Brain transcriptome analysis reveals novel long non-coding RNAs in Dryophytes arenicolor (Canyon Treefrog)

Anurans possess complex genomes, making molecular research challenging, particularly in non-model species. Transcriptomics offers a powerful tool for uncovering genomic responses to environmental changes through distinct transcriptional patterns. A sizeable portion of the transcriptome consists of non-coding RNAs, with long non-coding RNAs (lncRNAs) playing key roles in gene regulation. Here, we performed de novo transcriptome assembly from brain samples of Dryophytes arenicolor across 3 life stages: Pre-metamorphic, Metamorphic Climax, and Adults. By aligning our transcriptomes to LNCipedia, we identified 4,557 previously annotated lncRNAs with potential roles in gene regulation, macromolecule biosynthesis, and chromatin organization. To detect novel lncRNAs, we implemented a bioinformatic pipeline to filter out known mRNAs, small ncRNAs, sequences with coding potential, conserved protein domains, and previously identified D. arenicolor mRNAs, identifying 4,836 putative novel lncRNAs. To explore their functional roles, we performed Weighted Gene Correlation Analysis and gene enrichment analysis, revealing that these lncRNAs may be involved in protein heterodimerization, nucleosome assembly, and post-transcriptional regulation of gene expression. To our knowledge, this is the first study to characterize lncRNAs across multiple life stages in D. arenicolor, highlighting their potential regulatory functions.