A Web-based Bioinformatics Interface Applied to the GENOSOJA Project: Databases and Pipelines

Overview

Journal Genet Mol Biol

Specialty Genetics

Date 2012 Jul 18

PMID 22802706

Citations 12

Authors

Leandro Costa do Nascimento

Gustavo Gilson Lacerda Costa

Eliseu Binneck

Goncalo Amarante Guimaraes Pereira

Marcelo Falsarella Carazzolle

Affiliations

Soon will be listed here.

Abstract

The Genosoja consortium is an initiative to integrate different omics research approaches carried out in Brazil. Basically, the aim of the project is to improve the plant by identifying genes involved in responses against stresses that affect domestic production, like drought stress and Asian Rust fungal disease. To do so, the project generated several types of sequence data using different methodologies, most of them sequenced by next generation sequencers. The initial stage of the project is highly dependent on bioinformatics analysis, providing suitable tools and integrated databases. In this work, we describe the main features of the Genosoja web database, including the pipelines to analyze some kinds of data (ESTs, SuperSAGE, microRNAs, subtractive cDNA libraries), as well as web interfaces to access information about soybean gene annotation and expression.

Citing Articles

Harnessing the Potential of Forage Legumes, Alfalfa, Soybean, and Cowpea for Sustainable Agriculture and Global Food Security.

Kulkarni K, Tayade R, Asekova S, Song J, Shannon J, Lee J Front Plant Sci. 2018; 9:1314.

PMID: 30283466 PMC: 6157451. DOI: 10.3389/fpls.2018.01314.

De Novo Transcriptome Analysis for Kentucky Bluegrass Dwarf Mutants Induced by Space Mutation.

Gan L, Di R, Chao Y, Han L, Chen X, Wu C PLoS One. 2016; 11(3):e0151768.

PMID: 27010560 PMC: 4807101. DOI: 10.1371/journal.pone.0151768.

Abscisic-acid-dependent basic leucine zipper (bZIP) transcription factors in plant abiotic stress.

Banerjee A, Roychoudhury A Protoplasma. 2015; 254(1):3-16.

PMID: 26669319 DOI: 10.1007/s00709-015-0920-4.

Implications of ethylene biosynthesis and signaling in soybean drought stress tolerance.

Arraes F, Beneventi M, Lisei de Sa M, Roca Paixao J, Saliba Albuquerque E, Marin S BMC Plant Biol. 2015; 15:213.

PMID: 26335593 PMC: 4557918. DOI: 10.1186/s12870-015-0597-z.

Early transcriptional response of soybean contrasting accessions to root dehydration.

Ferreira Neto J, Pandolfi V, Guimaraes F, Benko-Iseppon A, Romero C, de Oliveira Silva R PLoS One. 2013; 8(12):e83466.

PMID: 24349513 PMC: 3861472. DOI: 10.1371/journal.pone.0083466.

References

Wanderley-Nogueira A, Belarmino L, Soares-Cavalcanti N, Bezerra-Neto J, Kido E, Pandolfi V . An overall evaluation of the Resistance (R) and Pathogenesis-Related (PR) superfamilies in soybean, as compared with Medicago and Arabidopsis. Genet Mol Biol. 2012; 35(1 (suppl)):260-71. PMC: 3392878. DOI: 10.1590/S1415-47572012000200007. View

Jenkinson A, Albrecht M, Birney E, Blankenburg H, Down T, Finn R . Integrating biological data--the Distributed Annotation System. BMC Bioinformatics. 2008; 9 Suppl 8:S3. PMC: 2500094. DOI: 10.1186/1471-2105-9-S8-S3. View

Molina L, da Fonseca G, Loss de Morais G, de Oliveira L, de Carvalho J, Kulcheski F . Metatranscriptomic analysis of small RNAs present in soybean deep sequencing libraries. Genet Mol Biol. 2012; 35(1 (suppl)):292-303. PMC: 3392881. DOI: 10.1590/S1415-47572012000200010. View

