ITAG2.4 Tomato Genome Annotation Release

Contents:
  1. Introduction
  2. Change log
  3. Files in this release

== 1. Introduction ==

The ITAG2.4 release of the official Tomato genome annotation (ITAG2.4), 
is a post-release update to ITAG2.3 covering approximately 84% of the genome,
with 34,725 gene models. This release includes updates to the gap sizes 
between scaffolds from FISH experiments.

This release file set was generated on February 23, 2014.

Please note that ITAG2.4 corresponds to build 2.5 of the tomato genome and ITAG2.3
corresponds to build 2.4. The genome release numbers and ITAG versions are not 
synchronized.

Please see ftp://ftp.solgenomics.net/tomato_genome/annotation/ITAG2.3_release/ITAG2.3_README.txt
for detailed description and statistics of ITAG2.3.

== 2. Change log ==

The following gene models were dropped from ITAG2.4 release
Solyc03g053140.1
Solyc12g032910.1

Please see ITAG2.4_dropped_features.gff3 for a complete list of features that were dropped in 
release ITAG 2.4.

== 3. Files in this release ==

* ITAG2.4_assembly.gff3
  GFF version 3 file containing chromsome features, as well as
  positions of scaffolds, contigs, and inter-scaffold
  (i.e. unknown-size) gaps.

  Analyses in this file:
    SL2.50_assembly

* ITAG2.4_cdna.fasta
  fasta-format sequence file of cDNA sequences.

* ITAG2.4_cdna_alignments.gff3
  GFF version 3 files containing alignments of existing EST and cDNA
  sequences to the genome.

  Analyses in this file: 
    ITAG_microtom_flcdnas
    ITAG_transcripts_sol
    ITAG_transcripts_tomato

* ITAG2.4_cds.fasta
  fasta-format sequence file of CDS sequences.

* ITAG2.4_de_novo_gene_finders.gff3
  GFF version 3 file containing predictions from several de novo gene
finders.  These were integrated into the final gene models by EuGene.

  Analyses in this file:
    ITAG_augustus
    ITAG_geneid_tomato
    ITAG_glimmerhmm_ath
    ITAG_glimmerhmm_tomato
    ITAG_trnascanse
    
* ITAG2.4_dropped_features.gff3
  GFF version 3 file listing features from the ITAG2 that could not be
  remapped from the SL2.40 assembly to the SL2.50 assembly.

* ITAG2.4_gene_models.gff3
  GFF version 3 file containing gene models in this release.

  Analyses in this file:
    ITAG_eugene
    
* ITAG2.4_genomic.fasta
  fasta-format sequence file of genomic contig sequences.

* ITAG2.4_genomic_reagents.gff3
  GFF version 3 file containing alignments to subclones or other
  intermediate materials used in the genome.

  Analyses in this file:
    ITAG_tomato_bacs
    DBolser_Dundee_BES_SSAHA

* ITAG2.4_infernal.gff3
  GFF version 3 file containing annotated small-RNA regions, produced
  by Infernal (http://infernal.janelia.org/).

  Analyses in this file:
    ITAG_infernal

* ITAG2.4_other_genomes.gff3
  GFF version 3 file containing alignments to other genomes or
  assemblies other than the one used as reference for this annotation.

  Analyses in this file:
    ITAG_itag1_ref
    ITAG_tobacco_contigs

* ITAG2.4_protein_functional.gff3
  GFF version 3 file containing annotations on protein sequences, such
  as protein domains.

  Analyses in this file:
    ITAG_blastp_ath_pep
    ITAG_blastp_refseq_pep
    ITAG_blastp_rice_pep
    ITAG_blastp_swissprot
    ITAG_blastp_trembl
    ITAG_interpro

* ITAG2.4_protein_reference.gff3
  GFF version 3 file containing reference features for each protein
  sequence.  Useful for loading features on the protein sequences into
  databases like Chado.

  Analyses in this file:
    none

* ITAG2.4_proteins.fasta
  fasta-format sequence file of protein sequences.

* ITAG2.4_proteins_full_desc.fasta

* ITAG2.4_repeats.gff3
  GFF version 3 file containing repetitive regions, at 'normal'
  stringency, meaning running it *with* the -nolow option, so that
  low-complexity and simple repeats are NOT masked.  The repeat set
  used for masking is available at
  ftp://ftp.sgn.cornell.edu/genomes/Solanum_lycopersicum/repeats/mipsREdat_8.8_solanaceae_TE.masked.gz.
     
  Analyses in this file:
    ITAG_repeats

* ITAG2.4_repeats_aggressive.gff3
  GFF version 3 file containing repetitive regions, at 'aggressive'
  stringency, meaning running it *without* the -nolow option, so that
  low-complexity and simple repeats ARE masked.  The repeat set used
  for masking is available at
  ftp://ftp.sgn.cornell.edu/genomes/Solanum_lycopersicum/repeats/mipsREdat_8.8_eudico_TEs.masked.gz.
     
  Analyses in this file:
    ITAG_repeats

* ITAG2.4_sgn_data.gff3
  GFF version 3 file containing alignments to sequences related to
  data on SGN.  Currently contains alignments to SGN unigenes, SGN
  marker sequences, and SGN locus sequences.

  Analyses in this file:
    ITAG_sgn_loci
    ITAG_sgn_markers
    ITAG_sgn_unigenes

* ITAG2.4_solCAP.gff3
  GFF version 3 file containing locations of the solCAP markers.

  Analyses in this file:
    ITAG_sgn_markers
    
* ITAG2.4.go.csv
  Comma separated value (CSV) file of the GO annotations for each ITAG24 gene model. This file was created by parsing the fasta headers from ftp://ftp.solgenomics.net/tomato_genome/annotation/ITAG2.3_release/ITAG2.3_proteins_full_desc.fasta