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Supplemental Information

R. delemar ATCC20344 RNA seq assembly fasta file

Fasta file of all de novo assembled transcripts obtained from the R. delemar ATCC 20344 transcriptomics experiment.

DOI: 10.7287/peerj.preprints.2742v1/supp-1

R. delemar ATCC20344 RNA seq assembly allORFs above cutoff 21 fasta file

In silico translation of de novo assembled transcripts from the R. delemar ATCC 20344 transcriptomics experiment. Minimun protein length >= 21 amino acids.

DOI: 10.7287/peerj.preprints.2742v1/supp-2

R. delemar ATCC20344 snapshot proteome

Relative protein abundance and average nucleotide coverage of enzymes identified in the proteomics data. Note that only enzymes that could be predicted by PRIAM are listed.

DOI: 10.7287/peerj.preprints.2742v1/supp-3

Metabolic pathway enrichment analysis

Metabolic pathway coverage and hypergeometric test results of proteins found in the R. delemar ATCC 20344 and R. delemar RA 99-880 in silico and snapshot proteomes.

DOI: 10.7287/peerj.preprints.2742v1/supp-4

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Dorett I Odoni conceived and designed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Juan A Tamayo-Ramos conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, reviewed drafts of the paper.

Jasper Sloothaak performed the experiments, analyzed the data, reviewed drafts of the paper.

Ruben G A van Heck analyzed the data, reviewed drafts of the paper.

Vitor A P Martins dos Santos conceived and designed the experiments, contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Leo H de Graaff conceived and designed the experiments, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.

Maria Suarez-Diez conceived and designed the experiments, reviewed drafts of the paper.

Peter J Schaap conceived and designed the experiments, reviewed drafts of the paper.

Data Deposition

The following information was supplied regarding data availability:

Proteomics data:

1) PRIDE

2) PXD004600

3) http://www.ebi.ac.uk/pride/archive/login

Accession details for review purposes:

Username: reviewer14653@ebi.ac.uk

Password: r1CpiwSv

RNA seq data:

1) EMBL-EBI

2) PRJEB14210

Note: not yet publicly available, but relevant data for revision was submitted as supplemental material.

Funding

This work has been carried out on a basis of a grant in the framework of the WUR IPOP Systems Biology program KB-17-003.02-026 “Genome-wide metabolic modelling and data integration of organic acid production in filamentous fungi” (DIO) and the BE-Basic (http://www.be-basic.org/) program F01.002 “Itaconic/fumaric acids: Novel economic and eco-efficient processes for the production of itaconic and fumaric acid” (JATR). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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