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Genome-wide identification of the Phaseolus vulgaris sRNAome using small RNA and degradome sequencing

Overview of attention for article published in BMC Genomics, June 2015
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  • Above-average Attention Score compared to outputs of the same age (53rd percentile)
  • Above-average Attention Score compared to outputs of the same age and source (52nd percentile)

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Title
Genome-wide identification of the Phaseolus vulgaris sRNAome using small RNA and degradome sequencing
Published in
BMC Genomics, June 2015
DOI 10.1186/s12864-015-1639-5
Pubmed ID
Authors

Damien Formey, Luis Pedro Iñiguez, Pablo Peláez, Yong-Fang Li, Ramanjulu Sunkar, Federico Sánchez, José Luis Reyes, Georgina Hernández

Abstract

MiRNAs and phasiRNAs are negative regulators of gene expression. These small RNAs have been extensively studied in plant model species but only 10 mature microRNAs are present in miRBase version 21, the most used miRNA database, and no phasiRNAs have been identified for the model legume Phaseolus vulgaris. Thanks to the recent availability of the first version of the common bean genome, degradome data and small RNA libraries, we are able to present here a catalog of the microRNAs and phasiRNAs for this organism and, particularly, we suggest new protagonists in the symbiotic nodulation events. We identified a set of 185 mature miRNAs, including 121 previously unpublished sequences, encoded by 307 precursors and distributed in 98 families. Degradome data allowed us to identify a total of 181 targets for these miRNAs. We reveal two regulatory networks involving conserved miRNAs: those known to play crucial roles in the establishment of nodules, and novel miRNAs present only in common bean, suggesting a specific role for these sequences. In addition, we identified 125 loci that potentially produce phased small RNAs, with 47 of them having all the characteristics of being triggered by a total of 31 miRNAs, including 14 new miRNAs identified in this study. We provide here a set of new small RNAs that contribute to the broader knowledge of the sRNAome of Phaseolus vulgaris. Thanks to the identification of the miRNA targets from degradome analysis and the construction of regulatory networks between the mature microRNAs, we present here the probable functional regulation associated with the sRNAome and, particularly, in N2-fixing symbiotic nodules.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 83 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
France 1 1%
Argentina 1 1%
Brazil 1 1%
Unknown 80 96%

Demographic breakdown

Readers by professional status Count As %
Student > Bachelor 18 22%
Student > Ph. D. Student 17 20%
Researcher 13 16%
Student > Master 9 11%
Other 5 6%
Other 9 11%
Unknown 12 14%
Readers by discipline Count As %
Agricultural and Biological Sciences 31 37%
Biochemistry, Genetics and Molecular Biology 27 33%
Computer Science 3 4%
Unspecified 2 2%
Medicine and Dentistry 2 2%
Other 2 2%
Unknown 16 19%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 3. 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 12 June 2015.
All research outputs
#13,205,434
of 22,811,321 outputs
Outputs from BMC Genomics
#4,764
of 10,651 outputs
Outputs of similar age
#123,533
of 267,772 outputs
Outputs of similar age from BMC Genomics
#106
of 246 outputs
Altmetric has tracked 22,811,321 research outputs across all sources so far. This one is in the 41st percentile – i.e., 41% of other outputs scored the same or lower than it.
So far Altmetric has tracked 10,651 research outputs from this source. They receive a mean Attention Score of 4.7. This one has gotten more attention than average, scoring higher than 53% 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 267,772 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 53% of its contemporaries.
We're also able to compare this research output to 246 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 52% of its contemporaries.