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Comprehensive Survey of Genetic Diversity in Chloroplast Genomes and 45S nrDNAs within Panax ginseng Species.

Kim K, Lee SC, Lee J, Lee HO, Joh HJ, Kim NH, Park HS, Yang TJ - PLoS ONE (2015)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea; Phyzen Genomics Institute, 501-1, Gwanak Century Tower, Gwanak-gu, Seoul, 151-836, Republic of Korea.

ABSTRACT
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.

No MeSH data available.


Assembly of complete 45S nrDNA unit.Schematic diagram of a representative complete 45S nrDNA. N indicates gap present in some IGS sequence of nine 45S nrDNAs except Chunpoong and Yunpoong. Polymorphic SNP sites are denoted as arrowheads. (1), (3), (4), and (5) are polymorphic sites among 11 P. ginseng cultivars and (2) is a heterogeneous site with co-appearance of G and C in P. ginseng cv. Gumpoong and Gopoong. Mapping of Gumpoong cultivar 11,067 bp raw reads on the 45S nrDNA sequence of Gumpoong. (Accession no. KM207667) GC contents for each region of 45S nrDNA sequence. GC contents were calculated from the GC composition in 100-bp sliding windows.
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pone.0117159.g003: Assembly of complete 45S nrDNA unit.Schematic diagram of a representative complete 45S nrDNA. N indicates gap present in some IGS sequence of nine 45S nrDNAs except Chunpoong and Yunpoong. Polymorphic SNP sites are denoted as arrowheads. (1), (3), (4), and (5) are polymorphic sites among 11 P. ginseng cultivars and (2) is a heterogeneous site with co-appearance of G and C in P. ginseng cv. Gumpoong and Gopoong. Mapping of Gumpoong cultivar 11,067 bp raw reads on the 45S nrDNA sequence of Gumpoong. (Accession no. KM207667) GC contents for each region of 45S nrDNA sequence. GC contents were calculated from the GC composition in 100-bp sliding windows.

Mentions: The 45S nrDNA unit sequences were highly homogeneous among the 11 Korean P. ginseng cultivars sequenced in this study (Table 1) with 10,095~11,091 bp single units (GenBank accession numbers for the 45S nrDNA of the cultivars are displayed in Table 1). We did not include the three Chinese collections in this analysis because of the lack of reported 45S nrDNA sequences. Some cultivars have a nucleotide gap in an IGS region that has high GC composition and lower WGS read depth (Fig 3). Comparison of 45S nrDNA sequences revealed five SNPs, one in the 5.8S rRNA region, three in IGS sequence, and one in 26S rRNA coding sequence that was heterogeneous, with co-appearance of G and C in cultivars Gumpoong and Gopoong (Table 2). Three SNPs were identified in both Gumpoong and Gopoong, and one SNP was unique to cultivar Sunpoong (Table 2). Large repeat sequences with 3.5 copies of 641-bp sub-repeat elements were identified in IGS regions of all 11 accessions.


Comprehensive Survey of Genetic Diversity in Chloroplast Genomes and 45S nrDNAs within Panax ginseng Species.

Kim K, Lee SC, Lee J, Lee HO, Joh HJ, Kim NH, Park HS, Yang TJ - PLoS ONE (2015)

Assembly of complete 45S nrDNA unit.Schematic diagram of a representative complete 45S nrDNA. N indicates gap present in some IGS sequence of nine 45S nrDNAs except Chunpoong and Yunpoong. Polymorphic SNP sites are denoted as arrowheads. (1), (3), (4), and (5) are polymorphic sites among 11 P. ginseng cultivars and (2) is a heterogeneous site with co-appearance of G and C in P. ginseng cv. Gumpoong and Gopoong. Mapping of Gumpoong cultivar 11,067 bp raw reads on the 45S nrDNA sequence of Gumpoong. (Accession no. KM207667) GC contents for each region of 45S nrDNA sequence. GC contents were calculated from the GC composition in 100-bp sliding windows.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4465672&req=5

pone.0117159.g003: Assembly of complete 45S nrDNA unit.Schematic diagram of a representative complete 45S nrDNA. N indicates gap present in some IGS sequence of nine 45S nrDNAs except Chunpoong and Yunpoong. Polymorphic SNP sites are denoted as arrowheads. (1), (3), (4), and (5) are polymorphic sites among 11 P. ginseng cultivars and (2) is a heterogeneous site with co-appearance of G and C in P. ginseng cv. Gumpoong and Gopoong. Mapping of Gumpoong cultivar 11,067 bp raw reads on the 45S nrDNA sequence of Gumpoong. (Accession no. KM207667) GC contents for each region of 45S nrDNA sequence. GC contents were calculated from the GC composition in 100-bp sliding windows.
Mentions: The 45S nrDNA unit sequences were highly homogeneous among the 11 Korean P. ginseng cultivars sequenced in this study (Table 1) with 10,095~11,091 bp single units (GenBank accession numbers for the 45S nrDNA of the cultivars are displayed in Table 1). We did not include the three Chinese collections in this analysis because of the lack of reported 45S nrDNA sequences. Some cultivars have a nucleotide gap in an IGS region that has high GC composition and lower WGS read depth (Fig 3). Comparison of 45S nrDNA sequences revealed five SNPs, one in the 5.8S rRNA region, three in IGS sequence, and one in 26S rRNA coding sequence that was heterogeneous, with co-appearance of G and C in cultivars Gumpoong and Gopoong (Table 2). Three SNPs were identified in both Gumpoong and Gopoong, and one SNP was unique to cultivar Sunpoong (Table 2). Large repeat sequences with 3.5 copies of 641-bp sub-repeat elements were identified in IGS regions of all 11 accessions.

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea; Phyzen Genomics Institute, 501-1, Gwanak Century Tower, Gwanak-gu, Seoul, 151-836, Republic of Korea.

ABSTRACT
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.

No MeSH data available.