Alexander Blinov

Molecular characterization of vernalization loci VRN1 in wild and cultivated wheats

BackgroundVariability of the VRN1 promoter region of the unique collection of spring polyploid and wild diploid wheat species together with diploid goatgrasses (donor of B and D genomes of polyploid wheats) were investigated. Accessions of wild diploid (T. boeoticum, T. urartu) and tetraploid (T. araraticum, T. timopheevii) species were studied for the first time.ResultsSequence analysis indicated great variability in the region from -62 to -221 nucleotide positions of the VRN1 promoter region. Different indels were found within this region in spring wheats. It was shown that VRN1 promoter region of B and G genome can also contain damages such as the insertion of the transposable element.Some transcription factor recognition sites including hybrid C/G-box for TaFDL2 protein known as the VRN1 gene upregulator were predicted inside the variable region. It was shown that deletions leading to promoter damage occurred in diploid and polyploid species independently. DNA transposon insertions first occurred in polyploid species. At the same time, the duplication of the promoter region was observed in A genomes of polyploid species.ConclusionsWe can conclude that supposed molecular mechanism of the VRN1 gene activating in cultivated diploid wheat species T. monococcum is common also for wild T. boeoticum and was inherited by T. monococcum. The spring polyploids are not related in their origin to spring diploids. The spring T. urartu and goatgrass accessions have another mechanism of flowering activation that is not connected with indels in VRN1 promoter region. All obtained data may be useful for detailed insight into origin of spring wheat forms in evolution and domestication process.

Non-LTR retrotransposons in fungi

Non-long terminal repeat (non-LTR) retrotransposons have contributed to shaping the structure and function of genomes. Fungi have small genomes, usually with limited amounts of repetitive DNA. In silico approach has been used to survey the non-LTR elements in 57 fungal genomes. More than 100 novel non-LTR retrotransposons were found, which belonged to five diverse clades. The present survey identified two novel clades of fungal non-LTR retrotransposons. The copy number of non-LTR retroelements varied widely. Some of the studied species contained a single copy of non-LTR retrotransposon, whereas others possessed a great number of non-LTR retrotransposon copies per genome. Although evolutionary relationships of most elements are congruent with phylogeny of host species, a new case of possible horizontal transfer was found between Eurotiomycetes and Sordariomycetes.

Vertical evolution and horizontal transfer of CR1 non- LTR retrotransposons and Tc1/mariner DNA transposons in Lepidoptera species.

Horizontal transfer (HT) is a complex phenomenon usually used as an explanation of phylogenetic inconsistence, which cannot be interpreted in terms of vertical evolution. Most examples of HT of eukaryotic genes involve transposable elements. An intriguing feature of HT is that its frequency differs among transposable elements classes. Although HT is well known for DNA transposons and long terminal repeat (LTR) retrotransposons, non-LTR retrotransposons rarely undergo HT, and their phylogenies are largely congruent to those of their hosts. Previously, we described HT of CR1-like non-LTR retrotransposons between butterflies (Maculinea) and moths (Bombyx), which occurred less than 5 million years ago (Novikova O, Sliwinska E, Fet V, Settele J, Blinov A, Woyciechowski M. 2007. CR1 clade of non-LTR retrotransposons from Maculinea butterflies (Lepidoptera: Lycaenidae): evidence for recent horizontal transmission. BMC Evol Biol. 7:93). In this study, we continued to explore the diversity of CR1 non-LTR retrotransposons among lepidopterans providing additional evidences to support HT hypothesis. We also hypothesized that DNA transposons could be involved in HT of non-LTR retrotransposons. Thus, we performed analysis of one of the groups of DNA transposons, mariner-like DNA elements, as potential vectors for HT of non-LTR retrotransposons. Our results demonstrate multiple HTs between Maculinea and Bombyx genera. Although we did not find strong evidence for our hypothesis of the involvement of DNA transposons in HT of non-LTR retrotransposons, we demonstrated that recurrent and/or simultaneous flow of TEs took place between distantly related moths and butterflies.

CR1 clade of non-LTR retrotransposons from Maculinea butterflies (Lepidoptera: Lycaenidae): evidence for recent horizontal transmission