Koski L, Gray M, Lang B, Burger G . AutoFACT: an automatic functional annotation and classification tool. BMC Bioinformatics. 2005; 6:151. PMC: 1182349. DOI: 10.1186/1471-2105-6-151. View

Umezawa T, Sakurai T, Totoki Y, Toyoda A, Seki M, Ishiwata A . Sequencing and analysis of approximately 40,000 soybean cDNA clones from a full-length-enriched cDNA library. DNA Res. 2008; 15(6):333-46. PMC: 2608845. DOI: 10.1093/dnares/dsn024. View

Audic S, Claverie J . The significance of digital gene expression profiles. Genome Res. 1997; 7(10):986-95. DOI: 10.1101/gr.7.10.986. View

Wang L, Feng Z, Wang X, Wang X, Zhang X . DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics. 2009; 26(1):136-8. DOI: 10.1093/bioinformatics/btp612. View

Rodrigues F, Marcolino-Gomes J, de Fatima Correa Carvalho J, do Nascimento L, Neumaier N, Farias J . Subtractive libraries for prospecting differentially expressed genes in the soybean under water deficit. Genet Mol Biol. 2012; 35(1 (suppl)):304-14. PMC: 3392882. DOI: 10.1590/S1415-47572012000200011. View

Kanehisa M, Goto S . KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 1999; 28(1):27-30. PMC: 102409. DOI: 10.1093/nar/28.1.27. View

10.

Cheng K, Stromvik M . SoyXpress: a database for exploring the soybean transcriptome. BMC Genomics. 2008; 9:368. PMC: 2536680. DOI: 10.1186/1471-2164-9-368. View

11.

Kulcheski F, de Oliveira L, Molina L, Almerao M, Rodrigues F, Marcolino J . Identification of novel soybean microRNAs involved in abiotic and biotic stresses. BMC Genomics. 2011; 12:307. PMC: 3141666. DOI: 10.1186/1471-2164-12-307. View

12.

Suzek B, Huang H, McGarvey P, Mazumder R, Wu C . UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics. 2007; 23(10):1282-8. DOI: 10.1093/bioinformatics/btm098. View

13.

Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy S . The Pfam protein families database. Nucleic Acids Res. 2001; 30(1):276-80. PMC: 99071. DOI: 10.1093/nar/30.1.276. View

14.

Dowell R, Jokerst R, Day A, Eddy S, Stein L . The distributed annotation system. BMC Bioinformatics. 2001; 2:7. PMC: 58584. DOI: 10.1186/1471-2105-2-7. View

15.

Schmutz J, Cannon S, Schlueter J, Ma J, Mitros T, Nelson W . Genome sequence of the palaeopolyploid soybean. Nature. 2010; 463(7278):178-83. DOI: 10.1038/nature08670. View

16.

Yorinori J, Paiva W, Frederick R, Costamilan L, Bertagnolli P, Hartman G . Epidemics of Soybean Rust (Phakopsora pachyrhizi) in Brazil and Paraguay from 2001 to 2003. Plant Dis. 2019; 89(6):675-677. DOI: 10.1094/PD-89-0675. View

17.

Li R, Yu C, Li Y, Lam T, Yiu S, Kristiansen K . SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics. 2009; 25(15):1966-7. DOI: 10.1093/bioinformatics/btp336. View

18.

Altschul S, Madden T, Schaffer A, Zhang J, Zhang Z, Miller W . Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997; 25(17):3389-402. PMC: 146917. DOI: 10.1093/nar/25.17.3389. View

19.

Smith T, Waterman M . Identification of common molecular subsequences. J Mol Biol. 1981; 147(1):195-7. DOI: 10.1016/0022-2836(81)90087-5. View

20.

Huang X, Madan A . CAP3: A DNA sequence assembly program. Genome Res. 1999; 9(9):868-77. PMC: 310812. DOI: 10.1101/gr.9.9.868. View