Computational identification of miRNAs, their targets and functions in three‐spined stickleback (Gasterosteus aculeatus)

An intriguing question in biology is how the evolution of gene regulation is shaped by natural selection in natural populations. Among the many known regulatory mechanisms, regulation of gene expression by microRNAs (miRNAs) is of critical importance. However, our understanding of their evolution in...

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Bibliographic Details
Published in:Molecular ecology resources 2014-07, Vol.14 (4), p.768-777
Main Authors: Chaturvedi, Anurag, Raeymaekers, Joost A. M, Volckaert, Filip A. M
Format: Article
Language:English
Subjects:
Adaptation, Biological
Animal behavior
Animals
Binding Sites
case studies
Computational Biology - methods
evolution
Evolution & development
Evolution, Molecular
Fish
freshwater
Gasterosteus aculeatus
Gene expression
Gene Expression Regulation
genes
Genomes
microRNA
MicroRNAs - genetics
Molecular Sequence Annotation
natural selection
prediction
Smegmamorpha - genetics
targets
three-spined stickleback
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Summary:An intriguing question in biology is how the evolution of gene regulation is shaped by natural selection in natural populations. Among the many known regulatory mechanisms, regulation of gene expression by microRNAs (miRNAs) is of critical importance. However, our understanding of their evolution in natural populations is limited. Studying the role of miRNAs in three‐spined stickleback, an important natural model for speciation research, may provide new insights into adaptive polymorphisms. However, lack of annotation of miRNA genes in its genome is a bottleneck. To fill this research gap, we used the genome of three‐spined stickleback to predict miRNAs and their targets. We predicted 1486 mature miRNAs using the homology‐based miRNA prediction approach. We then performed functional annotation and enrichment analysis of these targets, which identified over‐represented motifs. Further, a database resource (GAmiRdb) has been developed for dynamically searching miRNAs and their targets exclusively in three‐spined stickleback. Finally, the database was used in two case studies focusing on freshwater adaptation in natural populations. In the first study, we found 44 genomic regions overlapping with predicted miRNA targets. In the second study, we identified two SNPs altering the MRE seed site of sperm‐specific glyceraldehyde‐3‐phosphate gene. These findings highlight the importance of the GAmiRdb knowledge base in understanding adaptive evolution.
ISSN:1755-098X
1755-0998
DOI:10.1111/1755-0998.12223