Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken

David Wragg; Andrew S Mason; Le Yu; Richard Kuo; Raman A Lawal; Takele Taye Desta; Joram M Mwacharo; Chang-Yeon Cho; Steve Kemp; David W Burt; Olivier Hanotte

doi:10.1186/s12864-015-1954-x

Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken

David Wragg, Andrew S Mason, Le Yu, Richard Kuo, Raman A Lawal, Takele Taye Desta, Joram M Mwacharo, Chang-Yeon Cho, Steve Kemp, David W Burt, Olivier Hanotte

Biology

Research output: Contribution to journal › Article › peer-review

Abstract

BACKGROUND: EAV-HP is an ancient retrovirus pre-dating Gallus speciation, which continues to circulate in modern chicken populations, and led to the emergence of avian leukosis virus subgroup J causing significant economic losses to the poultry industry. We mapped EAV-HP integration sites in Ethiopian village chickens, a Silkie, Taiwan Country chicken, red junglefowl Gallus gallus and several inbred experimental lines using whole-genome sequence data.

RESULTS: An average of 75.22 ± 9.52 integration sites per bird were identified, which collectively group into 279 intervals of which 5 % are common to 90 % of the genomes analysed and are suggestive of pre-domestication integration events. More than a third of intervals are specific to individual genomes, supporting active circulation of EAV-HP in modern chickens. Interval density is correlated with chromosome length (P < 2.31(-6)), and 27 % of intervals are located within 5 kb of a transcript. Functional annotation clustering of genes reveals enrichment for immune-related functions (P < 0.05).

CONCLUSIONS: Our results illustrate a non-random distribution of EAV-HP in the genome, emphasising the importance it may have played in the adaptation of the species, and provide a platform from which to extend investigations on the co-evolutionary significance of endogenous retroviral genera with their hosts.

Original language	English
Article number	784
Number of pages	10
Journal	BMC Genomics
Volume	16
DOIs	https://doi.org/10.1186/s12864-015-1954-x
Publication status	Published - 14 Oct 2015

Keywords

Animals
Animals, Domestic/genetics
Chickens/genetics
Evolution, Molecular
Genome
Phylogeny
Poultry/genetics
Retroviridae/genetics
Virus Integration/genetics

Access to Document

10.1186/s12864-015-1954-x

Cite this

@article{b16aae3b788b4a42b3e1dff646965037,

title = "Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken",

abstract = "BACKGROUND: EAV-HP is an ancient retrovirus pre-dating Gallus speciation, which continues to circulate in modern chicken populations, and led to the emergence of avian leukosis virus subgroup J causing significant economic losses to the poultry industry. We mapped EAV-HP integration sites in Ethiopian village chickens, a Silkie, Taiwan Country chicken, red junglefowl Gallus gallus and several inbred experimental lines using whole-genome sequence data.RESULTS: An average of 75.22 ± 9.52 integration sites per bird were identified, which collectively group into 279 intervals of which 5 % are common to 90 % of the genomes analysed and are suggestive of pre-domestication integration events. More than a third of intervals are specific to individual genomes, supporting active circulation of EAV-HP in modern chickens. Interval density is correlated with chromosome length (P < 2.31(-6)), and 27 % of intervals are located within 5 kb of a transcript. Functional annotation clustering of genes reveals enrichment for immune-related functions (P < 0.05).CONCLUSIONS: Our results illustrate a non-random distribution of EAV-HP in the genome, emphasising the importance it may have played in the adaptation of the species, and provide a platform from which to extend investigations on the co-evolutionary significance of endogenous retroviral genera with their hosts.",

keywords = "Animals, Animals, Domestic/genetics, Chickens/genetics, Evolution, Molecular, Genome, Phylogeny, Poultry/genetics, Retroviridae/genetics, Virus Integration/genetics",

author = "David Wragg and Mason, {Andrew S} and Le Yu and Richard Kuo and Lawal, {Raman A} and Desta, {Takele Taye} and Mwacharo, {Joram M} and Chang-Yeon Cho and Steve Kemp and Burt, {David W} and Olivier Hanotte",

year = "2015",

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day = "14",

doi = "10.1186/s12864-015-1954-x",

language = "English",

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publisher = "BioMed Central",

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T1 - Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken

AU - Wragg, David

AU - Mason, Andrew S

AU - Yu, Le

AU - Kuo, Richard

AU - Lawal, Raman A

AU - Desta, Takele Taye

AU - Mwacharo, Joram M

AU - Cho, Chang-Yeon

AU - Kemp, Steve

AU - Burt, David W

AU - Hanotte, Olivier

PY - 2015/10/14

Y1 - 2015/10/14

N2 - BACKGROUND: EAV-HP is an ancient retrovirus pre-dating Gallus speciation, which continues to circulate in modern chicken populations, and led to the emergence of avian leukosis virus subgroup J causing significant economic losses to the poultry industry. We mapped EAV-HP integration sites in Ethiopian village chickens, a Silkie, Taiwan Country chicken, red junglefowl Gallus gallus and several inbred experimental lines using whole-genome sequence data.RESULTS: An average of 75.22 ± 9.52 integration sites per bird were identified, which collectively group into 279 intervals of which 5 % are common to 90 % of the genomes analysed and are suggestive of pre-domestication integration events. More than a third of intervals are specific to individual genomes, supporting active circulation of EAV-HP in modern chickens. Interval density is correlated with chromosome length (P < 2.31(-6)), and 27 % of intervals are located within 5 kb of a transcript. Functional annotation clustering of genes reveals enrichment for immune-related functions (P < 0.05).CONCLUSIONS: Our results illustrate a non-random distribution of EAV-HP in the genome, emphasising the importance it may have played in the adaptation of the species, and provide a platform from which to extend investigations on the co-evolutionary significance of endogenous retroviral genera with their hosts.

AB - BACKGROUND: EAV-HP is an ancient retrovirus pre-dating Gallus speciation, which continues to circulate in modern chicken populations, and led to the emergence of avian leukosis virus subgroup J causing significant economic losses to the poultry industry. We mapped EAV-HP integration sites in Ethiopian village chickens, a Silkie, Taiwan Country chicken, red junglefowl Gallus gallus and several inbred experimental lines using whole-genome sequence data.RESULTS: An average of 75.22 ± 9.52 integration sites per bird were identified, which collectively group into 279 intervals of which 5 % are common to 90 % of the genomes analysed and are suggestive of pre-domestication integration events. More than a third of intervals are specific to individual genomes, supporting active circulation of EAV-HP in modern chickens. Interval density is correlated with chromosome length (P < 2.31(-6)), and 27 % of intervals are located within 5 kb of a transcript. Functional annotation clustering of genes reveals enrichment for immune-related functions (P < 0.05).CONCLUSIONS: Our results illustrate a non-random distribution of EAV-HP in the genome, emphasising the importance it may have played in the adaptation of the species, and provide a platform from which to extend investigations on the co-evolutionary significance of endogenous retroviral genera with their hosts.

KW - Animals

KW - Animals, Domestic/genetics

KW - Chickens/genetics

KW - Evolution, Molecular

KW - Genome

KW - Phylogeny

KW - Poultry/genetics

KW - Retroviridae/genetics

KW - Virus Integration/genetics

U2 - 10.1186/s12864-015-1954-x

DO - 10.1186/s12864-015-1954-x

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JO - BMC Genomics

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