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Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal Publication Acceptance Date: 8/7/2015 Publication Date: 10/5/2015 Citation: Calla Zalles, B., Geib, S.M. 2015. MicroRNAs in the oriental fruit fly, Bactrocera dorsalis: extending Drosophilid miRNA clusters to the Tephritidae. Biomed Central (BMC) Genomics. doi:10.1186/s12864-015-1835-3. Interpretive Summary: Small RNAs have been shown to be involved in up to 30% of the protein coding genes in animal cells. While they are important to understanding gene regulation, there is virtually nothing known about small RNAs in the true fruit flies (Family Tephritidae). To gain a foundational understanding of the role of small RNAs in these flies, we identified novel small RNAs (including micro RNAs) in the oriental fruit fly (Bactrocera dorsalis) using high-throughput sequencing approaches. Of interest, we found microRNA clusters that were previously thought to be limited to only Drosophila to be present in B.dorsalis, as well as in the genomes of several other Tephritids. Also, by surveying small RNA expression over the development of the fly and predicting the genes that are targeted by the small RNA, we gained understanding of what role individual small RNA molecules play in development and regulation of gene expression in this species. Technical Abstract: The oriental fruit fly, Bactrocera dorsalis, is an important pest species in the family Tephritidae. It is a phytophagous species with broad host range, and while not established in the mainland United States, is a species of great concern for introduction. Despite of the vast amount of information available from the closely related model organism Drosophila melanogaster, information at the genome and transcriptome level is still very limited for this species. Small RNAs act as regulatory molecules capable of determining target genes fate with the most studied being micro RNAs, which may impact as much as 30% of all protein coding genes in animals. Results: We have sequenced sRNAs from the Tephritid fruit fly, Bactrocera dorsalis (Oriental fruit fly), specifically sRNAs corresponding to the 17 to 28 nucleotides long fraction of total RNA, looking at variation in composition and expression between different developmental stages, and between male and female sexes in the pupa stage. We were able to identify several miRNAs orthologous to known miRNAs and additional novel miRNAs which might be specific to the genera or to the Tephritid family. We constructed a profile of gene expression for the identified miRNAs, and used comparative analysis with D.melanogaster to support our expression data, identify conserved miRNA clusters in the genome, and to mine for potential transcript targets for this miRNAs. Conclusions: The data presented here, adds to our growing pool of information concerning the genome structure and characteristics of true fruit flies, it provides a basis for comparative studies in other Dipteran species, and can be used for applied research such as in the development of new control strategies based on gene silencing and transgenesis, and for the improvement of existing methods like the Sterile Insect Technique (SIT). Most interesting is the presence of miRNA clusters that previously have be thought to be limited to Drosophila. Comparative genomics to B.dorsalis and several other Tephritid species, presence of these clusters can be expanded to the Tephritidae. |
