The 3′ untranslated regions of Kamiti River virus and Cell fusing agent virus originated by self-duplication

Previously, it was shown that the 3′ untranslated region (3′UTR) of Kamiti River virus (KRV) is nearly twice as long as the 3′UTR of other flaviviruses (1208 nucleotides compared with 730 nucleotides for the longest 3′UTR of any virus in the Tick-borne encephalitis virus species). Additionally, KRV and the closely related Cell fusing agent virus (CFAV) were shown to contain two short, almost perfect repeat sequences of 67 nucleotides. However, the construction of a robust comparative nucleotide alignment has now revealed that the double-length 3′UTR and the direct repeats resulted from the virtually complete duplication of a primordial KRV 3′UTR. We also propose that the CFAV 3′UTR was derived from a KRV-like precursor sequence with a large deletion that nevertheless preserved the two direct repeat sequences. These data provide new insights into the evolution of the flavivirus 3′UTR.

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Conservation of a satellite DNA sequence (SATB) in the tilapiine and haplochromine genome (Pisces: Cichlidae)

Genome ◽

10.1139/g93-025 ◽

1993 ◽

Vol 36 (1) ◽

pp. 187-194 ◽

Cited By ~ 14

Author(s):

Jens P. C. Franck ◽

Jonathan M. Wright

Keyword(s):

Satellite Dna ◽

Direct Repeat ◽

Repeat Sequence ◽

South American ◽

Direct Repeats ◽

Core Motif ◽

Hindiii Fragment ◽

Sequence Identity ◽

Repeat Sequences ◽

Internal Component

We have cloned and sequenced a 1900-bp EcoRI fragment (SATB) from the tilapiine fish Oreochromis niloticus. The SATB sequence is highly reiterated in the tilapiine genome and organized in long tandem arrays. A 760-bp HindIII fragment, an internal component of SATB, has also been cloned and sequenced from the related tilapiine species Oreochromis hornorum. Hybridization of the radiolabeled 760-bp HindIII repeat detected the presence of the SATB repeat in the genomes of several tilapiine species as well as the haplochromine species Haplochromis (Protomelas) similis. The 760-bp HindIII fragment did not hybridize to genomic DNA of Etroplus maculatus (an Asian cichlid) or to that of Cichlasoma meeki (a South American cichlid). The SATB repeat sequence is 56% AT and constitutes 0.2–5% of the tilapiine genome depending on the species examined. Four imperfect 21-bp direct repeat sequences are present within the cloned 1900-bp EcoRI repeat. Alignment of the four direct repeats from the O. niloticus cloned 1900-bp DNA and the two homologous direct repeats from the O. hornorum 760-bp HindIII repeat revealed a core motif of 11 bp that exhibits 100% sequence identity between all of the direct repeats. The conservation of this motif in the SATB repeat suggests that this sequence may be under selective constraint.Key words: satellite DNA, Cichlidae, direct repeats.

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Ac induces homologous recombination at the maize P locus.

Genetics ◽

10.1093/genetics/128.1.163 ◽

1991 ◽

Vol 128 (1) ◽

pp. 163-173 ◽

Cited By ~ 2

Author(s):

P Athma ◽

T Peterson

Keyword(s):

Homologous Recombination ◽

Transposable Element ◽

Direct Repeat ◽

Null Alleles ◽

Direct Repeats ◽

Ac Element ◽

Repeat Sequences ◽

P Gene ◽

In Trans ◽

P Locus

Abstract The maize P gene conditions red phlobaphene pigmentation to the pericarp and cob. Starting from two unstable P alleles which carry insertions of the transposable element Ac, we have derived 51 P null alleles; 47 of the 51 null alleles have a 17-kb deletion which removes the 4.5-kb Ac element and 12.5 kb of P sequences flanking both sides of Ac. The deletion endpoints lie within two 5.2-kb homologous direct repeats which flank the P gene. A P allele which contains the direct repeats, but does not have an Ac insertion between the direct repeats, shows very little sporophytic or gametophytic instability. The apparent frequency of sporophytic mutations was not increased when Ac was introduced in trans. Southern analysis of DNA prepared from the pericarp tissue demonstrates that the deletions can occur premeiotically, in the somatic cells during development of the pericarp. Evidence is presented that the deletions occurred by homologous recombination between the two direct repeats, and that the presence of an Ac element at the P locus is associated with the recombination/deletion. These results add another aspect to the spectrum of activities of Ac: the destabilization of flanking direct repeat sequences.

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Variability in the 3′ untranslated regions of the genomes of the different tick-borne encephalitis virus subtypes

Virus Genes ◽

10.1007/s11262-019-01672-0 ◽

2019 ◽

Vol 55 (4) ◽

pp. 448-457 ◽

Cited By ~ 1

Author(s):

Vladimir A. Ternovoi ◽

Anastasia V. Gladysheva ◽

Eugenia P. Ponomareva ◽

Tamara P. Mikryukova ◽

Elena V. Protopopova ◽

...

