Publication Date:
2012-06-26
Description:
Background: The peanut (Arachis hypogaea) is an important crop cultivated worldwide for oil productionand food sources. Its complex genetic architecture (e.g., the large and tetraploid genomepossibly due to unique cross of wild diploid relatives and subsequent chromosomeduplication: 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 isthe most effective way to harness the genome structure and gene expression dynamics of thisnon-model species that has a limited genomic resource.DescriptionWith the development of next generation sequencing technologies such as 454 pyrosequencingand Illumina sequencing by synthesis, the transcriptomics data of peanut israpidly accumulated in both the public databases and private sectors. Integrating 187,636Sanger reads (103,685,419 bases), 1,165,168 Roche 454 reads (333,862,593 bases) and57,135,995 Illumina reads (4,073,740,115 bases), we generated the first release of our peanuttranscriptome assembly that contains 32,619 contigs. We provided EC, KEGG and GOfunctional annotations to these contigs and detected SSRs, SNPs and other geneticpolymorphisms for each contig. Based on both open-source and our in-house tools, PeanutDBpresents many seamlessly integrated web interfaces that allow users to search, filter, navigateand visualize easily the whole transcript assembly, its annotations and detectedpolymorphisms and simple sequence repeats. For each contig, sequence alignment ispresented in both bird¿s-eye view and nucleotide level resolution, with colorfully highlightedregions of mismatches, indels and repeats that facilitate close examination of assemblyquality, genetic polymorphisms, sequence repeats and/or sequencing errors. Conclusion: As a public genomic database that integrates peanut transcriptome data from differentsources, PeanutDB (http://bioinfolab.muohio.edu/txid3818v1) provides the Peanut researchcommunity with an easy-to-use web portal that will definitely facilitate genomics researchand molecular breeding in this less-studied crop.
Electronic ISSN:
1471-2229
Topics:
Biology
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