tools to visualize each data type and the metadata which can be used as is or customized as desired. The Chado Search module provides search and download functionality for the supported data types. Also included are the tools to visualize map and species summary. The use of materialized views in the Chado Search module enables better performance as well as flexibility of data modeling in Chado, allowing existing Tripal databases with different metadata types to utilize the module. These Tripal Extension modules are implemented in the Genome Database for Rosaceae (rosaceae.org), CottonGen (cottongen.org), Citrus Genome Database (citrusgenomedb.org), Genome Database for Vaccinium (vaccinium.org) and the Cool Season Food Legume Database (coolseasonfoodlegume.org). Database URL: https://www.citrusgenomedb.org/, https://www.coolseasonfoodlegume.org/, https://www.cottongen.org/, https://www.rosaceae.org/, https://www.vaccinium.org/.
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Affiliation(s)
- Sook Jung
- Department of Horticulture, Washington State University, Pullman, WA, 99164, USA
| | - Taein Lee
- Department of Horticulture, Washington State University, Pullman, WA, 99164, USA
| | - Chun-Huai Cheng
- Department of Horticulture, Washington State University, Pullman, WA, 99164, USA
| | - Stephen Ficklin
- Department of Horticulture, Washington State University, Pullman, WA, 99164, USA
| | - Jing Yu
- Department of Horticulture, Washington State University, Pullman, WA, 99164, USA
| | - Jodi Humann
- Department of Horticulture, Washington State University, Pullman, WA, 99164, USA
| | - Dorrie Main
- Department of Horticulture, Washington State University, Pullman, WA, 99164, USA
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31
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Andrews RJ, Baber L, Moss WN. RNAStructuromeDB: A genome-wide database for RNA structural inference. Sci Rep 2017; 7:17269. [PMID: 29222504 PMCID: PMC5722888 DOI: 10.1038/s41598-017-17510-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 11/27/2017] [Indexed: 12/30/2022] Open
Abstract
RNA plays important roles in almost every aspect of biology, and every aspect of RNA biology is influenced by its folding. This is a particularly important consideration in the era of high-throughput sequencing, when the discovery of novel transcripts far outpaces our knowledge of their functions. To gain a comprehensive picture of biology requires a structural framework for making functional inferences on RNA. To this end we have developed the RNA Structurome Database ( https://structurome.bb.iastate.edu ), a comprehensive repository of RNA secondary structural information that spans the entire human genome. Here, we compile folding information for every base pair of the genome that may be transcribed: coding, noncoding, and intergenic regions, as well as repetitive elements, telomeres, etc. This was done by fragmenting the GRCh38 reference genome into 154,414,320 overlapping sequence fragments and, for each fragment, calculating a set of metrics based on the sequence's folding properties. These data will facilitate a wide array of investigations: e.g. discovery of structured regulatory elements in differential gene expression data or noncoding RNA discovery, as well as allow genome-scale analyses of RNA folding.
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Affiliation(s)
- Ryan J Andrews
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, 2437 Pammel Drive, Ames, IA, 50011, USA
| | - Levi Baber
- Biology Information Technology, Iowa State University, 2310 Pammel Drive, Ames, IA, 50011, USA
| | - Walter N Moss
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, 2437 Pammel Drive, Ames, IA, 50011, USA.
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32
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Gonzalez S, Clavijo B, Rivarola M, Moreno P, Fernandez P, Dopazo J, Paniego N. ATGC transcriptomics: a web-based application to integrate, explore and analyze de novo transcriptomic data. BMC Bioinformatics 2017; 18:121. [PMID: 28222698 PMCID: PMC5320735 DOI: 10.1186/s12859-017-1494-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 01/21/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND In the last years, applications based on massively parallelized RNA sequencing (RNA-seq) have become valuable approaches for studying non-model species, e.g., without a fully sequenced genome. RNA-seq is a useful tool for detecting novel transcripts and genetic variations and for evaluating differential gene expression by digital measurements. The large and complex datasets resulting from functional genomic experiments represent a challenge in data processing, management, and analysis. This problem is especially significant for small research groups working with non-model species. RESULTS We developed a web-based application, called ATGC transcriptomics, with a flexible and adaptable interface that allows users to work with new generation sequencing (NGS) transcriptomic analysis results using an ontology-driven database. This new application simplifies data exploration, visualization, and integration for a better comprehension of the results. CONCLUSIONS ATGC transcriptomics provides access to non-expert computer users and small research groups to a scalable storage option and simple data integration, including database administration and management. The software is freely available under the terms of GNU public license at http://atgcinta.sourceforge.net .