Keyword(s):

Encephalitis Virus ◽

Untranslated Regions ◽

Tick Borne Encephalitis ◽

Tick Borne Encephalitis Virus

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Ac Insertion Site Affects the Frequency of Transposon-Induced Homologous Recombination at the Maize p1 Locus

Genetics ◽

10.1093/genetics/156.4.2007 ◽

2000 ◽

Vol 156 (4) ◽

pp. 2007-2017

Author(s):

Yong-Li Xiao ◽

Xianggan Li ◽

Thomas Peterson

Keyword(s):

Homologous Recombination ◽

Transposable Element ◽

Recombination Frequency ◽

Insertion Site ◽

Direct Repeat ◽

Red Pigment ◽

Direct Repeats ◽

Coding Region ◽

Repeat Sequences ◽

Gene Coding

Abstract The maize p1 gene regulates the production of a red pigment in the kernel pericarp, cob, and other maize floral tissues. Insertions of the transposable element Ac can induce recombination between two highly homologous 5.2-kb direct repeat sequences that flank the p1 gene-coding region. Here, we tested the effects of the Ac insertion site and orientation on the induction of recombination at the p1 locus. A collection of unique p1 gene alleles was used, which carry Ac insertions at different sites in and near the p1 locus, outside of the direct repeats, within the direct repeat sequences, and between the direct repeats, in both orientations. Recombination was scored by the numbers of colorless pericarp sectors (somatic frequency) and heritable mutations (germinal frequency). In both the somatic and germinal tests, the frequency of homologous recombination is significantly higher when Ac is inserted between the direct repeats than when Ac is inserted either within or outside the repeats. In contrast, Ac orientation had no significant effect on recombination frequency. We discuss these results in terms of the possible mechanisms of transposon-induced recombination.

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TBE in South Korea

Tick-borne encephalitis - The Book ◽

10.33442/978-981-14-0914-1_12b-31 ◽

2019 ◽

Author(s):

Joon Young Song

Keyword(s):

South Korea ◽

Human Case ◽

Encephalitis Virus ◽

Surveillance Studies ◽

Tick Borne Encephalitis ◽

Tick Borne Encephalitis Virus

Although no human case of tick-borne encephalitis (TBE) has been documented in South Korea to date, surveillance studies have been conducted to evaluate the prevalence of tick-borne encephalitis virus (TBEV) in wild ticks.

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TBE in Slovakia

Tick-borne encephalitis - The Book ◽

10.33442/978-981-14-0914-1_12b-29 ◽

2019 ◽

Author(s):

Jana Kerlik

Keyword(s):

Encephalitis Virus ◽

Tick Borne Encephalitis ◽

Tick Borne Encephalitis Virus

The former Czechoslovak Republic was one of the first countries in Europe where the tick-borne encephalitis virus (TBEV) was identified.

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TBE in Sweden

Tick-borne encephalitis - The Book ◽

10.33442/26613980_12b32-3 ◽

2020 ◽

Keyword(s):

Genetic Characterization ◽

Immunoglobulin M ◽

Enzyme Linked Immunosorbent Assay ◽

Second Phase ◽

Serum Samples ◽

Tick Borne Encephalitis ◽

Specific Immunoglobulin ◽

Tick Borne Encephalitis Virus ◽

First Time

Tick-borne encephalitis virus (TBEV) was isolated for the first time in Sweden in 1958 (from ticks and from 1 tick-borne encephalitis [TBE] patient).1 In 2003, Haglund and colleagues reported the isolation and antigenic and genetic characterization of 14 TBEV strains from Swedish patients (samples collected 1991–1994).2 The first serum sample, from which TBEV was isolated, was obtained 2–10 days after onset of disease and found to be negative for anti-TBEV immunoglobulin M (IgM) by enzyme-linked immunosorbent assay (ELISA), whereas TBEV-specific IgM (and TBEV-specific immunoglobulin G/cerebrospinal fluid [IgG/CSF] activity) was demonstrated in later serum samples taken during the second phase of the disease.

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Chapter 11: General epidemiology of TBE

Tick-borne encephalitis - The Book ◽

10.33442/26613980_11-3 ◽

2020 ◽

Keyword(s):

Eastern Siberia ◽

Genetic Lineages ◽

Phylogenetic Studies ◽

Tick Borne Encephalitis ◽

Natural Foci ◽

Genetic Sequences ◽

Tick Borne Encephalitis Virus ◽

Almost All ◽

Far Eastern ◽

Reservoir Hosts

Tick-borne encephalitis virus (TBEV) exists in natural foci, which are areas where TBEV is circulating among its vectors (ticks of different species and genera) and reservoir hosts (usually rodents and small mammals). Based on phylogenetic studies, four TBEV subtypes (Far-Eastern, Siberian, European, Baikalian) and two putative subtypes (Himalayan and “178-79” group) are known. Within each subtype, some genetic lineages are described. The European subtype (TBEV-EU) (formerly known also as the “Western subtype”) of TBEV is prevalent in Europe, but it was also isolated in Western and Eastern Siberia in Russia and South Korea. The Far-Eastern subtype (TBEV-FE) was preferably found in the territory of the far-eastern part of Eurasia, but some strains were isolated in other regions of Eurasia. The Siberian (TBEV-SIB) subtype is the most common and has been found in almost all TBEV habitat areas. The Baikalian subtype is prevalent around Lake Baikal and was isolated several times from ticks and rodents. In addition to the four TBEV subtypes, one single isolate of TBEV (178-79) and two genetic sequences (Himalayan) supposed to be new TBEV subtypes were described in Eastern Siberia and China. The data on TBEV seroprevalence in humans and animals can serve as an indication for the presence or absence of TBEV in studied area.

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