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Characterization of an extensive rainbow trout miRNA transcriptome by next generation sequencing

Overview of attention for article published in BMC Genomics, March 2016
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Title
Characterization of an extensive rainbow trout miRNA transcriptome by next generation sequencing
Published in
BMC Genomics, March 2016
DOI 10.1186/s12864-016-2505-9
Pubmed ID
Authors

Amelie Juanchich, Philippe Bardou, Olivier Rué, Jean-Charles Gabillard, Christine Gaspin, Julien Bobe, Yann Guiguen

Abstract

MicroRNAs (miRNAs) have emerged as important post-transcriptional regulators of gene expression in a wide variety of physiological processes. They can control both temporal and spatial gene expression and are believed to regulate 30 to 70 % of the genes. Data are however limited for fish species, with only 9 out of the 30,000 fish species present in miRBase. The aim of the current study was to discover and characterize rainbow trout (Oncorhynchus mykiss) miRNAs in a large number of tissues using next-generation sequencing in order to provide an extensive repertoire of rainbow trout miRNAs. A total of 38 different samples corresponding to 16 different tissues or organs were individually sequenced and analyzed independently in order to identify a large number of miRNAs with high confidence. This led to the identification of 2946 miRNA loci in the rainbow trout genome, including 445 already known miRNAs. Differential expression analysis was performed in order to identify miRNAs exhibiting specific or preferential expression among the 16 analyzed tissues. In most cases, miRNAs exhibit a specific pattern of expression in only a few tissues. The expression data from sRNA sequencing were confirmed by RT-qPCR. In addition, novel miRNAs are described in rainbow trout that had not been previously reported in other species. This study represents the first characterization of rainbow trout miRNA transcriptome from a wide variety of tissue and sets an extensive repertoire of rainbow trout miRNAs. It provides a starting point for future studies aimed at understanding the roles of miRNAs in major physiological process such as growth, reproduction or adaptation to stress. These rainbow trout miRNAs repertoire provide a novel resource to advance genomic research in salmonid species.

Twitter Demographics

The data shown below were collected from the profiles of 4 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 69 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Netherlands 1 1%
India 1 1%
Unknown 67 97%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 17 25%
Researcher 13 19%
Student > Master 10 14%
Student > Doctoral Student 6 9%
Other 3 4%
Other 8 12%
Unknown 12 17%
Readers by discipline Count As %
Agricultural and Biological Sciences 30 43%
Biochemistry, Genetics and Molecular Biology 15 22%
Environmental Science 3 4%
Pharmacology, Toxicology and Pharmaceutical Science 1 1%
Nursing and Health Professions 1 1%
Other 3 4%
Unknown 16 23%

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 05 March 2016.
All research outputs
#7,020,449
of 11,293,566 outputs
Outputs from BMC Genomics
#4,388
of 6,784 outputs
Outputs of similar age
#160,515
of 292,545 outputs
Outputs of similar age from BMC Genomics
#163
of 218 outputs
Altmetric has tracked 11,293,566 research outputs across all sources so far. This one is in the 23rd percentile – i.e., 23% of other outputs scored the same or lower than it.
So far Altmetric has tracked 6,784 research outputs from this source. They receive a mean Attention Score of 4.2. This one is in the 27th percentile – i.e., 27% 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 292,545 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 35th percentile – i.e., 35% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 218 others from the same source and published within six weeks on either side of this one. This one is in the 20th percentile – i.e., 20% of its contemporaries scored the same or lower than it.