BackgroundNon-long terminal repeat (non-LTR) retrotransposons are mobile genetic elements that propagate themselves by reverse transcription of an RNA intermediate. Non-LTR retrotransposons are known to evolve mainly via vertical transmission and random loss. Horizontal transmission is believed to be a very rare event in non-LTR retrotransposons. Our knowledge of distribution and diversity of insect non-LTR retrotransposons is limited to a few species – mainly model organisms such as dipteran genera Drosophila, Anopheles, and Aedes. However, diversity of non-LTR retroelements in arthropods seems to be much richer. The present study extends the analysis of non-LTR retroelements to CR1 clade from four butterfly species of genus Maculinea (Lepidoptera: Lycaenidae).The lycaenid genus Maculinea, the object of interest for evolutionary biologists and also a model group for European biodiversity studies, possesses a unique, specialized myrmecophilous lifestyle at larval stage. Their caterpillars, after three weeks of phytophagous life on specific food plants drop to the ground where they are adopted to the ant nest by Myrmica foraging workers.ResultsWe found that the genome of Maculinea butterflies contains multiple CR1 lineages of non-LTR retrotransposons, including those from MacCR1A, MacCR1B and T1Q families. A comparative analysis of RT nucleotide sequences demonstrated an extremely high similarity among elements both in interspecific and intraspecific comparisons. CR1A-like elements were found only in family Lycaenidae. In contrast, MacCR1B lineage clones were extremely similar to CR1B non-LTR retrotransposons from Bombycidae moths: silkworm Bombyx mori and Oberthueria caeca.ConclusionThe degree of coding sequence similarity of the studied elements, their discontinuous distribution, and results of divergence-versus-age analysis make it highly unlikely that these sequences diverged at the same time as their host taxa. The only reasonable alternative explanation is horizontal transfer. In addition, phylogenetic markers for population analysis of Maculinea could be developed based on the described non-LTR retrotransposons.

The Chironomus thummi genome contains a non-LTR retrotransposon

SummaryNineteen recombinant phages containing DNA from the region of Balbiani ring a (BRa), which develops on chromosome IV in cells of the special lobe of the Chironomus thummi salivary gland, were isolated from a Chironomus thummi genomic library. Three of the clones contained transposable element sequences that hybridized to more then 100 sites on all four Chironomus chromosomes, including constant and variable sites. Two handogous clones, λ24 (which lacks the transposable element) and λ43 (which contains this insertion) were investigated by nucleotide sequence analysis. The complete nucleotide sequence of the 4.8 kb transposable element from Chironomus thummi (NLR1Cth) is reported here. This element contains two overlapping open reading frames of 1887 (ORF1) and 2649 by (ORF2). Three cysteine motifs are found in the sequence of ORF1. Sequence similarity was found between ORF2 and known genes of viruses and transposable elements which encode reverse transcriptase. The NLR1Cth element has no long terminal repeats and is flanked by short direct repeats of the sequence TATCACTGACAAC. A 24 bp poly(dA) sequence was found at the 3′ end of the element. Based upon its structural organization and comparative analysis of its nucleotide sequence we suggest that this NLR1Cth element belongs to the class of non-LTR retrotransposons. The genomic clone pC6.10 was previously obtained by microdissection and cloning of DNA from polytene chromosome IV of Chironomus thummi. A 2.4 kb insertion contained part of the 3′ terminal region of the NLR1Cth element, but this differed in sequence from the first copy by several nucleotide substitutions and a shorter poly (dA) tract at the 3′ end. In addition, it was associated with a different target site duplication.

vasa-related genes and their expression in stem cells of colonial parasitic rhizocephalan barnacle Polyascus polygenea (Arthropoda: Crustacea: Cirripedia: Rhizocephala)

vasa (vas)‐related genes are members of the DEAD‐box protein family and are expressed in the germ cells of many Metazoa. We cloned vasa‐related genes (PpVLG, CpVLG) and other DEAD‐box family related genes (PpDRH1, PpDRH2, CpDRH, AtDRHr) from the colonial parasitic rhizocephalan barnacle Polyascus polygenea, the non‐colonial Clistosaccus paguri (Crustacea: Cirripedia: Rhizocephala), and the parasitic isopodan Athelgis takanoshimensis (Crustacea: Isopoda). The colonial Polyascus polygenea, a parasite of the coastal crabs Hemigrapsus sanguineus and Hemigrapsus longitarsis was used as a model object for further detailed investigations. Phylogenetic analysis suggested that PpVLG and CpVLG are closely related to vasa‐like genes of other Arthropoda. The rest of the studied genes form their own separate branch on the phylogenetic tree and have a common ancestry with the p68 and PL10 subfamilies. We suppose this group may be a new subfamily of the DEAD‐box RNA helicases that is specific for parasitic Crustacea. We found PpVLG and PpDRH1 expression products in stem cells from stolons and buds of internae, during asexual reproduction of colonial P. polygenea, and in germ cells from sexually reproducing externae, including male spermatogenic cells and female oogenic cells.

Molecular phylogeny of Palaearctic genera of Gomphocerinae grasshoppers (Orthoptera, Acrididae)

Abstract.  Molecular phylogenetic methods were used to examine morphologically based hypotheses concerning the taxonomic structure and relationships of the grasshopper subfamily Gomphocerinae. Two mitochondrial gene (cytochrome b and cytochrome oxidase subunit I) sequences were determined for twenty‐five species representing eleven Palaearctic genera. The studied Gomphocerinae species constituted a monophyletic group; furthermore, the earlier division of Gomphocerinae into tribes was supported, with each tribe monophyletic. There was no support for various systems uniting Stenobothrini and Gomphocerini into one tribe. Two separate clusters were discerned in Gomphocerini and two tribes were distinguished – Gomphocerini (genera Aeropus, Stauroderus, Chorthippus) and Stenobothrini (genera Omocestus, Stenobothrus).

