ArticleBMC genomics2015
RiTE database: a resource database for genus-wide rice genomics and evolutionary biology.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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39 citing papers in PubMed, 81 citations in OpenAlex.
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- CHH Methylation Islands: A Nonconserved Feature of Grass Genomes That Is Positively Associated with Transposable Elements but Negatively Associated with Gene-Body Methylation.Genome biology and evolution · 2021Article
- A cluster of Ankyrin and Ankyrin-TPR repeat genes is associated with panicle branching diversity in rice.PLoS genetics · 2021Article
- Xa7, a Small Orphan Gene Harboring Promoter Trap for AvrXa7, Leads to the Durable Resistance to Xanthomonas oryzae Pv. oryzae.Rice (New York, N.Y.) · 2021Article
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- Gene disruption by structural mutations drives selection in US rice breeding over the last century.PLoS genetics · 2021Article
- ThRSDB: a database of Thai rice starch composition, molecular structure and functionality.Database : the journal of biological databases and curation · 2020Article
- Genomic re-assessment of the transposable element landscape of the potato genome.Plant cell reports · 2020Article
- Genome-wide DNA hypomethylation shapes nematode pattern-triggered immunity in plants.The New phytologist · 2020Article
- Draft genomes of two outcrossing wild rice,Plant direct · 2020Article
- Evolution and Diversity of the Wild Rice Oryza officinalis Complex, across Continents, Genome Types, and Ploidy Levels.Genome biology and evolution · 2020Article
- Current status of genomic resources on wild relatives of rice.Breeding science · 2020Article
- Low Long Terminal Repeat (LTR)-Retrotransposon Expression in Leaves of the Marine PhanerogamLife (Basel, Switzerland) · 2020Article
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Authors and funding
24 authors at 12 institutions in 10 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundComparative 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.
resultsHere 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.
conclusionsThis 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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.