PeanutDB: an integrated bioinformatics web portal for Arachis hypogaea transcriptomics

BMC Plant Biology

Database

Lin Liu¹  Pei Li¹  Douglas Lenox²  Chun Liang²  Emily Schmidt²  Jie Zhang³  Changlong Shu³  Xiaohong Duan³ 

[1] Department of Botany, Miami University, 45056, Oxford, OH, USA;Department of Botany, Miami University, 45056, Oxford, OH, USA;Department of Computer Science and Software Engineering, Miami University, 45056, Oxford, OH, USA;State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, 100193, Beijing, China;

关键词: Peanut;    Arachis hypogaea;    Transcriptome sequencing;    Transcriptome assembly;    Database;    PeanutDB;    SNP;    SSR;    Functional annotation;   

DOI  :  10.1186/1471-2229-12-94

 received in 2012-02-05, accepted in 2012-06-05,  发布年份 2012

来源: Springer

【 摘 要 】

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.

【 授权许可】

Unknown   
© Duan et al.; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.