Evolutionary genetic approaches to analyze mucins

Mucins are heavily glycosylated proteins that form protective mucus barriers at host-environment interfaces. Mucin genes frequently contain exonic variable number tandem repeat (exVNTR) domains that encode peptides enriched in proline, threonine, and serine. These repeat domains create substantial challenges for comparative and population genetic analyses because short-read sequencing often collapses repeat arrays and obscures haplotype structure. Recent advances in long-read sequencing, pangenome resources, and specialized VNTR analysis tools now enable systematic investigation of mucin genetics and evolution. In this chapter, we present practical protocols for identifying candidate mucin genes across species, annotating mucin exVNTRs from long-read genome assemblies, and genotyping exVNTR alleles in large short-read sequencing cohorts. We further outline analytical strategies for evaluating natural selection acting on mucin repeat domains. Together, these protocols enable systematic identification, structural resolution, and evolutionary analysis of mucin variation across species and human populations.