- KOREAN
- E-ISSN2713-8615
- KCI
E-ISSN : 2713-8615
Plastid genome of Aster altaicus var. uchiyamae Kitam., an endanger species of Korean asterids
Won， Hyo-Sig
Jungho Lee
Abstract
Aster altaicus var. uchiyamae Kitam. is an endemic taxon of Korea and is protected by law as an endanger taxon. The genetic information of A. altaicus var. uchiyamae is unavailable in Genbank. Here we sequenced chloroplast genome of A. altaicus var. uchiyamae. The cp-genome of Aster altaicus var. uchiyamae was 152,446 bps in size: LSC was 84,240 bps, IR 25,005 bps, SSC 18,196 bps. The cp-genome contains 112 genes and 21 introns consisted of 79 protein coding genes (PCGs), 4 RNA genes, and 29 tRNA genes, with 20 group II introns and one group I intron. There were three pseudo-genes including ψ-ycf1, ψ-rps19, and ψ-trnT_GGU. Eighteen genes, five introns, and parts of two genes and an intron are found within the IR, which has two copies. The cp-DNA of Aster altaicus var. uchiyamae is distinguished from A. spathulifolius, only known cp-genome of the genus Aster, by 172 SNP in genic regions of 43 PCGs and 21 indels in 11 PCGs and SSU. The chloroplast genome sequence was deposited at GenBank (KX35265).
- keywords
- Aster altaicus, Asteraceae, chloroplast genome, Compositae, indel, SNP, ψ-trnT_GGU
Reference
Besendahl, A., Y.L. Qiu, J. Lee, J.D. Palmer and D. Bhattacharya. 2000. The endosymbiotic origin and vertical evolution of the plastid tRNA Leu group I intron. Curr. Genet. 37:12-23.
Chen, Y., L. Brouillet and J.C. Semple. 2008. Aster Linnaeus. Flora of China. In eFloras (2008). Published on the Internet http://www.efloras.org
Choi, K.S. and S. Park. 2015. The complete chloroplast genome sequence of Aster spathulifolius (Asteraceae);genomic features and relationship with Asteraceae. Gene 572:214-221.
Chung, G.Y. and Y.S. Kim. 1991a. A taxonomic study of pappus morphology on the genus Aster. L., and its allied groups in Korea. Kor. J. Plant Tax. 21(3):197-209.
Chung, G.Y. and Y.S. Kim. 1991b. A taxonomic study of the receptacle morphology on the genus Aster. L., and its allied groups in Korea. Kor. J. Plant Tax. 21(4):229-238.
Chung, G.Y. and Y.S. Kim. 1991c. A study on epidermal cells of the ligulate florets of the genus Aster. L., and its allied groups in Korea. Kor. J. Plant Tax. 21(4):239-250.
Chung, G.Y. and Y.S. Kim. 1993a. A study on the capitulum morphology of the genus Aster. L., and its allied taxa in Korea. Kor. J. Plant Tax. 23(3):105-118.
Chung, G.Y. and Y.S. Kim. 1993b. A taxonomic study of Korean Aster. L., and its allied taxa on the anatomical characters. Kor. J. Plant Tax. 23(3):119-130.
Conant, G.C. and K.H. Wolfe. 2008. GenomeVx: simple web-based creation of editable circular chromosome maps. Bioinformatics 24:861-862.
Dong, W., C. Xu, C. Li, J. Sun, Y. Zuo, S. Shi, T. Chang, J. Guo and S. Zhou. 2015. ycf1, the most promising plastid DNA barcode of land plants. Sientific Report 5:8348.
Fraser, K.A., L. Pachter, A. Poliakov, E.M. Rubin and I. Dubchak. 2004. VISTA: computational tools for comparative genomics. Nucleic Acids Research 32:W273-W279.
Hong, S.-Y., K.-S. Cho and K.-O. Yoo. 2012. Phylogenetic Analysis of Korean Native Aster Plants Based on Internal Transcribed Spacer (ITS) Sequences. Kor. J. Hort. Sci. Technol. 30(2):178-184.
Ito, M., A. Soejima and T. Nishino. 1994. Phylogeny and speciation of Asian Aster. Kor. J. Plant Tax. 24(3):133-143.
Ito, M., A. Soejima, M. Hasebe and K. Watanabe. 1995. A Chloroplast-DNA Phylogeny of Kalimeris and Aster, with Reference to the Generic Circumscription. J. Plant Res. 108:93-96.
Ito, M., A. Soejima and K. Watanabe. 1998. Phylogenetic Relationships of Japanese Aster (Asteraceae, Astereae)sensu lato Based on Chloroplast-DNA Restriction Site Mutations. J. Plant Res. 111:217-223.
Kitamura, S. 1937. Aster altaicus Willd., var. Uchiyamae Kitamura var. nov. Memoirs of the College of Science, Kyoto Imperial University, Series B. pp. 367-368.
Laslett, D. and B. Canback. 2004. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res. 32:11-16.
Lee, J. and J.R. Manhart. 2002a. Four embryophyte introns and psbB operon explains Chlorokybus as a basal lineage of streptophytes. Algae 17(1):53-58.
Lee, J. and J.R. Manhart. 2002b. The Chloroplast rpl23 gene cluster of Spirogyra maxima (Charophyceae) shares many similarities with the angiosperm rpl23 operon. Algae 17(1):59-68.
Lee, M., J. Park, H. Lee, S.-H. Sohn and J. Lee. 2015. Complete chloroplast genomic sequence of Citrus platymamma determined by combined analysis of Sanger and NGS data. Hortic. Environ. Biotechnol. 56(5):704-711.
Li, X., Y. Yang, R.J. Henry, M. Rosseto, Y. Wang and S. Chen. 2015. Plant DNA barcoding: from gene to genome. Biol. Rev. 90:157-166.
Lowe, T.M. and S.R. Eddy. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25:955-964.
Park, C.-W. 2007. The Genera of Vascular Plants of Korea. Academy Publishing Co., Seoul.
Park, J.H. and J. Lee. 2016. The complete plastid genome of Scopolia parviflora (Dunn.) Nakai (Solanaceae). Korean J. Pl. Taxon. 46(1):70-74.
Park, S.K., S.-J. Kwon, J. Park, M. Lee, S.Y. Won, Y.C. Kim, Y.-J. Hwang, S.-H. Sohn and J. Lee. 2015. Chloroplast genome of white wild chrysanthemum, Dendranthema sp. K247003, as genetic barcode. Journal of Species Research 4(2):152-158.
Suh, Y.B. and Y.J. Kim. 2014. Korean Red List of Threatened Species. 2nd ed. National Institute of Biological Resources, Korea.
Timme, R.E., V.K. Jennifer, L.B. Jefferey and K.J. Robert. 2007. A comparative analysis of the Lactuca and Helianthus (Asteraceae) plastid genomes: Identification of divergent regions and categorization of shared repeats. American Journal of Botany 94(3):302-312.
Wyman, S.K., R.K. Jansen and J.L. Boore. 2004. Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20:3252-3255.
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