Structure and distribution of the retrotransposon Bov-B LINE

Godakova, S. A.; Sevast’yanova, G. A.; Semenova, S. K.

doi:10.18821/0208-0613-2016-34-1-9-12

Cited by 3 publications

(5 citation statements)

References 44 publications

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“…For a long time, BovB was considered to be ruminant specific but it turned out that BovB originally appeared in the reptiles' genomes, from which it was introduced in ruminant genomes by horizontal transfer [8,9,17,18]. Modern studies also confirm the BovB presence in marsupials [19,20] and relate it to the horizontal transfer as well.…”

Section: Discussionmentioning

confidence: 99%

Candidate vectors of horizontal transfer of BovB retrotransposon

Skobel¹,

Kosovsky²,

Glazko³

2022

BIO Web Conf.

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The horizontal transfer of retrotransposons has a significant impact on the regulatory system of a multicellular organism, but the biological basis of horizontal transfer has been sufficiently studied up to date. Earlier, we identified the conserved sequence of retrotransposons recombination products of the bovine chromosome 1 nucleotide sequence region. This conserved sequence has a high percent identity with LINE BovB, which is widely known as horizontal transfer participant. The current study analyzes the presence of the conserved sequence of retrotransposons recombination products of cattle in members of different taxonomic groups to detect potential vectors of horizontal transfer. It was shown that the conserved sequence with a high percent identity can be found in 43 members of different species, including eukaryotes, prokaryotes and viruses. The identified potential vectors of horizontal retrotransposon transfer associated with various diseases of farm animals are of particular interest. Such potential vectors are hemiparasites Babesia ovata and Babesia bigemina (pathogens causing babesiosis), bacterium Clostridium botulinum (the causative agent of botulism), Jaagsiekte sheep retrovirus (the causative agent of lung cancer in sheep). They all have regions with a high percent identity (not lower than 95%) to the studied bovine conserved sequence. Thus, we identify new potential vectors of horizontal retrotransposon transfer as well as the possible influence of retrotransposons on regulatory networks affecting host protection from infectious diseases.

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Section: Discussionmentioning

confidence: 99%

Candidate vectors of horizontal transfer of BovB retrotransposon

Skobel¹,

Kosovsky²,

Glazko³

2022

BIO Web Conf.

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“…Generally, all the copies of Bov-B LINE found in different vertebrates do not exceed a length of about 3.1 kb. Based on the most conservative sequence of reverse transcriptase (RT) domain, all the LINEs are classified into several clades [49]. DNA fragments of Bov-B LINE sequences were amplified using primers specific for Bov-B LINE (BovB_VA2 F 5 -GCTACACTCAATTTGCCAGCA-3 and BovB_VA2 R 5 -CCAGTTCTCCCTGTTGCTTC-3 ).…”

Section: Polymerase Chain Reaction Amplification and Molecular Cloning Of Bov-b Linementioning

confidence: 99%

“…However, the noise of random biological variation/association, especially with relatively small sample sizes could not be ruled out. Additionally, a full-length Bov-B LINE sequence is over 3kb in length [49]. Using a ranging of 330-385 bp RT domain to estimate Bov-B LINE copy number will likely retrieve most of the full-length copies present in the genome but may miss fragments or Bov-B LINE copies with a mutated RT domain region [17,95].…”

Section: Independent Copy Number Variation Among Snake Speciesmentioning

confidence: 99%

Existence of Bov-B LINE Retrotransposons in Snake Lineages Reveals Recent Multiple Horizontal Gene Transfers with Copy Number Variation

Puinongpo

Singchat

Petpradub

et al. 2020

Genes

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Transposable elements (TEs) are dynamic elements present in all eukaryotic genomes. They can “jump” and amplify within the genome and promote segmental genome rearrangements on both autosomes and sex chromosomes by disruption of gene structures. The Bovine-B long interspersed nuclear element (Bov-B LINE) is among the most abundant TE-retrotransposon families in vertebrates due to horizontal transfer (HT) among vertebrate lineages. Recent studies have shown multiple HTs or the presence of diverse Bov-B LINE groups in the snake lineage. It is hypothesized that Bov-B LINEs are highly dynamic and that the diversity reflects multiple HTs in snake lineages. Partial sequences of Bov-B LINE from 23 snake species were characterized. Phylogenetic analysis resolved at least two Bov-B LINE groups that might correspond to henophidian and caenophidian snakes; however, the tree topology differed from that based on functional nuclear and mitochondrial gene sequences. Several Bov-B LINEs of snakes showed greater than 80% similarity to sequences obtained from insects, whereas the two Bov-B LINE groups as well as sequences from the same snake species classified in different Bov-B LINE groups showed sequence similarities of less than 80%. Calculation of estimated divergence time and pairwise divergence between all individual Bov-B LINE copies suggest invasion times ranging from 79.19 to 98.8 million years ago in snakes. Accumulation of elements in a lineage-specific fashion ranged from 9 × 10−6% to 5.63 × 10−2% per genome. The genomic proportion of Bov-B LINEs varied among snake species but was not directly associated with genome size or invasion time. No differentiation in Bov-B LINE copy number between males and females was observed in any of the snake species examined. Incongruence in tree topology between Bov-B LINEs and other snake phylogenies may reflect past HT events. Sequence divergence of Bov-B LINEs between copies suggests that recent multiple HTs occurred within the same evolutionary timeframe in the snake lineage. The proportion of Bov-B LINEs varies among species, reflecting species specificity in TE invasion. The rapid speciation of snakes, coinciding with Bov-B LINE invasion in snake genomes, leads us to better understand the effect of Bov-B LINEs on snake genome evolution.