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Affiliation(s)
- Sergio Gonzalez
- Instituto de Biotecnología, Centro Investigación en Ciencias Veterinarias y Agronómicas (CICVyA) INTA, Hurlingham, Buenos Aires Argentina
| | | | - Máximo Rivarola
- Instituto de Biotecnología, Centro Investigación en Ciencias Veterinarias y Agronómicas (CICVyA) INTA, Hurlingham, Buenos Aires Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, Buenos Aires, C1425FQB Argentina
| | - Patricio Moreno
- Instituto de Ingeniería Biomédica, Facultad de Ingeniería, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Paula Fernandez
- Instituto de Biotecnología, Centro Investigación en Ciencias Veterinarias y Agronómicas (CICVyA) INTA, Hurlingham, Buenos Aires Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, Buenos Aires, C1425FQB Argentina
- Escuela de Ciencia y Tecnología, Universidad Nacional de San Martín, San Martín, Buenos Aires Argentina
| | - Joaquín Dopazo
- Computational Genomics Department, Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Norma Paniego
- Instituto de Biotecnología, Centro Investigación en Ciencias Veterinarias y Agronómicas (CICVyA) INTA, Hurlingham, Buenos Aires Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, Buenos Aires, C1425FQB Argentina
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Watts NA, Feltus FA. Big Data Smart Socket (BDSS): a system that abstracts data transfer habits from end users. Bioinformatics 2017; 33:627-628. [PMID: 27797780 PMCID: PMC5408802 DOI: 10.1093/bioinformatics/btw679] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 08/30/2016] [Accepted: 10/25/2016] [Indexed: 01/16/2023] Open
Abstract
Motivation The ability to centralize and store data for long periods on an end user's computational resources is increasingly difficult for many scientific disciplines. For example, genomics data is increasingly large and distributed, and the data needs to be moved into workflow execution sites ranging from lab workstations to the cloud. However, the typical user is not always informed on emerging network technology or the most efficient methods to move and share data. Thus, the user defaults to using inefficient methods for transfer across the commercial internet. Results To accelerate large data transfer, we created a tool called the Big Data Smart Socket (BDSS) that abstracts data transfer methodology from the user. The user provides BDSS with a manifest of datasets stored in a remote storage repository. BDSS then queries a metadata repository for curated data transfer mechanisms and optimal path to move each of the files in the manifest to the site of workflow execution. BDSS functions as a standalone tool or can be directly integrated into a computational workflow such as provided by the Galaxy Project. To demonstrate applicability, we use BDSS within a biological context, although it is applicable to any scientific domain. Availability and Implementation BDSS is available under version 2 of the GNU General Public License at https://github.com/feltus/BDSS . Contact ffeltus@clemson.edu.
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Affiliation(s)
| | - Frank A Feltus
- Clemson University Department of Genetics & Biochemistry, Clemson, SC, USA
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Wytko C, Soto B, Ficklin SP. blend4php: a PHP API for galaxy. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2017; 2017:baw154. [PMID: 28077564 PMCID: PMC5225400 DOI: 10.1093/database/baw154] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 10/12/2016] [Accepted: 11/01/2016] [Indexed: 01/17/2023]
Abstract
Galaxy is a popular framework for execution of complex analytical pipelines typically for large data sets, and is a commonly used for (but not limited to) genomic, genetic and related biological analysis. It provides a web front-end and integrates with high performance computing resources. Here we report the development of the blend4php library that wraps Galaxy’s RESTful API into a PHP-based library. PHP-based web applications can use blend4php to automate execution, monitoring and management of a remote Galaxy server, including its users, workflows, jobs and more. The blend4php library was specifically developed for the integration of Galaxy with Tripal, the open-source toolkit for the creation of online genomic and genetic web sites. However, it was designed as an independent library for use by any application, and is freely available under version 3 of the GNU Lesser General Public License (LPGL v3.0) at https://github.com/galaxyproject/blend4php. Database URL:https://github.com/galaxyproject/blend4php
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Affiliation(s)
- Connor Wytko
