Endogenous Retrovirus EAV-HP Linked to Blue Egg Phenotype in Mapuche Fowl

Wragg, David; Mwacharo, Joram M.; Alcalde, José Antonio; Wang, Chen; Han, Jianlin; Gongora, Jaime; Gourichon, David; Tixier‐Boichard, Michèle; Hanotte, Olivier

doi:10.1371/journal.pone.0071393

Cited by 57 publications

(62 citation statements)

References 46 publications

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“…In the event that two breakpoints were observed within an interval, they were found either to be 6 bp apart, corresponding to the size of a target-site duplication and so might be attributed to soft-clipped reads from the LTR at either end of the virus (chr2:129,140,825–129,141,707 and chr3:84,550,518–84,551,452; S9), or the integration was present in the reference genome and the breakpoints corresponded closely with the LTR alignment (chr1:182,715,565–183,138,508; S10). This is in contrast to that which has been recently observed at the oocyan locus for Chinese and South American chicken populations [ 8 , 9 ].…”

Section: Resultscontrasting

confidence: 99%

“…Desfarges and Ciuffi [ 6 ] indicate that alpharetroviruses display a weak preference for integration in transcription units of genes and CpG islands, which are enriched in gene-rich regions. This is consistent with the EAV-HP integration sites identified for the oocyan phenotype in chicken [ 8 , 9 ], which integrates into the promoter region of SLCO1B3 . Bolisetty et al [ 7 ] report a near random distribution of ERV integration sites, although this may be an artefact of the preferences of different retrovirus genera.…”

Section: Introductionsupporting

confidence: 88%

“…This gene transfer format file includes all of the coding and non-coding transcripts annotated on Ensembl's genome browser for Galgal4 . The rationale for selecting genes within 5 kb is that this is likely to cover the promoter region, as evidenced by the recent discovery of an EAV-HP integration site ~ 4 kb upstream of SLCO1B3 in chickens possessing the oocyan phenotype [ 8 , 9 ]. Functional annotation of genes was assessed using DAVID Bioinformatics Resources v6.7 [ 54 ], specifically the functional annotation clustering enrichment threshold for EASE was set to 1.3 with stringency set to HIGH; from the resulting clusters only those with an enrichment score ≥ 1.3 ( P < 0.05) were retained.…”

Section: Methodsmentioning

confidence: 99%

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

Wragg

Mason

Yu³

et al. 2015

BMC Genomics

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BackgroundEAV-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.ResultsAn 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).ConclusionsOur 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1954-x) contains supplementary material, which is available to authorized users.

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Section: Resultscontrasting

confidence: 99%

Section: Introductionsupporting

confidence: 88%

Section: Methodsmentioning

confidence: 99%

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

Wragg

Mason

Yu³

et al. 2015

BMC Genomics

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“…All the variation in the coloration of birds' eggshells is thus far known to be the product of just two ancient and highly conserved [ 17 ], tetrapyrrole pigments: biliverdin IXα, and protoporphyrin IX [ 18 – 21 ]. While the genetic and biochemical mechanisms by which colorful eggshell pigments are formed are not yet fully understood [ 22 ], the prevailing consensus is that protoporphyrin, a cyclic tetrapyrrole which produces red-brown maculation [ 23 ], is an immediate precursor of the heme molecule, whereas biliverdin, a linear tetrapyrrole which gives the eggshell a blue-green hue, is a byproduct of hemoglobin breakdown [ 18 – 20 , 24 ]. The basic biochemistry of avian eggshell pigments has received considerable attention [ 17 , 19 – 21 ] and subsequently, the presence or absence of protoporphyrin and biliverdin in eggshells has been documented for several extinct moa species [ 17 ] and more than 100 species of extant birds [ 18 ].…”

