RCPedia: a global resource for studying and exploring retrocopies in diverse species

Abstract

Motivation: Gene retrocopies arise from the reverse transcription and genomic insertion of processed mRNA transcripts. These elements have significantly contributed to genetic diversity and novelties throughout the evolution of many species. However, the study of retrocopies has been challenging, owing to the absence of comprehensive, complete, and user-friendly databases for diverse species.

Results: Here, we introduce an improved version of RCPedia, an integrative database meticulously designed for the study of retrocopies. RCPedia offers an extensive catalog of retrocopies identified across 44 species, which includes 13 primates, 4 rodents, 6 chiropterans, 12 other mammals, 4 birds, turtles, lizards, frogs, zebrafish, and Drosophila. The database offers the most complete compilation of retrocopies per species, accompanied by detailed genomic annotations, expression data, and links to other data portals. Furthermore, RCPedia features a streamlined representation of data and an efficient querying system, establishing it as an invaluable tool for researchers in the fields of genomics, evolutionary biology, and transposable elements (TEs). In summary, RCPedia aims to enhance the investigation of retrocopies and their pivotal roles in shaping the genomic landscapes of diverse species.

Availability and implementation: RCPedia is available at https://www.rcpediadb.org.

Figure 1.

Overview of RCPedia’s features and data. (A) The retrocopy identification workflow in RCPedia. This schematic delineates the algorithm’s main steps for identifying retrocopies, beginning with mRNA alignment and followed by sequential filtering based on a match threshold, parental gene distance, presence of exon-exon junctions, and exclusion of repetitive elements. (B) The user interface and data presentation in RCPedia. Illustrated here is a sample of the comprehensive information available for each retrocopy and its parental gene, including summary statistics, genomic coordinates, cross-species homology, RNA-seq expression levels, and genomic context. (C) Distribution of retrocopy numbers across different species groups. The box plots demonstrate the range and median values of retrocopies identified within groups of primates, rodents, chiropterans, other mammals, birds, and additional vertebrate species.