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Increased sequencing depth does not increase captured diversity of arbuscular mycorrhizal fungi

Overview of attention for article published in Mycorrhiza, July 2017
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  • Above-average Attention Score compared to outputs of the same age and source (53rd percentile)

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Title
Increased sequencing depth does not increase captured diversity of arbuscular mycorrhizal fungi
Published in
Mycorrhiza, July 2017
DOI 10.1007/s00572-017-0791-y
Pubmed ID
Authors

Martti Vasar, Reidar Andreson, John Davison, Teele Jairus, Mari Moora, Maido Remm, J. P. W. Young, Martin Zobel, Maarja Öpik

Abstract

The arrival of 454 sequencing represented a major breakthrough by allowing deeper sequencing of environmental samples than was possible with existing Sanger approaches. Illumina MiSeq provides a further increase in sequencing depth but shorter read length compared with 454 sequencing. We explored whether Illumina sequencing improves estimates of arbuscular mycorrhizal (AM) fungal richness in plant root samples, compared with 454 sequencing. We identified AM fungi in root samples by sequencing amplicons of the SSU rRNA gene with 454 and Illumina MiSeq paired-end sequencing. In addition, we sequenced metagenomic DNA without prior PCR amplification. Amplicon-based Illumina sequencing yielded two orders of magnitude higher sequencing depth per sample than 454 sequencing. Initial analysis with minimal quality control recorded five times higher AM fungal richness per sample with Illumina sequencing. Additional quality control of Illumina samples, including restriction of the marker region to the most variable amplicon fragment, revealed AM fungal richness values close to those produced by 454 sequencing. Furthermore, AM fungal richness estimates were not correlated with sequencing depth between 300 and 30,000 reads per sample, suggesting that the lower end of this range is sufficient for adequate description of AM fungal communities. By contrast, metagenomic Illumina sequencing yielded very few AM fungal reads and taxa and was dominated by plant DNA, suggesting that AM fungal DNA is present at prohibitively low abundance in colonised root samples. In conclusion, Illumina MiSeq sequencing yielded higher sequencing depth, but similar richness of AM fungi in root samples, compared with 454 sequencing.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 118 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 118 100%

Demographic breakdown

Readers by professional status Count As %
Researcher 22 19%
Student > Ph. D. Student 21 18%
Student > Master 19 16%
Student > Bachelor 8 7%
Student > Doctoral Student 8 7%
Other 16 14%
Unknown 24 20%
Readers by discipline Count As %
Agricultural and Biological Sciences 65 55%
Environmental Science 8 7%
Biochemistry, Genetics and Molecular Biology 8 7%
Computer Science 1 <1%
Psychology 1 <1%
Other 2 2%
Unknown 33 28%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 1. 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 30 October 2017.
All research outputs
#17,288,665
of 25,387,480 outputs
Outputs from Mycorrhiza
#401
of 691 outputs
Outputs of similar age
#205,503
of 320,103 outputs
Outputs of similar age from Mycorrhiza
#7
of 15 outputs
Altmetric has tracked 25,387,480 research outputs across all sources so far. This one is in the 21st percentile – i.e., 21% of other outputs scored the same or lower than it.
So far Altmetric has tracked 691 research outputs from this source. They receive a mean Attention Score of 3.8. This one is in the 34th percentile – i.e., 34% of its peers scored the same or lower than it.
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 320,103 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 27th percentile – i.e., 27% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 15 others from the same source and published within six weeks on either side of this one. This one has gotten more attention than average, scoring higher than 53% of its contemporaries.