Seasonal tissue-specific transcriptomic responses of the Andean Killifish Orestias ascotanensis

The Andean killifish Orestias ascotanensis inhabits the high-altitude Ascotán Salt Pan, an environment with variable salinity, high UV exposure, low oxygen, and extreme daily temperature fluctuations. These conditions make it an excellent model for studying high-altitude fish biology. However, the transcriptomic responses of O. ascotanensis to seasonal acclimation remain unexplored. To investigate seasonal and tissue-specific transcriptomic profiles, RNA-seq was performed on 42 libraries from gills, skin, and muscle tissues of 14 individuals collected in summer (n=7) and winter (n=7). Each library had a median of 105 million reads. Principal component analysis revealed strong tissue-specific expression, and seasonal differential expression analyses identified significant transcriptomic changes within each tissue. Additionally, a bioinformatics pipeline identified 10,365 high-confidence long non-coding RNAs (lncRNAs), predicted by at least three computational tools. Compared to protein-coding genes, lncRNAs exhibited higher tissue specificity, with a predominance of monoexonic structures and shorter exon lengths. This dataset provides the first comprehensive view of seasonal mRNA and lncRNA expression in O. ascotanensis tissues. Total RNA was extracted from three different tissues (gills, skin, and muscle) samples obtained from each of the 14 individuals captured during either summer (n=7) or winter (n=7), using TRIzol (Invitrogen) following the manufacturer's protocol. The concentration and quality of the extracted RNA were assessed using a Qubit fluorometer (Invitrogen) and a Bioanalyzer 2100 (Agilent), determining the integrity and purity of each sample. Unstranded poly-A libraries were prepared from each tissue sample using the Illumina TruSeq RNA sample preparation kit (Illumina) according to the manufacturer’s instructions. The prepared RNA samples were sent to Quick Biology (Pasadena, CA, USA) for sequencing, where they were processed on the Illumina HiSeq 4000 platform to generate 150 bp paired-end reads.