Abstract
Multilocus microsatellite genotyping of Plasmodium knowlesi isolates previously indicated 2 divergent parasite subpopulations in humans on the island of Borneo, each associated with a different macaque reservoir host species. Geographic divergence was also apparent, and independent sequence data have indicated particularly deep divergence between parasites from mainland Southeast Asia and Borneo. To resolve the overall population structure, multilocus microsatellite genotyping was conducted on a new sample of 182 P. knowlesi infections (obtained from 134 humans and 48 wild macaques) from diverse areas of Malaysia, first analyzed separately and then in combination with previous data. All analyses confirmed 2 divergent clusters of human cases in Malaysian Borneo, associated with long-tailed macaques and pig-tailed macaques, and a third cluster in humans and most macaques in peninsular Malaysia. High levels of pairwise divergence between each of these sympatric and allopatric subpopulations have implications for the epidemiology and control of this zoonotic species.
Highlights
Most short-reads mappers for next-generation sequencing (NGS) data were developed when sequence reads were about 36bp in length
Fast moving NGS technologies keep pressing for the development of new alignment algorithms
2.1.1 Seeding and re-seeding BWA-MEM follows the canonical seed-and-extend paradigm. It initially seeds an alignment with supermaximal exact matches (SMEMs) using an algorithm we found previously (Li, 2012, Algorithm 5), which essentially finds at each query position the longest exact match covering the position
Summary
Most short-reads mappers for next-generation sequencing (NGS) data were developed when sequence reads were about 36bp in length. Fast moving NGS technologies keep pressing for the development of new alignment algorithms In this background, a few long-read alignment algorithms, notably including BWA-SW (Li and Durbin, 2010), Bowtie (Langmead and Salzberg, 2012), Cushaw (Liu and Schmidt, 2012) and GEM (Marco-Sola et al, 2012), have been developed. A few long-read alignment algorithms, notably including BWA-SW (Li and Durbin, 2010), Bowtie (Langmead and Salzberg, 2012), Cushaw (Liu and Schmidt, 2012) and GEM (Marco-Sola et al, 2012), have been developed Very few algorithms are able to align sequences of such variable lengths at high accuracy and to be robust to translocations in the assembly All these concerns motivated us to explore a new alignment algorithm
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