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In sum, Nsp appears to be one of the most polymorphic coding genes known in Insecta.
The genes of the major histocompatibility (MH) complex (MHC) encode proteins that play a crucial role in the vertebrate immune response (Klein 1986), and possibly as a result of pathogen-driven balancing selection, MHC genes are the most polymorphic coding regions known in vertebrates (Grimholt et al. 2003; Wegner 2008).
The peptide-binding region (PBR) for each HLA is the most polymorphic coding region in the human genome, and this variation is thought to be primarily maintained by balancing selection (Hughes and Nei 1988 , 1989 Hughes and Yeager 1998; Klein et al. 2007).
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Although our analysis was focused on whole genes (leading to an underestimation of positive selection), it is notable that the genes with significant dN/dS > 1 were mainly incs and T3SS effectors encoding genes, whereas the most polymorphic ones code essentially for membrane and hypothetical proteins.
As illustrated Fig. 9, we identified most polymorphic positions in the coding sequence (18 out of a total of 29 which are reported) among which 9 SNPs induce amino acid change.
No SNPs were found by EcoTILLING in EU39 and DQ66, a J. curcas seed maturation gene (Smp1) and a chloroplast omega-3 fatty acid (FA) desaturase, respectively, while the most polymorphic locus, AF, a curcin gene coding for a ribosome inactivating protein from J. curcas, revealed 20 SNPs.
Major histocompatibility complex (MHC) proteins constitute an essential component of the vertebrate immune response, and are coded by the most polymorphic of the vertebrate genes.
We concluded that MSs within intronic regions are most polymorphic, and followed by UTR, intergenic, and coding regions.
The remaining instances of intra-specific polymorphism were scored using polymorphic coding (0/1; Wiens, 2000).
The MSP1 gene codes for one of the most polymorphic proteins in P. falciparum.
We restricted our analyses to the PBR (Peptide Binding Region) coding exon(s) which are the most polymorphic amongst HLA classical genes and which are screened through most typing protocols (Table 1).
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