Evidence for the loss of plasminogen receptor KT gene in chicken.

The loss of conserved genes has the potential to alter phenotypes drastically. Screening of vertebrate genomes for lineage-specific gene loss events has identified numerous natural knockouts associated with specific phenotypes. We provide evidence for the loss of a multi-exonic plasminogen receptor KT (PLGRKT) protein-encoding gene located on the Z chromosome in chicken. Exons 1 and 2 are entirely missing; remnants of exon 3 and a mostly intact exon 4 are identified in an assembly gap-free region in chicken with conserved synteny across species and verified using transcriptome and genome sequencing. PLGRKT gene disrupting changes are present in representative species from all five galliform families. In contrast to this, the presence of an intact transcriptionally active PLGRKT gene in species such as mallard, swan goose, and Anolis lizard suggests that gene loss occurred in the galliform lineage sometime between 68 and 80 Mya. The presence of galliform specific chicken repeat 1 (CR1) insertion at the erstwhile exon 2 of PLGRKT gene suggests repeat insertion-mediated loss. However, at least nine other independent PLGRKT coding frame disrupting changes in other bird species are supported by genome sequencing and indicate a role for relaxed purifying selection before CR1 insertion. The recurrent loss of a conserved gene with a role in the regulation of macrophage migration, efferocytosis, and blood coagulation is intriguing. Hence, we propose potential candidate genes that might be compensating the function of PLGRKT based on the presence of a C-terminal lysine residue, transmembrane domains, and gene expression patterns.