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Trichoderma reesei complete genome sequence, repeat-induced point mutation, and partitioning of CAZyme gene clusters

Overview of attention for article published in Biotechnology for Biofuels, July 2017
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About this Attention Score

  • In the top 25% of all research outputs scored by Altmetric
  • Good Attention Score compared to outputs of the same age (72nd percentile)
  • High Attention Score compared to outputs of the same age and source (99th percentile)

Mentioned by

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5 tweeters
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1 patent

Citations

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61 Dimensions

Readers on

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90 Mendeley
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Title
Trichoderma reesei complete genome sequence, repeat-induced point mutation, and partitioning of CAZyme gene clusters
Published in
Biotechnology for Biofuels, July 2017
DOI 10.1186/s13068-017-0825-x
Pubmed ID
Authors

Wan-Chen Li, Chien-Hao Huang, Chia-Ling Chen, Yu-Chien Chuang, Shu-Yun Tung, Ting-Fang Wang

Abstract

Trichoderma reesei (Ascomycota, Pezizomycotina) QM6a is a model fungus for a broad spectrum of physiological phenomena, including plant cell wall degradation, industrial production of enzymes, light responses, conidiation, sexual development, polyketide biosynthesis, and plant-fungal interactions. The genomes of QM6a and its high enzyme-producing mutants have been sequenced by second-generation-sequencing methods and are publicly available from the Joint Genome Institute. While these genome sequences have offered useful information for genomic and transcriptomic studies, their limitations and especially their short read lengths make them poorly suited for some particular biological problems, including assembly, genome-wide determination of chromosome architecture, and genetic modification or engineering. We integrated Pacific Biosciences and Illumina sequencing platforms for the highest-quality genome assembly yet achieved, revealing seven telomere-to-telomere chromosomes (34,922,528 bp; 10877 genes) with 1630 newly predicted genes and >1.5 Mb of new sequences. Most new sequences are located on AT-rich blocks, including 7 centromeres, 14 subtelomeres, and 2329 interspersed AT-rich blocks. The seven QM6a centromeres separately consist of 24 conserved repeats and 37 putative centromere-encoded genes. These findings open up a new perspective for future centromere and chromosome architecture studies. Next, we demonstrate that sexual crossing readily induced cytosine-to-thymine point mutations on both tandem and unlinked duplicated sequences. We also show by bioinformatic analysis that T. reesei has evolved a robust repeat-induced point mutation (RIP) system to accumulate AT-rich sequences, with longer AT-rich blocks having more RIP mutations. The widespread distribution of AT-rich blocks correlates genome-wide partitions with gene clusters, explaining why clustering of genes has been reported to not influence gene expression in T. reesei. Compartmentation of ancestral gene clusters by AT-rich blocks might promote flexibilities that are evolutionarily advantageous in this fungus' soil habitats and other natural environments. Our analyses, together with the complete genome sequence, provide a better blueprint for biotechnological and industrial applications.

Twitter Demographics

The data shown below were collected from the profiles of 5 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 90 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 90 100%

Demographic breakdown

Readers by professional status Count As %
Researcher 14 16%
Student > Master 12 13%
Student > Doctoral Student 10 11%
Student > Bachelor 10 11%
Student > Ph. D. Student 8 9%
Other 16 18%
Unknown 20 22%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 28 31%
Agricultural and Biological Sciences 25 28%
Chemistry 4 4%
Computer Science 2 2%
Immunology and Microbiology 1 1%
Other 8 9%
Unknown 22 24%

Attention Score in Context

This research output has an Altmetric Attention Score of 6. 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 15 December 2021.
All research outputs
#5,125,500
of 21,322,016 outputs
Outputs from Biotechnology for Biofuels
#330
of 1,379 outputs
Outputs of similar age
#77,922
of 283,086 outputs
Outputs of similar age from Biotechnology for Biofuels
#1
of 5 outputs
Altmetric has tracked 21,322,016 research outputs across all sources so far. Compared to these this one has done well and is in the 75th percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 1,379 research outputs from this source. They receive a mean Attention Score of 4.7. This one has done well, scoring higher than 75% 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 283,086 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 72% of its contemporaries.
We're also able to compare this research output to 5 others from the same source and published within six weeks on either side of this one. This one has scored higher than all of them