Abstract
Through RNA-Seq analyses, we identified 137 genes that are missing in chicken, including the long-sought-after nephrin and tumor necrosis factor genes. These genes tended to cluster in GC-rich regions that have poor coverage in genome sequence databases. Hence, the occurrence of syntenic groups of vertebrate genes that have not been observed in Aves does not prove the evolutionary loss of such genes.Please see related Research article: http://dx.doi.org/10.1186/s13059-014-0565-1 and Please see response from Lovell et al: https://www.dx.doi.org/10.1186/s13059-017-1234-y
Highlights
Through RNA-Seq analyses, we identified 137 genes that are missing in chicken, including the long-sought-after nephrin and tumor necrosis factor genes
These transcripts were characterized on the basis of sequence similarity to known genes in other vertebrates using the Trinotate pipeline, which searches for sequences encoding known protein domains, transmembrane domains, and signal peptides (Additional file 1: Tables S2 and S3a)
Among the remaining 38 genes (Additional file 1: Table S6) with no sequence similarity to any genome build are the tumor necrosis factor (TNF) and nephrin (NPHS1), which have been reported as missing from birds in several studies (Table 1) but which are critically important in vertebrate biology and have extensively been studied in non-avian vertebrates
Summary
Correspondence on Lovell et al.: identification of chicken genes previously assumed to be evolutionarily lost. Burgess, Manfred Grabherr, Miriam Friedman-Einat3* and Leif Andersson1,6,7*.
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