Comprehensive Survey of Genetic Diversity in Chloroplast Genomes and 45S nrDNAs within Panax ginseng Species.
We report complete sequences of chloroplast (cp) genome and 45S nuclear ribosomal DNA (45S nrDNA) for 11 Panax ginseng cultivars. We have obtained complete sequences of cp and 45S nrDNA, the representative barcoding target sequences for cytoplasm and nuclear genome, respectively, based on low covera...
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2015-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC4465672?pdf=render |
| _version_ | 1818041380063150080 |
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| author | Kyunghee Kim Sang-Choon Lee Junki Lee Hyun Oh Lee Ho Jun Joh Nam-Hoon Kim Hyun-Seung Park Tae-Jin Yang |
| author_facet | Kyunghee Kim Sang-Choon Lee Junki Lee Hyun Oh Lee Ho Jun Joh Nam-Hoon Kim Hyun-Seung Park Tae-Jin Yang |
| author_sort | Kyunghee Kim |
| collection | DOAJ |
| description | We report complete sequences of chloroplast (cp) genome and 45S nuclear ribosomal DNA (45S nrDNA) for 11 Panax ginseng cultivars. We have obtained complete sequences of cp and 45S nrDNA, the representative barcoding target sequences for cytoplasm and nuclear genome, respectively, based on low coverage NGS sequence of each cultivar. The cp genomes sizes ranged from 156,241 to 156,425 bp and the major size variation was derived from differences in copy number of tandem repeats in the ycf1 gene and in the intergenic regions of rps16-trnUUG and rpl32-trnUAG. The complete 45S nrDNA unit sequences were 11,091 bp, representing a consensus single transcriptional unit with an intergenic spacer region. Comparative analysis of these sequences as well as those previously reported for three Chinese accessions identified very rare but unique polymorphism in the cp genome within P. ginseng cultivars. There were 12 intra-species polymorphisms (six SNPs and six InDels) among 14 cultivars. We also identified five SNPs from 45S nrDNA of 11 Korean ginseng cultivars. From the 17 unique informative polymorphic sites, we developed six reliable markers for analysis of ginseng diversity and cultivar authentication. |
| first_indexed | 2024-12-10T08:29:30Z |
| format | Article |
| id | doaj.art-b296a40c8a8343288dcedbf1dc54d1f0 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-10T08:29:30Z |
| publishDate | 2015-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-b296a40c8a8343288dcedbf1dc54d1f02022-12-22T01:56:09ZengPublic Library of Science (PLoS)PLoS ONE1932-62032015-01-01106e011715910.1371/journal.pone.0117159Comprehensive Survey of Genetic Diversity in Chloroplast Genomes and 45S nrDNAs within Panax ginseng Species.Kyunghee KimSang-Choon LeeJunki LeeHyun Oh LeeHo Jun JohNam-Hoon KimHyun-Seung ParkTae-Jin YangWe report complete sequences of chloroplast (cp) genome and 45S nuclear ribosomal DNA (45S nrDNA) for 11 Panax ginseng cultivars. We have obtained complete sequences of cp and 45S nrDNA, the representative barcoding target sequences for cytoplasm and nuclear genome, respectively, based on low coverage NGS sequence of each cultivar. The cp genomes sizes ranged from 156,241 to 156,425 bp and the major size variation was derived from differences in copy number of tandem repeats in the ycf1 gene and in the intergenic regions of rps16-trnUUG and rpl32-trnUAG. The complete 45S nrDNA unit sequences were 11,091 bp, representing a consensus single transcriptional unit with an intergenic spacer region. Comparative analysis of these sequences as well as those previously reported for three Chinese accessions identified very rare but unique polymorphism in the cp genome within P. ginseng cultivars. There were 12 intra-species polymorphisms (six SNPs and six InDels) among 14 cultivars. We also identified five SNPs from 45S nrDNA of 11 Korean ginseng cultivars. From the 17 unique informative polymorphic sites, we developed six reliable markers for analysis of ginseng diversity and cultivar authentication.http://europepmc.org/articles/PMC4465672?pdf=render |
| spellingShingle | Kyunghee Kim Sang-Choon Lee Junki Lee Hyun Oh Lee Ho Jun Joh Nam-Hoon Kim Hyun-Seung Park Tae-Jin Yang Comprehensive Survey of Genetic Diversity in Chloroplast Genomes and 45S nrDNAs within Panax ginseng Species. PLoS ONE |
| title | Comprehensive Survey of Genetic Diversity in Chloroplast Genomes and 45S nrDNAs within Panax ginseng Species. |
| title_full | Comprehensive Survey of Genetic Diversity in Chloroplast Genomes and 45S nrDNAs within Panax ginseng Species. |
| title_fullStr | Comprehensive Survey of Genetic Diversity in Chloroplast Genomes and 45S nrDNAs within Panax ginseng Species. |
| title_full_unstemmed | Comprehensive Survey of Genetic Diversity in Chloroplast Genomes and 45S nrDNAs within Panax ginseng Species. |
| title_short | Comprehensive Survey of Genetic Diversity in Chloroplast Genomes and 45S nrDNAs within Panax ginseng Species. |
| title_sort | comprehensive survey of genetic diversity in chloroplast genomes and 45s nrdnas within panax ginseng species |
| url | http://europepmc.org/articles/PMC4465672?pdf=render |
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