The Genome Database for Rosaceae (GDR): year 10 update

Abstract

The Genome Database for Rosaceae (GDR, http:/www.rosaceae.org), the long-standing central repository and data mining resource for Rosaceae research, has been enhanced with new genomic, genetic and breeding data, and improved functionality. Whole genome sequences of apple, peach and strawberry are available to browse or download with a range of annotations, including gene model predictions, aligned transcripts, repetitive elements, polymorphisms, mapped genetic markers, mapped NCBI Rosaceae genes, gene homologs and association of InterPro protein domains, GO terms and Kyoto Encyclopedia of Genes and Genomes pathway terms. Annotated sequences can be queried using search interfaces and visualized using GBrowse. New expressed sequence tag unigene sets are available for major genera, and Pathway data are available through FragariaCyc, AppleCyc and PeachCyc databases. Synteny among the three sequenced genomes can be viewed using GBrowse_Syn. New markers, genetic maps and extensively curated qualitative/Mendelian and quantitative trait loci are available. Phenotype and genotype data from breeding projects and genetic diversity projects are also included. Improved search pages are available for marker, trait locus, genetic diversity and publication data. New search tools for breeders enable selection comparison and assistance with breeding decision making.

MYB107 and MYB9 Homologs Regulate Suberin Deposition in Angiosperms

“…Data were acquired for the various species from the following databases, making use of the gene IDs curated by these databases: SOL Genomics Network database (Fernandez-Pozo et al, 2015), Grape Genome Database (Vitulo et al, 2014), Spud DB (Hirsch et al, 2014), The Arabidopsis Information Resource (Lamesch et al, 2012), Rice Genome Annotation Project (Kawahara et al, 2013), and Genome Database for Rosaceae (Jung et al, 2014). Orthology between species was determined via alignment of relevant protein sequences with the ortholog database from the PLAZA Comparative Genomics Platform (Proost et al, 2015).…”

“…Library preparation was performed according to previously described methods (Zhong et al, 2011) and samples run on the Illumina HiSeq 2000 under default parameters generating 50-bp single end reads. Reads were mapped to either the apple (Malus x domestica; Jung et al, 2014), tomato (Fernandez-Pozo et al, 2015), or Arabidopsis (Lamesch et al, 2012) predicted transcriptome according to methods described previously (Itkin et al, 2013), generating normalized RPKM values for each gene.…”

Analysis of codon usage patterns inMorus notabilisbased on genome and transcriptome data

“…The genome and coding sequences (CDSs) were obtained from the Morus genome database (Tian et al 2014), Genome Database for Rosaceae (Jung et al 2013), and GenBank. CDSs that contained premature translation termination codons were ruled out and only those that had correct initiation codons and termination codons were included in the dataset.…”

Isolation, cloning, and expression of five genes related to nitrogen metabolism in peach (Prunus persicaL. Batsch)

“…These sequences were used as queries to BLAST-search the peach genome database (https://www.rosaceae.org/peach/genome; Jung et al, 2014) to identify homologous genes in peach. The coding sequences (CDS) of the five genes identified in peach (Gene ID: Ppa003265m, Ppa006457m, Ppa007728m, Ppa003315m, and Ppa001113m) were obtained from the Genome Database for Rosaceae (GDR; https://www.rosaceae.org/peach/genome).…”