RiTE database: a resource database for genus-wide rice genomics and evolutionary biology - CNRS - Centre national de la recherche scientifique Accéder directement au contenu
Article Dans Une Revue BMC Genomics Année : 2015

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

Elena Barghini
  • Fonction : Auteur
Rosa Cossu
  • Fonction : Auteur
Carlos Maldonado L.
  • Fonction : Auteur
Stefan Roffler
  • Fonction : Auteur
Hajime Ohyanagi
  • Fonction : Auteur
Mingsheng Chen
  • Fonction : Auteur
Robert Henry
  • Fonction : Auteur
Nori Kurata
  • Fonction : Auteur
Wen Wang
  • Fonction : Auteur
  • PersonId : 858635
Rod Wing
  • Fonction : Auteur

Résumé

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.
Fichier principal
Vignette du fichier
12864_2015_Article_1762.pdf (1.52 Mo) Télécharger le fichier
Origine : Fichiers éditeurs autorisés sur une archive ouverte

Dates et versions

hal-02099881 , version 1 (25-10-2023)

Identifiants

Citer

Dario Copetti, Jianwei Zhang, Moaine El Baidouri, Dongying Gao, Jun Wang, et al.. RiTE database: a resource database for genus-wide rice genomics and evolutionary biology. BMC Genomics, 2015, 16 (1), pp.538. ⟨10.1186/s12864-015-1762-3⟩. ⟨hal-02099881⟩
60 Consultations
6 Téléchargements

Altmetric

Partager

Gmail Facebook X LinkedIn More