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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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Manhattan plot showing the rate of SNVs and InDels per 500kbp window for the autosomes and sex chromosome.The red line denotes the top 1% of empirical distribution.
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pone-0114763-g001: Manhattan plot showing the rate of SNVs and InDels per 500kbp window for the autosomes and sex chromosome.The red line denotes the top 1% of empirical distribution.

Mentions: The overall average mapping rate for the five chicken samples was 97.52% and the percentage of reads with one concordant mapping to the reference genome was 87.43% (Table S3 in S1 File). Mean coverage depth was 35.04 and the average calculated insert size was 268.8 (Figure S3 in S1 File). After variant calling and filtering, 1.3 million InDels and 10.9 million SNVs were retained. Of the 10.9 million SNVs identified in this study, 6.3 million SNVs have previously been reported (57.62%) while 4.6 million SNVs were novel variants (42.37%) based on Ensembl database ver.74. Figure S4 in S1 File shows the distribution of both novel and previously reported SNVs in each chromosome. The number of strain specific variants is summarized in Table S4 in S1 File. KNC_L(40) had a higher number of strain specific variants than the other four KNC strains. The proportion of strain specific SNVs made up 28% of all identified SNVs and 21% of the total identified SNVs were common to all strains (Figure S5 in S1 File). For InDel variants, 20% of the identified INDELs were strain specific while 30% were common to all five KNC strains (Figure S6 in S1 File). The ratios of the number of chromosomal variants to the total number of variants are displayed in Figure S7 in S1 File with the chromosomal length ratio distribution. The ratio of variants showed similar distribution patterns with the ratio of chromosome length. Most of the SNVs and InDels were located in the intergenic region and the intron region had the next highest proportion of variants (Figure S8 in S1 File). The number of SNVs and InDels per 500kbp window was calculated for each chromosome and the results are represented in Fig. 1. The top 1% of mutation rates was used to distinguish the significant peaks on the SNP and InDel distributions (the top 1% is marked off with a red line). In the plot, SNV rates showed peak points on chromosome 6 and 9, in all five strains and the overall distributions of InDel rates showed peak points in chromosome 5, 6, and 8. There were 25 and 16 genes in the highly variable SNVs and InDels windows where to be in common to all five KNC strains. The name of genes and number of variants in each gene were summarized in Table 2. The positions of synonymous and non-synonymous variants in each gene are summarized in Table S5 in S1 File.


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)

Manhattan plot showing the rate of SNVs and InDels per 500kbp window for the autosomes and sex chromosome.The red line denotes the top 1% of empirical distribution.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0114763-g001: Manhattan plot showing the rate of SNVs and InDels per 500kbp window for the autosomes and sex chromosome.The red line denotes the top 1% of empirical distribution.
Mentions: The overall average mapping rate for the five chicken samples was 97.52% and the percentage of reads with one concordant mapping to the reference genome was 87.43% (Table S3 in S1 File). Mean coverage depth was 35.04 and the average calculated insert size was 268.8 (Figure S3 in S1 File). After variant calling and filtering, 1.3 million InDels and 10.9 million SNVs were retained. Of the 10.9 million SNVs identified in this study, 6.3 million SNVs have previously been reported (57.62%) while 4.6 million SNVs were novel variants (42.37%) based on Ensembl database ver.74. Figure S4 in S1 File shows the distribution of both novel and previously reported SNVs in each chromosome. The number of strain specific variants is summarized in Table S4 in S1 File. KNC_L(40) had a higher number of strain specific variants than the other four KNC strains. The proportion of strain specific SNVs made up 28% of all identified SNVs and 21% of the total identified SNVs were common to all strains (Figure S5 in S1 File). For InDel variants, 20% of the identified INDELs were strain specific while 30% were common to all five KNC strains (Figure S6 in S1 File). The ratios of the number of chromosomal variants to the total number of variants are displayed in Figure S7 in S1 File with the chromosomal length ratio distribution. The ratio of variants showed similar distribution patterns with the ratio of chromosome length. Most of the SNVs and InDels were located in the intergenic region and the intron region had the next highest proportion of variants (Figure S8 in S1 File). The number of SNVs and InDels per 500kbp window was calculated for each chromosome and the results are represented in Fig. 1. The top 1% of mutation rates was used to distinguish the significant peaks on the SNP and InDel distributions (the top 1% is marked off with a red line). In the plot, SNV rates showed peak points on chromosome 6 and 9, in all five strains and the overall distributions of InDel rates showed peak points in chromosome 5, 6, and 8. There were 25 and 16 genes in the highly variable SNVs and InDels windows where to be in common to all five KNC strains. The name of genes and number of variants in each gene were summarized in Table 2. The positions of synonymous and non-synonymous variants in each gene are summarized in Table S5 in S1 File.

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