This article is part of the supplement: Computational Intelligence in Bioinformatics and Biostatistics: new trends from the CIBB conference series

Open Access Research

Expression dynamics and genome distribution of osmoprotectants in soybean: identifying important components to face abiotic stress

Ederson A Kido1, José RC Ferreira Neto1, Roberta LO Silva1, Luis C Belarmino1, João P Bezerra Neto1, Nina M Soares-Cavalcanti1, Valesca Pandolfi1, Manassés D Silva1, Alexandre L Nepomuceno2 and Ana M Benko-Iseppon1*

Author Affiliations

1 Departament of Genetics/Biological Sciences Center, Federal University of Pernambuco, Recife, Pernambuco, CEP 50.670-420, Brazil

2 Embrapa Soybean, Brazilian Agricultural Research Corporation, Londrina, PR, CEP 86001-970, Brazil

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BMC Bioinformatics 2013, 14(Suppl 1):S7  doi:10.1186/1471-2105-14-S1-S7

Published: 14 January 2013

Additional files

Additional file 1:

Table S1. BLASTx (Identity % and e-value) results regarding nucleotide sequences involved in the biosynthesis pathway and corresponding best hit (cut-off e-10) in the Uniprot-SwissProt and Phytozome (v.8 Glycine max) databases, represented by the respective loci/transcripts in soybean (Glyma) as well as their annotation.

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Additional file 2:

Table S2. BLASTn results (Identity %, e-value) using HT-SuperSAGE 26-bp tags against Glycine max seed sequences given in Table S1. Libraries consisted of soybean cultivar Embrapa 48, tolerant (T) against drought, with roots submitted to water deficit after 1-6 h of stress submission (TS) as compared with the tolerant non stressed control (TC). The same treatment was given to the drought sensible cultivar (BR-16) considering stressed (SS) and its respective control (SC). Tag annotation occurred against transcripts on the soybean Phytozome database. For each library normalized frequencies were considered (tpm: tags per million). Regarding comparisons among different treatments, fold change (FC), regulation (reg) [including upregulated (UR, in red) downregulated (DR, in green) and also non significant differential expression (ns), at 5% level] are given, as well as the tag-mapping position in the respective soybean transcript (Glyma).

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Additional file 3:

Table S3. Main soybean transcripts similar to known osmoprotectants-genes (I.) from Arabidopsis thaliana (used as seed sequences). II. tBLASTn results and sequence evaluation of soybean Osmoprotectants-genes. Information available include number of hits, best match of each gene class and features of hits: size range (maximal and minimal) in nucleotides (n), ORF (Open Reading Frame) size range in amino-acids (aa), e-value range based on SoyBase web resource, as well as number of matching HT-SuperSAGE tags.

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