Identification of chicken genes previously assumed to be evolutionarily lost

RNA-Seq data of visceral fat, pituitary and hypothalamus from two different strains of chicken were assembled and filtered against known genes in chicken, and candidate novel transcripts were screened for similarities to known genes in other vertebrate species. Using stringent filtering, we identified 190 genes that were missing in the chicken galgal4 assembly. These genes had an average GC content of 68% significantly higher than the average GC content of 46% for chicken genes. Two of these, which have been intensively sought, encode nephrin (NPHS1) and tumor necrosis factor (TNFA). Full length cDNA deduced for NPHS1 and TNF was confirmend by PCR and expression profiling. Mass-spectrometry analysis of visceral fat confirmed the expression of several of the novel genes. The recently released galgal5 genome assembly revealed 54 of the novel genes, thus validated our approach. Novel genes with defined mapping position were found at high tendency in clusters and in microchromosomes.

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