Molecular genotyping, diversity studies and high-resolution molecular markers unveiled by microsatellites in Giardia duodenalis

Abstract

BackgroundGiardia duodenalis (synonyms G. lamblia and G. intestinalis) is an enteric protozoan parasite of a wide range of mammalian hosts, including humans and various domestic and wild animals. There is considerable genetic variability in G. duodenalis and isolates of this parasite have been divided into eight genetic assemblages. Microsatellites markers can be used to discriminate isolates with a high level of sensitivity. This study was conducted to identify and characterize genomic microsatellites (simple sequence repeats—SSRs), sequences of one- to six-nucleotide motifs repeated in tandem, present in the available genomes of G. duodenalis and to develop new markers that can serve as a tool for detection and for characterizing the genetic diversity of this parasite.Methodology/ Principal findingsFor each genetic assemblage, polymorphism levels for the microsatellite markers were evaluated. After performing the analysis using the MISA and SciRoKo software, 1,853 simple sequence repeats (SSRs) were identified. In all the genomes, trinucleotide repeats were the most common class followed by tetranucleotide. Many of the SSR loci are assemblage-specific, and 36 SSR loci shared among all the genomes were identified. Together with hypothetical proteins, variant-specific surface proteins represented nearly half of the annotated SSR loci. The results regarding the most common repeat among the SSRs led us to infer that positive selection occurred to avoid frameshift mutations. Additionally, based on inter- and intra-genetic assemblages polymorphism analyses, we unveiled previously undetected genetic variation, indicating that the microsatellite markers we developed are useful molecular tools for epidemiological inferences based on population genetics patterns and processes.ConclusionsThere is increasing demand for the development of new molecular markers and for the characterization of pathogens at a higher resolution level. In this study, we present 60 G. duodenalis microsatellites markers that exhibited high polymerase chain reaction (PCR) amplification efficiency among the different genetic assemblages. Twenty of these markers presented nucleotide sequence polymorphisms and may be used as a genotyping tool. The monomorphic markers can be used for the detection of the parasite at the species and genetic assemblage level. These polymorphic markers revealed a genetic diversity that was previously undetectable, thus they can be considered valuable molecular tools for high resolution markers in future studies investigating Giardia and may also be used for epidemiological inferences based on populations genetics patterns and processes.

Comprehensive analysis of SSRs and database construction using all complete gene-coding sequences in major horticultural and representative plants

“…Since molecular marker technology was developed in the 1980s, an increasing number of molecular marker types have been identified, which has rapidly accelerated genetic improvements in species 1 . The development and comparative analysis of molecular markers could help us reveal genetic variation underlying various biological functional genes 2 – 4 . To date, researchers have found several molecular markers, such as restriction fragment length polymorphisms, random amplified polymorphism DNA, sequence tag sites, amplified fragment length polymorphism, diversity array technology markers, single-nucleotide polymorphisms, specific locus amplified fragments, and simple sequence repeats (SSRs) 1 , 5 , 6 .…”

Genotypes of Giardia duodenalis in Household Dogs and Cats from Poland

“…The assemblages A and B are further divided into sub-genotypes AI, AII, AIII, BIII and BIV. Typical genotypes in dogs are C and D, but A and B can also be found, and exceptionally even E and F ones [ 6 , 9 , 12 , 14 , 20 ]. Genotype F is common in cats, which can be infected also by genotype A, E and rarely C [ 6 , 21 , 24 ].…”

Giardiasis in Human and Animals

“…The research done so far on giardiasis has been mainly focused on its molecular characterization in various animals in order to identify the reservoir host and calculate the zoonotic risk of disease. At present, identification of specific genotype in animals and humans is possible due to the development of molecular markers (Durigan et al 2018). Giardiasis is an important disease, affecting both human and animals, and having millions of cases every year.…”