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“…In most mammalian species, including bovine cattle, retrotransposons (RTs) dominate in the genomes among mobile genetic elements, which for their movement use the mechanisms of reproduction of exogenous retroviruses [1]. One of the reptile units as Squamata could be the source of a number of mobile genetic elements for ruminants [2][3][4]. It is assumed that the horizontal transfer of RTs between taxonomically removed forms is promoted by the common habitat [5].…”

mentioning

confidence: 99%

“…In ruminants and marsupials, LINE RTE encodes proteins required for transpositions of SINE BovA, the (BOV-A2, Bov-tA1, 2, 3)/SINE ART2A or SINE RTE, respectively. RTE LINE contains BovB repeats, suggesting that they are horizontally transferred from reptiles to ruminants and marsupials [4,[9][10][11]. Ancient clusters of L2/MIR repeats form domains that are conserved in human and bovine genomes, and there are no younger repetitions, such as RTE/ART2A, in such domains.…”

mentioning

confidence: 99%

Domain Distribution of Mobile Genetic Elements in the Bovine Genome

Glazko¹,

Skobel²,

Kosovsky³

et al. 2017

S-h. biol.

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Genetic landscape of bovine genome attracts a lot of attention in recent years. This is due to the complexity of genomic selection task solution, i.e. the use of multilocus genotypes in order to simplify and hasten breeding. Accumulated data show that there is high evolutionary speed of different genetic elements and also they have structure functional polymorphism intensity (L. Chen et al., 2017). It was shown that interspersed repeats account for about 50 % of nucleotide sequence of the bovine genome (R.L. Tellam et al., 2009). Also it was found that some of the interspersed repeats cluster into conservative domains along the bovine genome due to joint localization (D.L. Adelson et al., 2009). The characteristics of domain distribution are still not fully studied despite the fact that it is very important to identify conservative and variable domains throughout the bovine genome to solve traditional tasks of their genetic resources management and controlling. In this work domain distribution of mobile genetic elements and their products of recombination in nucleotide sequences of 13,436,028 nucleotides of bovine chromosome 1 were analyzed by means of Repeat Masker mobile genetic elements database and Integrated Genome Browser software. It was revealed that the most prevalent types throughout analyzed region are SINE/tRNA-Core-RTE, LINE/RTE-BovB, LINE/L1 and LTR/ERV. Their joint localization in bovine genome has complicated structure. The most common pairwise clusters are SINE and LINE, SINE/tRNA-Core-RTE and LTR EVR, (LTR/ERVK)/(LINE/RTE-BovB), (LTR/ERVK)/(LINE/L1). Two last pairs are the bases for such triple clusters as (LINE/RTE-BovB)/(BTLTR1)/(LINE/RTE-BovB) and (LINE/L1)/(BTLTR1J)/(LINE/L1). It should be mentioned that there is no such clustering with other retrotransposons. It was revealed that there is some certain bias of these triple clusters high density to the distal end of studied region of chromosome 1. By the means of Integrated Genome Browser software the localization of obtained triple products of recombination between LINE and LTR ERV to structural genes was analyzed. It was found that only 34 clusters are localized in 12 structural genes (other are located in intergenic space). Besides, 10 and 12 copies are located in two genes that are closely connected with the function of central nervous system in mammals, grik1 and app. The fact that 9 copies of triple gene construct (LINE/RTE-BovB)/(BTLTR1)/(LINE/RTE-BovB) are found in each of two genes and (LINE/L1)/(BTLTR1J)/(LINE/L1) had only 1 copy in grik1 and 3 copies in app, suggests that these genes are ancestral targets for such insertions and their conservations. It also should be mentioned that (LINE/L1)/(BTLTR1J)/(LINE/L1) construct was found only in these two genes but not in other 10 genes where (LINE/RTE-BovB)/(BTLTR1)/(LINE/RTE-BovB) is also located. Specific features of distribution of products of recombination between LINE and LTR ERV throughout the studied chromosome 1 area and their localization in structural genes suggest the possible...

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Structure and distribution of the retrotransposon Bov-B LINE

Cited by 3 publications

References 44 publications

Candidate vectors of horizontal transfer of BovB retrotransposon

Candidate vectors of horizontal transfer of BovB retrotransposon

Existence of Bov-B LINE Retrotransposons in Snake Lineages Reveals Recent Multiple Horizontal Gene Transfers with Copy Number Variation

Domain Distribution of Mobile Genetic Elements in the Bovine Genome

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