MGERT: a pipeline to retrieve coding sequences of mobile genetic elements from genome assemblies

Abstract Background Genomes of eukaryotes are inhabited by myriads of mobile genetic elements (MGEs) – transposons and retrotransposons - which play a great role in genome plasticity and evolution. A lot of computational tools were developed to annotate them either in genomic assemblies or raw reads using de novo or homology-based approaches. But there has been no pipeline enabling users to get coding and flanking sequences of MGEs suitable for a downstream analysis from genome assemblies. Results We developed a new pipeline, MGERT (Mobile Genetic Elements Retrieving Tool), that automates all the steps necessary to obtain protein-coding sequences of mobile genetic elements from genomic assemblies even if no previous knowledge on MGE content of a particular genome is available. Conclusions Using MGERT, researchers can easily find MGEs, their coding and flanking sequences in the genome of interest. Thus, this pipeline helps researchers to focus on the biological analysis of MGEs rather than excessive scripting and pipelining

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

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

Schematic representation of the SP network that reflects relationship between genotypes 1–9 in <i>D. dahli.</i>

<p>Complete sequences of <i>D. dahli</i> genotypes were analyzed using TCS software version 1.21. Genotypes 10 and 11 are plotted separately. Population distribution of the genotypes is shown by different colours. The black circles show, unsampled, but computer-predicted genotypes.</p

Sample size, genotype composition, diversity and distribution in the populations of D. <i>rostombekowi</i>.

<p>Sample size, genotype composition, diversity and distribution in the populations of D. <i>rostombekowi</i>.</p

Allelic variations of microsatellite containing loci Du215, Du281, and Du323 in parthenogenetic <i>D. dahli</i> species.

1<p>Distances before (−) and after (+) microsatellite cluster are given in bp.</p

Schematic representation of 11 genotypes formed by allelic combinations of microsatellite loci Du215, Du281, and Du323 in 111 <i>D. dahli</i> individuals.

<p>Parental-specific SNV markers are shown in square. Variable microsatellite clusters are shown in each of two alleles.</p