- Department of Horticulture and.,School of Electrical Engineering and Computer Science, Washington State University, Pullman, WA 99164, USA
| | - Brian Soto
- Department of Horticulture and.,School of Electrical Engineering and Computer Science, Washington State University, Pullman, WA 99164, USA
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Ankenbrand MJ, Weber L, Becker D, Förster F, Bemm F. TBro: visualization and management of de novo transcriptomes. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw146. [PMID: 28025338 PMCID: PMC5199188 DOI: 10.1093/database/baw146] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 10/12/2016] [Accepted: 10/18/2016] [Indexed: 01/24/2023]
Abstract
RNA sequencing (RNA-seq) has become a powerful tool to understand molecular mechanisms and/or developmental programs. It provides a fast, reliable and cost-effective method to access sets of expressed elements in a qualitative and quantitative manner. Especially for non-model organisms and in absence of a reference genome, RNA-seq data is used to reconstruct and quantify transcriptomes at the same time. Even SNPs, InDels, and alternative splicing events are predicted directly from the data without having a reference genome at hand. A key challenge, especially for non-computational personnal, is the management of the resulting datasets, consisting of different data types and formats. Here, we present TBro, a flexible de novo transcriptome browser, tackling this challenge. TBro aggregates sequences, their annotation, expression levels as well as differential testing results. It provides an easy-to-use interface to mine the aggregated data and generate publication-ready visualizations. Additionally, it supports users with an intuitive cart system, that helps collecting and analysing biological meaningful sets of transcripts. TBro’s modular architecture allows easy extension of its functionalities in the future. Especially, the integration of new data types such as proteomic quantifications or array-based gene expression data is straightforward. Thus, TBro is a fully featured yet flexible transcriptome browser that supports approaching complex biological questions and enhances collaboration of numerous researchers. Database URL: tbro.carnivorom.com
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Affiliation(s)
- Markus J Ankenbrand
- Department of Animal Ecology and Tropical Biology, Biocenter, Am Hubland, 97074 Würzburg, Germany
| | - Lorenz Weber
- Department of Bioinformatics, Biocenter, Am Hubland, 97074 Würzburg, Germany.,Center for Computational and Theoretical Biology, University of Würzburg, 97074 Würzburg, Germany
| | - Dirk Becker
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, 97082 Würzburg, Germany
| | - Frank Förster
- Department of Bioinformatics, Biocenter, Am Hubland, 97074 Würzburg, Germany.,Center for Computational and Theoretical Biology, University of Würzburg, 97074 Würzburg, Germany
| | - Felix Bemm
- Department of Bioinformatics, Biocenter, Am Hubland, 97074 Würzburg, Germany .,Department Molecular Biology (Detlef Weigel), Max-Planck-Institute for Developmental Biology, 72076 Tübingen, Germany
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36
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Jung S, Lee T, Ficklin S, Yu J, Cheng CH, Main D. Chado use case: storing genomic, genetic and breeding data of Rosaceae and Gossypium crops in Chado. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw010. [PMID: 26989146 PMCID: PMC4795932 DOI: 10.1093/database/baw010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 01/21/2016] [Indexed: 11/12/2022]
Abstract
The Genome Database for Rosaceae (GDR) and CottonGen are comprehensive online data repositories that provide access to integrated genomic, genetic and breeding data through search, visualization and analysis tools for Rosaceae crops and Gossypium (cotton). These online databases use Chado, an open-source, generic and ontology-driven database schema for biological data, as the primary data storage platform. Chado is highly normalized and uses ontologies to indicate the 'types' of data. Therefore, Chado is flexible such that it has been used to house genomic, genetic and breeding data for GDR and CottonGen. These data include whole genome sequence and annotation, transcripts, molecular markers, genetic maps, Quantitative Trait Loci, Mendelian Trait Loci, traits, germplasm, pedigrees, large scale phenotypic and genotypic data, ontologies and publications. We provide information about how to store these types of data in Chado using GDR and CottonGen as examples sites that were converted from an older legacy infrastructure. Database URL: GDR (www.rosaceae.org), CottonGen (www.cottongen.org).
