RetroTector online, a rational tool for analysis of retroviral elements in small and medium size vertebrate genomic sequences

Sperber, Göran; Lövgren, Anders; Eriksson, Nils-Einar; Benachenhou, Farid; Blomberg, Jonas

doi:10.1186/1471-2105-10-s6-s4

Cited by 38 publications

(40 citation statements)

References 9 publications

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“…As for retroviruses, the HMMs constructed here can also be used for detection of many groups of LTR retrotransposons if they are combined with detection of other motifs as is done by the RetroTector © program [57,58]. Implementation of large-scale parallel execution of HMM detection is required, because of speed limitations of HMM algorithms.…”

Section: Resultsmentioning

confidence: 99%

Conserved structure and inferred evolutionary history of long terminal repeats (LTRs)

et al. 2013

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BackgroundLong terminal repeats (LTRs, consisting of U3-R-U5 portions) are important elements of retroviruses and related retrotransposons. They are difficult to analyse due to their variability.The aim was to obtain a more comprehensive view of structure, diversity and phylogeny of LTRs than hitherto possible.ResultsHidden Markov models (HMM) were created for 11 clades of LTRs belonging to Retroviridae (class III retroviruses), animal Metaviridae (Gypsy/Ty3) elements and plant Pseudoviridae (Copia/Ty1) elements, complementing our work with Orthoretrovirus HMMs. The great variation in LTR length of plant Metaviridae and the few divergent animal Pseudoviridae prevented building HMMs from both of these groups.Animal Metaviridae LTRs had the same conserved motifs as retroviral LTRs, confirming that the two groups are closely related. The conserved motifs were the short inverted repeats (SIRs), integrase recognition signals (5´TGTTRNR…YNYAACA 3´); the polyadenylation signal or AATAAA motif; a GT-rich stretch downstream of the polyadenylation signal; and a less conserved AT-rich stretch corresponding to the core promoter element, the TATA box. Plant Pseudoviridae LTRs differed slightly in having a conserved TATA-box, TATATA, but no conserved polyadenylation signal, plus a much shorter R region.The sensitivity of the HMMs for detection in genomic sequences was around 50% for most models, at a relatively high specificity, suitable for genome screening.The HMMs yielded consensus sequences, which were aligned by creating an HMM model (a ‘Superviterbi’ alignment). This yielded a phylogenetic tree that was compared with a Pol-based tree. Both LTR and Pol trees supported monophyly of retroviruses. In both, Pseudoviridae was ancestral to all other LTR retrotransposons. However, the LTR trees showed the chromovirus portion of Metaviridae clustering together with Pseudoviridae, dividing Metaviridae into two portions with distinct phylogeny.ConclusionThe HMMs clearly demonstrated a unitary conserved structure of LTRs, supporting that they arose once during evolution. We attempted to follow the evolution of LTRs by tracing their functional foundations, that is, acquisition of RNAse H, a combined promoter/ polyadenylation site, integrase, hairpin priming and the primer binding site (PBS). Available information did not support a simple evolutionary chain of events.

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Section: Resultsmentioning

confidence: 99%

Conserved structure and inferred evolutionary history of long terminal repeats (LTRs)

et al. 2013

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“…Comparison between neighbour-joining trees of human gammaretroviruslike (ERV1 in RepBase) LTR sequences (a consensus cladogram) and the corresponding pol sequences (a phylogram). The latter were extracted from internal retroviral RepBase entries using RetroTector Online Sperber et al, 2009). Not all internal RepBase consensus sequences yielded a pol sequence with ROL.…”

Section: Methodsmentioning

confidence: 99%

The phylogeny of orthoretroviral long terminal repeats (LTRs)

Benachenhou

Blikstad

Blomberg

2009

Gene

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“…Using RetroTector10 program [29], we evaluated the genomic structure and function of full-length GGERV10 elements. The program is able to identify open reading frames (ORFs) in chicken ERV elements.…”

Section: Resultsmentioning

confidence: 99%

Chicken (Gallus gallus) endogenous retrovirus generates genomic variations in the chicken genome

et al. 2017

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BackgroundTransposable elements (TEs) comprise ~10% of the chicken (Gallus gallus) genome. The content of TEs is much lower than that of mammalian genomes, where TEs comprise around half of the genome. Endogenous retroviruses are responsible for ~1.3% of the chicken genome. Among them is Gallus gallus endogenous retrovirus 10 (GGERV10), one of the youngest endogenous retrovirus families, which emerged in the chicken genome around 3 million years ago.ResultsWe identified a total of 593 GGERV10 elements in the chicken reference genome using UCSC genome database and RepeatMasker. While most of the elements were truncated, 49 GGERV10 elements were full-length retaining 5′ and 3′ LTRs. We examined in detail their structural features, chromosomal distribution, genomic environment, and phylogenetic relationships. We compared LTR sequence among five different GGERV10 subfamilies and found sequence variations among the LTRs. Using a traditional PCR assay, we examined a polymorphism rate of the 49 full-length GGERV10 elements in three different chicken populations of the Korean domestic chicken, Leghorn, and Araucana. The result found a breed-specific GGERV10B insertion locus in the Korean domestic chicken, which could be used as a Korean domestic chicken-specific marker.ConclusionsGGERV10 family is the youngest ERV family and thus might have contributed to recent genomic variations in different chicken populations. The result of this study showed that one of GGERV10 elements integrated into the chicken genome after the divergence of Korean domestic chicken from other closely related chicken populations, suggesting that GGERV10 could be served as a molecular marker for chicken breed identification.Electronic supplementary materialThe online version of this article (doi:10.1186/s13100-016-0085-5) contains supplementary material, which is available to authorized users.

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RetroTector online, a rational tool for analysis of retroviral elements in small and medium size vertebrate genomic sequences

Cited by 38 publications

References 9 publications

Conserved structure and inferred evolutionary history of long terminal repeats (LTRs)

Conserved structure and inferred evolutionary history of long terminal repeats (LTRs)

The phylogeny of orthoretroviral long terminal repeats (LTRs)

Chicken (Gallus gallus) endogenous retrovirus generates genomic variations in the chicken genome

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