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Endogenous avian leukosis virus subgroup E elements of the chicken reference genome.
Poult Sci. 2020 Jun; 99(6):2911-2915.PS

Abstract

The chicken reference genome contains 2 endogenous avian leukosis virus subgroup E (ALVE) insertions, but gaps and unresolved repetitive sequences in previous assemblies have hindered their precise characterization. Detailed analysis of the most recent reference genome (GRCg6a) now shows both ALVEs within contiguous chromosome assemblies for the first time. ALVE6 (ALVE-JFevA) and ALVE-JFevB are both located on chromosome 1, with ALVE6 close to the p-arm telomere. ALVE-JFevB is a structurally intact element containing the ALVE gag, pol, and env genes and is capable of forming replication competent viruses. In contrast, ALVE6 contains a 3,352 bp 5' truncation and lacks the entire 5' long terminal repeat and gag gene. Despite this, ALVE6 remains able to produce intact envelope protein, likely due to a mutation in the recognition site for a known inhibitory miRNA (miR-155). Whole genome resequencing data sets from layers, broilers, and 3 independent sources of wild-caught red junglefowl were surveyed for the presence of each of these reference genome ALVEs. ALVE-JFevB was found in no other chicken or red junglefowl genomes, whereas ALVE6 was identified in some layers, broilers, and native breeds but not within any other red junglefowl genome. Improved assembly contiguity has facilitated better characterization of the 2 ALVEs of the chicken reference genome. However, both the limited ALVE content and unique presence of ALVE-JFevB suggests that the reference individual is unrepresentative of ancestral Gallus gallus ALVE diversity.

Authors+Show Affiliations

Department of Biology, The University of York, York YO10 5DD, UK; The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian EH25 9RG, UK. Electronic address: andrew.mason@york.ac.uk.Hy-Line International, Dallas Center, IA 50063, USA.The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian EH25 9RG, UK.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

32475424

Citation

Mason, Andrew S., et al. "Endogenous Avian Leukosis Virus Subgroup E Elements of the Chicken Reference Genome." Poultry Science, vol. 99, no. 6, 2020, pp. 2911-2915.
Mason AS, Fulton JE, Smith J. Endogenous avian leukosis virus subgroup E elements of the chicken reference genome. Poult Sci. 2020;99(6):2911-2915.
Mason, A. S., Fulton, J. E., & Smith, J. (2020). Endogenous avian leukosis virus subgroup E elements of the chicken reference genome. Poultry Science, 99(6), 2911-2915. https://doi.org/10.1016/j.psj.2019.12.074
Mason AS, Fulton JE, Smith J. Endogenous Avian Leukosis Virus Subgroup E Elements of the Chicken Reference Genome. Poult Sci. 2020;99(6):2911-2915. PubMed PMID: 32475424.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Endogenous avian leukosis virus subgroup E elements of the chicken reference genome. AU - Mason,Andrew S, AU - Fulton,Janet E, AU - Smith,Jacqueline, Y1 - 2020/04/02/ PY - 2019/07/29/received PY - 2019/11/08/revised PY - 2019/12/31/accepted PY - 2020/6/2/entrez KW - ALVE KW - ALVE-JFevB KW - ALVE6 KW - ERV KW - reference genome SP - 2911 EP - 2915 JF - Poultry science JO - Poult. Sci. VL - 99 IS - 6 N2 - The chicken reference genome contains 2 endogenous avian leukosis virus subgroup E (ALVE) insertions, but gaps and unresolved repetitive sequences in previous assemblies have hindered their precise characterization. Detailed analysis of the most recent reference genome (GRCg6a) now shows both ALVEs within contiguous chromosome assemblies for the first time. ALVE6 (ALVE-JFevA) and ALVE-JFevB are both located on chromosome 1, with ALVE6 close to the p-arm telomere. ALVE-JFevB is a structurally intact element containing the ALVE gag, pol, and env genes and is capable of forming replication competent viruses. In contrast, ALVE6 contains a 3,352 bp 5' truncation and lacks the entire 5' long terminal repeat and gag gene. Despite this, ALVE6 remains able to produce intact envelope protein, likely due to a mutation in the recognition site for a known inhibitory miRNA (miR-155). Whole genome resequencing data sets from layers, broilers, and 3 independent sources of wild-caught red junglefowl were surveyed for the presence of each of these reference genome ALVEs. ALVE-JFevB was found in no other chicken or red junglefowl genomes, whereas ALVE6 was identified in some layers, broilers, and native breeds but not within any other red junglefowl genome. Improved assembly contiguity has facilitated better characterization of the 2 ALVEs of the chicken reference genome. However, both the limited ALVE content and unique presence of ALVE-JFevB suggests that the reference individual is unrepresentative of ancestral Gallus gallus ALVE diversity. SN - 1525-3171 UR - https://www.unboundmedicine.com/medline/citation/32475424/Endogenous_avian_leukosis_virus_subgroup_E_elements_of_the_chicken_reference_genome_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S0032-5791(20)30118-8 DB - PRIME DP - Unbound Medicine ER -
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