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Affiliation(s)
- Sook Jung
- Department of Horticulture, Washington State University Pullman, WA, USA
| | - Taein Lee
- Department of Horticulture, Washington State University Pullman, WA, USA
| | - Stephen Ficklin
- Department of Horticulture, Washington State University Pullman, WA, USA
| | - Jing Yu
- Department of Horticulture, Washington State University Pullman, WA, USA
| | - Chun-Huai Cheng
- Department of Horticulture, Washington State University Pullman, WA, USA
| | - Dorrie Main
- Department of Horticulture, Washington State University Pullman, WA, USA
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Dash S, Campbell JD, Cannon EKS, Cleary AM, Huang W, Kalberer SR, Karingula V, Rice AG, Singh J, Umale PE, Weeks NT, Wilkey AP, Farmer AD, Cannon SB. Legume information system (LegumeInfo.org): a key component of a set of federated data resources for the legume family. Nucleic Acids Res 2015; 44:D1181-8. [PMID: 26546515 PMCID: PMC4702835 DOI: 10.1093/nar/gkv1159] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 10/19/2015] [Indexed: 12/02/2022] Open
Abstract
Legume Information System (LIS), at http://legumeinfo.org, is a genomic data portal (GDP) for the legume family. LIS provides access to genetic and genomic information for major crop and model legumes. With more than two-dozen domesticated legume species, there are numerous specialists working on particular species, and also numerous GDPs for these species. LIS has been redesigned in the last three years both to better integrate data sets across the crop and model legumes, and to better accommodate specialized GDPs that serve particular legume species. To integrate data sets, LIS provides genome and map viewers, holds synteny mappings among all sequenced legume species and provides a set of gene families to allow traversal among orthologous and paralogous sequences across the legumes. To better accommodate other specialized GDPs, LIS uses open-source GMOD components where possible, and advocates use of common data templates, formats, schemas and interfaces so that data collected by one legume research community are accessible across all legume GDPs, through similar interfaces and using common APIs. This federated model for the legumes is managed as part of the ‘Legume Federation’ project (accessible via http://legumefederation.org), which can be thought of as an umbrella project encompassing LIS and other legume GDPs.
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Affiliation(s)
- Sudhansu Dash
- National Center for Genome Resources, Santa Fe, NM 87505, USA
| | | | | | - Alan M Cleary
- National Center for Genome Resources, Santa Fe, NM 87505, USA Dept. of Computer Science, Montana State University, Bozeman, MT 59715, USA
| | - Wei Huang
- Dept. of Agronomy, Iowa State University, Ames, IA 50011, USA
| | - Scott R Kalberer
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Crop Genome Informatics Lab, Iowa State University, Ames, IA 50011, USA
| | - Vijay Karingula
- Dept. of Agronomy, Iowa State University, Ames, IA 50011, USA
| | - Alex G Rice
- National Center for Genome Resources, Santa Fe, NM 87505, USA
| | - Jugpreet Singh
- ORISE Fellow, USDA-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, USA
| | - Pooja E Umale
- National Center for Genome Resources, Santa Fe, NM 87505, USA
| | - Nathan T Weeks
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Crop Genome Informatics Lab, Iowa State University, Ames, IA 50011, USA
| | - Andrew P Wilkey
- Dept. of Agronomy, Iowa State University, Ames, IA 50011, USA
| | - Andrew D Farmer
- National Center for Genome Resources, Santa Fe, NM 87505, USA
| | - Steven B Cannon
- Dept. of Agronomy, Iowa State University, Ames, IA 50011, USA USDA-ARS Corn Insects and Crop Genetics Research Unit, Crop Genome Informatics Lab, Iowa State University, Ames, IA 50011, USA
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Krishnakumar V, Kim M, Rosen BD, Karamycheva S, Bidwell SL, Tang H, Town CD. MTGD: The Medicago truncatula genome database. PLANT & CELL PHYSIOLOGY 2015; 56:e1. [PMID: 25432968 DOI: 10.1093/pcp/pcu179] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Medicago truncatula, a close relative of alfalfa (Medicago sativa), is a model legume used for studying symbiotic nitrogen fixation, mycorrhizal interactions and legume genomics. J. Craig Venter Institute (JCVI; formerly TIGR) has been involved in M. truncatula genome sequencing and annotation since 2002 and has maintained a web-based resource providing data to the community for this entire period. The website (http://www.MedicagoGenome.org) has seen major updates in the past year, where it currently hosts the latest version of the genome (Mt4.0), associated data and legacy project information, presented to users via a rich set of open-source tools. A JBrowse-based genome browser interface exposes tracks for visualization. Mutant gene symbols originally assembled and curated by the Frugoli lab are now hosted at JCVI and tie into our community annotation interface, Medicago EuCAP (to be integrated soon with our implementation of WebApollo). Literature pertinent to M. truncatula is indexed and made searchable via the Textpresso search engine. The site also implements MedicMine, an instance of InterMine that offers interconnectivity with other plant 'mines' such as ThaleMine and PhytoMine, and other model organism databases (MODs). In addition to these new features, we continue to provide keyword- and locus identifier-based searches served via a Chado-backed Tripal Instance, a BLAST search interface and bulk downloads of data sets from the iPlant Data Store (iDS). Finally, we maintain an E-mail helpdesk, facilitated by a JIRA issue tracking system, where we receive and respond to questions about the website and requests for specific data sets from the community.
