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If you have information about misannotated or unannotated genes, please contact TAIR.

Table of Contents

Genome Annotation Methods at TAIR

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The TAIR10 release contains 27,416 protein coding genes, 4827 pseudogenes or transposable element genes and 1359 ncRNAs (33,602 genes in all, 41,671 gene models). A total of 126 new loci and 2099 new gene models were added.

Eighteen percent (5885) of Arabidopsis genes now have annotated splice variants. Updates were made to 1184 gene models of which 707 had CDS updates. There were 41 gene splits and 37 gene merges. No changes were made to the Arabidopsis genome assembly for the TAIR10 release.

Gene annotation utilized available proteomics data (Baerenfaller et al., 2008 and Castellana et al., 2008) and RNA-seq data from the Ecker and Mockler labs (Lister et al. 2008, Filichkin et al. 2010). RNA-seq data was mapped to the Arabidopsis genome using TopHat, HashMatch or supersplat. After quality and low complexity filtering a total of ~200 million RNA-seq reads were successfully mapped to the genome. Of these, ~9 million represent spliced reads. Proteomics data and spliced RNA-seq reads were provided to Augustus and the resulting gene models categorised and manually reviewed. Validated gene updates, novel genes and novel splice variants were incorporated into the TAIR10 release. Additional spliced RNA-seq reads not already incorporated into gene models by Augustus were supplied to TAU. The resulting TAU models were again reviewed for potential novel splice variants. Transcript assemblies were generated via Cufflinks using all spliced reads and unspliced reads from the Ecker sets. Transcript assemblies were filtered and compared to existing gene models, resulting in the addition of 56 novel genes. Additional new proteome data provided to us by Katja Baerenfaller was used to directly update 24 gene models.

Gene models created using the Gnomon pipeline were provided to TAIR by NCBI. Reanalysis of these models for TAIR10 resulted in 11 additional novel genes, 67 additional alternative splice variants and 178 updates to existing genes.

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In agreement with our reference genome policy corrections to the reference assembly were only made if supported by at least two independently derived sequence libraries from the Columbia ecotype.

The following updates were made to the chromosome sequences for the TAIR9 release:

• 227 single nucleotide substitutions were made to the assembly sequence based on re-sequencing data provided by Richard Clark (Ossowski et al. 2008) and Joe Ecker.
• 341 indels were made to the assembly sequence based on re-sequencing data provided by Richard Clark and EST and cDNA sequences deposited in Genbank that supported the insertion/deletion.
• 14 regions previously identified in TAIR8 as either vector, E.coli or rice contamination, and where the existing sequence had been substituted with the equivalent number of IUPAC ambiguity code 'N's were standardized (via deletion) to a set size of 100bp.
• All five nuclear chromosomes were updated for TAIR9 details of the golden path length of each chromosome can be found at

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• here.

Further details of these TAIR 9 assembly changes and earlier TAIR8 updates can be found at ftp://ftp.arabidopsis.org/home/tair/Sequences/whole_chromosomes/ Assembly updates and gap information can also be viewed in TAIRs GBrowse (see Assembly tracks section). are linked.

We would like to thank all those who contributed to the latest release by providing submissions for new and incorrectly annotated genes. TAIR wishes to thank Cornell University for use of the computer clusters at the Cornell Center for Advanced Computing (CAC).

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The fully annotated chromosome sequences in TIGR xml format or GFF format, along with Fasta FASTA files of cDNA, CDS, genomic and protein sequences, and lists of added, deleted and updated genes are available from the TAIR ftp Download site.

Previous TIGR annotation is available from both the TIGR FTP site and TAIR FTP TAIR Download site.

For a summary of the different genome version statistics see table All Genome Versions Statistics below. Fasta

FASTA formatted files for all TAIR sequence analysis datasets including sets of intron, intergenic, UTR, upstream and downstream sequences are also available in the blast BLAST datasets directory of the TAIR Download Section.

Datasets are also available from TAIR's Bulk Download tool Advanced Gene Search; paste in or upload a list of AGI identifiers (such as At1g01010) and download the corresponding sequences. A graphic display of the Arabidopsis sequence and annotation can be viewed using TAIR's genome browsers GBrowse and Seqviewer.

Transposon genes and Transposable elements

Prior to TAIR8 all non transposon related pseudogenes and transposon genes were categorised as locus type pseudogene. For TAIR8, transposon related genes were reclassified into a distinct transposable element gene class.

Transposable element annotations provided by Hadi Quesneville were combined with pre-existing annotations to create a composite set of Arabidopsis transposons. These have been assigned a unique identifier (e.g. AT3TE53245) that indicates relative position on the chromosome. Under defined criteria (see additional readme-transposons) we have associated transposons to overlapping transposable element genes e.g. genes AT3G32022, AT3G32024, AT3G32026, AT3G32027 and AT3G32028 are associated to transposon AT3TE53245. Transposons can be viewed in TAIR's GBrowse genome browsers and additional information can be found on the Transposon and Transposon family detail pages.

TAIR10 Genome Statistics

All Genome Versions Statistics

Graphical Views of Annotation Data

TAIR GBrowse

Search or browse a map of the Arabidopsis genome (including genes, cDNAs and ESTs, insertion mutants, SNPs, markers, BACs, VISTA sequence similarity plots and more) or upload your own annotation track. Tracks can be easily customized by turning on and off specific data types, collapsing and expanding tracks, or changing track order.

TAIR SeqViewer

A graphic display of the latest Arabidopsis sequence and annotation can be viewed using TAIRs genome browser. Browse the chromosomes, search for names or short sequences and view search hits on the whole genome, in a close-up view or on a nucleotide level.

TAIR MapViewer

Displays ORFs at zoom levels of 200x and higher, and allows wildcard and alias searching on clone names, ORF names, genes and markers.

NCBI Map Viewer

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