Abstract
BackgroundAvian leukosis virus subgroup E (ALVE) insertions are endogenous retroviruses (ERV) that are restricted to the domestic chicken and its wild progenitor. In commercial chickens, ALVE are known to have a detrimental effect on productivity and provide a source for recombination with exogenous retroviruses. The wider diversity of ALVE in non-commercial chickens and the role of these elements in ERV-derived immunity (EDI) are yet to be investigated.ResultsIn total, 974 different ALVE were identified from 407 chickens sampled from village populations in Ethiopia, Iraq, and Nigeria, using the recently developed obsERVer bioinformatics identification pipeline. Eighty-eight percent of all identified ALVE were novel, bringing the known number of ALVE integrations to more than 1300 across all analysed chickens. ALVE content was highly lineage-specific and populations generally exhibited a large diversity of ALVE at low frequencies, which is typical for ERV involved in EDI. A significantly larger number of ALVE was found within or near coding regions than expected by chance, although a relative depletion of ALVE was observed within coding regions, which likely reflects selection against deleterious integrations. These effects were less pronounced than in previous analyses of chickens from commercial lines.ConclusionsIdentification of more than 850 novel ALVE has trebled the known diversity of these retroviral elements. This work provides the basis for future studies to fully quantify the role of ALVE in immunity against exogenous ALV, and development of programmes to improve the productivity and welfare of chickens in developing economies.
Highlights
Avian leukosis virus subgroup E (ALVE) insertions are endogenous retroviruses (ERV) that are restricted to the domestic chicken and its wild progenitor
Distribution of ALVE across populations ALVE were detected from the Whole-genome (re)sequencing (WGS) data of 407 individual chickens that were sampled from village populations in Ethiopia, Iraq, and Nigeria
All selected integration sites were successfully validated by PCR, which confirmed an obsERVer false detection rate (FDR) of 0% and that obsERVer is highly specific for the detection of ERV from WGS data
Summary
Avian leukosis virus subgroup E (ALVE) insertions are endogenous retroviruses (ERV) that are restricted to the domestic chicken and its wild progenitor. ALVE are known to have a detrimental effect on productivity and provide a source for recombination with exogenous retroviruses. If a retrovirus integrates within the genome of the germline, these “endogenous” retroviruses (ERV) are inherited vertically, and can continue to affect the host organism over large evolutionary timescales. In chickens (Gallus gallus), where ERV represent about 3% of the genome [18, 19], the only retrovirus with recurrent exogenous and endogenous activity is the avian leukosis virus (ALV) [20, 21]. ALV can infect all galliform birds, subgroup E (ALVE) integrations are found only in the domestic chicken and its wild progenitor, the red junglefowl (RJF) [22]. ALVE have long been known to facilitate EDI [23, 24], but they have been primarily studied in commercial layer lines, where any selective benefit is masked by their typically negative association with productivity traits, and the absence of ALV infection in commercial stock [25,26,27,28]
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