Section: Introductionmentioning

confidence: 99%

Nature’s Palette: Characterization of Shared Pigments in Colorful Avian and Mollusk Shells

et al. 2015

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Pigment-based coloration is a common trait found in a variety of organisms across the tree of life. For example, calcareous avian eggs are natural structures that vary greatly in color, yet just a handful of tetrapyrrole pigment compounds are responsible for generating this myriad of colors. To fully understand the diversity and constraints shaping nature’s palette, it is imperative to characterize the similarities and differences in the types of compounds involved in color production across diverse lineages. Pigment composition was investigated in eggshells of eleven paleognath bird taxa, covering several extinct and extant lineages, and shells of four extant species of mollusks. Birds and mollusks are two distantly related, calcareous shell-building groups, thus characterization of pigments in their calcareous structures would provide insights to whether similar compounds are found in different phyla (Chordata and Mollusca). An ethylenediaminetetraacetic acid (EDTA) extraction protocol was used to analyze the presence and concentration of biliverdin and protoporphyrin, two known and ubiquitous tetrapyrrole avian eggshell pigments, in all avian and molluscan samples. Biliverdin was solely detected in birds, including the colorful eggshells of four tinamou species. In contrast, protoporphyrin was detected in both the eggshells of several avian species and in the shells of all mollusks. These findings support previous hypotheses about the ubiquitous deposition of tetrapyrroles in the eggshells of various bird lineages and provide evidence for its presence also across distantly related animal taxa.

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“…Subsequent research found that ChERV plays an important role in both qualitative and quantitative traits as follows. ChERVs have been found to be involved in blue eggshell [9,10], recessive white [11], late feathering [12] and henny feathering phenotype [13]. In addition, the effects of ChERVs on exogenous avian tumor viruses infection including leukosis virus (ALV), reticuloendotheliosis viruses (REV) and Marek's disease virus (MDV) have also been documented [14][15][16][17].…”

Section: Introductionmentioning

confidence: 99%

Endogenous retroviruses transcriptomes in response to four avian pathogenic microorganisms infection in chicken

Dai¹,

Xie

Feng

et al. 2020

Preprint

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Background Endogenous retroviruses (ERVs) are common in the genomes of vertebrates and have been implicated in a variety of host responses such as immunity, phenotypic character and disease occurrence. However, the impact of ERVs on chicken disease is not well understood. In particular, the expression profiles of chicken ERVs (ChERVs) in the infection of pathogenic microorganisms are not clear. Results In the present study, we systematically identified 436 full-length ChERVs from the chicken genome and analyzed their neighboring genes. Subsequently, ChERV transcriptomes were analyzed in chicken after subgroup J avian leukosis virus (ALV-J), avian influenza virus (AIV), Marek’s disease virus (MDV) and avian pathogenic escherichia coli (APEC) infection. We found that about 50%-68% of ChERVs were transcriptionally active in infected-samples and uninfected-samples, although the abundance of most ChERVs is relatively low. Moreover, compared to uninfected-samples, a few ChERVs were significantly differentially expressed in ALV-J (49 ChERVs), AIV (18 ChERVs), MDV (66 ChERVs) and APEC (17 ChERVs) infected-samples. Of these differentially expressed ChERVs, only ChERV-3 was simultaneously down-regulated in the four ERV transcriptomes analysis after ALV-J, AIV, MDV and APEC infection. Further verification experiments found that both the exogenous and endogenous expression of ChERV-3 env gene was inhibited after ALV-J infection in chicken fibroblasts. However, overexpression of ChERV-3 env could induce the expression of interferon-stimulated genes (ISGs), but did not affect the replication of ALV-J. Conclusions To our knowledge, this study systematically revealed the expression profile of ChERVS for the first time after the pathogenic microorganism infection in chicken. These findings may be of significance for understanding the role and function of ChERVs to response the pathogenic microorganism infection.

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Endogenous Retrovirus EAV-HP Linked to Blue Egg Phenotype in Mapuche Fowl

Cited by 57 publications

References 46 publications

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

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

Nature’s Palette: Characterization of Shared Pigments in Colorful Avian and Mollusk Shells

Endogenous retroviruses transcriptomes in response to four avian pathogenic microorganisms infection in chicken

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