Molecular genetic characteristics of Darevskia portschinskii lizard populations based on microsatellite markers analysis

The Caucasian rock lizard species Darevskia portschinskii is one of the bisexual species participating in interspecific hybridisation as the paternal ancestor with the maternal ancestors D. mixta and D. raddei resulting in the successful formation of the parthenogenetic D. dahli and D. rostombekowi, respectively. Populations of D. portschinskii have been previously divided into two subspecies, D. p. portschinskii and D. p. nigrita according to their geographical distribution and the morphological data, but they have not been characterised genetically. Here, we used ten microsatellite markers to determine the genetic structure of the D. portschinskii populations. The utility of the developed microsatellite markers for investigating the genetic variability within and among populations with a heterogeneous spatial distribution was demonstrated. Our results showed that the intra- and interspecific differentiation of the studied populations were consistent with the morphological data on the subspecies status of the D. p. portschinskii and D. p. nigrita populations. A potential applicability of the developed microsatellite markers to study genetic diversity of Darevskia species and subspecies complexes is suggested

Genetic Variation and De Novo Mutations in the Parthenogenetic Caucasian Rock Lizard Darevskia unisexualis

Unisexual all-female lizards of the genus Darevskia that are well adapted to various habitats are known to reproduce normally by true parthenogenesis. Although they consist of unisexual lineages and lack effective genetic recombination, they are characterized by some level of genetic polymorphism. To reveal the mutational contribution to overall genetic variability, the most straightforward and conclusive way is the direct detection of mutation events in pedigree genotyping. Earlier we selected from genomic library of D. unisexualis two polymorphic microsatellite containg loci Du281 and Du215. In this study, these two loci were analyzed to detect possible de novo mutations in 168 parthenogenetic offspring of 49 D. unisexualis mothers and in 147 offspring of 50 D. armeniaca mothers . No mutant alleles were detected in D. armeniaca offspring at both loci, and in D. unisexualis offspring at the Du215 locus. There were a total of seven mutational events in the germ lines of four of the 49 D. unisexualis mothers at the Du281 locus, yielding the mutation rate of 0.1428 events per germ line tissue. Sequencing of the mutant alleles has shown that most mutations occur via deletion or insertion of single microsatellite repeat being identical in all offspring of the family. This indicates that such mutations emerge at the early stages of embryogenesis. In this study we characterized single highly unstable (GATA)n containing locus in parthenogenetic lizard species D. unisexualis. Besides, we characterized various types of mutant alleles of this locus found in the D. unisexualis offspring of the first generation. Our data has shown that microsatellite mutations at highly unstable loci can make a significant contribution to population variability of parthenogenetic lizards

Allelic variants of microsatellite clusters of <i>Du281</i> locus in parthenogenetic lizard families <i>D. unisexualis</i>.

<p>Variations in microsatellite clusters are denoted by bold letters. T-A-T and C-G-C are haplotypes specific for allelic variants of <i>D. unisexualis</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0002730#pone.0002730-Korchagin1" target="_blank">[24]</a>. In Family 2 the observed changes were the same in all offspring (1–5). In family 3 the observed changes were the same in all offspring(1, 2). In Family 4 the observed changes are the same in three offspring (1, 3 and 4).</p

Examples of families where where no intrafamily variation of PCR products was revealed.

<p>a – Du281 locus, <i>D. armeniaca</i> family; b – 215 locus, <i>D. armeniaca</i> family; c – 215 locus, <i>D. unisexualis</i> family. Maternal DNAs are marked by M, offspring DNAs are shown by arrows and numbered in each family.</p

The origin of multiple clones in the parthenogenetic lizard species Darevskia rostombekowi.

The all-female Caucasian rock lizard Darevskia rostombekowi and other unisexual species of this genus reproduce normally via true parthenogenesis. Typically, diploid parthenogenetic reptiles exhibit some amount of clonal diversity. However, allozyme data from D. rostombekowi have suggested that this species consists of a single clone. Herein, we test this hypothesis by evaluating variation at three variable microsatellite loci for 42 specimens of D. rostombekowi from four populations in Armenia. Analyses based on single nucleotide polymorphisms of each locus reveal five genotypes or presumptive clones in this species. All individuals are heterozygous at the loci. The major clone occurs in 24 individuals and involves three populations. Four rare clones involve one or several individuals from one or two populations. Most variation owes to parent-specific single nucleotide polymorphisms, which occur as heterozygotes. This result fails to reject the hypothesis of a single hybridization founder event that resulted in the initial formation of one major clone. The other clones appear to have originated via post-formation microsatellite mutations of the major clone

Characterization of Streptococcus pneumoniae strains causing invasive infections using whole-genome sequencing

