Complete Chloroplast Genome Sequences from Korean Ginseng (Panax schinseng Nees) and Comparative Analysis of Sequence Evolution among 17 Vascular Plants

Abstract

The nucleotide sequence of Korean ginseng (Panax schinseng Nees) chloroplast genome has been completed (AY582139). The circular double-stranded DNA, which consists of 156,318 bp, contains a pair of inverted repeat regions (IRa and IRb) with 26,071 bp each, which are separated by small and large single copy regions of 86,106 bp and 18,070 bp, respectively. The inverted repeat region is further extended into a large single copy region which includes the 5' parts of the rpsl9 gene. Four short inversions associated with short palindromic sequences that form stem-loop structures were also observed in the chloroplast genome of P. schinseng compared to that of Nicotiana tabacum. The genome content and the relative positions of 114 genes (75 peptide-encoding genes, 30 tRNA genes, 4 rRNA genes, and 5 conserved open reading frames [ycfs]), however, are identical with the chloroplast DNA of N. tabacum. Sixteen genes contain one intron while two genes have two introns. Of these introns, only one (trnL-UAA) belongs to the self-splicing group I; all remaining introns have the characteristics of six domains belonging to group II. Eighteen simple sequence repeats have been identified from the chloroplast genome of Korean ginseng. Several of these SSR loci show infra-specific variations. A detailed comparison of 17 known completed chloroplast genomes from the vascular plants allowed the identification of evolutionary modes of coding segments and intron sequences, as well as the evaluation of the phylogenetic utilities of chloroplast genes. Furthermore, through the detailed comparisons of several chloroplast genomes, evolutionary hotspots predominated by the inversion end points, indel mutation events, and high frequencies of base substitutions were identified. Large-sized indels were often associated with direct repeats at the end of the sequences facilitating intra-molecular recombination.

Complete plastid genome sequences of Abeliophyllum distichum Nakai (Oleaceae), a Korea endemic genus

“…The organization, size and gene content of A. distichum plastome was similar to most angiosperm plastome (Kim & Lee 2004;Kim et al 2009). The plastome of A. distichum was 155,982 bp in length, including a large single copy (LSC) region of 86,742 bp and a small single copy (SSC) region of 17,834 bp separated by two IR regions of 25,703 bp, respectively (NCBI acc.…”

Phylogenetic utility of ycf1 in orchids: a plastid gene more variable than matK

“…4 ), there are no distinct regions of hypervariability such as those seen in ITS (Baldwin et al 1995 ;Whitten et al 2000 ). In Panax , ycf 1 exhibits relatively long indels associated with short direct repeats (Kim and Lee 2004 ) resulting from illegitimate recombination events that have been observed in several plastid genomes (Ogihara et al 1988 ;Milligan et al 1989 ;Shimada and Sugiura 1989 ). Many indels were found in ycf 1 of orchids, but they were dissimilar in that the indels were usually relatively short repeats of adjacent nucleotides.…”

The complete plastome sequence of Pentactina rupicola Nakai (Rosaceae), a genus endemic to Korea

“…The structure, gene content, gene order, and AT content of the P. rupicola plastome are similar to those of a typical angiosperm plastome (Kim & Lee 2004;Kim et al 2009). The P. rupicola plastome is 156,612 bp in length, including a large singlecopy (LSC) region of 84,970 bp and a small single-copy (SSC) region of 18,940 bp separated by two inverted repeat (IR) regions, each of 26,351 bp (NCBI acc.…”

“…A combination of short-and long-range PCRs and continuous sequencing of PCR products using primer walking was utilized for whole plastome sequencing. The amplification primers were designed on the basis of the plastomes of Nicotiana, Panax, and Morus (Kim & Lee 2004;Yukawa et al 2005;Ravi et al 2006). The PCR products were purified using the MEGAquick-spin kit (iNtRON, Seoul, Korea), and the cleaned products were sequenced using a series of primers oriented in both directions at intervals of 300-800 bp, using an ABI 3730XL automatic sequencer.…”