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Affiliation(s)
- Vivek Krishnakumar
- Plant Genomics Group, J. Craig Venter Institute, 9704 Medical Center Dr, Rockville, MD 20850, USA
| | - Maria Kim
- Plant Genomics Group, J. Craig Venter Institute, 9704 Medical Center Dr, Rockville, MD 20850, USA
| | - Benjamin D Rosen
- Plant Genomics Group, J. Craig Venter Institute, 9704 Medical Center Dr, Rockville, MD 20850, USA
| | - Svetlana Karamycheva
- Plant Genomics Group, J. Craig Venter Institute, 9704 Medical Center Dr, Rockville, MD 20850, USA
| | - Shelby L Bidwell
- Plant Genomics Group, J. Craig Venter Institute, 9704 Medical Center Dr, Rockville, MD 20850, USA
| | - Haibao Tang
- Plant Genomics Group, J. Craig Venter Institute, 9704 Medical Center Dr, Rockville, MD 20850, USA
| | - Christopher D Town
- Plant Genomics Group, J. Craig Venter Institute, 9704 Medical Center Dr, Rockville, MD 20850, USA
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Krishnakumar V, Hanlon MR, Contrino S, Ferlanti ES, Karamycheva S, Kim M, Rosen BD, Cheng CY, Moreira W, Mock SA, Stubbs J, Sullivan JM, Krampis K, Miller JR, Micklem G, Vaughn M, Town CD. Araport: the Arabidopsis information portal. Nucleic Acids Res 2014; 43:D1003-9. [PMID: 25414324 PMCID: PMC4383980 DOI: 10.1093/nar/gku1200] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The Arabidopsis Information Portal (https://www.araport.org) is a new online resource for plant biology research. It houses the Arabidopsis thaliana genome sequence and associated annotation. It was conceived as a framework that allows the research community to develop and release ‘modules’ that integrate, analyze and visualize Arabidopsis data that may reside at remote sites. The current implementation provides an indexed database of core genomic information. These data are made available through feature-rich web applications that provide search, data mining, and genome browser functionality, and also by bulk download and web services. Araport uses software from the InterMine and JBrowse projects to expose curated data from TAIR, GO, BAR, EBI, UniProt, PubMed and EPIC CoGe. The site also hosts ‘science apps,’ developed as prototypes for community modules that use dynamic web pages to present data obtained on-demand from third-party servers via RESTful web services. Designed for sustainability, the Arabidopsis Information Portal strategy exploits existing scientific computing infrastructure, adopts a practical mixture of data integration technologies and encourages collaborative enhancement of the resource by its user community.
