Development of a Multilocus Sequence Typing Scheme for Giardia intestinalis

Abstract

<jats:p>Giardia intestinalis is an intestinal protozoan most commonly found in humans. It has been grouped into 8 assemblages (A-H). Markers such as the glutamate dehydrogenase gene, triose phosphate isomerase and beta-giardin (β-giardin) have been widely used for genotyping. In addition, different genetic targets have been proposed as a valuable alternative to assess diversity and genetics of this microorganism. Thus, our objective was to evaluate new markers for the study of the diversity and intra-taxa genetic structure of G. intestinalis in silico and in DNA obtained from stool samples. We analysed nine constitutive genes in 80 complete genome sequences and in a group of 24 stool samples from Colombia. Allelic diversity was evaluated by locus and for the concatenated sequence of nine loci that could discriminate up to 53 alleles. Phylogenetic reconstructions allowed us to identify AI, AII and B assemblages. We found evidence of intra- and inter-assemblage recombination events. Population structure analysis showed genetic differentiation among the assemblages analysed.</jats:p>

Subspecific Nomenclature of Giardia duodenalis in the Light of a Compared Population Genomics of Pathogens

“…However, if genetic exchange obtains in G. duodenalis , it does not affect either the discreteness or stability of the assemblages, in accordance with the statement by Tsui et al [ 5 ]. These properties of the assemblages (NCs) have been corroborated by many independent studies relying on different tools and samplings [ 3 , 4 , 10 , 14 , 25 , 26 , 27 , 28 , 29 , 30 , 31 ].…”

Genetic Diversity and Population Structure of Anopheles funestus in Western Kenya Based on Mitochondrial DNA Marker COII

“…The DnaSP Version 6.12.03 [ 25 ] was used to compute genetic diversity indices [haplotype diversity (Hd), the number of haplotypes (h), nucleotide diversity (Π), the number of segregating sites (S) and the mean number of pairwise difference (k)] and neutrality tests (Tajima’s D, Fu and Li’s D, Fu and Li’s F, and Fu’s Fs statistics). Gamma ST measurements, including an inbuilt algorithm with DnaSP software, were used to estimate the gene flow and genetic differentiation [ 26 , 27 ]. The analysis of molecular variance (AMOVA) was performed in Arlequin version 3.5.2 [ 28 ] to partition genetic variations among groups (Port Victoria, Migori, Bungoma, and Kombewa) and within groups.…”