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Honey bee microRNAs respond to infection by the microsporidian parasite Nosema ceranae.

Huang Q, Chen Y, Wang RW, Schwarz RS, Evans JD - Sci Rep (2015)

Bottom Line: In order to study the effects of Nosema ceranae infection on honey bee microRNA (miRNA) expression, we deep-sequenced honey bee miRNAs daily across a full 6-day parasite reproduction cycle.Based on Enzyme Code analysis, nine biological pathways were identified by screening target genes against the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, seven of which involved metabolism.Our results suggest that differentially expressed miRNAs regulate metabolism related genes of host honey bees in response to N. ceranae infection.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Science, Kunming, 650223, China.

ABSTRACT
In order to study the effects of Nosema ceranae infection on honey bee microRNA (miRNA) expression, we deep-sequenced honey bee miRNAs daily across a full 6-day parasite reproduction cycle. Seventeen miRNAs were differentially expressed in honey bees infected by N. ceranae that potentially target over 400 genes predicted to primarily involve ion binding, signaling, the nucleus, transmembrane transport, and DNA binding. Based on Enzyme Code analysis, nine biological pathways were identified by screening target genes against the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, seven of which involved metabolism. Our results suggest that differentially expressed miRNAs regulate metabolism related genes of host honey bees in response to N. ceranae infection.

No MeSH data available.


Related in: MedlinePlus

Associations between miRNAs and target genes at expression levels.By co-expression analysis, 371 target genes of 17 miRNAs were clustered into three groups. 36 target genes showed co-expression and were clustered into group 1 (blue). Another 319 target genes showed co-expression and were clustered into group 2 (turquoise). The remaining 16 target gene did not show co-expression were clustered into group 3 (grey). If the target prediction is true, the miRNAs should be correlated with target genes at the expression levels. We then quantified the correlation between the each of miRNAs with three groups of target genes. Each row corresponds to a co-expressed gene group and each column corresponds to a miRNA. Each cell contains the corresponding correlation and p-value. The table is color – coded by correlation according to the color legend on the right side.
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f1: Associations between miRNAs and target genes at expression levels.By co-expression analysis, 371 target genes of 17 miRNAs were clustered into three groups. 36 target genes showed co-expression and were clustered into group 1 (blue). Another 319 target genes showed co-expression and were clustered into group 2 (turquoise). The remaining 16 target gene did not show co-expression were clustered into group 3 (grey). If the target prediction is true, the miRNAs should be correlated with target genes at the expression levels. We then quantified the correlation between the each of miRNAs with three groups of target genes. Each row corresponds to a co-expressed gene group and each column corresponds to a miRNA. Each cell contains the corresponding correlation and p-value. The table is color – coded by correlation according to the color legend on the right side.

Mentions: By matching seed regions (2–8 bp) of mature miRNAs to 3′UTRs of honey bee genes, 413 predicted genes could be targeted by the 17 differentially expressed miRNAs. We expected a dynamic correlation between miRNA and its direct or indirect target mRNAs during the six day infection period. Therefore, we quantified the expression levels of honey bee transcripts in infected and uninfected honey bee workers from 1 to 6 dpi using RNA-seq data from NCBI bio-project PRJNA282511. Out of the 413 predicted gene targets, 371 were expressed according to three groups (Fig. 1). Group 1 (blue) and Group 2 (turquoise) consisted of 36 and 319 genes, respectively, and showed co-expression within each group. The remaining genes were clustered in a third (grey) group. Out of 17 miRNAs, 5 showed a significant correlation with group 1 (blue) and 2 miRNAs showed a significant correlation with group 2 (turquoise). No significant correlation was detected between miRNAs and group 3 (grey) (Fig. 1, Additional file 2).


Honey bee microRNAs respond to infection by the microsporidian parasite Nosema ceranae.

Huang Q, Chen Y, Wang RW, Schwarz RS, Evans JD - Sci Rep (2015)

Associations between miRNAs and target genes at expression levels.By co-expression analysis, 371 target genes of 17 miRNAs were clustered into three groups. 36 target genes showed co-expression and were clustered into group 1 (blue). Another 319 target genes showed co-expression and were clustered into group 2 (turquoise). The remaining 16 target gene did not show co-expression were clustered into group 3 (grey). If the target prediction is true, the miRNAs should be correlated with target genes at the expression levels. We then quantified the correlation between the each of miRNAs with three groups of target genes. Each row corresponds to a co-expressed gene group and each column corresponds to a miRNA. Each cell contains the corresponding correlation and p-value. The table is color – coded by correlation according to the color legend on the right side.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4664923&req=5

f1: Associations between miRNAs and target genes at expression levels.By co-expression analysis, 371 target genes of 17 miRNAs were clustered into three groups. 36 target genes showed co-expression and were clustered into group 1 (blue). Another 319 target genes showed co-expression and were clustered into group 2 (turquoise). The remaining 16 target gene did not show co-expression were clustered into group 3 (grey). If the target prediction is true, the miRNAs should be correlated with target genes at the expression levels. We then quantified the correlation between the each of miRNAs with three groups of target genes. Each row corresponds to a co-expressed gene group and each column corresponds to a miRNA. Each cell contains the corresponding correlation and p-value. The table is color – coded by correlation according to the color legend on the right side.
Mentions: By matching seed regions (2–8 bp) of mature miRNAs to 3′UTRs of honey bee genes, 413 predicted genes could be targeted by the 17 differentially expressed miRNAs. We expected a dynamic correlation between miRNA and its direct or indirect target mRNAs during the six day infection period. Therefore, we quantified the expression levels of honey bee transcripts in infected and uninfected honey bee workers from 1 to 6 dpi using RNA-seq data from NCBI bio-project PRJNA282511. Out of the 413 predicted gene targets, 371 were expressed according to three groups (Fig. 1). Group 1 (blue) and Group 2 (turquoise) consisted of 36 and 319 genes, respectively, and showed co-expression within each group. The remaining genes were clustered in a third (grey) group. Out of 17 miRNAs, 5 showed a significant correlation with group 1 (blue) and 2 miRNAs showed a significant correlation with group 2 (turquoise). No significant correlation was detected between miRNAs and group 3 (grey) (Fig. 1, Additional file 2).

Bottom Line: In order to study the effects of Nosema ceranae infection on honey bee microRNA (miRNA) expression, we deep-sequenced honey bee miRNAs daily across a full 6-day parasite reproduction cycle.Based on Enzyme Code analysis, nine biological pathways were identified by screening target genes against the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, seven of which involved metabolism.Our results suggest that differentially expressed miRNAs regulate metabolism related genes of host honey bees in response to N. ceranae infection.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Science, Kunming, 650223, China.

ABSTRACT
In order to study the effects of Nosema ceranae infection on honey bee microRNA (miRNA) expression, we deep-sequenced honey bee miRNAs daily across a full 6-day parasite reproduction cycle. Seventeen miRNAs were differentially expressed in honey bees infected by N. ceranae that potentially target over 400 genes predicted to primarily involve ion binding, signaling, the nucleus, transmembrane transport, and DNA binding. Based on Enzyme Code analysis, nine biological pathways were identified by screening target genes against the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, seven of which involved metabolism. Our results suggest that differentially expressed miRNAs regulate metabolism related genes of host honey bees in response to N. ceranae infection.

No MeSH data available.


Related in: MedlinePlus