RNA-Seq reveals differential expression profiles and functional annotation of genes involved in retinal degeneration in Pde6c mutant Danio rerio

• Published in: BMC genomics 2020-02, Vol.21 (1), p.132-132, Article 132
• Main Authors: Saddala, Madhu Sudhana, Lennikov, Anton, Bouras, Adam, Huang, Hu
• Format: Article
• Language: English
• Subjects: Abnormalities; Adapters; Adaptor proteins; Animals; Annotations; Apoptosis; Biochemistry; Biological activity; Biosynthesis; Calcium; Cardiomyocytes; Citric acid; Criminal investigation; Cyclic Nucleotide Phosphodiesterases, Type 6 - genetics; Danio rerio; Degeneration; Degenerative diseases; Diseases; Disruption; Encyclopedias; Epithelium; FastQC; Gene expression; Gene Ontology; Gene Regulatory Networks; Genes; Genetic aspects; Genetic research; Genomes; Genomics; Gluconeogenesis; Glycolysis; Health aspects; Heart cells; Immunology; Insulin; KEGG; Light Signal Transduction - genetics; Messenger RNA; Mutants; Mutation; Neurodegeneration; Oxidative phosphorylation; Pathogenesis; Pde6c; Peptidase; Phosphodiesterase; Phosphorylation; Photoreceptors; Phototransduction; Proteins; Retina; Retina - metabolism; Retinal degeneration; Retinal Degeneration - genetics; Retinal pigment epithelium; Rhodopsin; Ribonucleic acid; RNA; RNA sequencing; RNA transport; RNA-Seq; Signal transduction; Signaling; Systems development; Tricarboxylic acid cycle; Trinity; Zebrafish; Zebrafish - genetics; Zebrafish Proteins - genetics
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-020-6550-z

Retinal degenerative diseases affect millions of people and represent the leading cause of vision loss around the world. Retinal degeneration has been attributed to a wide variety of causes, such as disruption of genes involved in phototransduction, biosynthesis, folding of the rhodopsin molecule, and the structural support of the retina. The molecular pathogenesis of the biological events in retinal degeneration is unclear; however, the molecular basis of the retinal pathological defect can be potentially determined by gene-expression profiling of the whole retina. In the present study, we analyzed the differential gene expression profile of the retina from a wild-type zebrafish and phosphodiesterase 6c (pde6c) mutant. The datasets were downloaded from the Sequence Read Archive (SRA), and adaptors and unbiased bases were removed, and sequences were checked to ensure the quality. The reads were further aligned to the reference genome of zebrafish, and the gene expression was calculated. The differentially expressed genes (DEGs) were filtered based on the log fold change (logFC) (±4) and p-values (p