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Affiliation(s)
| | - Matthew R Hanlon
- Texas Advanced Computing Center, The University of Texas, Austin, TX 78758, USA
| | - Sergio Contrino
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB2 1QR, UK
| | - Erik S Ferlanti
- Plant Genomics, J. Craig Venter Institute, Rockville, MD 20850, USA
| | | | - Maria Kim
- Plant Genomics, J. Craig Venter Institute, Rockville, MD 20850, USA
| | - Benjamin D Rosen
- Plant Genomics, J. Craig Venter Institute, Rockville, MD 20850, USA
| | - Chia-Yi Cheng
- Plant Genomics, J. Craig Venter Institute, Rockville, MD 20850, USA
| | - Walter Moreira
- Texas Advanced Computing Center, The University of Texas, Austin, TX 78758, USA
| | - Stephen A Mock
- Texas Advanced Computing Center, The University of Texas, Austin, TX 78758, USA
| | - Joseph Stubbs
- Texas Advanced Computing Center, The University of Texas, Austin, TX 78758, USA
| | - Julie M Sullivan
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB2 1QR, UK
| | | | - Jason R Miller
- Plant Genomics, J. Craig Venter Institute, Rockville, MD 20850, USA
| | - Gos Micklem
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB2 1QR, UK
| | - Matthew Vaughn
- Texas Advanced Computing Center, The University of Texas, Austin, TX 78758, USA
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Poelchau M, Childers C, Moore G, Tsavatapalli V, Evans J, Lee CY, Lin H, Lin JW, Hackett K. The i5k Workspace@NAL--enabling genomic data access, visualization and curation of arthropod genomes. Nucleic Acids Res 2014; 43:D714-9. [PMID: 25332403 DOI: 10.1093/nar/gku983] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The 5000 arthropod genomes initiative (i5k) has tasked itself with coordinating the sequencing of 5000 insect or related arthropod genomes. The resulting influx of data, mostly from small research groups or communities with little bioinformatics experience, will require visualization, dissemination and curation, preferably from a centralized platform. The National Agricultural Library (NAL) has implemented the i5k Workspace@NAL (http://i5k.nal.usda.gov/) to help meet the i5k initiative's genome hosting needs. Any i5k member is encouraged to contact the i5k Workspace with their genome project details. Once submitted, new content will be accessible via organism pages, genome browsers and BLAST search engines, which are implemented via the open-source Tripal framework, a web interface for the underlying Chado database schema. We also implement the Web Apollo software for groups that choose to curate gene models. New content will add to the existing body of 35 arthropod species, which include species relevant for many aspects of arthropod genomic research, including agriculture, invasion biology, systematics, ecology and evolution, and developmental research.
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Affiliation(s)
| | | | - Gary Moore
- National Agricultural Library, Beltsville, MD 20705, USA
| | | | - Jay Evans
- Bee Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD 20705, USA
| | - Chien-Yueh Lee
- National Agricultural Library, Beltsville, MD 20705, USA Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan
| | - Han Lin
- National Agricultural Library, Beltsville, MD 20705, USA Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan
| | - Jun-Wei Lin
- National Agricultural Library, Beltsville, MD 20705, USA Graduate Institute of Electrical Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Kevin Hackett
- Crop Production and Protection, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD 20705, USA
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Jung S, Ficklin SP, Lee T, Cheng CH, Blenda A, Zheng P, Yu J, Bombarely A, Cho I, Ru S, Evans K, Peace C, Abbott AG, Mueller LA, Olmstead MA, Main D. The Genome Database for Rosaceae (GDR): year 10 update. Nucleic Acids Res 2013; 42:D1237-44. [PMID: 24225320 PMCID: PMC3965003 DOI: 10.1093/nar/gkt1012] [Citation(s) in RCA: 154] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The Genome Database for Rosaceae (GDR, http:/www.rosaceae.org), the long-standing central repository and data mining resource for Rosaceae research, has been enhanced with new genomic, genetic and breeding data, and improved functionality. Whole genome sequences of apple, peach and strawberry are available to browse or download with a range of annotations, including gene model predictions, aligned transcripts, repetitive elements, polymorphisms, mapped genetic markers, mapped NCBI Rosaceae genes, gene homologs and association of InterPro protein domains, GO terms and Kyoto Encyclopedia of Genes and Genomes pathway terms. Annotated sequences can be queried using search interfaces and visualized using GBrowse. New expressed sequence tag unigene sets are available for major genera, and Pathway data are available through FragariaCyc, AppleCyc and PeachCyc databases. Synteny among the three sequenced genomes can be viewed using GBrowse_Syn. New markers, genetic maps and extensively curated qualitative/Mendelian and quantitative trait loci are available. Phenotype and genotype data from breeding projects and genetic diversity projects are also included. Improved search pages are available for marker, trait locus, genetic diversity and publication data. New search tools for breeders enable selection comparison and assistance with breeding decision making.
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Affiliation(s)
- Sook Jung
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA, Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA, Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, NY 14853, USA, Department of Computer Science, Saginaw Valley State University, University Center, MI 48710, USA and Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
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