Dataset Information

Nucleotide sequence and genomic organization of bird minisatellites.

ABSTRACT: Two minisatellite loci from a Eurasian songbird, the willow warbler (Phylloscopus trochilus) were isolated, sequenced and used as probes to detect more than 20 related hypervariable loci. In addition, a sequence flanking one of the minisatellite loci was isolated, and used to study a VNTR locus. The bird minisatellites have a repeat unit of either 12 (AGGGAAGGGCTC) or 17 bp (GGGGACAGGGGACACCC), repeated in tandem 40-100 times per locus, and shows partial similarity to the sequence motifs of human minisatellites. These sequences are among the most variable minisatellites known, with the incidence per gamete of new length alleles estimated from family studies of warblers to about 5.6% per locus. The bird minisatellite alleles show mendelian inheritance and segregation analysis indicates that they are derived from families of sequences with members on several autosomal linkage groups. Some of the warbler core sequences cross-hybridize to hypervariable loci in other species of birds, mammals and fishes.

SUBMITTER: Gyllensten UB

PROVIDER: S-EPMC317590 | biostudies-other | 1989 Mar

REPOSITORIES: biostudies-other

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Nucleotide sequence and genomic organization of bird minisatellites.

Gyllensten U B UB Jakobsson S S Temrin H H Wilson A C AC

Nucleic acids research 19890301 6

Two minisatellite loci from a Eurasian songbird, the willow warbler (Phylloscopus trochilus) were isolated, sequenced and used as probes to detect more than 20 related hypervariable loci. In addition, a sequence flanking one of the minisatellite loci was isolated, and used to study a VNTR locus. The bird minisatellites have a repeat unit of either 12 (AGGGAAGGGCTC) or 17 bp (GGGGACAGGGGACACCC), repeated in tandem 40-100 times per locus, and shows partial similarity to the sequence motifs of huma ...[more]

PMID: 2704618

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Project description:BackgroundOnly very few viruses of Oomycetes have been studied in detail. Isometric virions were found in different isolates of the oomycete Plasmopara halstedii, the downy mildew pathogen of sunflower. However, complete nucleotide sequences and data on the genome organization were lacking.MethodsViral RNA of different P. halstedii isolates was subjected to nucleotide sequencing and analysis of the viral genome. The N-terminal sequence of the viral coat protein was determined using Top-Down MALDI-TOF analysis.ResultsThe complete nucleotide sequences of both single-stranded RNA segments (RNA1 and RNA2) were established. RNA1 consisted of 2793 nucleotides (nt) exclusive its 3' poly(A) tract and a single open-reading frame (ORF1) of 2745 nt. ORF1 was framed by a 5' untranslated region (5' UTR) of 18 nt and a 3' untranslated region (3' UTR) of 30 nt. ORF1 contained motifs of RNA-dependent RNA polymerases (RdRp) and showed similarities to RdRp of Scleropthora macrospora virus A (SmV A) and viruses within the Nodaviridae family. RNA2 consisted of 1526 nt exclusive its 3' poly(A) tract and a second ORF (ORF2) of 1128 nt. ORF2 coded for the single viral coat protein (CP) and was framed by a 5' UTR of 164 nt and a 3' UTR of 234 nt. The deduced amino acid sequence of ORF2 was verified by nano-LC-ESI-MS/MS experiments. Top-Down MALDI-TOF analysis revealed the N-terminal sequence of the CP. The N-terminal sequence represented a region within ORF2 suggesting a proteolytic processing of the CP in vivo. The CP showed similarities to CP of SmV A and viruses within the Tombusviridae family. Fragments of RNA1 (ca. 1.9 kb) and RNA2 (ca. 1.4 kb) were used to analyze the nucleotide sequence variation of virions in different P. halstedii isolates. Viral sequence variation was 0.3% or less regardless of their host's pathotypes, the geographical origin and the sensitivity towards the fungicide metalaxyl.ConclusionsThe results showed the presence of a single and new virus type in different P. halstedii isolates. Insignificant viral sequence variation indicated that the virus did not account for differences in pathogenicity of the oomycete P. halstedii.

Project description:The merozoite surface protein-1 (MSP1) is a prime candidate for an asexual blood stage vaccine against malaria. However, polymorphism in this antigen could compromise the vaccine's efficacy. Although the extent of sequence variation in MSP1 has been analyzed from various Plasmodium species, little is known about structural organization and diversity of this locus in Plasmodium malariae (PmMSP1). Herein, we have shown that PmMSP1 contained five conserved and four variable blocks based on analysis of the complete coding sequences. Variable blocks were characterized by short insertion and deletion variants (block II), polymorphic nonrepeat sequences (block IV), complex repeat structure with size variation (block VI) and degenerate octapeptide repeats (block VIII). Like other malarial MSP1s, evidences of intragenic recombination have been found in PmMSP1. The rate of nonsynonymous nucleotide substitutions significantly exceeded that of synonymous nucleotide substitutions in block IV, suggesting positive selection in this region. Codon-based analysis of deviation from neutrality has identified a codon under purifying selection located in close proximity to the homologous region of the 38 kDa/42 kDa cleavage site of P. falciparum MSP1. A number of predicted linear B-cell epitopes were identified across both conserved and variable blocks of the protein. However, polymorphism in repeat-containing blocks resulted in alteration of the predicted linear B-cell epitope scores across variants. Although a number of predicted HLA-class II-binding peptides were identified in PmMSP1, all variants of block IV seemed not to be recognized by common HLA-class II alleles among Thai population, suggesting that diversity in this positive selection region could probably affect host immune recognition. The data on structural diversity in PmMSP1 could be useful for further studies such as vaccine development and strain characterization of this neglected malaria parasite.

Dataset Information

Nucleotide sequence and genomic organization of bird minisatellites.

Publications

Nucleotide sequence and genomic organization of bird minisatellites.

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