Chloroplast genome of white wild chrysanthemum, Dendranthema sp. K247003, as genetic barcode
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초록
Dendranthema boreale and D. indicum are easily distinguished from other Korean Dendranthema spp. by having yellow flowers. We have found a putative new taxon of Dendranthema having white flowers, except for sharing most characters with Dendranthema boreale. The chloroplast (cp) genome of the putative new taxon of Dendranthema, Dendranthema sp. K247003, registered in National Agro-Biodiversity Center (ABC), was completely characterized as a genetic barcode. The cp-genome of Dendranthema sp. K247003 was 151,175-bp in size: LSC was 82,886-bp, IR 24,971-bp, SSC 18,347-bp. The cp-genome of Dendranthema sp. K247003 contains 113 genes and 21 introns consisted of 79 protein coding genes, 4 RNA genes, and 30 tRNA genes, with 20 group II introns and one group I intron. Some of the genes and there introns were duplicated in IR. The cp-DNA of Dendranthema sp. K247003 is distinguished from that of D. boreale IT121002 by 67 SNPs in genic regions of 24 protein coding genes and by a 9-bp INDEL in ycf1. Further cp-DNA study will give us better information on genetic markers of Dendranthema species.
Abstract
Dendranthema boreale and D. indicum are easily distinguished from other Korean Dendranthema spp. by having yellow flowers. We have found a putative new taxon of Dendranthema having white flowers, except for sharing most characters with Dendranthema boreale. The chloroplast (cp) genome of the putative new taxon of Dendranthema, Dendranthema sp. K247003, registered in National Agro-Biodiversity Center (ABC), was completely characterized as a genetic barcode. The cp-genome of Dendranthema sp. K247003 was 151,175-bp in size: LSC was 82,886-bp, IR 24,971-bp, SSC 18,347-bp. The cp-genome of Dendranthema sp. K247003 contains 113 genes and 21 introns consisted of 79 protein coding genes, 4 RNA genes, and 30 tRNA genes, with 20 group II introns and one group I intron. Some of the genes and there introns were duplicated in IR. The cp-DNA of Dendranthema sp. K247003 is distinguished from that of D. boreale IT121002 by 67 SNPs in genic regions of 24 protein coding genes and by a 9-bp INDEL in ycf1. Further cp-DNA study will give us better information on genetic markers of Dendranthema species.
참고문헌 (25)
- Besendahl, A., "The endosymbiotic origin and vertical evolution of the plastid tRNA Leu group I intron", Curr. Genet, 37, pp.12~23 (2000)
- Bock, D.G., "Genome skimming reveals the origin of the Jerusalem Artichoke tuber crop species: neither from Jerusalem nor an artichoke", New Phytol, 201(3), pp.1021~1030 (2014)
- Conant, G.C., "GenomeVx: simple webbased creation of editable circular chromosome maps", Bioinformatics, 24, pp.861~862 (2008)
- Dempewolf, H., "Establishing genomic tools and resources for Guizotia abyssinica (L.f.)Cass.-the development of a library of expressed sequence tags, microsatellite loci, and the sequencing of its chloroplast genome", Mol. Ecol. Resour, 10(6), pp.1048~1058 (2010)
- Dong, W., "ycf1, the most promising plastid DNA barcode of land plants", Sientific Report, 5, pp.8348~ (2015)
- Doorduin, L., "The Complete Chloroplast Genome of 17 Individuals of Pest Species Jacobaea vulgaris: SNPs, Microsatellites and Barcoding Markers for Population and Phylogenetic Studies", DNA Res, 18(2), pp.93~105 (2011)
- Fraser, K.A., "VISTA: computational tools for comparative genomics", Nucleic Acids Research, 32, pp.W273~W279 (2004)
- 황윤정, "Karyomorphological Analysis of Wild Chrysanthemum boreale Collected from Four Natural Habitats in Korea", 화훼연구, 21(4), pp.182~189 (2013), 한국화훼학회[DOI]
- Jeong, H., "Plastid and mitochondrion genomic sequences from Arctic Chlorella sp. ArM0029B", BMC Genomics, 15, pp.286~299 (2014)
- Laslett, D., "ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences", Nucleic Acids Res, 32, pp.11~16 (2004)
- Lee, J., "Gene clusters and introns of Spirogyra maxima chloroplast and other charophytes and their phylogenetic implications in green plants", 박사, pp.1997
- 이정호, "Four Embryophyte Introns and psbB Operon Indicate Chlorokybus as a Basal Streptophyte Lineage", ALGAE, 17(1), pp.53~58 (2002), 한국조류학회I
- 이정호, "The Chloroplast rpl23 Gene Cluster of Spirogyra maxima (Charophyceae) Shares Many Similarities with the Angiosperm rpl23 Operon", ALGAE, 17(1), pp.59~68 (2002), 한국조류학회I
- Li, X., "Plant DNA barcoding: from gene to genome", Biol. Rev, 90, pp.157~166 (2015)
- Liu, P.-L., "Phylogeny of the Genus Chrysanthemum L.: Evidence from Single-Copy Nuclear Gene and Chloroplast DNA Sequences", PLoS One, 7(11), pp.e48970~ (2012)
- Liu, Y., "Complete Chloroplast Genome Sequences of Mongolia Medicine Artemisia frigida and Phylogenetic Relationships with Other Plants", PLoS One, 8(2), pp.e57533~ (2013)
- Lowe, T.M., "tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence", Nucleic Acids Res, 25, pp.955~964 (1997)
- Nie, X., "Complete chloroplast genome sequence of a major invasive species, crofton weed (Ageratina adenophora)", PLoS One, 7(5), pp.e36869~ (2012)
- Nock, C.J., "Chloroplast genome sequences from total DNA for plant identification", Plant Biotechnol. J, 9(3), pp.328~333 (2011)
- Park, C.-W., "The Genera of Vascular Plants of Korea" (2007), Academy Publishing Co
- Park, J.-H., "The Genera of Vascular Plants of Korea", pp.1024~1026 (2007), Academy Publishing Co
- Shaw, J., "Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: The tortoise and the hare III", American Journal of Botany, 94(3), pp.275~288 (2007)
- Timme, R.E., "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), pp.302~312 (2007)
- Walker, J.F., "Comparative analysis of complete chloroplast genome sequence and inversion variation in Lasthenia burkei (Madieae, Asteraceae)", Am. J. Bot, 101(4), pp.722~729 (2014)
- Wyman, S.K., "Automatic annotation of organellar genomes with DOGMA", Bioinformatics, 20, pp.3252~3255 (2004)
