Whole Genome Re-Sequencing of Three Domesticated Chicken Breeds

Oh, Do Hoon; Son, Bongjun; Mun, Seyoung; Oh, Man Hwan; Oh, Sejong; Ha, Jae Jung; Yi, Junkoo; Lee, Seunguk; Han, Kyudong

doi:10.2108/zs150071

Cited by 12 publications

(12 citation statements)

References 19 publications

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“…To detect new transposition events, we aligned the published resequencing data of the White Leghorn genome with ~100X coverage (Oh et al, 2016) to the Red Jungle Fowl reference genome. 503 putative TE insertions, absent in Red Jungle Fowl, were distributed throughout the chicken genome (Figure 1D, Supplementary file 1).…”

Section: Resultsmentioning

confidence: 99%

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Domestic chickens activate a piRNA defense against avian leukosis virus

Sun

Xie

Zhuo³

et al. 2017

eLife

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PIWI-interacting RNAs (piRNAs) protect the germ line by targeting transposable elements (TEs) through the base-pair complementarity. We do not know how piRNAs co-evolve with TEs in chickens. Here we reported that all active TEs in the chicken germ line are targeted by piRNAs, and as TEs lose their activity, the corresponding piRNAs erode away. We observed de novo piRNA birth as host responds to a recent retroviral invasion. Avian leukosis virus (ALV) has endogenized prior to chicken domestication, remains infectious, and threatens poultry industry. Domestic fowl produce piRNAs targeting ALV from one ALV provirus that was known to render its host ALV resistant. This proviral locus does not produce piRNAs in undomesticated wild chickens. Our findings uncover rapid piRNA evolution reflecting contemporary TE activity, identify a new piRNA acquisition modality by activating a pre-existing genomic locus, and extend piRNA defense roles to include the period when endogenous retroviruses are still infectious.DOI: http://dx.doi.org/10.7554/eLife.24695.001

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Section: Resultsmentioning

confidence: 99%

“…We analyzed the previously published genome resequencing libraries from White Leghorn (SRX1121834, SRX1121835, SRX1121836) (Oh et al, 2016) and we combined the three replicates to increase detection sensitivity. The new transposition events were analyzed by TEMP (Khurana et al, 2011; Zhuang et al, 2014, SCR_001788).…”

Section: Materials and Methodsmentioning

confidence: 99%

Domestic chickens activate a piRNA defense against avian leukosis virus

Sun

Xie

Zhuo³

et al. 2017

eLife

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“…It suggests that GGERV10 elements could be served as a genetic marker [32]. It suggests the possibility that any of the full-length GGERV10 elements could be breed-specific locus.…”

Section: Resultsmentioning

confidence: 99%

Chicken (Gallus gallus) endogenous retrovirus generates genomic variations in the chicken genome

et al. 2017

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BackgroundTransposable elements (TEs) comprise ~10% of the chicken (Gallus gallus) genome. The content of TEs is much lower than that of mammalian genomes, where TEs comprise around half of the genome. Endogenous retroviruses are responsible for ~1.3% of the chicken genome. Among them is Gallus gallus endogenous retrovirus 10 (GGERV10), one of the youngest endogenous retrovirus families, which emerged in the chicken genome around 3 million years ago.ResultsWe identified a total of 593 GGERV10 elements in the chicken reference genome using UCSC genome database and RepeatMasker. While most of the elements were truncated, 49 GGERV10 elements were full-length retaining 5′ and 3′ LTRs. We examined in detail their structural features, chromosomal distribution, genomic environment, and phylogenetic relationships. We compared LTR sequence among five different GGERV10 subfamilies and found sequence variations among the LTRs. Using a traditional PCR assay, we examined a polymorphism rate of the 49 full-length GGERV10 elements in three different chicken populations of the Korean domestic chicken, Leghorn, and Araucana. The result found a breed-specific GGERV10B insertion locus in the Korean domestic chicken, which could be used as a Korean domestic chicken-specific marker.ConclusionsGGERV10 family is the youngest ERV family and thus might have contributed to recent genomic variations in different chicken populations. The result of this study showed that one of GGERV10 elements integrated into the chicken genome after the divergence of Korean domestic chicken from other closely related chicken populations, suggesting that GGERV10 could be served as a molecular marker for chicken breed identification.Electronic supplementary materialThe online version of this article (doi:10.1186/s13100-016-0085-5) contains supplementary material, which is available to authorized users.

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“…Here, we focus our discussion on several examples of variation in epidermal appendage structure and morphology that have resulted from long-term selective breeding in domestic avian species. In addition to structural variation, several recent studies elucidate the genetic and genomic basis of plumage color variation in avian populations, and this important topic is addressed elsewhere (Bed’hom et al, 2012; Domyan et al, 2014; Gunnarsson et al, 2011; Hellström et al, 2010; Lopes et al, 2016; Mundy et al, 2016; Oh et al, 2016). …”

Section: Variation In Epidermal Appendage Structurementioning

confidence: 99%

Genomic determinants of epidermal appendage patterning and structure in domestic birds

Boer

Hollebeke

Shapiro

2017

Developmental Biology

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Variation in regional identity, patterning, and structure of epidermal appendages contributes to skin diversity among many vertebrate groups, and is perhaps most striking in birds. In pioneering work on epidermal appendage patterning, John Saunders and his contemporaries took advantage of epidermal appendage diversity within and among domestic chicken breeds to establish the importance of mesoderm-ectoderm signaling in determining skin patterning. Diversity in chickens and other domestic birds, including pigeons, is driving a new wave of research to dissect the molecular genetic basis of epidermal appendage patterning. Domestic birds are not only outstanding models for embryonic manipulations, as Saunders recognized, but they are also ideal genetic models for discovering the specific genes that control normal development and the mutations that contribute to skin diversity. Here, we review recent genetic and genomic approaches to uncover the basis of epidermal macropatterning, micropatterning, and structural variation. We also present new results that confirm expression changes in two limb identity genes in feather-footed pigeons, a case of variation in appendage structure and identity.

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Whole Genome Re-Sequencing of Three Domesticated Chicken Breeds

Cited by 12 publications

References 19 publications

Domestic chickens activate a piRNA defense against avian leukosis virus

Domestic chickens activate a piRNA defense against avian leukosis virus

Chicken (Gallus gallus) endogenous retrovirus generates genomic variations in the chicken genome

Genomic determinants of epidermal appendage patterning and structure in domestic birds

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