RiTE database: a resource database for genus-wide rice genomics and evolutionary biology

Persistent Link:
http://hdl.handle.net/10150/610281
Title:
RiTE database: a resource database for genus-wide rice genomics and evolutionary biology
Author:
Copetti, Dario; Zhang, Jianwei; El Baidouri, Moaine; Gao, Dongying; Wang, Jun; Barghini, Elena; Cossu, Rosa M.; Angelova, Angelina; Maldonado L., Carlos E.; Roffler, Stefan; Ohyanagi, Hajime; Wicker, Thomas; Fan, Chuanzhu; Zuccolo, Andrea; Chen, Mingsheng; Costa de Oliveira, Antonio; Han, Bin; Henry, Robert; Hsing, Yue-ie; Kurata, Nori; Wang, Wen; Jackson, Scott A.; Panaud, Olivier; Wing, Rod A.
Affiliation:
Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona; International Rice Research Institute, Genetic Resource Center; Laboratoire Génome et Développement des Plantes and CNRS and Laboratoire Génome et Développements des Plantes, Université de Perpignan Via Domitia; Center for Applied Genetic Technologies, University of Georgia; Department of Biological Sciences, Wayne State University; Department of Agriculture, Food, and Environment, University of Pisa; Institute of Life Sciences, Scuola Superiore Sant’Anna; School of Life Sciences, Heriot-Watt University; Institute of Plant Biology, University of Zürich; Plant Genetics Laboratory, National Institute of Genetics; State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology Chinese Academy of Sciences; Plant Genomics and Breeding Center, Federal University of Pelotas; National Center for Gene Research and Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences; Queensland Alliance for Agriculture and Food Innovation, University of Queensland; Institute of Plant and Microbial Biology, Academia Sinica; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences and University of Chinese Academy of Sciences
Issue Date:
2015
Publisher:
BioMed Central Ltd
Citation:
Copetti et al. BMC Genomics (2015) 16:538 DOI 10.1186/s12864-015-1762-3
Journal:
BMC Genomics
Rights:
© 2015 Copetti et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0)
Collection Information:
This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.
Abstract:
BACKGROUND: Comparative evolutionary analysis of whole genomes requires not only accurate annotation of gene space, but also proper annotation of the repetitive fraction which is often the largest component of most if not all genomes larger than 50 kb in size. RESULTS: Here we present the Rice TE database (RiTE-db) - a genus-wide collection of transposable elements and repeated sequences across 11 diploid species of the genus Oryza and the closely-related out-group Leersia perrieri. The database consists of more than 170,000 entries divided into three main types: (i) a classified and curated set of publicly-available repeated sequences, (ii) a set of consensus assemblies of highly-repetitive sequences obtained from genome sequencing surveys of 12 species; and (iii) a set of full-length TEs, identified and extracted from 12 whole genome assemblies. CONCLUSIONS: This is the first report of a repeat dataset that spans the majority of repeat variability within an entire genus, and one that includes complete elements as well as unassembled repeats. The database allows sequence browsing, downloading, and similarity searches. Because of the strategy adopted, the RiTE-db opens a new path to unprecedented direct comparative studies that span the entire nuclear repeat content of 15 million years of Oryza diversity.
EISSN:
1471-2164
DOI:
10.1186/s12864-015-1762-3
Keywords:
Rice; Oryza; Transposable elements; Repeats; Genome; RiTE-db
Version:
Final published version
Additional Links:
http://www.biomedcentral.com/1471-2164/16/538

