Evidence for the loss of plasminogen receptor KT gene in chicken
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Evidence for the loss of plasminogen receptor KT gene in chicken Sandhya Sharma1 · Sagar Sharad Shinde1 · Lokdeep Teekas1 · Nagarjun Vijay1 Received: 1 June 2020 / Accepted: 3 November 2020 © Springer-Verlag GmbH Germany, part of Springer Nature 2020
Abstract The loss of conserved genes has the potential to alter phenotypes drastically. Screening of vertebrate genomes for lineagespecific 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. Keywords Chicken · Gene loss · Plasminogen receptor · PLGRKT · Insulin resistance · Platelet Chicken genome has ~2-fold smaller introns and intergenic regions as compared to the human genome (Kapusta et al. 2017). The major histocompatibility complex (MHC) in chicken is also more compact than humans, with a ~20fold smaller size in chicken (Kaufman et al. 1999). This constrained genome size of birds is hypothesized to result from higher metabolic flux associated with flight (Hughes and Hughes 1995; Wright et al. 2014). The smaller genome size and lack of genomic sequence corresponding to several hundred protein-coding genes in bird genome assemblies compared to mammalian genome assemblies initially served as evidence of massive gene loss in birds (Hughes and Friedman 2008; Lovell et al. 2014). Surprisingly, ensuing studies could reconstruct several hundred missing genes relying upon de novo assembly of transcriptome sequencing * Nagarjun Vijay [email protected] 1
Computational Evolutionary Genomics Lab, Department of Biological Sciences, IISER Bhopal, Bhauri, Madhya Pradesh, India
datasets (Hron et al. 2015; Borne
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