Evidence for a prokaryotic insertion-sequence contamination in eukaryotic sequences registered in different databases

G. Astua-Monge, A. Lyznik, V. Jones, S. A. Mackenzie, C. E. Vallejos

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

An insertion-sequence of prokaryotic origin was detected in a genomic clone obtained from a Phaseolus vulgaris bacterial artificial chromosome (BAC) library. This BAC clone, characterized as part of a contig constructed near a virus resistance gene, exhibited restriction fragment length polymorphism with an overlapping clone of the contig. Restriction analysis of DNA obtained from individual colonies of the stock culture indicated the presence of a mixed population of wild-type and insertional mutants. Sequence analysis of both members of the population revealed the presence of IS10R, an insertion-sequence from Escherichia coli. A BLAST search for IS10-like sequences detected unexpected homologies with a large number of eukaryotic sequences from Homo sapiens, Arabidopsis thaliana, Drosophila melanogaster and Caenorhabditis elegans. Southern analysis of a random sample of BAC clones failed to detect IS10 in the BAC DNA. However, prolonged subculturing of a set of 15 clones resulted in transposition into the BAC DNA. Eventually, all cultures acquired a 2.3-kb fragment that hybridized strongly with IS10. Sequence analysis revealed the presence of a preferred site for transposition in the BAC vector. These results indicate that a large number, if not all, of the BAC libraries from different organisms are contaminated with IS10R. The source of this element has been identified as the DH10B strain of E. coli used as the host for BAC libraries.

Original languageEnglish (US)
Pages (from-to)48-53
Number of pages6
JournalTheoretical and Applied Genetics
Volume104
Issue number1
DOIs
StatePublished - Dec 1 2002

Fingerprint

Bacterial Artificial Chromosomes
bacterial artificial chromosomes
Insertional Mutagenesis
transposons
Databases
Clone Cells
clones
transposition (genetics)
Sequence Analysis
DNA
sequence analysis
Escherichia coli
Phaseolus
Caenorhabditis elegans
Drosophila melanogaster
Arabidopsis
Restriction Fragment Length Polymorphisms
Population
Phaseolus vulgaris
restriction fragment length polymorphism

Keywords

  • BAC libraries
  • IS10
  • Tn10

ASJC Scopus subject areas

  • Biotechnology
  • Agronomy and Crop Science
  • Genetics

Cite this

Evidence for a prokaryotic insertion-sequence contamination in eukaryotic sequences registered in different databases. / Astua-Monge, G.; Lyznik, A.; Jones, V.; Mackenzie, S. A.; Vallejos, C. E.

In: Theoretical and Applied Genetics, Vol. 104, No. 1, 01.12.2002, p. 48-53.

Research output: Contribution to journalArticle

Astua-Monge, G. ; Lyznik, A. ; Jones, V. ; Mackenzie, S. A. ; Vallejos, C. E. / Evidence for a prokaryotic insertion-sequence contamination in eukaryotic sequences registered in different databases. In: Theoretical and Applied Genetics. 2002 ; Vol. 104, No. 1. pp. 48-53.
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