The Plant Orthology Browser: An Orthology and Gene‐Order Visualizer for Plant Comparative Genomics

Abstract

© Crop Science Society of America. Worldwide genome sequencing efforts for plants with medium and large genomes require identification and visualization of orthologous genes, while their syntenic conservation becomes the pinnacle of any comparative and functional genomics study. Using gene models for 20 fully sequenced plant genomes, including model organisms and staple crops such as Aegilops tauschii Coss., Arabidopsis thaliana (L.) Heynh., Brachypodium distachyon (L.) Beauv., turnip (Brassica rapa L.), barley (Hordeum vulgare L.), rice (Oryza sativa L.), sorghum [Sorghum bicolor (L.) Moench], wheat (Triticum aestivum L.), red wild einkorn (Triticum urartu Tumanian ex Gandilyan), and maize (Zea mays L.), we computationally predicted 1,021,611 orthologs using stringent sequence similarity criteria. For each pair of plant species, we determined sets of conserved synteny blocks using strand orientation and physical mapping. Gene ontology (GO) annotations are added for each gene. Plant Orthology Browser (POB) includes three interconnected modules: (i) a gene-order visualization module implementing an interactive environment for exploration of gene order between any pair of chromosomes in two plant species, (ii) a synteny visualization module providing unique interactive dot plot representations of orthologous genes between a pair of chromosomes in two distinct plant species, and (iii) a search module that interconnects all modules via free-text search capability with online as-you-type suggestions and highlighting that allows exploration of the underlining information without constraint of interface-dependent search fields. The POB is a web-based orthology and annotation visualization tool, which currently supports 20 completely sequenced plant species with considerably large genomes and offers intuitive and highly interactive pairwise comparison and visualization of genomic traits via gene orthology.