Identification and Characterization of Microsatellite Markers Derived from the Whole Genome Analysis of Taenia solium

Abstract

BackgroundInfections with Taenia solium are the most common cause of adult acquired seizures worldwide, and are the leading cause of epilepsy in developing countries. A better understanding of the genetic diversity of T. solium will improve parasite diagnostics and transmission pathways in endemic areas thereby facilitating the design of future control measures and interventions. Microsatellite markers are useful genome features, which enable strain typing and identification in complex pathogen genomes. Here we describe microsatellite identification and characterization in T. solium, providing information that will assist in global efforts to control this important pathogen.MethodsFor genome sequencing, T. solium cysts and proglottids were collected from Huancayo and Puno in Peru, respectively. Using next generation sequencing (NGS) and de novo assembly, we assembled two draft genomes and one hybrid genome. Microsatellite sequences were identified and 36 of them were selected for further analysis. Twenty T. solium isolates were collected from Tumbes in the northern region, and twenty from Puno in the southern region of Peru. The size-polymorphism of the selected microsatellites was determined with multi-capillary electrophoresis. We analyzed the association between microsatellite polymorphism and the geographic origin of the samples.ResultsThe predicted size of the hybrid (proglottid genome combined with cyst genome) T. solium genome was 111 MB with a GC content of 42.54%. A total of 7,979 contigs (>1,000 nt) were obtained. We identified 9,129 microsatellites in the Puno-proglottid genome and 9,936 in the Huancayo-cyst genome, with 5 or more repeats, ranging from mono- to hexa-nucleotide. Seven microsatellites were polymorphic and 29 were monomorphic within the analyzed isolates. T. solium tapeworms were classified into two genetic groups that correlated with the North/South geographic origin of the parasites.Conclusions/SignificanceThe availability of draft genomes for T. solium represents a significant step towards the understanding the biology of the parasite. We report here a set of T. solium polymorphic microsatellite markers that appear promising for genetic epidemiology studies.

Genome-wide characterization and analysis of microsatellite sequences in camelid species

“…In addition, this finding is consistent with the previous report that mononucleotide SSR repeats are more frequent in eukaryotic genomes than other SSR repeat types (Sharma et al 2007). However, dinucleotide SSR repeats are the most frequent type in dicotyledons (Kumpatla and Mukhopadhyay 2005), Taenia solium (Pajuelo et al 2015), Drosophila (Katti et al 2001), and rodents (Toth 2000), while trinucleotide SSR repeats are the most prevalent type in a number of prokaryotes (Kim et al 2008;Sharma et al 2007) and yeast (Katti et al 2001). The second most frequent SSRs in camelid genomes are dinucleotides, accounting for 25.08-33.94% of all SSRs.…”

A conventional PCR for differentiating common taeniid species of dogs based on in silico microsatellite analysis

“…This is in agreement with the fact that the coding regions have less frequent microsatellites than the non-coding ones 22 . In addition, ITS1 dinucleotide motifs were the most abundant in taeniids as previously shown in other species 35 .…”

“…Accordingly, in ITS1 region, a higher GT content was found in the study in agreement with Pajuelo et al . 35 .…”

Clustering of Necropsy-Confirmed Porcine Cysticercosis Surrounding Taenia solium Tapeworm Carriers in Peru

“…Future research using microsatellite DNA markers to link cysts found in pigs to their specific parent tapeworm may help to better understand the spatial and environmental mechanism of T. solium transmission. 33 In conclusion, we demonstrated significant clustering of viable porcine cysticercosis infection in the immediate surroundings of confirmed T. solium tapeworm carriers. This study contributes to a growing body of evidence that T. solium tapeworm carriers represent important sources of infection to pigs raised in their immediate vicinity.…”