Full metadata record

DC FieldValue Language
dc.contributor.authorCopetti, Darioen
dc.contributor.authorZhang, Jianweien
dc.contributor.authorEl Baidouri, Moaineen
dc.contributor.authorGao, Dongyingen
dc.contributor.authorWang, Junen
dc.contributor.authorBarghini, Elenaen
dc.contributor.authorCossu, Rosa M.en
dc.contributor.authorAngelova, Angelinaen
dc.contributor.authorMaldonado L., Carlos E.en
dc.contributor.authorRoffler, Stefanen
dc.contributor.authorOhyanagi, Hajimeen
dc.contributor.authorWicker, Thomasen
dc.contributor.authorFan, Chuanzhuen
dc.contributor.authorZuccolo, Andreaen
dc.contributor.authorChen, Mingshengen
dc.contributor.authorCosta de Oliveira, Antonioen
dc.contributor.authorHan, Binen
dc.contributor.authorHenry, Roberten
dc.contributor.authorHsing, Yue-ieen
dc.contributor.authorKurata, Norien
dc.contributor.authorWang, Wenen
dc.contributor.authorJackson, Scott A.en
dc.contributor.authorPanaud, Olivieren
dc.contributor.authorWing, Rod A.en
dc.date.accessioned2016-05-20T09:03:06Z-
dc.date.available2016-05-20T09:03:06Z-
dc.date.issued2015en
dc.identifier.citationCopetti et al. BMC Genomics (2015) 16:538 DOI 10.1186/s12864-015-1762-3en
dc.identifier.doi10.1186/s12864-015-1762-3en
dc.identifier.urihttp://hdl.handle.net/10150/610281-
dc.description.abstractBACKGROUND: Comparative evolutionary analysis of whole genomes requires not only accurate annotation of gene space, but also proper annotation of the repetitive fraction which is often the largest component of most if not all genomes larger than 50 kb in size. RESULTS: Here we present the Rice TE database (RiTE-db) - a genus-wide collection of transposable elements and repeated sequences across 11 diploid species of the genus Oryza and the closely-related out-group Leersia perrieri. The database consists of more than 170,000 entries divided into three main types: (i) a classified and curated set of publicly-available repeated sequences, (ii) a set of consensus assemblies of highly-repetitive sequences obtained from genome sequencing surveys of 12 species; and (iii) a set of full-length TEs, identified and extracted from 12 whole genome assemblies. CONCLUSIONS: This is the first report of a repeat dataset that spans the majority of repeat variability within an entire genus, and one that includes complete elements as well as unassembled repeats. The database allows sequence browsing, downloading, and similarity searches. Because of the strategy adopted, the RiTE-db opens a new path to unprecedented direct comparative studies that span the entire nuclear repeat content of 15 million years of Oryza diversity.en
dc.language.isoenen
dc.publisherBioMed Central Ltden
dc.relation.urlhttp://www.biomedcentral.com/1471-2164/16/538en
dc.rights© 2015 Copetti et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0)en
dc.subjectRiceen
dc.subjectOryzaen
dc.subjectTransposable elementsen
dc.subjectRepeatsen
dc.subjectGenomeen
dc.subjectRiTE-dben
dc.titleRiTE database: a resource database for genus-wide rice genomics and evolutionary biologyen
dc.typeArticleen
dc.identifier.eissn1471-2164en
dc.contributor.departmentArizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizonaen
dc.contributor.departmentInternational Rice Research Institute, Genetic Resource Centeren
dc.contributor.departmentLaboratoire Génome et Développement des Plantes and CNRS and Laboratoire Génome et Développements des Plantes, Université de Perpignan Via Domitiaen
dc.contributor.departmentCenter for Applied Genetic Technologies, University of Georgiaen
dc.contributor.departmentDepartment of Biological Sciences, Wayne State Universityen
dc.contributor.departmentDepartment of Agriculture, Food, and Environment, University of Pisaen
dc.contributor.departmentInstitute of Life Sciences, Scuola Superiore Sant’Annaen
dc.contributor.departmentSchool of Life Sciences, Heriot-Watt Universityen
dc.contributor.departmentInstitute of Plant Biology, University of Zürichen
dc.contributor.departmentPlant Genetics Laboratory, National Institute of Geneticsen
dc.contributor.departmentState Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology Chinese Academy of Sciencesen
dc.contributor.departmentPlant Genomics and Breeding Center, Federal University of Pelotasen
dc.contributor.departmentNational Center for Gene Research and Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciencesen
dc.contributor.departmentQueensland Alliance for Agriculture and Food Innovation, University of Queenslanden
dc.contributor.departmentInstitute of Plant and Microbial Biology, Academia Sinicaen
dc.contributor.departmentState Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences and University of Chinese Academy of Sciencesen
dc.identifier.journalBMC Genomicsen
dc.description.collectioninformationThis item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.en
dc.eprint.versionFinal published versionen
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