Phylogenetic Relationships of the Siberian Iris Species Inferred from Noncoding Chloroplast DNA Sequences

A study of phylogenetic relationships of Iris species has been complicated because of extreme morpho‐ecological diversity, wide distribution of the genus, multiple hybridizations, and convergent evolution processes in the genus. In order to get an insight into the evolutionary history of Iris and to clarify some contradictions of contemporary classifications, we performed a molecular analysis of the phylogenetic relationships of a heterogeneous group of Iris species occurring in Siberia and covering major taxonomic groups of the genus Iris. According to contemporary classifications, these species belong to the subgenera Limniris (Tausch) Spach, Xyridion (Tausch) Spach, Iris, and Pardanthopsis (Hance) Baker. However, the position of Pardanthopsis within the genus Iris and the position of Xyridion as a distinct subgenus or a part of Limniris are disputable. Based on an analysis of 56 RAPD markers in 12 Siberian Iris species and comparative analysis of trnL intron and trnL‐trnF intergenic spacer noncoding chloroplast DNA sequences in all 22 Siberian Iris species, we reconstructed the phylogenetic relationships of Siberian Iris species. In general, the species grouping coincides with contemporary classifications. According to our results, Pardanthopsis dichotoma forms a separate branch on the phylogenetic trees based on sequences of chloroplast DNA and RAPD analysis, which supports its position as a distinct genus. All of the Siberian Iris species are clustered into four phylogenetic groups. Our results indicate that the phylogeny and taxonomic structure of the genus Iris may need reconsideration.

Novel clades of chromodomain-containing Gypsy LTR retrotransposons from mosses (Bryophyta).

Retrotransposons are the major component of plant genomes. Chromodomain-containing Gypsy long terminal repeat (LTR) retrotransposons are widely distributed in eukaryotes. Four distinct clades of chromodomain-containing Gypsy retroelements are known from the vascular plants: Reina, CRM, Galadriel and Tekay. At the same time, almost nothing is known about the repertoire of LTR retrotransposons in bryophyte genomes. We have combined a search of chromodomain-containing Gypsy retroelements in Physcomitrella genomic sequences and an experimental investigation of diverse moss species. The computer-based mining of the chromodomain-containing LTR retrotransposons allowed us to describe four different elements from Physcomitrella. Four novel clades were identified that are evolutionarily distinct from the chromodomain-containing Gypsy LTR retrotransposons of other plants.

Acquisition of an Archaea-like ribonuclease H domain by plant L1 retrotransposons supports modular evolution

Significance Transposons are jumping genes that constitute a sizeable fraction of eukaryotic genomes. They drive genome evolution and can cause genetic diseases and cancer. Although transposons were first discovered in plants and much of our knowledge about them stems from plants, the most abundant human transposon, L1, has barely been investigated in plants. In this study, we identify plant L1 retrotransposons from a variety of plant genomes and show that, similar to viruses, they evolved in a modular fashion by gaining and losing various protein-coding domains. Moreover, we find that plant L1s carry an active Archaea-like ribonuclease H (RNH) domain, suggesting that they shuttle RNH between plants, bacteria, and Archaea. Although a variety of non-LTR retrotransposons of the L1 superfamily have been found in plant genomes over recent decades, their diversity, distribution, and evolution have yet to be analyzed in depth. Here, we perform comprehensive comparative and evolutionary analyses of L1 retrotransposons from 29 genomes of land plants covering a wide range of taxa. We identify numerous L1 elements in these genomes and detect a striking diversity of their domain composition. We show that all known land plant L1 retrotransposons can be grouped into five major families based on their phylogenetic relationships and domain composition. Moreover, we trace the putative evolution timeline that created the current variants and reveal that evolutionary events included losses and acquisitions of diverse putative RNA-binding domains and the acquisition of an Archaea-like ribonuclease H (RNH) domain. We also show that the latter RNH domain is autonomously active in vitro and speculate that retrotransposons may play a role in the horizontal transfer of RNH between plants, Archaea, and bacteria. The acquisition of an Archaea-like RNH domain by plant L1 retrotransposons negates the hypothesis that RNH domains in non-LTR retrotransposons have a single origin and provides evidence that acquisition happened at least twice. Together, our data indicate that the evolution of the investigated retrotransposons can be mainly characterized by repeated events of domain rearrangements and identify modular evolution as a major trend in the evolution of plant L1 retrotransposons.