SpudDB

SpudDB houses potato genome sequence and annotation, with the doubled monoploid DM 1-3 516 R44 genome serving as the reference genome and haplotype for cultivated tetraploid potato.

Key Features:

• Gene Report Pages: Diverse annotation data types for DM genes are provided including gene expression profiles across 438 potato samples.
• Gene Co-expression Modules: 65 gene co-expression modules permit identification of tightly co-regulated genes within DM across development and responses to wounding, abiotic stress, and biotic stress.
• Genome Browser Views: Genome browser views of DM and 28 other potato genomes are provided.
• Data Download: A download page for genome sequence and annotation is available.
• Syntelog Identification: Syntelogs were identified across 25 cultivated potato genomes to link syntenic genes within and between haplotypes.

Scientific Applications:

• Gene Expression Analysis: Researchers can access gene expression profiles across 438 potato samples to study gene activity patterns.
• Co-regulation Studies: The 65 gene co-expression modules enable identification of tightly co-regulated genes involved in development, wounding, abiotic stress, and biotic stress responses.
• Comparative Genomics: Genome browser views of DM and 28 other potato genomes support cross-genome comparisons and synteny analysis.
• Potato Improvement: The database enables potato biologists, geneticists, and breeders to improve this key food crop through access to genome sequences and associated annotations.

Methodology:

Gene co-expression modules were constructed for annotating potato genes based on expression. Syntelogs were identified across 25 cultivated potato genomes to link syntenic genes within and between haplotypes.