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Uncovering Genomic Features and Maternal Origin of Korean Native Chicken by Whole Genome Sequencing
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 SNV...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4263466/ https://www.ncbi.nlm.nih.gov/pubmed/25501044 http://dx.doi.org/10.1371/journal.pone.0114763 |
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author | Kwak, Woori Song, Ki-Duk Oh, Jae-Don Heo, Kang-Nyeong Lee, Jun-Heon Lee, Woon Kyu Yoon, Sook Hee Kim, Heebal Cho, Seoae Lee, Hak-Kyo |
author_facet | Kwak, Woori Song, Ki-Duk Oh, Jae-Don Heo, Kang-Nyeong Lee, Jun-Heon Lee, Woon Kyu Yoon, Sook Hee Kim, Heebal Cho, Seoae Lee, Hak-Kyo |
author_sort | Kwak, Woori |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-4263466 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-42634662014-12-19 Uncovering Genomic Features and Maternal Origin of Korean Native Chicken by Whole Genome Sequencing Kwak, Woori Song, Ki-Duk Oh, Jae-Don Heo, Kang-Nyeong Lee, Jun-Heon Lee, Woon Kyu Yoon, Sook Hee Kim, Heebal Cho, Seoae Lee, Hak-Kyo PLoS One Research Article 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. Public Library of Science 2014-12-11 /pmc/articles/PMC4263466/ /pubmed/25501044 http://dx.doi.org/10.1371/journal.pone.0114763 Text en © 2014 Kwak et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Kwak, Woori Song, Ki-Duk Oh, Jae-Don Heo, Kang-Nyeong Lee, Jun-Heon Lee, Woon Kyu Yoon, Sook Hee Kim, Heebal Cho, Seoae Lee, Hak-Kyo Uncovering Genomic Features and Maternal Origin of Korean Native Chicken by Whole Genome Sequencing |
title | Uncovering Genomic Features and Maternal Origin of Korean Native Chicken by Whole Genome Sequencing |
title_full | Uncovering Genomic Features and Maternal Origin of Korean Native Chicken by Whole Genome Sequencing |
title_fullStr | Uncovering Genomic Features and Maternal Origin of Korean Native Chicken by Whole Genome Sequencing |
title_full_unstemmed | Uncovering Genomic Features and Maternal Origin of Korean Native Chicken by Whole Genome Sequencing |
title_short | Uncovering Genomic Features and Maternal Origin of Korean Native Chicken by Whole Genome Sequencing |
title_sort | uncovering genomic features and maternal origin of korean native chicken by whole genome sequencing |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4263466/ https://www.ncbi.nlm.nih.gov/pubmed/25501044 http://dx.doi.org/10.1371/journal.pone.0114763 |
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