Long non-coding RNA transcripts in crucian carp Brain – annotation and expression patterns in anoxia and reoxygenation

Long non-coding RNAs (lncRNAs) regulate diverse cellular processes, yet their role in anoxia-induced transcriptomic changes in crucian carp (Carassius carassius) – a species that endures months without oxygen at low temperatures – remains unclear. Because existing genome annotations focus on protein-coding genes, we aimed to annotate lncRNAs in crucian carp, assess their potential for involvement in mRNA regulation during anoxia and reoxygenation, and characterize differentially regulated lncRNAs and nearby putative interaction partners (IPs). Using next-generation RNA sequencing of the brain across normoxia, anoxia, and reoxygenation (n = 10 per group), we assembled 145,264 transcripts with a reference-guided approach. With CPC2, CNCI, CPAT, and FEELnc, we identified 6072 lncRNAs. Anoxia elicited a robust transcriptomic response: 56,440 transcripts were differentially expressed (adjusted p-value 0.38), including 1321 lncRNAs. FEELnc classification highlighted proximal RNA transcripts suggestive of cis-acting lncRNA functions. Most (60%) DElncRNA – IP interaction sites were intergenic, predominantly on the same strand within intergenic subtypes, with many features nested within genic contexts. Notably, log2-fold changes in RNA abundance of predicted DE IPs positively correlated with those of their corresponding DElncRNAs. These results provide a comprehensive lncRNA annotation for crucian carp and reveal extensive lncRNA co-expression with nearby genes during anoxia and reoxygenation, supporting a potential cis-regulatory role in the adaptive transcriptomic response to oxygen deprivation.