Uncovering Genomic Features and Maternal Origin of Korean Native Chicken by Whole Genome Sequencing
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{"title"=>"Uncovering genomic features and maternal origin of Korean Native Chicken by whole genome sequencing", "type"=>"journal", "authors"=>[{"first_name"=>"Woori", "last_name"=>"Kwak", "scopus_author_id"=>"56367563800"}, {"first_name"=>"Ki Duk", "last_name"=>"Song", "scopus_author_id"=>"7401740590"}, {"first_name"=>"Jae Don", "last_name"=>"Oh", "scopus_author_id"=>"7402155301"}, {"first_name"=>"Kang Nyeong", "last_name"=>"Heo", "scopus_author_id"=>"35740334900"}, {"first_name"=>"Jun Heon", "last_name"=>"Lee", "scopus_author_id"=>"56156473900"}, {"first_name"=>"Woon Kyu", "last_name"=>"Lee", "scopus_author_id"=>"36081923500"}, {"first_name"=>"Sook Hee", "last_name"=>"Yoon", "scopus_author_id"=>"56446064300"}, {"first_name"=>"Heebal", "last_name"=>"Kim", "scopus_author_id"=>"56493773500"}, {"first_name"=>"Seoae", "last_name"=>"Cho", "scopus_author_id"=>"16644772000"}, {"first_name"=>"Hak Kyo", "last_name"=>"Lee", "scopus_author_id"=>"34968239000"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84917733114", "doi"=>"10.1371/journal.pone.0114763", "pui"=>"600738338", "pmid"=>"25501044", "scopus"=>"2-s2.0-84917733114", "issn"=>"19326203", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)"}, "id"=>"189dd7de-04ba-372e-a49c-722233ac9846", "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.", "link"=>"http://www.mendeley.com/research/uncovering-genomic-features-maternal-origin-korean-native-chicken-whole-genome-sequencing", "reader_count"=>6, "reader_count_by_academic_status"=>{"Researcher"=>2, "Student > Ph. D. Student"=>2, "Other"=>1, "Student > Master"=>1}, "reader_count_by_user_role"=>{"Researcher"=>2, "Student > Ph. D. Student"=>2, "Other"=>1, "Student > Master"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Biochemistry, Genetics and Molecular Biology"=>1, "Agricultural and Biological Sciences"=>3, "Medicine and Dentistry"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>3}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}}, "reader_count_by_country"=>{"Japan"=>1}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1839145"], "description"=>"<p>Coverage was calculated based on the size of reference genome Galgal4(1046.93MB).</p><p>Summary of sequencing information and rawdata QC result using trimmomatic.</p>", "links"=>[], "tags"=>["origin", "PIK", "chicken breed imports", "mitochondrial genome sequences", "Whole Genome Sequencing", "3c", "5 strains", "PCHD", "cisd", "KNC", "Korean Native Chicken", "Genomic Features", "Uncovering Genomic Features", "snv", "nucb"], "article_id"=>1267643, "categories"=>["Biological Sciences"], "users"=>["Woori Kwak", "Ki-Duk Song", "Jae-Don Oh", "Kang-Nyeong Heo", "Jun-Heon Lee", "Woon Kyu Lee", "Sook Hee Yoon", "Heebal Kim", "Seoae Cho", "Hak-Kyo Lee"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0114763.t001", "stats"=>{"downloads"=>4, "page_views"=>37, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_sequencing_information_and_rawdata_QC_result_using_trimmomatic_/1267643", "title"=>"Summary of sequencing information and rawdata QC result using trimmomatic.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-12-11 02:42:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/1839143"], "description"=>"<p>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.</p>", "links"=>[], "tags"=>["origin", "PIK", "chicken breed imports", "mitochondrial genome sequences", "Whole Genome Sequencing", "3c", "5 strains", "PCHD", "cisd", "KNC", "Korean Native Chicken", "Genomic Features", "Uncovering Genomic Features", "snv", "nucb"], "article_id"=>1267642, "categories"=>["Biological Sciences"], "users"=>["Woori Kwak", "Ki-Duk Song", "Jae-Don Oh", "Kang-Nyeong Heo", "Jun-Heon Lee", "Woon Kyu Lee", "Sook Hee Yoon", "Heebal Kim", "Seoae Cho", "Hak-Kyo Lee"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0114763.g002", "stats"=>{"downloads"=>3, "page_views"=>78, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_tree_using_75_whole_MT_genome_sequences_including_five_Korean_Native_Chickens_from_this_study_/1267642", "title"=>"Phylogenetic tree using 75 whole MT genome sequences, including five Korean Native Chickens from this study.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-11 02:42:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/1839138"], "description"=>"<p>The red line denotes the top 1% of empirical distribution.