A New Look at the LTR Retrotransposon Content of the Chicken Genome

Long Terminal Repeat (LTR) retrotransposons are Eukaryotic autonomous repetitive elements which facilitate horizontal gene transfer and chromosomal rearrangements, and modify gene expression profiles. Furthermore, LTR retrotransposons (particularly endogenous retroviruses – ERVs) are known to alter the immunological response to exogenous retrovirus infection with diverse effects. This is particularly relevant in the domestic chicken, where recombination between ERVs and exogenous retroviruses has produced novel exogenous strains such as Avian Leukosis Virus (ALV)-J, whilst other ERVs confer immunological tolerance or, conversely, induce persistent viremia.

We present a new, fully integrated identification of LTR retrotransposons in the chicken galGal4 assembly, using existing homology and structure based techniques. We have annotated some 35Mbp of the genome; double the previous best annotation with levels similar to those seen in other bird species. Elements have been further studied to analyse retrotransposon positional clustering, proximity to genes and the likelihood of active retrotransposition and/or viral protein expression. This work forms the basis of future comparative genomics projects to assess the variation and evolutionary history of ERVs within the avian lineage, and between commercial chicken lines.

Our analysis pipeline is transferrable to all assembled genomes and has been made freely available for use in other LTR retrotransposon identification projects.

This work was supported as part of a Biotechnology and Biological Sciences Research Council (BBSRC) CASE studentship in association with Hy-Line International.