WGS of Aspergillus calidoustus
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| CDMC01.dat.gz | Other | |||
| CDMC01.fasta.gz | Fasta.gz | |||
| CDMC01.master.dat | Other | |||
| ERR675099_1.fastq.gz | Fastqsanger.gz | |||
| ERR675099_2.fastq.gz | Fastqsanger.gz |
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Project description:Vongsangnak2008 - Genome-scale metabolic
network of Aspergillus oryzae (iWV1314)
This model is described in the article:
Improved annotation through
genome-scale metabolic modeling of Aspergillus oryzae.
Vongsangnak W, Olsen P, Hansen K,
Krogsgaard S, Nielsen J.
BMC Genomics 2008; 9: 245
Abstract:
BACKGROUND: Since ancient times the filamentous fungus
Aspergillus oryzae has been used in the fermentation industry
for the production of fermented sauces and the production of
industrial enzymes. Recently, the genome sequence of A. oryzae
with 12,074 annotated genes was released but the number of
hypothetical proteins accounted for more than 50% of the
annotated genes. Considering the industrial importance of this
fungus, it is therefore valuable to improve the annotation and
further integrate genomic information with biochemical and
physiological information available for this microorganism and
other related fungi. Here we proposed the gene prediction by
construction of an A. oryzae Expressed Sequence Tag (EST)
library, sequencing and assembly. We enhanced the function
assignment by our developed annotation strategy. The resulting
better annotation was used to reconstruct the metabolic network
leading to a genome scale metabolic model of A. oryzae.
RESULTS: Our assembled EST sequences we identified 1,046 newly
predicted genes in the A. oryzae genome. Furthermore, it was
possible to assign putative protein functions to 398 of the
newly predicted genes. Noteworthy, our annotation strategy
resulted in assignment of new putative functions to 1,469
hypothetical proteins already present in the A. oryzae genome
database. Using the substantially improved annotated genome we
reconstructed the metabolic network of A. oryzae. This network
contains 729 enzymes, 1,314 enzyme-encoding genes, 1,073
metabolites and 1,846 (1,053 unique) biochemical reactions. The
metabolic reactions are compartmentalized into the cytosol, the
mitochondria, the peroxisome and the extracellular space.
Transport steps between the compartments and the extracellular
space represent 281 reactions, of which 161 are unique. The
metabolic model was validated and shown to correctly describe
the phenotypic behavior of A. oryzae grown on different carbon
sources. CONCLUSION: A much enhanced annotation of the A.
oryzae genome was performed and a genome-scale metabolic model
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This model is hosted on
BioModels Database
and identified by:
MODEL1507180056.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2015-07-30 | MODEL1507180056 | BioModels
Project description:Investigation of whole genome gene expression level changes in Aspergillus nidulans OE::rsmA compared to wild-type RDIT9.32 (veA).
2012-01-17 | GSE34220 | GEO
Project description:Aspergillus display an amazing level of diversity in physiologies, and environments that they occupy. Strategies for coping with diverse environmental stresses have evolved in different Aspergillus species. Therefore, Aspergillus are considered to be good models for investigating the adaptation and response to many natural and anthropogenic environmental stressors. Recent genome sequencing projects in several Aspergillus have provided insights into the molecular and genetic mechanisms underlying their responses to some environmental stressors. However, to better clarify the conserved and differentiated features of the adaptive response to specific stresses and to trace the evolutionary process of environmental adaptation and response in Aspergillus, insight from more Aspergillus species with different evolutionary positions, such as A. glaucus, and thus offer a large number of models of adaptation and response to various environmental stresses. Here, we report a high-quality reference genome assembly of A. glaucus CCHA from the surface of wild vegetation around saltern of Jilin, China, based on sequence data from whole-genome shotgun (WGS) sequencing platforms of Illumina solexa technologies. This assembly contains 106 scaffolds ( >1 Kb; N50 = ~0.795 Mb), has a length of ~28.9 Mb and covers ~97% of the predicted genome size (~120 Mb). Together with the data analyses from comprehensive transcriptomic surveys and comparative genomic analyses, we aim to obtain new insights into molecular mechanisms of the adaptation to living at high salt in the saltern
2017-09-26 | GSE104102 | GEO
Project description:Investigation of whole genome gene expression level changes in Aspergillus nidulans AN1599 (PbcR) overexpression mutant, compared to the FGSC A4 wild-type strain. Overexpression of the Zn(II)2Cys6 –type transcription factor, AN1599.4 (PbcR, pimaradiene biosynthetic cluster regulator), activates a secondary metabolite gene cluster in Aspergillus nidulans. Activation of the pathway in Aspergillus nidulans lead to a production of ent-pimara-8(14),15-diene.
2012-04-16 | GSE32954 | GEO
Project description:David2008 - Genome-scale metabolic network of
Aspergillus nidulans (iHD666)
This model is described in the article:
Analysis of Aspergillus
nidulans metabolism at the genome-scale.
David H, Ozçelik IS, Hofmann G,
Nielsen J.