Purpose: antigenic and genetic characterization of Streptococcus pneumoniae strains isolated from patients with invasive forms of pneumococcal infection using whole-genome sequencing.Materials and Methods. The study was performed on 46 S. pneumoniae strains isolated during the PEHASus multicenter studies in 2015-2018. Sequencing was performed using Illumina protocols and equipment. The SPAdes, SeroBA, PneumoCaT software were used for data processing, as well as BIGSdb software (PubMLST.org).Results and Discussion. Whole-genome sequences of strains were obtained; the information was entered into the PubMLST database (id: 51080-51125). Ten (21%) strains were found to have serotype 3. Five (11%) strains belonged to serotype 19F and five to serogroup 6; two of them belonged to serotype 6A; one strain had 6B and 1 had 6BE serotype; 1 strain showed discordant result (6A or 6BE). Serotype 15B was identified in 3 (6.5%) strains. Serotypes 7F, 8, 9V, 14, 22F, 23F and 28A were identified in two strains each; serotypes 1, 4, 9N, 10C, 12F, 18C, 35F, 37 and 38 were found once. The proportion of strains with serotypes included in PCV13 and PPV23 vaccines was 65% and 80%, respectively. 36 sequence types were found in strains; out of them, 6 sequence types were found for the first time. A dominant sequence type or clone complexes could not be identified using multilocus sequence typing except for serotype 3 strains. The inability to identify clonal complexes is in congruence with the previously obtained data on the absence of S. pneumoniae clones associated with pneumococcal meningitis in Russia.Conclusion. The information about serotypes of S. pneumoniae causing invasive infections together with epidemiologic data about strain sources and vaccination allows us to evaluate the effectiveness of pneumococcal vaccines and provide information for improving the PCR-based routine serotyping

Clonal diversity and clone formation in the parthenogenetic Caucasian rock Lizard Darevskia dahli [corrected].

The all-female Caucasian rock lizard species Darevskia dahli and other parthenogenetic species of this genus reproduce normally via true parthenogenesis. Previously, the genetic diversity of this species was analyzed using allozymes, mitochondrial DNA, and DNA fingerprint markers. In the present study, variation at three microsatellite loci was studied in 111 specimens of D. dahli from five populations from Armenia, and new information regarding clonal diversity and clone formation in D. dahli was obtained that suggests a multiple hybridization origin. All individuals but one were heterozygous at the loci studied. Based on specific allele combinations, 11 genotypes were identified among the individuals studied. Individuals with the same genotypes formed distinct clonal lineages: one major clone was represented by 72 individuals, an intermediate clone was represented by 21 individuals, and nine other clones were rare and represented by one or several individuals. A new approach based on the detection and comparison of genotype-specific markers formed by combinations of parental-specific markers was developed and used to identify at least three hybridization founder events that resulted in the initial formation of one major and two rare clones. All other clones, including the intermediate and seven rare clones, probably arose through postformation microsatellite mutations of the major clone. This approach can be used to identify hybridization founder events and to study clone formation in other unisexual taxa

Genetic similarity between the sequences of alleles Du281 (a) and Du323 (b) for the species <i>D</i>. <i>portschinskii</i> (D. port), <i>D</i>. <i>rostombekowi</i> (D. rost) and <i>D</i>. <i>raddei</i> (D. rad).

<p>NJ/p-distance/Pairwise deletions/IB = 500.</p

The population indices of gene diversity for three studied loci in four sampled populations of <i>D</i>. <i>rostombekowi</i>.

<p>The population indices of gene diversity for three studied loci in four sampled populations of <i>D</i>. <i>rostombekowi</i>.</p

Map of Armenia showing the localities from which populations of parthenogenetic <i>Darevskia rostombekowi</i> and bisexual parental species <i>D</i>. <i>raddei</i> and <i>D</i>. <i>portschinskii</i> were collected.

<p>Sampling localities are indicated by the following colors: <i>D</i>. <i>rostombekowi</i>–yellow; <i>D</i>. <i>raddei raddei</i>–blue; <i>D</i>. <i>raddei nairensis</i>–red; <i>D</i>. <i>portschinskii portschinskii</i>–green; <i>D</i>. <i>portschinskii nigrita</i>–black. Numbers indicate populations: 1 –Gosh (40°42'20.3"N 45°00'57.7"E); 2 –Tsovak (40°10'45.0"N 45°37'22.7"E); 3 –Papanino (40°42'27.7"N 44°45'43.8"E); 4 –Spitak (40°48'50.0"N 44°16'48.7"E); 5 –Geghard (40°08'49.4"N 44°48'26.9"E); 6 –Goris (39°33'09.5"N 46°21'19.7"E); 7 –Doroga (39°22'53.9"N 46°21'06.6"E); 8 –Yeghegnadzor (39°47'48.4"N 45°19'52.4"E); 9 –Kelbajar (40°06'03.1"N 45°59'27.1"E); 10 –Tatev (39°23'13.2"N 46°15'11.2"E); 11 –Ayrivank (40°26'02.3"N 45°06'27.2"E); 12 –Bjni (40°27'42.6"N 44°39'07.3"E); 13 –Yerevan (40°10'37.0"N 44°36'09.3"E); 14 –Lchap (40°28'02.4"N 45°03'43.5"E); 15 –Lchashen (40°30'45.9"N 44°54'03.2"E); 16 –Pyunik (40°36'49.9"N 44°35'06.4"E); 17 –Zuar (40°04'39.0"N 46°13'47.0"E); 18 –Dzoraget (40°54'15.0"N 44°40'37.7"E).</p