ITAG3.0 Tomato Genome Annotation Release

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

== 1. Introduction ==

ITAG3.2 release of new annotation on the tomato genome assembly SL3.0. This release includes 35,768 gene models.

Release Date: June 15, 2017

== 2. Change log ==

Following are the changes in ITAG3.2 compared to ITAG2.40.
Number of ITAG2.4 genes preserved    =	 30,866
Number of dropped genes		     =	  3,859
Number of updated genes		     =	 20,766
Number of novel genes		     =	  4,900

== 3. Files in this release ==
*	ITAG3.2_CDS.fasta
	fasta-format sequence file of CDS sequences.

*	ITAG3.2_cDNA.fasta
	fasta-format sequence file of cDNA sequences.

*	ITAG3.2_gene_models.gff
	GFF version 3 file containing gene models in this release. 

*	ITAG3.2_proteins.fasta
	fasta-format sequence file of protein sequences.

*	ITAG3.2_REPET_repeats_agressive.gff
	GFF version 3 file containing repetitive regions. This contains repeats identified by REPET
	pipeline and contains comprehensive repeat annotation.

*	ITAG3.2_RepeatModeler_repeats_light.gff
	GFF version 3 file containing repetitive regions. ITAG3.0 protein-coding gene models were
	identified after masking genome with this file. This contains repeats identified by RepeatMasker
	using RepeatModeler generated custom repeat library. Known proteins were identified in the repeat
	library to improve chances of protein-coding gene identification.

*       ITAG3.2_RepeatModeler_repeats_light.classified
	Tabular file with repeat classification

*       ITAG3.2_proteins_interproscan.tsv
	Interproscan results generated with interproscan-5.22-61
		
*       ITAG3.2_proteins_go.tsv
	Tabular separated value (TSV) file of the GO annotations for each ITAG3.2 gene model. This file was created from ITAG3.2_proteins_interproscan.tsv

*	ITAG2.40_Solyc.dropped.ID.txt
	List of genes dropped from ITAG2.4