</p>", "links"=>[], "tags"=>["origin", "PIK", "chicken breed imports", "mitochondrial genome sequences", "Whole Genome Sequencing", "3c", "5 strains", "PCHD", "cisd", "KNC", "Korean Native Chicken", "Genomic Features", "Uncovering Genomic Features", "snv", "nucb"], "article_id"=>1267637, "categories"=>["Biological Sciences"], "users"=>["Woori Kwak", "Ki-Duk Song", "Jae-Don Oh", "Kang-Nyeong Heo", "Jun-Heon Lee", "Woon Kyu Lee", "Sook Hee Yoon", "Heebal Kim", "Seoae Cho", "Hak-Kyo Lee"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0114763.g001", "stats"=>{"downloads"=>2, "page_views"=>27, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Manhattan_plot_showing_the_rate_of_SNVs_and_InDels_per_500kbp_window_for_the_autosomes_and_sex_chromosome_/1267637", "title"=>"Manhattan plot showing the rate of SNVs and InDels per 500kbp window for the autosomes and sex chromosome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-11 02:42:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/1839151"], "description"=>"<p>List of commonly predicted genes from assembled sequences of each sample.</p>", "links"=>[], "tags"=>["origin", "PIK", "chicken breed imports", "mitochondrial genome sequences", "Whole Genome Sequencing", "3c", "5 strains", "PCHD", "cisd", "KNC", "Korean Native Chicken", "Genomic Features", "Uncovering Genomic Features", "snv", "nucb"], "article_id"=>1267650, "categories"=>["Biological Sciences"], "users"=>["Woori Kwak", "Ki-Duk Song", "Jae-Don Oh", "Kang-Nyeong Heo", "Jun-Heon Lee", "Woon Kyu Lee", "Sook Hee Yoon", "Heebal Kim", "Seoae Cho", "Hak-Kyo Lee"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0114763.t003", "stats"=>{"downloads"=>5, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_List_of_commonly_predicted_genes_from_assembled_sequences_of_each_sample_/1267650", "title"=>"List of commonly predicted genes from assembled sequences of each sample.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-12-11 02:42:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/1839164"], "description"=>"<div><p>The <u>Korean Native Chicken</u> (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 <i><u>PCHD15</u></i>, <i><u>CISD1</u></i>, <i><u>PIK3C2A</u></i>, and <i><u>NUCB2</u></i> 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 <u>unaligned reads</u>, 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 <u>maternal origin</u> 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.</p></div>", "links"=>[], "tags"=>["origin", "PIK", "chicken breed imports", "mitochondrial genome sequences", "Whole Genome Sequencing", "3c", "5 strains", "PCHD", "cisd", "KNC", "Korean Native Chicken", "Genomic Features", "Uncovering Genomic Features", "snv", "nucb"], "article_id"=>1267663, "categories"=>["Biological Sciences"], "users"=>["Woori Kwak", "Ki-Duk Song", "Jae-Don Oh", "Kang-Nyeong Heo", "Jun-Heon Lee", "Woon Kyu Lee", "Sook Hee Yoon", "Heebal Kim", "Seoae Cho", "Hak-Kyo Lee"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0114763", "stats"=>{"downloads"=>4, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Uncovering_Genomic_Features_and_Maternal_Origin_of_Korean_Native_Chicken_by_Whole_Genome_Sequencing_/1267663", "title"=>"Uncovering Genomic Features and Maternal Origin of Korean Native Chicken by Whole Genome Sequencing", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-12-11 02:42:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/1839147"], "description"=>"<p>The number of variants was based on the result of multi-sample calling from GATK.</p><p>List of genes and the number of variants in the highly variable regions of SNVs and InDels.</p>", "links"=>[], "tags"=>["origin", "PIK", "chicken breed imports", "mitochondrial genome sequences", "Whole Genome Sequencing", "3c", "5 strains", "PCHD", "cisd", "KNC", "Korean Native Chicken", "Genomic Features", "Uncovering Genomic Features", "snv", "nucb"], "article_id"=>1267645, "categories"=>["Biological Sciences"], "users"=>["Woori Kwak", "Ki-Duk Song", "Jae-Don Oh", "Kang-Nyeong Heo", "Jun-Heon Lee", "Woon Kyu Lee", "Sook Hee Yoon", "Heebal Kim", "Seoae Cho", "Hak-Kyo Lee"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0114763.t002", "stats"=>{"downloads"=>5, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_List_of_genes_and_the_number_of_variants_in_the_highly_variable_regions_of_SNVs_and_InDels_/1267645", "title"=>"List of genes and the number of variants in the highly variable regions of SNVs and InDels.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-12-11 02:42:10"}

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