Identification and characterisation of endogenous Avian Leukosis Virus subgroup E (ALVE) insertions in chicken whole genome sequencing data

Ashlee R. Lund,Janet E. Fulton,Paul M. Hocking,David W. Burt,Andrew S. Mason

doi:10.1186/s13100-020-00216-w

Abstract

BackgroundEndogenous retroviruses (ERVs) are the remnants of retroviral infections which can elicit prolonged genomic and immunological stress on their host organism. In chickens, endogenous Avian Leukosis Virus subgroup E (ALVE) expression has been associated with reductions in muscle growth rate and egg production, as well as providing the potential for novel recombinant viruses. However, ALVEs can remain in commercial stock due to their incomplete identification and association with desirable traits, such as ALVE21 and slow feathering. The availability of whole genome sequencing (WGS) data facilitates high-throughput identification and characterisation of these retroviral remnants.ResultsWe have developed obsERVer, a new bioinformatic ERV identification pipeline which can identify ALVEs in WGS data without further sequencing. With this pipeline, 20 ALVEs were identified across eight elite layer lines from Hy-Line International, including four novel integrations and characterisation of a fast feathered phenotypic revertant that still contained ALVE21. These bioinformatically detected sites were subsequently validated using new high-throughput KASP assays, which showed that obsERVer was highly precise and exhibited a 0% false discovery rate. A further fifty-seven diverse chicken WGS datasets were analysed for their ALVE content, identifying a total of 322 integration sites, over 80% of which were novel. Like exogenous ALV, ALVEs show site preference for proximity to protein-coding genes, but also exhibit signs of selection against deleterious integrations within genes.ConclusionsobsERVer is a highly precise and broadly applicable pipeline for identifying retroviral integrations in WGS data. ALVE identification in commercial layers has aided development of high-throughput diagnostic assays which will aid ALVE management, with the aim to eventually eradicate ALVEs from high performance lines. Analysis of non-commercial chicken datasets with obsERVer has revealed broad ALVE diversity and facilitates the study of the biological effects of these ERVs in wild and domesticated populations.

Highlights

Endogenous retroviruses (ERVs) are the remnants of retroviral infections which can elicit prolonged genomic and immunological stress on their host organism
Detection of Avian Leukosis Virus subgroup E (ALVE) integrations in HL elite layer lines by obsERVer We have developed obsERVer, a focused bioinformatic pipeline for the detection of ALVE integrations in whole genome sequencing (WGS) datasets, which utilises popular, freely available tools for processing generation sequencing data. obsERVer was initially used to identify twenty different ALVEs across eight elite layer lines from Hy-Line International, of which four ALVEs were novel to this study (Table 1)
The novel ALVE_ros007, was initially identified by obsERVer as two separate sites 1939 bp apart due to a post-integration deletion of over 8 kbp, excising the absent genomic sequence and over 80% of the ALVE integration (Figure S3)

Summary

Introduction

Endogenous retroviruses (ERVs) are the remnants of retroviral infections which can elicit prolonged genomic and immunological stress on their host organism. Endogenous Avian Leukosis Virus subgroup E (ALVE) expression has been associated with reductions in muscle growth rate and egg production, as well as providing the potential for novel recombinant viruses. ERVs may continue to express their own retroviral genes (gag, pol, and env), driven by promoters with the potential for bidirectional effects in the flanking long terminal repeats (LTRs). They can re-emerge from the genome by recombination to pose novel exogenous threats, such as Avian Leukosis Virus (ALV) subgroup J in chickens [1, 4, 11, 13, 15, 16]

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Conclusion