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

Area of Science:

• Genomics
• Evolutionary Biology
• Bioinformatics

Background:

• Accurate whole-genome analysis necessitates comprehensive annotation of both gene space and repetitive DNA sequences.
• Repetitive fractions constitute a significant portion of many eukaryotic genomes, impacting evolutionary studies.

Purpose of the Study:

• To establish a genus-wide database of transposable elements (TEs) and repeated sequences for the genus Oryza.
• To facilitate comparative evolutionary analyses by providing a unified resource for repeat content.

Main Methods:

• Compiled a genus-wide collection of TEs and repeated sequences from 11 diploid Oryza species and one out-group.
• Integrated publicly available sequences, consensus assemblies from genome surveys, and full-length TEs from whole genome assemblies.
• Developed a database with over 170,000 entries, including classified sequences, consensus assemblies, and identified full-length TEs.

Main Results:

• The Rice TE database (RiTE-db) contains over 170,000 entries, representing a broad spectrum of repeat variability within the Oryza genus.
• The database includes classified public repeats, consensus assemblies of highly repetitive sequences, and full-length transposable elements.
• RiTE-db provides tools for sequence browsing, downloading, and similarity searches.

Conclusions:

• RiTE-db is the first comprehensive repeat dataset covering extensive variability within an entire genus, including complete and unassembled elements.
• This resource enables unprecedented direct comparative studies of nuclear repeat content across 15 million years of Oryza evolution.
• The database significantly advances the study of repetitive DNA in comparative genomics and evolutionary biology.