Generic Genome Browser (GBrowse) Databases

Solanaceae Comparative Genome Database

This database contains all public genomic contig sequence data for the Solanaceae available from GenBank. Currently, our Solanaceae Comparative Genome Database includes the DM1-3 516R44 (Doubled Monoploid) Potato Genome sequence available from the Potato Genome Sequencing Consortium, as well as BACs from the Tomato Genome Initiative and the Potato Genome Initiative.

The DM potato genome annotation is provided by the Potato Genome Sequencing Consortium. More details can be found in the published Nature paper by the PGSC. The BAC sequences are run through the MAKER pipeline to provide gene models, in addition to any previously annotated gene models from the public data.

Annotation of the PGSC DM genome includes:

Loci, gene models, and isoforms
Alignments of UniRef100 proteins to the genome assembly
Repeatmasker predicted repeats and putative SSRS
SolCAP Infinium platform SNPs
Alignment to assembled Solanaceae transcript sequences (PUTs) obtained from PlantGDB

Data and analyses results for the BAC-based annotation include:

Assembled Solanaceae transcript sequences obtained from PlantGDB (PUTs) aligned to the genomic sequence (11 species)
UniProt's SwissProt and UniRef protein databases aligned to the genomic sequence
Top hits for the Solanaceae gene models against model dicot proteomes (Arabidopsis, Grape, Medicago, Poplar)
InterProScan results on the models
Predicted repeat features (using RepeatMasker and ssr.pl from Gramene)
Predicted ncRNA features (using tRNAscan-SE and RNAmmer)
Results of additional computational analyses

Model Dicot Genome Comparative Databases

Genome databases for the current public releases of model dicot genomes with tracks of data from comparative analyses against Solanaceae sequence.

Arabidopsis Genome Database

TAIR8 release of the Arabidopsis thaliana genome.

Grape Genome Database

Genoscope v1.1 release of the Vitis vinifera genome.

Poplar Genome Database

DOE JGI v2 release of the Populus trichocarpa genome.