ITAG4.0 Tomato Genome Annotation Release

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

== 1. Introduction ==

ITAG4.0 release of new annotation on the tomato genome assembly SL4.0 assembled from long reads. This release includes 34,075 gene models.

Release Date: Sep 6, 2019

== 2. Change log ==

Following are the changes in ITAG4.0 compared to ITAG2.40.
Number of ITAG2.4 genes preserved    =	 29,281
Number of dropped genes		     =	  5,444
Number of updated genes		     =	 21,375
Number of novel genes		     =	  4,794

== 3. Files in this release ==
*	ITAG4.0_CDS.fasta
	fasta-format sequence file of CDS sequences.

*	ITAG4.0_cDNA.fasta
	fasta-format sequence file of cDNA sequences.

*	ITAG4.0_gene_models.gff
	GFF version 3 file containing gene models in this release. 

*	ITAG4.0_proteins.fasta
	fasta-format sequence file of protein sequences.

*	ITAG4.0_REPET_repeats_agressive.gff
	GFF version 3 file containing repetitive regions. This contains repeats identified by REPET
	pipeline and contains comprehensive repeat annotation.

*	ITAG4.0_RepeatModeler_repeats_light.gff
	GFF version 3 file containing repetitive regions. ITAG4.0 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.

*       ITAG4.0_RepeatModeler_repeats_light.classified
	Tabular file with repeat classification

*	solcap.SL4.0gff
	GFF version 3 file containing the Solcap markers on SL4.0