BMC Genomics 2008; 9: 163
Abstract:
BACKGROUND: Aspergillus nidulans is a member of a diverse
group of filamentous fungi, sharing many of the properties of
its close relatives with significance in the fields of
medicine, agriculture and industry. Furthermore, A. nidulans
has been a classical model organism for studies of development
biology and gene regulation, and thus it has become one of the
best-characterized filamentous fungi. It was the first
Aspergillus species to have its genome sequenced, and automated
gene prediction tools predicted 9,451 open reading frames
(ORFs) in the genome, of which less than 10% were assigned a
function. RESULTS: In this work, we have manually assigned
functions to 472 orphan genes in the metabolism of A. nidulans,
by using a pathway-driven approach and by employing comparative
genomics tools based on sequence similarity. The central
metabolism of A. nidulans, as well as biosynthetic pathways of
relevant secondary metabolites, was reconstructed based on
detailed metabolic reconstructions available for A. niger and
Saccharomyces cerevisiae, and information on the genetics,
biochemistry and physiology of A. nidulans. Thereby, it was
possible to identify metabolic functions without a gene
associated, and to look for candidate ORFs in the genome of A.
nidulans by comparing its sequence to sequences of
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of interest. A classification system, based on defined
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among the candidates, in an objective and systematic manner.
The functional assignments served as a basis to develop a
mathematical model, linking 666 genes (both previously and
newly annotated) to metabolic roles. The model was used to
simulate metabolic behavior and additionally to integrate,
analyze and interpret large-scale gene expression data
concerning a study on glucose repression, thereby providing a
means of upgrading the information content of experimental data
and getting further insight into this phenomenon in A.
nidulans. CONCLUSION: We demonstrate how pathway modeling of A.
nidulans can be used as an approach to improve the functional
annotation of the genome of this organism. Furthermore we show
how the metabolic model establishes functional links between
genes, enabling the upgrade of the information content of
transcriptome data.
This model is hosted on
BioModels Database
and identified by:
MODEL1507180016.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2015-07-30 | MODEL1507180016 | BioModels
Project description:Given the facilities for whole genome sequencing with next-generation sequencers, structural and functional gene annotation is now only based on automated prediction. However, errors in terms of gene structure are still frequently reported especially for the correct determination of initiation start codons. Here, we propose a strategy to enrich and detect protein N-termini by mass spectrometry in order to refine genome annotation. After selective protein N-termini derivatization using (N-Succinimidyloxycarbonylmethyl)tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPPAc-OSu) as labeling reagent, protein digestion was performed with three proteases in parallel. TMPP-labeled N-terminal-most peptides were further resolved from internal peptides by the COmbined FRActional DIagonal Chromatography (COFRADIC) sorting methodology before analysis with tandem mass spectrometry. We refined the annotation of the genome of a model marine bacterium, Roseobacter denitrificans.
2014-02-19 | PXD000337 | Pride
Project description:Investigation of whole genome gene expression level changes in Aspergillus nidulans OE::rsmA compared to wild-type RDIT9.32 (veA). A twelve array study using total RNA recovered from six separate cultures of Aspergillus nidulans wild-type RDIT9.32 (veA) and six separate cultures of Aspergillus nidulans overexpressing rsmA (restorer of secondary metabolism A), using custom-designed, four-plex arrays. The experiment was divided into two runs. In the first run, three biological replicates each of Aspergillus nidulans wild-type RDIT9.32 (veA) and Aspergillus nidulans carrying a plasmid overexpressing rsmA under the control of the gpdA promoter were assayed. In the second run, three biological replicates each of Aspergillus nidulans wild-type RDIT9.32 (veA) and Aspergillus nidulans overexpressing rsmA at the native locus under the control of the gpdA promoter were assayed.
2012-01-17 | E-GEOD-34220 | biostudies-arrayexpress
Project description:Using transcriptomics, the strain-specific metabolism was mapped for two whole-genome sequenced strains of Aspergillus niger Keywords: Strain comparison
2011-03-07 | GSE10983 | GEO
Project description:Lack of comprehensive genome structural- and functional-annotation significantly prevents researchers from exploiting the full potential of the chicken genome model system for comparative and functional genomic studies. Comprehensive genome structural- and functional-annotation must be made easily accessible for the chicken genome sequence to reach its full potential to contribute to human health and well-being. To this end we collected a variety of tissues from 2 (1 male, 1 female) healthy 2-year-old red jungle fowls. We performed mRNA sequencing, small RNA sequencing, proteomics and proteogeomic mapping on each of these tissues to further elucidate tissue and sex specific expression and to improve upon current gene models.
2015-12-16 | E-MTAB-1826 | biostudies-arrayexpress
Project description:Investigation of whole genome gene expression level changes in Aspergillus nidulans AN1599 (PbcR) overexpression mutant, compared to the FGSC A4 wild-type strain. Overexpression of the Zn(II)2Cys6 M-bM-^@M-^Stype transcription factor, AN1599.4 (PbcR, pimaradiene biosynthetic cluster regulator), activates a secondary metabolite gene cluster in Aspergillus nidulans. Activation of the pathway in Aspergillus nidulans lead to a production of ent-pimara-8(14),15-diene. 12x135K array of two separate cultures of FGSC A4 and two separate cultures of oe:AN1599(PbcR) with three separate RNA extractions from each culture. Each 135K array measures expression level of 10,546 genes with 6 probes/transcript. In addition, the array format contains tiling probes for 36 longer transcripts. All probes are in duplicates, giving the total number of 137,562 probes per array.
2012-04-15 | E-GEOD-32954 | biostudies-arrayexpress