Endogenous avian leukosis virus subgroup E elements of the chicken reference genome
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...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2020-06-01
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| Series: | Poultry Science |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S0032579120301188 |
| _version_ | 1819229889116504064 |
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| author | Andrew S. Mason Janet E. Fulton Jacqueline Smith |
| author_facet | Andrew S. Mason Janet E. Fulton Jacqueline Smith |
| author_sort | Andrew S. Mason |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-23T11:20:20Z |
| format | Article |
| id | doaj.art-34bf77cca9a94a4d90b5742a47ccd929 |
| institution | Directory Open Access Journal |
| issn | 0032-5791 |
| language | English |
| last_indexed | 2024-12-23T11:20:20Z |
| publishDate | 2020-06-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Poultry Science |
| spelling | doaj.art-34bf77cca9a94a4d90b5742a47ccd9292022-12-21T17:49:06ZengElsevierPoultry Science0032-57912020-06-0199629112915Endogenous avian leukosis virus subgroup E elements of the chicken reference genomeAndrew S. Mason0Janet E. Fulton1Jacqueline Smith2Department 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; Corresponding author:Hy-Line International, Dallas Center, IA 50063, USAThe Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian EH25 9RG, UKThe 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.http://www.sciencedirect.com/science/article/pii/S0032579120301188ALVEreference genomeERVALVE6ALVE-JFevB |
| spellingShingle | Andrew S. Mason Janet E. Fulton Jacqueline Smith Endogenous avian leukosis virus subgroup E elements of the chicken reference genome Poultry Science ALVE reference genome ERV ALVE6 ALVE-JFevB |
| title | Endogenous avian leukosis virus subgroup E elements of the chicken reference genome |
| title_full | Endogenous avian leukosis virus subgroup E elements of the chicken reference genome |
| title_fullStr | Endogenous avian leukosis virus subgroup E elements of the chicken reference genome |
| title_full_unstemmed | Endogenous avian leukosis virus subgroup E elements of the chicken reference genome |
| title_short | Endogenous avian leukosis virus subgroup E elements of the chicken reference genome |
| title_sort | endogenous avian leukosis virus subgroup e elements of the chicken reference genome |
| topic | ALVE reference genome ERV ALVE6 ALVE-JFevB |
| url | http://www.sciencedirect.com/science/article/pii/S0032579120301188 |
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