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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.


Related in: MedlinePlus

Validation of copy number variation (CNV) of TRs in rps16 ~ trnUUG region.(A) Schematic diagram of CNV of TR units among 11 P. ginseng cultivars and P. quinquefolius. Arrowheads and polygons indicate TR units of 13 bp and 33 bp, respectively. P. ginseng cv. SH and P. ginseng other cvs. indicate cultivar Sunhyang and the remaining 11 accessions listed in Table 1 and P. quinquefolius. (B) PCR analysis of CNV regions using 097f2*r primer set in 11 P. ginseng cultivars and P. quinquefolius. Abbreviated cultivar names (defined in Table 1) are denoted on the gel. PQ and M denote P. quinquefolius and 100-bp DNA ladder, respectively.
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pone.0117159.g004: Validation of copy number variation (CNV) of TRs in rps16 ~ trnUUG region.(A) Schematic diagram of CNV of TR units among 11 P. ginseng cultivars and P. quinquefolius. Arrowheads and polygons indicate TR units of 13 bp and 33 bp, respectively. P. ginseng cv. SH and P. ginseng other cvs. indicate cultivar Sunhyang and the remaining 11 accessions listed in Table 1 and P. quinquefolius. (B) PCR analysis of CNV regions using 097f2*r primer set in 11 P. ginseng cultivars and P. quinquefolius. Abbreviated cultivar names (defined in Table 1) are denoted on the gel. PQ and M denote P. quinquefolius and 100-bp DNA ladder, respectively.

Mentions: We identified 118 tandem repeats (TRs) (6-57bp) in cp genome sequences of 11 P. ginseng cultivars. Copy number variation of various TRs played major role in InDel polymorphism. Three of four cultivar-unique polymorphic InDel regions were derived from copy number variations among cultivars. One InDel at intergenic regions of rps16-trnUUG derived from copy number variance of two kinds of TRs, 13 bp and 33 bp TRs, was identified in one Korean inbred cultivar ‘Sunhyang’ and P. quinquefolius. PCR analysis for the target with pgcp097f2*r showed the expected band size differences, with unique bands in ginseng cultivar Sunhyang and P. quinquifolius (Fig 4A and 4B). A 13-bp TR-based InDel marker, 139f*r2, derived from rpl32-trnUAG clearly distinguished Chunpoong from other ginseng cultivars (Tables 2 and 3). The 57-bp TR-based InDel marker pgycf1f*r derived from the ycf1 gene clearly distinguished Chunpoong and Hwangsook from other P. ginseng Korean cultivars as well as P. quinquefolius (Fig 5A). Meanwhile, one 59-bp unique inserted sequence was identified at trnUUC-trnGGU in cultivar Sunhyang among all 14 accessions (Fig 5B).


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)

Validation of copy number variation (CNV) of TRs in rps16 ~ trnUUG region.(A) Schematic diagram of CNV of TR units among 11 P. ginseng cultivars and P. quinquefolius. Arrowheads and polygons indicate TR units of 13 bp and 33 bp, respectively. P. ginseng cv. SH and P. ginseng other cvs. indicate cultivar Sunhyang and the remaining 11 accessions listed in Table 1 and P. quinquefolius. (B) PCR analysis of CNV regions using 097f2*r primer set in 11 P. ginseng cultivars and P. quinquefolius. Abbreviated cultivar names (defined in Table 1) are denoted on the gel. PQ and M denote P. quinquefolius and 100-bp DNA ladder, respectively.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0117159.g004: Validation of copy number variation (CNV) of TRs in rps16 ~ trnUUG region.(A) Schematic diagram of CNV of TR units among 11 P. ginseng cultivars and P. quinquefolius. Arrowheads and polygons indicate TR units of 13 bp and 33 bp, respectively. P. ginseng cv. SH and P. ginseng other cvs. indicate cultivar Sunhyang and the remaining 11 accessions listed in Table 1 and P. quinquefolius. (B) PCR analysis of CNV regions using 097f2*r primer set in 11 P. ginseng cultivars and P. quinquefolius. Abbreviated cultivar names (defined in Table 1) are denoted on the gel. PQ and M denote P. quinquefolius and 100-bp DNA ladder, respectively.
Mentions: We identified 118 tandem repeats (TRs) (6-57bp) in cp genome sequences of 11 P. ginseng cultivars. Copy number variation of various TRs played major role in InDel polymorphism. Three of four cultivar-unique polymorphic InDel regions were derived from copy number variations among cultivars. One InDel at intergenic regions of rps16-trnUUG derived from copy number variance of two kinds of TRs, 13 bp and 33 bp TRs, was identified in one Korean inbred cultivar ‘Sunhyang’ and P. quinquefolius. PCR analysis for the target with pgcp097f2*r showed the expected band size differences, with unique bands in ginseng cultivar Sunhyang and P. quinquifolius (Fig 4A and 4B). A 13-bp TR-based InDel marker, 139f*r2, derived from rpl32-trnUAG clearly distinguished Chunpoong from other ginseng cultivars (Tables 2 and 3). The 57-bp TR-based InDel marker pgycf1f*r derived from the ycf1 gene clearly distinguished Chunpoong and Hwangsook from other P. ginseng Korean cultivars as well as P. quinquefolius (Fig 5A). Meanwhile, one 59-bp unique inserted sequence was identified at trnUUC-trnGGU in cultivar Sunhyang among all 14 accessions (Fig 5B).

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.


Related in: MedlinePlus