Mol. Cells 2009; 27(3): 365-381
Published online March 19, 2009
https://doi.org/10.1007/s10059-009-0047-6
© The Korean Society for Molecular and Cellular Biology
The chloroplast DNA sequences of Megaleranthis saniculifolia, an endemic and monotypic endangered plant species, were completed in this study (GenBank FJ597983). The genome is 159,924 bp in length. It harbors a pair of IR regions consisting of 26,608 bp each. The lengths of the LSC and SSC regions are 88,326 bp and 18,382 bp, respectively. The structural organizations, gene and intron contents, gene orders, AT contents, codon usages, and transcription units of the Megaleranthis chloroplast genome are similar to those of typical land plant cp DNAs. However, the detailed features of Megaleranthis chloroplast genomes are substantially different from that of Ranunculus, which belongs to the same family, the Ranunculaceae. First, the Megaleranthis cp DNA was 4,797 bp longer than that of Ranunculus due to an expanded IR region into the SSC region and duplicated sequence elements in several spacer regions of the Megaleranthis cp genome. Second, the chloroplast genomes of Megaleranthis and Ranuncu-lus evidence 5.6% sequence divergence in the coding regions, 8.9% sequence divergence in the intron regions, and 18.7% sequence divergence in the intergenic spacer regions, respectively. In both the coding and noncoding regions, average nucleotide substitution rates differed markedly, depending on the genome position. Our data strongly implicate the positional effects of the evolutionary modes of chloroplast genes. The genes evidencing higher levels of base substitutions also have higher incidences of indel mutations and low Ka/Ks ratios. A total of 54 simple sequence repeat loci were identified from the Megaleranthis cp genome. The existence of rich cp SSR loci in the Megaleranthis cp genome provides a rare opportunity to study the population genetic structures of this endangered species. Our phylogenetic trees based on the two independent markers, the nuclear ITS and chloroplast matK sequences, strongly support the inclusion of the Megale-ranthis to the Trollius. Therefore, our molecular trees support Ohwi’s original treatment of Megaleranthis saniculifolia to Trollius chosenensis Ohwi.
Keywords base substitution rate, chloroplast genome, endangered genus in Korea, indel mutation, Megalreanthis, phylogeny, positional effect, simple sequence repeat, Trollius
Mol. Cells 2009; 27(3): 365-381
Published online March 31, 2009 https://doi.org/10.1007/s10059-009-0047-6
Copyright © The Korean Society for Molecular and Cellular Biology.
Young-Kyu Kim, Chong-wook Park, and Ki-Joong Kim
The chloroplast DNA sequences of Megaleranthis saniculifolia, an endemic and monotypic endangered plant species, were completed in this study (GenBank FJ597983). The genome is 159,924 bp in length. It harbors a pair of IR regions consisting of 26,608 bp each. The lengths of the LSC and SSC regions are 88,326 bp and 18,382 bp, respectively. The structural organizations, gene and intron contents, gene orders, AT contents, codon usages, and transcription units of the Megaleranthis chloroplast genome are similar to those of typical land plant cp DNAs. However, the detailed features of Megaleranthis chloroplast genomes are substantially different from that of Ranunculus, which belongs to the same family, the Ranunculaceae. First, the Megaleranthis cp DNA was 4,797 bp longer than that of Ranunculus due to an expanded IR region into the SSC region and duplicated sequence elements in several spacer regions of the Megaleranthis cp genome. Second, the chloroplast genomes of Megaleranthis and Ranuncu-lus evidence 5.6% sequence divergence in the coding regions, 8.9% sequence divergence in the intron regions, and 18.7% sequence divergence in the intergenic spacer regions, respectively. In both the coding and noncoding regions, average nucleotide substitution rates differed markedly, depending on the genome position. Our data strongly implicate the positional effects of the evolutionary modes of chloroplast genes. The genes evidencing higher levels of base substitutions also have higher incidences of indel mutations and low Ka/Ks ratios. A total of 54 simple sequence repeat loci were identified from the Megaleranthis cp genome. The existence of rich cp SSR loci in the Megaleranthis cp genome provides a rare opportunity to study the population genetic structures of this endangered species. Our phylogenetic trees based on the two independent markers, the nuclear ITS and chloroplast matK sequences, strongly support the inclusion of the Megale-ranthis to the Trollius. Therefore, our molecular trees support Ohwi’s original treatment of Megaleranthis saniculifolia to Trollius chosenensis Ohwi.
Keywords: base substitution rate, chloroplast genome, endangered genus in Korea, indel mutation, Megalreanthis, phylogeny, positional effect, simple sequence repeat, Trollius
Dong-Keun Yi, Hae-Lim Lee, Byung-Yun Sun, Mi Yoon Chung, and Ki-Joong Kim*
Mol. Cells 2012; 33(5): 497-508 https://doi.org/10.1007/s10059-012-2281-6Hyun A Kim, Ah-Young Shin, Min-Seon Lee, Hee-Jeong Lee, Heung-Ryul Lee, Jongmoon Ahn, Seokhyeon Nahm, Sung-Hwan Jo, Jeong Mee Park, and Suk-Yoon Kwon
Mol. Cells 2016; 39(2): 141-148 https://doi.org/10.14348/molcells.2016.2264Hyejung Lee, Woogeun Song, Hae-Ryun Kwak, Jae-deok Kim, Jungan Park, Chung-Kyoon Auh, Dae-Hyun Kim, Kyeong-yeoll Lee, Sukchan Lee*, and Hong-Soo Choi*
Mol. Cells 2010; 30(5): 467-476 https://doi.org/10.1007/s10059-010-0143-7