In the next folders are included the genomic data for Nicotiana tabacum published by Sierro, et al. 2014 in Nature Communications.


assembly: includes the genome sequences in FASTA format (compressed using gzip) for the superscaffolds for the three varieties of tobacco sequenced; Basma Xanthi (BX), K326 (Flue-cured) and TN90 (Burley).


Ntab-BX_AWOK-SS.fa.gz   -> genome sequence for the superscaffolds from Nicotiana tabacum Basma Xanthi
Ntab-K326_AWOJ-SS.fa.gz -> genome sequence for the superscaffolds from Nicotiana tabacum K326 Flue-cured
Ntab-TN90_AYMY-SS.fa.gz -> genome sequence for the superscaffolds from Nicotiana tabacum TN90 Burley


annotation: contains the gff3 files for the three varieties of tobacco sequenced and, for each one of them, gene models predicted by Cufflinks, and BLAT mappings with tomato (ITAG 2.4), potato (PGSC) and arabidopsis thaliana (TAIR10).

Ntab-TN90.gff3.tar.gz                  -> All gff3 files for TN90 compressed
Ntab-TN90_AYMY-SS_NGS_rnaseq.gff3      -> Cufflinks gene models based on RNA-seq data from 9 tissues (ie Dry Capsule, Immature Flower, Mature Flower, Mature Leaf Middle Stalk, Root, Senescent Flower, Senescent Leaf Lower Stalk, Stem, Young Leaf Upper Stalk)
Ntab-TN90_AYMY-SS_TN90_rnaseq.gff3     -> gene models from Cufflinks based on RNA-seq data from leaf and root
Ntab-TN90_AYMY-SS_itag_2.4_.80-80.gff3 -> BLAT mapping of tomato genes (ITAG 2.3) on TN90
Ntab-TN90_AYMY-SS_pgsc.80-80.gff3      -> BLAT mapping of potato genes (PGSC) on TN90
Ntab-TN90_AYMY-SS_tair10.80-60.gff3    -> BLAT mapping of A. thaliana genes (TAIR 10) on TN90

Ntab-TN90.fasta.tar.gz                 -> All FASTA files for TN90 annotations compressed
Ntab-TN90_AYMY-SS_NGS.cds.fna          -> TN90 coding sequences (CDS), based on Cufflinks prediction using 9 tissues
Ntab-TN90_AYMY-SS_NGS.mrna.fna         -> TN90 mRNA (includes UTR), based on Cufflinks prediction using 9 tissues
Ntab-TN90_AYMY-SS_NGS.proteins.faa     -> TN90 proteins, based on Cufflinks prediction using 9 tissues
Ntab-TN90_AYMY-SS_TN90.cds.fna         -> TN90 coding sequences (CDS), based on Cufflinks prediction using leaf and root
Ntab-TN90_AYMY-SS_TN90.mrna.fna        -> TN90 mRNA (includes UTR), based on Cufflinks prediction using leaf and root
Ntab-TN90_AYMY-SS_TN90.proteins.faa    -> TN90 proteins, based on Cufflinks prediction using leaf and root

Ntab-BX.gff3.tar.gz                    -> All gff3 files for BX compressed
Ntab-BX_AWOK-SS_Basma_rnaseq.gff3      -> Cufflinks gene models based on RNA-seq data from leaf and root
Ntab-BX_AWOK-SS_itag_2.4_.80-80.gff3   -> BLAT mapping of tomato genes (ITAG 2.3) on BX
Ntab-BX_AWOK-SS_pgsc.80-80.gff3        -> BLAT mapping of potato genes (PGSC) on BX
Ntab-BX_AWOK-SS_tair10.80-60.gff3      -> BLAT mapping of A. thaliana genes (TAIR 10) on BX

Ntab-BX.fasta.tar.gz                   -> All FASTA files for BX annotations compressed
Ntab-BX_AWOK-SS_Basma.cds.fna          -> BX coding sequences (CDS), based on Cufflinks prediction using leaf and root
Ntab-BX_AWOK-SS_Basma.mrna.fna         -> BX mRNA (includes UTR), based on Cufflinks prediction using leaf and root
Ntab-BX_AWOK-SS_Basma.proteins.faa     -> BX proteins, based on Cufflinks prediction using leaf and root

Ntab-K326.gff3.tar.gz                  -> All gff3 files for K326 compressed
Ntab-K326_AWOJ-SS_K326_rnaseq.gff3     -> Cufflinks gene models based on RNA-seq data from leaf and root
Ntab-K326_AWOJ-SS_itag_2.4_.80-80.gff3 -> BLAT mapping of tomato genes (ITAG 2.3) on K326
Ntab-K326_AWOJ-SS_pgsc.80-80.gff3      -> BLAT mapping of potato genes (PGSC) on K326
Ntab-K326_AWOJ-SS_tair10.80-60.gff3    -> BLAT mapping of A. thaliana genes (TAIR 10) on K326

Ntab-K326.fasta.tar.gz                 -> All FASTA files for K326 annotations compressed
Ntab-K326_AWOJ-SS_K326.cds.fna         -> K326 coding sequences (CDS), based on Cufflinks prediction using leaf and root
Ntab-K326_AWOJ-SS_K326.mrna.fna        -> K326 mRNA (includes UTR), based on Cufflinks prediction using leaf and root
Ntab-K326_AWOJ-SS_K326.proteins.faa    -> K326 proteins, based on Cufflinks prediction using leaf and root

previous_versions: includes old files, see README file in that folder for more information.

Tobacco Genome reference:
N. Sierro, J. N. Battey, S. Ouadi, N. Bakaher, L. Bovet, A. Willig, S. Goepfert, M. C. Peitsch, N. V. Ivanov, The tobacco genome sequence and its comparison with those of tomato and potato. Nat. Commun. 5, 3833 (2014).