Abstract
Abstract
Long non-coding RNAs (lncRNAs) are key regulatory molecules that control gene expression and developmental processes in Eukaryotes. Past studies have shown that lncRNAs are highly tissue- and condition-specific. Therefore, understanding their functional roles in tissues and conditions will help to unveil the molecular mechanisms underlying the development of complex phenotypes in
Drosophila melanogaster
(Fruit fly). Using our in-house pipeline, LncRAnalyzer, we identified lncRNAs and novel protein-coding transcripts (NPCTs) in FlyAtlas 2 and wild-type (WT) and germline testis mutant (
bam, tut, bgcn
) datasets. To curate tissue- and condition-specific lncRNAs, differential gene expression analysis was performed, and the tissue specificity index (τ) was calculated. The results identified upregulated lncRNAs candidates in reproductive and neuronal tissues, which highlights their possible role in tissues development. Additionally, the identified lncRNAs exhibited contrasting expression patterns across wild-type (WT) and germline testis mutants, suggesting that they could be contributor to mutant phenotype. We performed Weighted Gene Co-expression Network Analysis (WGCNA) and identified lncRNA-gene interaction modules associated with tissue types and germline mutants. The WGCNA module-trait correlations analysis confirmed the tissue- and condition-specific expression of the identified lncRNAs, suggesting that those lncRNAs could be major contributors to phenotype development. This study provides a comprehensive catalogue of identified tissue- and condition-specific lncRNAs. These lncRNAs could be major contributors to tissue development and spermatogenesis in the fruit fly. Their association with known genes highlights their regulatory roles and provides a foundation for future functional studies.