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A complete annotation of the chromosomes of the cellulase producer Trichoderma reesei provides insights in gene clusters, their expression and reveals genes required for fitness

Overview of attention for article published in Biotechnology for Biofuels, March 2016
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  • In the top 25% of all research outputs scored by Altmetric
  • Good Attention Score compared to outputs of the same age (76th percentile)

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Title
A complete annotation of the chromosomes of the cellulase producer Trichoderma reesei provides insights in gene clusters, their expression and reveals genes required for fitness
Published in
Biotechnology for Biofuels, March 2016
DOI 10.1186/s13068-016-0488-z
Pubmed ID
Authors

Irina S. Druzhinina, Alexey G. Kopchinskiy, Eva M. Kubicek, Christian P. Kubicek

Abstract

Investigations on a few eukaryotic model organisms showed that many genes are non-randomly distributed on chromosomes. In addition, chromosome ends frequently possess genes that are important for the fitness of the organisms. Trichoderma reesei is an industrial producer of enzymes for food, feed and biorefinery production. Its seven chromosomes have recently been assembled, thus making an investigation of its chromosome architecture possible. We manually annotated and mapped 9194 ORFs on their respective chromosomes and investigated the clustering of the major gene categories and of genes encoding carbohydrate-active enzymes (CAZymes), and the relationship between clustering and expression. Genes responsible for RNA processing and modification, amino acid metabolism, transcription, translation and ribosomal structure and biogenesis indeed showed loose clustering, but this had no impact on their expression. A third of the genes encoding CAZymes also occurred in loose clusters that also contained a high number of genes encoding small secreted cysteine-rich proteins. Five CAZyme clusters were located less than 50 kb apart from the chromosome ends. These genes exhibited the lowest basal (but not induced) expression level, which correlated with an enrichment of H3K9 methylation in the terminal 50 kb areas indicating gene silencing. No differences were found in the expression of CAZyme genes present in other parts of the chromosomes. The putative subtelomeric areas were also enriched in genes encoding secreted proteases, amino acid permeases, enzyme clusters for polyketide synthases (PKS)-non-ribosomal peptide synthase (NRPS) fusion proteins (PKS-NRPS) and proteins involved in iron scavenging. They were strongly upregulated during conidiation and interaction with other fungi. Our findings suggest that gene clustering on the T. reesei chromosomes occurs but generally has no impact on their expression. CAZyme genes, located in subtelomers, however, exhibited a much lower basal expression level. The gene inventory of the subtelomers suggests a major role of competition for nitrogen and iron supported by antibiosis for the fitness of T. reesei. The availability of fully annotated chromosomes will facilitate the use of genetic crossings in identifying still unknown genes responsible for specific traits of T. reesei.

Twitter Demographics

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Mendeley readers

The data shown below were compiled from readership statistics for 54 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Mexico 2 4%
Thailand 1 2%
Unknown 51 94%

Demographic breakdown

Readers by professional status Count As %
Student > Doctoral Student 11 20%
Researcher 9 17%
Student > Ph. D. Student 8 15%
Student > Master 7 13%
Student > Bachelor 4 7%
Other 8 15%
Unknown 7 13%
Readers by discipline Count As %
Agricultural and Biological Sciences 20 37%
Biochemistry, Genetics and Molecular Biology 14 26%
Medicine and Dentistry 2 4%
Chemistry 2 4%
Computer Science 1 2%
Other 7 13%
Unknown 8 15%

Attention Score in Context

This research output has an Altmetric Attention Score of 7. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 29 March 2018.
All research outputs
#3,301,086
of 17,359,532 outputs
Outputs from Biotechnology for Biofuels
#236
of 1,243 outputs
Outputs of similar age
#62,305
of 270,004 outputs
Outputs of similar age from Biotechnology for Biofuels
#3
of 4 outputs
Altmetric has tracked 17,359,532 research outputs across all sources so far. Compared to these this one has done well and is in the 80th percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 1,243 research outputs from this source. They receive a mean Attention Score of 4.5. This one has done well, scoring higher than 80% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 270,004 tracked outputs that were published within six weeks on either side of this one in any source. This one has done well, scoring higher than 76% of its contemporaries.
We're also able to compare this research output to 4 others from the same source and published within six weeks on either side of this one.