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== About the CDS and protein sequences: ==
==========================================

The Spimpinellifolium_genome.CDS.fa file contains reconstructed 
S. pimpinellifolium CDSs. The CDSs are reconstructed by replacing the 
S. lycopersicum cv. Heinz reference CDS sites with SNPs (and other variants) 
called from mapping S. pimpinellifolium genomic short reads to the reference. 
The reconstruction is only performed within protein coding regions, i .e. 
from start codon to stop codon. So there is no reconstructed UTRs, introns or 
intergenic regions. To streamline the reconstruction process, for genes not 
detected in S. pimpinellifolium, the CDSs are identifical with the reference. 
There is no information on presence/absence differences between the two 
species in this data set. 

The Spimpinellifolium_genome.protein.fa contains the translations from the
CDS file. These gene models have not been corrected, so some of the protein
sequences have early stop codons (or don't have any).




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== Disclaimers and data access agreement ==
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WILD TOMATO SPECIES GENOME SEQUENCE RELEASE. PLEASE READ BEFORE ACCESSING THE 
PRE-PUBLICATION SEQUENCE OF SOLANUM PIMPINELLIFOLIUM: The research groups of 
D. Ware, W.R. McCombie, and Z. B. Lippman at Cold Spring Harbor Laboratory are
pleased to provide to the Solanaceae and broader plant biology communities a 
pre-publication draft genome sequence of the Solanum pimpinellifolium wild 
tomato species genome. S. pimpinellifolium is the proposed wild progenitor of 
domesticated tomato, and its draft sequence provides a rich resource of 
genomic data for biological discovery of the processes of plant domestication 
and evolution. The sequence was generated using Illumina/Solexa sequencing 
technology to obtain approximately 20-fold genome coverage, and combined with 
mRNA-seq data to enrich for gene space. The data are provided freely for both 
public and private use, but with the understanding that users will respect the
rights of Cold Spring Harbor Laboratory to describe the genome and its 
comparison to the domesticated Heinz tomato genome in a peer-reviewed 
publication. This description includes genome level analyses on genes, gene 
families, repetitive sequences, SNP diversity, etc. We encourage users to 
review NIH-NHGRI guidelines on distribution and use of pre-publication genome 
sequence at http://www.genome.gov/page.cfm?pageID=10506537. Any use of the 
S. pimpinellifolium genome sequence prior to its publication should credit 
"D. Ware, W. R. McCombie, and Z. B. Lippman at Cold Spring Harbor Laboratory".
Please contact D. Ware or Z. B. Lippman (E-mail: ware@cshl.edu or 
lippman@cshl.edu) with any questions.


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Note: Annotations in protein file Spimpinellifolium_genome_protein_annot.fa are simply the ITAG 2.3 S. lycopersicum genome annotations substituted into the Spimpinellifolium_genome.protein.fa (performed by SRS).