GDR (Genome Database for Rosaceae): integrated web-database for Rosaceae genomics and genetics data

Abstract

The Genome Database for Rosaceae (GDR) is a central repository of curated and integrated genetics and genomics data of Rosaceae, an economically important family which includes apple, cherry, peach, pear, raspberry, rose and strawberry. GDR contains annotated databases of all publicly available Rosaceae ESTs, the genetically anchored peach physical map, Rosaceae genetic maps and comprehensively annotated markers and traits. The ESTs are assembled to produce unigene sets of each genus and the entire Rosaceae. Other annotations include putative function, microsatellites, open reading frames, single nucleotide polymorphisms, gene ontology terms and anchored map position where applicable. Most of the published Rosaceae genetic maps can be viewed and compared through CMap, the comparative map viewer. The peach physical map can be viewed using WebFPC/WebChrom, and also through our integrated GDR map viewer, which serves as a portal to the combined genetic, transcriptome and physical mapping information. ESTs, BACs, markers and traits can be queried by various categories and the search result sites are linked to the mapping visualization tools. GDR also provides online analysis tools such as a batch BLAST/FASTA server for the GDR datasets, a sequence assembly server and microsatellite and primer detection tools. GDR is available at http://www.rosaceae.org.

Genome-wide analysis of the AP2/ERF superfamily in peach (Prunus persica)

“…The AP2 family contains a similar number of genes in grapevine (20), cucumber (20), Arabidopsis (18), and peach (21), while it is 29 in rice (Table 1). The gene number in each family of peach does not differ much from that of other species, despite the fact that peach has a large genome of 220-230 Mbp (Jung et al, 2008), which is larger than that of A. thaliana (145 Mbp) (Huala et al, 2001) and shorter than that of Oryza sativa (430 Mbp) (Goff et al, 2002), cucumber (367 Mbp) (Ren et al, 2009), and grapevine (475 Mb) (Velasco et al, 2007). This observation is clearly illustrated by the gene numbers in the RAV family, which remain relatively constant among most species.…”

“…The numbers, names, and locations of the conserved domains contained in each AP2/ERF protein sequence of peach were also recorded. Finally, CDS sequences corresponding to the predicted AP2/ERF superfamily proteins were extracted from total CDS sequences of peach downloaded from the GDR database (Jung et al, 2008).…”

“…The distinct advantages of peach make it suitable as a model genome species for Prunus, as well as for other species in the Rosaceae. Since the release of the peach genome sequence in 2010, current estimates indicate that peach has 28,689 transcripts and 27,852 genes (Jung et al, 2008). However, the biological functions of only a few of these genes are well known.…”

Genome-wide analysis of the homeodomain-leucine zipper (HD-ZIP) gene family in peach (Prunus persica)

“…The numbers, names, and locations of conserved domains that were contained in each HD-ZIP protein sequence of peach were also recorded. Finally, coding DNA sequences (CDSs) corresponding to the HD-ZIP family proteins that were predicted above were extracted from total CDSs of peach and downloaded from the GDR database (Jung et al, 2008).…”

“…In addition to its ecological and high economic importance, peach is also emerging as a model tree species for comparative genomic studies, evolutionary studies, and plant development research because of its small genome size of 220-230 Mbp (about twice the size of the A. thaliana genome) and the relatively short reproductive time. Since the release of the peach genome sequence in 2010, current estimates indicate that peach has 28,689 transcripts and 27,852 genes (Jung et al, 2008). The functional annotation of these genes predicted that peach also contains some HD-ZIP genes.…”