Unveiling the world of bee microRNAs: computational identification and characterization of pathway genes, conserved microRNAs, and their targets

• Published in: International journal of tropical insect science Vol. 44; no. 1; pp. 237 - 251
• Main Authors: de Araujo, Carlos Bruno, Pereira, Paulo Vinícius Rocha, Sousa, Thais Gonzaga, Filho, Antonio Carlos Facciolo, Silva, Gustavo Caetano, do Amaral, Laurence Rodrigues, Gandolfi, Peterson Elizandro, Bonetti, Ana Maria, Ueira-Vieira, Carlos, Bertarini, Pedro Luiz Lima, de Souza Gomes, Matheus
• Format: Journal Article
• Language: English
• Published: Cham Springer International Publishing 01.02.2024; Springer Nature B.V
• Subjects: active sites; Algorithms; Amino acids; Apis mellifera; Bees; biogenesis; Biomedical and Life Sciences; Bombus impatiens; Computer applications; Dufourea novaeangliae; embryogenesis; Entomology; Eufriesea mexicana; Gene expression; Gene sequencing; genes; Genomes; Habropoda laboriosa; Lasioglossum albipes; Life Sciences; Megachile rotundata; microRNA; MicroRNAs; miRNA; non-coding RNA; Original Research Article; Phylogeny; Post-transcription; Proteins; species; Structural analysis; Target recognition; Vertebrates; Vitellogenin; microRNAs; In-silico analysis; Bioinformatics; Bees
• ISSN: 1742-7592; 1742-7584; 1742-7592
• DOI: 10.1007/s42690-023-01158-5

MicroRNAs (miRNAs) are noncoding RNA sequences crucial for post-transcriptional gene expression control and regulation. This study employs a comprehensive genome-wide computational approach to predict miRNAs and enhance our understanding of their occurrence and function across eight bee species. Initial steps involve genome scanning techniques, revealing hundreds of conserved miRNAs in Apis mellifera, Bombus impatiens, Duforea novaengliae, Eufrisea mexicana, Habropoda laboriosa, Lasioglossum albipes, and Megachile rotundata. An optimized algorithm identifies miRNA precursors within these genomes, followed by detailed structural analysis of a selected subset of miRNAs. Additionally, we investigate key proteins in the miRNA biogenesis pathway (Argonaute, Dicer, and Drosha) by comparing them with orthologs in the subject bee species. Our focus lies on verifying conservation levels of active site amino acid residues, key domains, and conducting phylogenetic analyses. Among functional proteins in bees, Vitellogenin (Vg) stands out due to its roles in embryo development and serving as a nutritional reserve in nonmammalian vertebrates. Seven potential miRNAs are identified, implicated in the regulation of the Vg gene through miRNA target identification. Results not only offer insights into miRNA biology in bees but also pave the way for further investigations in this field.