pATsi: Paralogs and Singleton Genes from Arabidopsis thaliana

Evolutionary Bioinformatics Online
Luca AmbrosinoMaria Luisa Chiusano

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.

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Citations

Apr 18, 2018·American Journal of Botany·Matthew B ParksAndrew J Alverson
Jul 10, 2019·Frontiers in Plant Science·Mateusz ZelkowskiVeit Schubert
Jul 1, 2019·G3 : Genes - Genomes - Genetics·Prasad VaddepalliKay Schneitz

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Software Mentioned

Cytoscape
Ensembl Compara Homologene
BLASTp
pATsi
InnoDb
EPGD
CytoscapeWeb
MySql
Plaza

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