Phylogenetic Distribution of CMP-Neu5Ac Hydroxylase (CMAH), the Enzyme Synthetizing the Proinflammatory Human Xenoantigen Neu5Gc

Peri, Sateesh; Kulkarni, Asmita; Feyertag, Felix; Berninsone, Patricia M; Alvarez-Ponce, David

Gene annotations, particularly for nonmodel organisms, are known to be subjected to high rates of error (Devos and Valencia 2001; Tu et al. 2012) . For each CMAH homolog, the nucleotide sequence of the coding region (CDS) was translated in silico and aligned with the chimpanzee sequence using ProbCons, version 1.12 (Do et al. 2005) . The resulting protein sequence alignment was used to guide the alignment of the CDSs. The CDS alignments were visualized using BioEdit, version 7.0.0 (Hall 1999) . Where possible, all gene annotation errors were fixed manually. Erroneous and extra exons (not showing significant similarity to the chimpanzee sequence) were removed. Missing exons (present in the chimpanzee sequence but not in the species of interest) were searched for in the genome using the chimpanzee sequence as query in TBLASTN or BLASTN searches. If the missing exon could not be detected, a careful analysis was conducted to determine whether the exon had been lost or it was part of an unsequenced region. Given the small size of the coding segment of exon 1 (only eight nucleotides), no attempt was made to annotate this exon.