Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release

Over the course of three years, TIGR has completed its effort to standardize the structural and functional annotation of the Arabidopsis genome. Using both manual and automated methods, Arabidopsis gene structures were refined and gene products were renamed and assigned to Gene Ontology categories. We present an overview of the methods employed, tools developed, and protocols followed, summarizing the contents of each data release with special emphasis on our final annotation release (version 5).Over the entire period, several thousand new genes and pseudogenes were added to the annotation. Approximately one third of the originally annotated gene models were significantly refined yielding improved gene structure annotations, and every protein-coding gene was manually inspected and classified using Gene Ontology terms.Arabidopsis thaliana has long been considered the foremost model organism in plant biology. It is favored for its short generation time, plentiful seeds, conveniently small stature, and ease of genetic transformation using Agrobacterium tumefaciens. Its comparatively small genome size, estimated at 140 million base pairs, and low repetitive sequence content drove the choice of Arabidopsis as a target for complete genome sequencing in the early nineties. Ten years later, the genome sequence was completed [1], providing a valuable resource for furthering the understanding of Arabidopsis biology and providing a reference sequence from which results in Arabidopsis could be extended to other plants.Since its publication, the Arabidopsis genome has been mined for clues to numerous important metabolic pathways and biological processes, many of which are documented in peer-reviewed publications including the Arabidopsis Book [2]. Additionally, the Arabidopsis genome has been used extensively as a tool for comparative genomics, both for genome-wide comparisons and to study specific processes among a wide range of plant species, including the gametophytic transcr