We developed a procedure for reconstructing full genotypic information (number of gene copies) at each KIR locus from the standard KIR gene content.
Average imputation accuracies were split into categories of the closest recent ancestor genotyped and calculated over 10 replications; mean of imputation accuracy calculated as the correlation between true genotypes and imputed genotype dosages, both uncorrected for the mean gene content; standard deviation.
The array features analyzed represent only 5689 genes, a fraction 25-300% of a standard vertebrate genome) of predicted total gene content for these species.
Even if striking exceptions to this standard are known [ 4- 10], most differences among animal mtDNAs involve gene content and arrangement.
Protein domain content, the overall collection of domains in a given proteome, was successfully used to reconstruct a phylogenetic tree of life that was equivalent to standard phylogenies derived from molecular sequences and phylogenomic trees based on gene content and gene order [ 9].
We may have a better estimate of the gene content once full-length gene sequences and a gold standard reference sequence of wheat becomes available allowing us to differentiate between genes and gene fragments.
Our results reveal that, despite widespread use, evolutionary relationships inferred from the standard seven-gene multilocus sequence typing (MLST) method could not predict virulence gene content or strain phenotype.
Inspection of the sequence reveals that while U. maydis has a streamlined gene content, it appears to contain a full repertoire of the standard signaling cascades present in other fungi.
Stated another way, the phylogenetic tree of life reconstructed based on PDC is comparable to standard phylogenetic methods based on molecular markers (such as rRNA) and other phylogenomic approaches such as gene content and gene order [5].
