Search and understanding of biological mechanisms through in silico analysis of the Apis mellifera transcriptome
Year: 2021
Type: dissertation
Abstract: Honey bees are excellent pollinating agents and producers of honey, royal jelly, apitoxins and propolis. In recent years, its activity has been affected due to the exacerbated use of pesticides in commercial plantation areas. Based on this, the analysis of genetic and environmental effects, as well as an interaction between these two factors, contribute to the understanding of how phenotypic changes caused by the use of pesticides. Although the environmental effect is a limiting factor to be measured, transcriptome studies can help in breeding programs. However, despite these insects being considered model organisms for several fields of science, very little is known about the molecular mechanisms that govern the biology of these insects. At the molecular level, lncRNAs are gaining prominence due to their involvement in epigenetic expression, even transcriptional and translational. Due to the great importance of these molecules, this work aims to characterize and evaluate potential lncRNAs involved in the biological system of the bee. The data set of bees exposed to cypermethrin (cypermethrin 0.3 ng/bee and cypermethrin 3 ng/bee) was selected to carry out the transcriptome analyzes using computational methods. For this, the quality control analysis of the samples (FastQC and Trim Galore!), mapping of the sequences (Hisat2) against the reference genome Amel_HAv3.1 was carried out, then the quantification (Htseq-count) was performed from the annotation of the Apis mellifera RNA set. For the differential expression of RNAs between samples, the EdgeR software was used. Afterwards, normalization of the sequences and analysis of the coexpression network were carried out to identify the interaction of transcripts (mRNA and lncRNA) using Cytoscape and, respectively, the functions of lncRNA molecules were analyzed using the ClueGO tool. The correlated transcripts were submitted to predictive analysis of subcellular localization by iLoc-LncRNA. Thus, a total of 21 lncRNAs differentially expressed in cypermethrin (3 ng) were observed, while 2 lncRNAs were differentially expressed in lower dose cypermethrin (0.3 ng). Part of these lncRNAs differentially expressed in cypermethrin 3 ng are correlated with mRNAs, in pathways such as dorsoventral axial formation and mRNA catabolic process. Furthermore, according to the analysis of the subcellular localization of lncRNAs, it was observed that most of these molecules are in the nucleus and cytoplasm. The results demonstrate a possible involvement of these molecules at the transcriptional level. Therefore, although there is evidence of the action of these molecules, further studies are needed to understand the biology of honey bees, especially regarding the effect of pesticides.
Author: Quintino, Larissa Fernanda
Language: Portuguese
Subfield: Insect Science
Domain: Life Sciences
SDG: Zero hunger
Open Access status: green
OpenAlex ID: W7155455133