Molecular phylogeny and systematics of drosophila retrotransposons and retroviruses

Нефедова, Л. Н.; Kim, A. I.

doi:10.1134/s0026893309050069

Cited by 13 publications

(11 citation statements)

References 26 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…A comparative analysis of integrase sequences, which was performed for 24 of the most typical representatives of LTR-retrotransposons, confirmed the previously constructed phylogeny [18]. In the most numerous gypsy subgroup, a similarity between certain retrotransposons with two and three ORFs was observed, an indicator of their close relationship (Fig.…”

Section: Resultsmentioning

confidence: 76%

“…1). According to the previously obtained data, retrotransposons of the 412 subgroups without an env gene are capable of horizontal transfer between different Drosophila species (even phylogenetically distant) [18]. This fact appears to be an indicator of their ability to use a foreign env gene for viral particles assembly.…”

Section: Resultsmentioning

confidence: 80%

“…A comparative analysis of reverse transcriptase domain sequences allows all LTR-retrotransposons to be subdivided into three groups: the gypsy group, the copia group, and the BEL group [17]. The gypsy group (27 MGE families) is represented by retrotransposons with one, two, or three ORFs [18]. The copia group (4 MGE families) and the BEL group (5 MGE families) contain retrotransposons with a single ORF (Fig.…”

Section: Resultsmentioning

confidence: 99%

See 2 more Smart Citations

Integration specificity of LTR-retrotransposons and retroviruses in the Drosophila melanogaster genome

2011

Self Cite

View full text Add to dashboard Cite

Integration of DNA copies in a host genome is a necessary stage in the life cycle of retroviruses and LTR-retrotransposons. There is still no clear understanding of integration specificity of retroelements into a target site. The selection of the target DNA is believed to potentially affect a number of factors such as transcriptional status, association with histones and other DNA-binding proteins, and DNA bending. The authors performed a comprehensive computer analysis of the integration specificity of Drosophila melanogaster LTR-retrotransposons and retroviruses including an analysis of the nucleotide composition of targets, terminal sequences of LTRs, and integrase sequences. A classification of LTR-retrotransposons based on the integration specificity was developed. All the LTR-retrotransposons of the gypsy group with three open frames (errantiviruses) and their derivatives with two open frames demonstrate strict specificity to a target DNA selection. Such specificity correlates with the structural features of the target DNA: bendability, A-philicity, or protein-induced deformability. The remaining LTR-retrotransposons (copia and BEL groups, blastopia and 412 subgroups of the gypsy group) do not show specificity of integration. Chromodomain is present in the integrase structures of blastopia and 412 subgroup LTR-retrotransposons and may facilitate the process of non-specific integration.

show abstract

Section: Resultsmentioning

confidence: 76%

Section: Resultsmentioning

confidence: 80%

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Integration specificity of LTR-retrotransposons and retroviruses in the Drosophila melanogaster genome

2011

Self Cite

View full text Add to dashboard Cite

show abstract

“…Later, other gypsy related retroelements were found in the genome of D. melanogaster (Kaminker et al, 2002). Their phylogenetic relationships were revealed by bioinformatic analysis (Nefedova, Kim, 2009). Although some of them contain ORF3, only gypsy (Kim at al., 1994) and ZAM (Leblanc et al, 2000) have been shown to possess infectious proper ties.…”

Section: Introductionmentioning

confidence: 99%

Analysis of the tissue- and stage-specific transportation of the Drosophila melanogaster gypsy retrotransposon

Urusov

Нефедова

Kim

2011

Russ J Genet Appl Res

Self Cite

View full text Add to dashboard Cite

“…50 U3 contains the enhancer and promoter sequences that drive viral transcription [11]. However, due to 51 the lack of env protein, LTR retrotransposons are not infectious; they are obligate intracellular elements [12]. 52…”

mentioning

confidence: 99%

Superiorab initioIdentification, Annotation and Characterisation of TEs and Segmental Duplications from Genome Assemblies

Zeng

Kortschak

Raison

et al. 2017

Preprint

View full text Add to dashboard Cite

Transposable Elements (TEs) are mobile DNA sequences that make up significant fractions of amniote genomes. However, they are difficult to detect and annotate ab initio because of their variable features, lengths and clade-specific variants. We have addressed this problem by refining and developing a Comprehensive ab initio Repeat Pipeline (CARP) to identify and cluster TEs and other repetitive sequences in genome assemblies. The pipeline begins with a pairwise alignment using krishna, a custom aligner. Single linkage clustering is then carried out to produce families of repetitive elements. Consensus sequences are then filtered for protein coding genes and then annotated using Repbase and a custom library of retrovirus and reverse transcriptase sequences. This process yields three types of family: fully annotated, partially annotated and unannotated. Fully annotated families reflect recently diverged/young known TEs present in Repbase. The remaining two types of families contain a mixture of novel TEs and segmental duplications. These can be resolved by aligning these consensus sequences back to the genome to assess copy number vs. length distribution. Our pipeline has three significant advantages compared to other methods for ab initio repeat identification: 1) we generate not only consensus sequences, but keep the genomic intervals for the original aligned sequences, allowing straightforward analysis of evolutionary dynamics, 2) consensus sequences represent low-divergence, recently/currently active TE families, 3) segmental duplications are annotated as a useful by-product. We have compared our ab initio repeat annotations for 7 genome assemblies (1 unpublished) to other methods and demonstrate that CARP compares favourably with RepeatModeler, the most widely used repeat annotation package. Lu et.al 1/21 Transposable elements (TEs) are interspersed repetitive DNA sequences, also known as 'jumping genes', 1 because of their ability to replicate in to new genomic locations. TEs account for a significant proportion 2 of all eukaryotic genomes. Previous studies have found that TE insertions have contributed to new genes, 3 coding sequences and regulatory regions. They also play an important role in genome evolution. Therefore, 4we developed a novel, ab initio approach for identifying and annotating repetitive elements. The idea 5 is simple: define a "repeat" as any sequence that occurs at least twice in the genome. Our ab initio 6 method is able to identify species-specific TEs with high sensitivity and accuracy including both TEs and 7 segmental duplications. Because of the high degree of sequence identity used in our method, the TEs 8 we find are less diverged and may still be active. We also retain all the information that links identified 9 repeat consensus sequences to their genome intervals, permiting direct evolutionary analysis of the TE 10 families we identify. 11 21 22 Repetitive DNA sequences can be divided into three major categories: tandem repeats, segmental 23 duplications and transposable elements...

show abstract

Molecular phylogeny and systematics of drosophila retrotransposons and retroviruses

Cited by 13 publications

References 26 publications

Integration specificity of LTR-retrotransposons and retroviruses in the Drosophila melanogaster genome

Integration specificity of LTR-retrotransposons and retroviruses in the Drosophila melanogaster genome

Analysis of the tissue- and stage-specific transportation of the Drosophila melanogaster gypsy retrotransposon

Superiorab initioIdentification, Annotation and Characterisation of TEs and Segmental Duplications from Genome Assemblies

Contact Info

Product

Resources

About