The Arabidopsis Information Resource (TAIR) has announced the release of the latest version of the Arabidopsis genome annotation (TAIR9) at TAIR and NCBI. The latest release builds upon the gene structures of the previous TAIR8 release. This version is available for ftp download.

The TAIR9 release contains 27,379 protein coding genes, 4827 pseudogenes or transposable elements and 1312 ncRNAs (33,518 genes in all, 39,640 gene models). A total of 282 new loci and 739 new gene models were added. Fourteen percent (4626) of Arabidopsis genes now have annotated splice variants. Updates were made to 1254 gene models of which 774 had CDS updates; a total of 1144 exons were modified and 1056 new exons incorporated. There were 13 gene splits and 46 gene merges. Changes to chromosome sequences include deletion of 14 regions previously found to contain vector/Ecoli contamination. In addition there were 227 single nucleotide substitutions and 341 indels. Additional details can be viewed on the TAIR website.

Arabidopsis thaliana is a small flowering plant of mustard family, brassicaceae (Cruciferae). It was selected as a model organism for genome sequencing in plants based on the fact that it has (1) a small genome of ~120 Mb with a simple structure having few repeated sequences and high gene density (2) short generation time of six weeks from seed germination to seed set (3) produces large number of seeds, and (4) is easy to transform. The sequencing was done by an international collaboration, collectively termed the Arabidopsis Genome Initiative (AGI). It consisted of research groups in the U.S., Europe and Japan. The project was initiated in 1996 and completed in 2000 (Nature, 408:796-815).

Available Documentation:

• NCBI Handbook: Map Viewer chapter - resource description
• NCBI Handbook: Map Viewer Exercises - tutorials and examples
• Map Viewer Help - details about navigation and customizing your display
• Genome Assembly - description of genome assembly and annotation process
• Gnomon - description of NCBI's Hidden Markov Model (HMM) ab initio prediction program

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