PFusionDB: a comprehensive database of plant-specific fusion transcripts.

Area of Science:

• Plant genomics and transcriptomics
• Bioinformatics and database development
• Molecular biology

Background:

• Fusion transcripts (FTs) are recognized cancer biomarkers but are understudied in plants.
• A comprehensive resource for plant FTs is needed to facilitate research in this area.
• Existing tools for FT identification require adaptation for plant-specific analyses.

Purpose of the Study:

• To develop PFusionDB, a novel, plant-specific database for fusion transcripts.
• To provide a comprehensive repository of FTs identified across multiple plant species.
• To offer tools for searching, analyzing, and mapping fusion transcript data.

Main Methods:

• RNA-Seq data from 1280 Arabidopsis thaliana, 637 Oryza sativa japonica, 697 Oryza sativa indica, and 181 Cicer arietinum samples were analyzed.
• Five distinct tools (EricScript-Plants, STAR-Fusion, TrinityFusion, SQUID, MapSplice) were employed for FT identification.
• Data integration and curation into the PFusionDB platform, including development of search and alignment modules.

Main Results:

• PFusionDB hosts 80,170 (A. thaliana), 39,108 (O. sativa japonica), 83,330 (O. sativa indica), and 11,500 (C. arietinum) unique FTs.
• A significant number of non-recurrent FTs (unique to a single sample) were identified across all species.
• The database includes detailed information on parental genes, junction sequences, expression levels, and genomic coordinates.

Conclusions:

• PFusionDB is a valuable and comprehensive resource for plant fusion transcript research.
• The database facilitates the exploration of FTs in plants, supporting further functional and evolutionary studies.
• It provides essential tools for researchers to query, analyze, and map plant fusion transcript data.