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

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.

The complete chloroplast genome ofSolanum berthaultii, one of the potato wild relative species

“…An Illumina paired-end (PE) genomic library was constructed with total genomic DNA according to the PE standard protocol (Illumina, San Diego, CA) and sequenced using an Illumina HiSeq2000 at Macrogen (http://www.macrogen.com/kor/). Low-quality bases with raw scores of 20 or less were removed and then approximately 2.5 Gbp of high-quality of PE reads were assembled by a CLC genome assembler (CLC Inc, Rarhus, Denmark) (Kim et al 2015). The principal contigs representing the chloroplast genome were retrieved from the total contigs using Nucmer (Kurtz et al 2004) with the chloroplast genome sequence of S. tuberosum (KM489056) as the reference sequence ).…”

The complete chloroplast genome sequence of Ligularia fischeri (Ledeb.) Turcz. (Asteraceae)

“…A pair-end (PE) library was constructed and sequenced using an Illumina MiSeq platform by Lab Genomics, Inc. (Seongnam, Korea). Approximately 1.01 Gb of sequencing data were obtained, and de novo assembled by a CLC genome assembler (v. beta 4.6, CLC Inc., Rarhus, Denmark), as reported in Kim et al (2015aKim et al ( , 2015b. Compared with the chloroplast sequence of Artemisia frigida (NC_020607) as a reference, eight representative chloroplast contigs were selected and joined into a single draft sequence.…”

The complete chloroplast genome of Korean popular Citrus hybrid Hallabong mandarin [(Citrus unshiu×C. sinensis)×C. reticulate] (Rutaceae)

“…PE reads of 3 Gb were obtained and assembled by a CLC genome assembler (ver. 4.06 beta, CLC Inc, Aarhus, Denmark), as mentioned in Kim et al (2015aKim et al ( , 2015b. The representative chloroplast contigs were collected, ordered and merged into a single draft sequence, through comparison with the chloroplast sequence of C. sinensis (DQ864733, Bausher et al 2006) as a reference.…”