A universal method for the study of CR1 retroposons in nonmodel bird genomes

Alexander Suh, Jan Ole Kriegs, Stephen Donnellan, Jürgen Brosius, Jürgen Schmitz

Research output: Contribution to journalArticlepeer-review

18 Citations (Scopus)

Abstract

Presence/absence patterns of retroposon insertions at orthologous genomic loci constitute straightforward markers for phylogenetic or population genetic studies. In birds, the convenient identification and utility of these markers has so far been mainly restricted to the lineages leading to model birds (i.e., chicken and zebra finch). We present an easy-to-use, rapid, and cost-effective method for the experimental isolation of chicken repeat 1 (CR1) insertions from virtually any bird genome and potentially nonavian genomes. The application of our method to the little grebe genome yielded insertions belonging to new CR1 subfamilies that are scattered all across the phylogenetic tree of avian CR1s. Furthermore, presence/absence analysis of these insertions provides the first retroposon evidence grouping flamingos + grebes as Mirandornithes and several markers for all subsequent branching events within grebes (Podicipediformes). Five markers appear to be species-specific insertions, including the hitherto first evidence in birds for biallelic CR1 insertions that could be useful in future population genetic studies.

Original languageEnglish
Pages (from-to)2899-2903
Number of pages5
JournalMolecular Biology and Evolution
Volume29
Issue number10
DOIs
Publication statusPublished - Oct 2012

Keywords

  • biallelic insertion
  • birds
  • CR1
  • genomic library
  • inverse PCR
  • retroposon extraction

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