Genome-Wide Insights Into Long Non-Coding Rna Responses to Co₂ Stress in Nannochloropsis Oceanica

Microalgae are photosynthetic, microscopic, mostly unicellular organisms found in freshwater and marine environments. Long non-coding RNAs (lncRNAs) are emerging as critical regulators of gene expression in eukaryotes, particularly in response to environmental stresses. However, their functional roles in microalgae remain poorly understood. In this study, strand-specific RNA sequencing was performed to investigate genome-wide lncRNA responses in the marine microalga Nannochloropsis oceanica under fluctuating carbon dioxide (CO₂) conditions. A total of 134 lncRNAs were identified, among which 51 exhibited significant differential expression between high and low CO₂ treatments, including 33 upregulated and 18 downregulated transcripts. Functional enrichment analysis revealed that CO₂-responsive lncRNAs are associated with cellulose, glucan, and polysaccharide metabolism, as well as transmembrane transport processes. Furthermore, lncRNA–mRNA co-expression and co-location network analyses suggested potential roles in transcriptional regulation, protein expression, and epigenetic modulation. A total of 2051 alternative splicing events were detected under CO₂ stress, indicating a possible regulatory interplay between lncRNAs and splicing mechanisms. Collectively, these findings provide new insights into lncRNA-mediated regulatory responses to CO₂ stress and offer potential targets for improving carbon utilization and stress tolerance in microalgal biotechnology.