Abstract
BackgroundThe peanut (Arachis hypogaea) is an important crop cultivated worldwide for oil production and food sources. Its complex genetic architecture (e.g., the large and tetraploid genome possibly due to unique cross of wild diploid relatives and subsequent chromosome duplication: 2n = 4x = 40, AABB, 2800 Mb) presents a major challenge for its genome sequencing and makes it a less-studied crop. Without a doubt, transcriptome sequencing is the most effective way to harness the genome structure and gene expression dynamics of this non-model species that has a limited genomic resource.DescriptionWith the development of next generation sequencing technologies such as 454 pyro-sequencing and Illumina sequencing by synthesis, the transcriptomics data of peanut is rapidly accumulated in both the public databases and private sectors. Integrating 187,636 Sanger reads (103,685,419 bases), 1,165,168 Roche 454 reads (333,862,593 bases) and 57,135,995 Illumina reads (4,073,740,115 bases), we generated the first release of our peanut transcriptome assembly that contains 32,619 contigs. We provided EC, KEGG and GO functional annotations to these contigs and detected SSRs, SNPs and other genetic polymorphisms for each contig. Based on both open-source and our in-house tools, PeanutDB presents many seamlessly integrated web interfaces that allow users to search, filter, navigate and visualize easily the whole transcript assembly, its annotations and detected polymorphisms and simple sequence repeats. For each contig, sequence alignment is presented in both bird’s-eye view and nucleotide level resolution, with colorfully highlighted regions of mismatches, indels and repeats that facilitate close examination of assembly quality, genetic polymorphisms, sequence repeats and/or sequencing errors.ConclusionAs a public genomic database that integrates peanut transcriptome data from different sources, PeanutDB (http://bioinfolab.muohio.edu/txid3818v1) provides the Peanut research community with an easy-to-use web portal that will definitely facilitate genomics research and molecular breeding in this less-studied crop.
Highlights
ConclusionAs a public genomic database that integrates peanut transcriptome data from different sources, PeanutDB (http://bioinfolab.muohio.edu/txid3818v1) provides the Peanut research community with an easy-to-use web portal that will definitely facilitate genomics research and molecular breeding in this less-studied crop
The peanut (Arachis hypogaea) is an important crop cultivated worldwide for oil production and food sources
We provided Gene Ontology (GO), Enzyme Commission (EC) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation to these contigs, and identified extensively the potential polymorphisms, both single base (e.g., Single Nucleotide Polymorphism (SNP) and single indels) and multiple bases, and simple sequences repeats for each contig
Summary
With many easy-to-use and powerful web tools, PeanutDB provides the research community with a bioinformatics platform that will empower individual researchers in data integration, visualization and analysis/ mining. Incorporating the most comprehensive datasets of peanut transcriptome sequences, our database is capable to present a new perspective about peanut genome dynamics. Using both open-source and our in-house tools, PeanutDB presents many seamlessly integrated web interfaces that allow users to search, filter, navigate and visualize the whole transcript assembly, its annotations, and detected polymorphisms and simple sequence repeats. We have tested our web interfaces using Google Chrome, Mozilla FireFox (8.0 or above) and Microsoft Internet Explorer (9.0 or above). For the best visualization effect and performance, we recommend Google Chrome and Mozilla FireFox. PeanutDB has an open access and all data can be downloaded through the website.
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