Characterisation of highly duplicated genes, such as those of the major histocompatibility complex (MHC), remains a challenging task, yet these genes play a crucial role in coevolution of parasites with their hosts, and may affect the susceptibility of endangered species to disease. In a recent article in Molecular Ecology Resources (link) A. Sebastian, M. Migalska and J. Radwan (Evolutionary Biology Group) together with A. Biedrzycka (Institute of Nature Conservation of PAS) and H. Westerdahl (Lund University) showed that studying such complex gene families in wild-living species is now possible due to advances in high-throughput amplicon sequencing technology.
The tested the effect of amplicon coverage (range: 500-20 000 reads) on the repeatability of genotyping using four different protocols. They concluded that reliable genotyping of even dozens of co-amplifying loci can be achieved above the threshold of 5 000 reads per amplicon. The Adjustable Clustering (AC) method with AmpliSAS, developed earlier by the team, (see Sebastian et al. 2016) proved to be the most effective. Moreover, the AC can easily be implemented with existing on-line software AmpliSAS (link).
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