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Uncovering genomic features and maternal origin of korean native chicken by whole genome sequencing.

Kwak W, Song KD, Oh JD, Heo KN, Lee JH, Lee WK, Yoon SH, Kim H, Cho S, Lee HK - PLoS ONE (2014)

Bottom Line: Through the analysis, we found that the highly variable region common to all 5 strains had genes like PCHD15, CISD1, PIK3C2A, and NUCB2 that might be related to the phenotypic traits of the chicken such as auditory sense, growth rate and egg traits.Our results revealed that the KNC has multiple maternal origins which are in agreement with Korea's history of chicken breed imports.The results presented here provide a valuable basis for future research on genomic features of KNC and further understanding of KNC's origin.

View Article: PubMed Central - PubMed

Affiliation: C & K genomics, Seoul, Republic of Korea; Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea.

ABSTRACT
The Korean Native Chicken (KNC) is an important endemic biological resource in Korea. While numerous studies have been conducted exploring this breed, none have used next-generation sequencing to identify its specific genomic features. We sequenced five strains of KNC and identified 10.9 million SNVs and 1.3 million InDels. Through the analysis, we found that the highly variable region common to all 5 strains had genes like PCHD15, CISD1, PIK3C2A, and NUCB2 that might be related to the phenotypic traits of the chicken such as auditory sense, growth rate and egg traits. In addition, we assembled unaligned reads that could not be mapped to the reference genome. By assembling the unaligned reads, we were able to present genomic sequences characteristic to the KNC. Based on this, we also identified genes related to the olfactory receptors and antigen that are common to all 5 strains. Finally, through the reconstructed mitochondrial genome sequences, we performed phylogenomic analysis and elucidated the maternal origin of the artificially restored KNC. Our results revealed that the KNC has multiple maternal origins which are in agreement with Korea's history of chicken breed imports. The results presented here provide a valuable basis for future research on genomic features of KNC and further understanding of KNC's origin.

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Phylogenetic tree using 75 whole MT genome sequences, including five Korean Native Chickens from this study.Box a shows the morphology and plumage color of the different KNC strains. Box b shows the legend (sample type and locality) for the phylogenetic tree in c. In the phylogentic tree, values (Bayesian posterior probability <0.8 or bootstrap value <600) were marked with a “-“ symbol.
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pone-0114763-g002: Phylogenetic tree using 75 whole MT genome sequences, including five Korean Native Chickens from this study.Box a shows the morphology and plumage color of the different KNC strains. Box b shows the legend (sample type and locality) for the phylogenetic tree in c. In the phylogentic tree, values (Bayesian posterior probability <0.8 or bootstrap value <600) were marked with a “-“ symbol.

Mentions: A phylogenetic tree was constructed using MrBayes based on Bayesian inferences with 75 whole mitochondrial genome sequences from commercial chicken breeds of China, Japan, Southeast Asia, South Asia, and the KNCs (Fig. 2). The constructed tree showed that the 75 OTUs were broadly divided into five groups. Although the topology of the NJ tree (Figure S9 in S1 File) showed different ordering of groups, the branching pattern of each group was consistent with the tree constructed using Bayesian inference methods.


Uncovering genomic features and maternal origin of korean native chicken by whole genome sequencing.

Kwak W, Song KD, Oh JD, Heo KN, Lee JH, Lee WK, Yoon SH, Kim H, Cho S, Lee HK - PLoS ONE (2014)

Phylogenetic tree using 75 whole MT genome sequences, including five Korean Native Chickens from this study.Box a shows the morphology and plumage color of the different KNC strains. Box b shows the legend (sample type and locality) for the phylogenetic tree in c. In the phylogentic tree, values (Bayesian posterior probability <0.8 or bootstrap value <600) were marked with a “-“ symbol.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4263466&req=5

pone-0114763-g002: Phylogenetic tree using 75 whole MT genome sequences, including five Korean Native Chickens from this study.Box a shows the morphology and plumage color of the different KNC strains. Box b shows the legend (sample type and locality) for the phylogenetic tree in c. In the phylogentic tree, values (Bayesian posterior probability <0.8 or bootstrap value <600) were marked with a “-“ symbol.
Mentions: A phylogenetic tree was constructed using MrBayes based on Bayesian inferences with 75 whole mitochondrial genome sequences from commercial chicken breeds of China, Japan, Southeast Asia, South Asia, and the KNCs (Fig. 2). The constructed tree showed that the 75 OTUs were broadly divided into five groups. Although the topology of the NJ tree (Figure S9 in S1 File) showed different ordering of groups, the branching pattern of each group was consistent with the tree constructed using Bayesian inference methods.

Bottom Line: Through the analysis, we found that the highly variable region common to all 5 strains had genes like PCHD15, CISD1, PIK3C2A, and NUCB2 that might be related to the phenotypic traits of the chicken such as auditory sense, growth rate and egg traits.Our results revealed that the KNC has multiple maternal origins which are in agreement with Korea's history of chicken breed imports.The results presented here provide a valuable basis for future research on genomic features of KNC and further understanding of KNC's origin.

View Article: PubMed Central - PubMed

Affiliation: C & K genomics, Seoul, Republic of Korea; Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea.

ABSTRACT
The Korean Native Chicken (KNC) is an important endemic biological resource in Korea. While numerous studies have been conducted exploring this breed, none have used next-generation sequencing to identify its specific genomic features. We sequenced five strains of KNC and identified 10.9 million SNVs and 1.3 million InDels. Through the analysis, we found that the highly variable region common to all 5 strains had genes like PCHD15, CISD1, PIK3C2A, and NUCB2 that might be related to the phenotypic traits of the chicken such as auditory sense, growth rate and egg traits. In addition, we assembled unaligned reads that could not be mapped to the reference genome. By assembling the unaligned reads, we were able to present genomic sequences characteristic to the KNC. Based on this, we also identified genes related to the olfactory receptors and antigen that are common to all 5 strains. Finally, through the reconstructed mitochondrial genome sequences, we performed phylogenomic analysis and elucidated the maternal origin of the artificially restored KNC. Our results revealed that the KNC has multiple maternal origins which are in agreement with Korea's history of chicken breed imports. The results presented here provide a valuable basis for future research on genomic features of KNC and further understanding of KNC's origin.

Show MeSH