Duan X, Schmidt E, Li P, Lenox D, Liu L, Shu C, Zhang J and Liang C (2012) PeanutDB: An integrated bioinformatics web portal for Arachis hypogaea transcriptomics.
BMC Plant Biology, 12:94
As in July 15, 2011, there were a total of 198,156 nucleotide sequences for Arachis hypogaea in NCBI GenBank, including 39,854 Nucleotide (Core Nucleotide Sequences), 150,177 EST (Expressed Sequence Tag), and 8,125 GSS (Genome Survey Sequence). Based on previously available 79,559 Sanger ESTs and 37,621 mRNAs, NCBI UniGene Build#2 was developed on Jon 09 2011, which contains 33,015 UniGene clusters, with 17,256 singletons that are supported by only one cDNA or mRNA read.
With the next generation sequencing like 454 pyrosequencing and Illumina SBS, more and more genomics resources are being generated for peanut. For example, there are a total of 596.5 million bases (3.6 GB) 454 ESTs available in NCBI SRA. Recently, Illumina sequencing of peanut transcriptome has been conducted in Institute of Plant Protection, Chinese Academy of Agricultural Sciences and generated a total of 5 GB sequence data (~80 million reads) for peanut.
As a public genomic database that integrates peanut transcriptomics data from different sources (i.e., Sanger, 454 and Illumina sequences), PeanutDB currently focuses on the transcriptomics analysis of Arachis hypogaea. Using all aformentioned cDNA and mRNA data, we have created our first release of peanut transriptome assembly consisting of 32,619 contigs. Not only we provided GO, KEGG and EC annotation to these contigs, but also we identified extensively the potential polymorphisms, both single base (e.g., SNPs and single indel) and multiple bases (e.g., mismatches/indels of multiple bases), and simple sequence repeats for each contig.
Currently, development of PeanutDB is a collabortion project between Liang Lab at Miami University, Ohio, USA and Institute of Plant Protection, Chinese Academy of Agricultural Sciences, China. We are open to more collabration from the peanut research community worldwide, with the goal of making PeanutDB an open-access, biologist-friendly bioinformatics web portal that will facilitate genomics, proteomics, metabolomics researches in peanut.