PATsi: Paralogs and Singleton Genes from Arabidopsis thaliana. (January 2016)

• Record Type: Journal Article
• Authors: Ambrosino, Luca; Bostan, Hamed; di Salle, Pasquale; Sangiovanni, Mara; vigilante, Alessandra; Chiusano, Maria L.
• Is Part Of: Evolutionary bioinformatics online. Volume 12(2016)
• Publication Date: 2016-01
• Subjects: Arabidopsis thaliana -- paralogs -- singletons; Bioinformatics -- Periodicals; Evolutionary computation -- Periodicals; Genetic programming (Computer science) -- Periodicals; Computational Biology; Evolution, Molecular; Bioinformatics; Electronic journals; Periodicals; Fulltext; Internet Resources; Periodicals; Periodicals; 576.8
• DOI: 10.4137/EBO.S32536
• Languages: English
• ISSNs: 1176-9343

Abstract

Arabidopsis thaliana is widely accepted as a model species in plant biology. Its genome, due to its small size and diploidy, was the first to be sequenced among plants, making this species also a reference for plant comparative genomics. Nevertheless, the evolutionary mechanisms that shaped the Arabidopsis genome are still controversial. Indeed, duplications, translocations, inversions, and gene loss events that contributed to the current organization are difficult to be traced. A reliable identification of paralogs and single-copy genes is essential to understand these mechanisms. Therefore, we implemented a dedicated pipeline to identify paralog genes and classify single-copy genes into opportune categories. PATsi, a web-accessible database, was organized to allow the straightforward access to the paralogs organized into networks and to the classification of single-copy genes. This permits to efficiently explore the gene collection of Arabidopsis for evolutionary investigations and comparative genomics.