A web-based bioinformatics interface applied to the GENOSOJA project: databases and pipelines

Nascimento, Leandro Costa do; Costa, Gustavo G.L.; Binneck, Eliseu; Pereira, Gonçalo Amarante Guimarães; Carazzolle, Marcelo Falsarella

doi:10.1590/s1415-47572012000200002

Cited by 12 publications

(16 citation statements)

References 22 publications

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“…Using the DESeq Bioconductor package [ 35 ], a FPKM cut-off value of 0.5 was employed to define the unigenes expressed in sequenced samples [ 36 ], and the expression levels of the selected reciprocal hits were analyzed for statistical significance. P-value < 0.05 was adjusted for multiple testing in this study.…”

Section: Resultsmentioning

confidence: 99%

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

Gan

Chao

et al. 2016

PLoS ONE

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Kentucky bluegrass (Poa pratensis L.) is a major cool-season turfgrass requiring frequent mowing. Utilization of cultivars with slow growth is a promising method to decrease mowing frequency. In this study, two dwarf mutant selections of Kentucky bluegrass (A12 and A16) induced by space mutation were analyzed for the differentially expressed genes compared with the wild type (WT) by the high-throughput RNA-Seq technology. 253,909 unigenes were obtained by de novo assembly. 24.20% of the unigenes had a significant level of amino acid sequence identity to Brachypodium distachyon proteins, followed by Hordeum vulgare with 18.72% among the non-redundant (NR) Blastx top hits. Assembled unigenes were associated with 32 pathways using KEGG orthology terms and their respective KEGG maps. Between WT and A16 libraries, 4,203 differentially expressed genes (DEGs) were identified, whereas there were 883 DEGs between WT and A12 libraries. Further investigation revealed that the DEG pathways were mainly involved in terpenoid biosynthesis and plant hormone metabolism, which might account for the differences of plant height and leaf blade color between dwarf mutant and WT plants. Our study presents the first comprehensive transcriptomic data and gene function analysis of Poa pratensis L., providing a valuable resource for future studies in plant dwarfing breeding and comparative genome analysis for Pooideae plants.

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Section: Resultsmentioning

confidence: 99%

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

Gan

Chao

et al. 2016

PLoS ONE

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“…The reads from sequencing were aligned against the GENOSOJA database (http://www.lge.ibi.unicamp.br/soybean) [61]. The generated sequences were assembled and preliminarily analyzed at the LGE (Laboratory of Genomic and Expression at UNICAMP, Campinas, São Paulo, Brazil).…”

Section: Methodsmentioning

confidence: 99%

Transcriptional analysis of genes involved in nodulation in soybean roots inoculated with Bradyrhizobium japonicumstrain CPAC 15

et al. 2013

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BackgroundBiological nitrogen fixation in root nodules is a process of great importance to crops of soybean [Glycine max (L.) Merr.], as it may provide the bulk of the plant’s needs for nitrogen. Legume nodulation involves several complex steps and, although studied for many decades, much remains to be understood.ResultsThis research aimed at analyzing the global expression of genes in soybean roots of a Brazilian cultivar (Conquista) inoculated with Bradyrhizobium japonicum CPAC 15, a strain broadly used in commercial inoculants in Brazil. To achieve this, we used the suppressive subtractive hybridization (SSH) technique combined with Illumina sequencing. The subtractive library (non-inoculated x inoculated) of soybean roots resulted in 3,210 differentially expressed transcripts at 10 days after inoculation were studied. The data were grouped according to the ontologies of the molecular functions and biological processes. Several classes of genes were confirmed as related to N2 fixation and others were reported for the first time.ConclusionsDuring nodule formation, a higher percentage of genes were related to primary metabolism, cell-wall modifications and the antioxidant defense system. Putative symbiotic functions were attributed to some of these genes for the first time.

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“…To construct the subtractive libraries, the samples were grouped, and the L1 (25 and 50 min of dehydration), L2 (75 and 100 min of dehydration), and L3 (125 and 150 min of dehydration) leaf samples and the corresponding R1, R2, and R3 root samples were formed. The differentially expressed transcripts that were obtained were sequenced by Next Generation Sequencing, and the data were deposited in the Genosoja Soybean Database (http://lge.ibi.unicamp.br/soybean) [26], which was created by a Brazilian Consortium for the Soybean Genome (Genosoja project) and used to search for differentially expressed genes. For the qPCR analysis, we used the same experimental design, but each period of exposure to dehydration (25, 50, 75, 100, 125, and 150 min) was evaluated individually.…”

Section: Methodsmentioning

confidence: 99%

Expression Patterns of GmAP2/EREB-Like Transcription Factors Involved in Soybean Responses to Water Deficit

et al. 2013

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Soybean farming has faced several losses in productivity due to drought events in the last few decades. However, plants have molecular mechanisms to prevent and protect against water deficit injuries, and transcription factors play an important role in triggering different defense mechanisms. Understanding the expression patterns of transcription factors in response to water deficit and to environmental diurnal changes is very important for unveiling water deficit stress tolerance mechanisms. Here, we analyzed the expression patterns of ten APETALA2/Ethylene Responsive Element Binding-like (AP2/EREB-like) transcription factors in two soybean genotypes (BR16: drought-sensitive; and Embrapa 48: drought-tolerant). According to phylogenetic and domain analyses, these genes can be included in the DREB and ERF subfamilies. We also analyzed a GmDRIP-like gene that encodes a DREB negative regulator. We detected the up-regulation of 9 GmAP2/EREB-like genes and identified transcriptional differences that were dependent on the levels of the stress applied and the tissue type analyzed (the expression of the GmDREB1F-like gene, for example, was four times higher in roots than in leaves). The GmDRIP-like gene was not induced by water deficit in BR16 during the longest periods of stress, but was significantly induced in Embrapa 48; this suggests a possible genetic/molecular difference between the responses of these cultivars to water deficit stress. Additionally, RNAseq gene expression analysis over a 24-h time course indicates that the expression patterns of several GmDREB-like genes are subject to oscillation over the course of the day, indicating a possible circadian regulation.

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A web-based bioinformatics interface applied to the GENOSOJA project: databases and pipelines

Cited by 12 publications

References 22 publications

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

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

Transcriptional analysis of genes involved in nodulation in soybean roots inoculated with Bradyrhizobium japonicumstrain CPAC 15

Expression Patterns of GmAP2/EREB-Like Transcription Factors Involved in Soybean Responses to Water Deficit

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