Journal of Species Research

The National Institute of Biological Resources (국립생물자원관)
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Chloroplast genome of white wild chrysanthemum, Dendranthema sp. K247003, as genetic barcode

  • Park, Sang Kun (Floriculture Research Division, National Institute of Horticultural and Herbal Science (NIHHS), RDA) ;
  • Kwon, Soo-Jin (Genomics Division, National Academy of Agricultural Science (NAAS), RDA) ;
  • Park, Jihye (Green Plant Institute, B-301, Heungdeok IT Valley) ;
  • Lee, Minjee (Green Plant Institute, B-301, Heungdeok IT Valley) ;
  • Won, So Youn (Genomics Division, National Academy of Agricultural Science (NAAS), RDA) ;
  • Kim, Young Chul (Korea Botanic Garden) ;
  • Hwang, Yoon-Jung (Department of Life Science, Sahmyook University) ;
  • Sohn, Seong-Han (Genomics Division, National Academy of Agricultural Science (NAAS), RDA) ;
  • Lee, Jungho (Green Plant Institute, B-301, Heungdeok IT Valley)
  • Received : 2015.07.01
  • Accepted : 2015.07.27
  • Published : 2015.08.30
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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.

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References

  1. 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. https://doi.org/10.1007/s002940050002
  2. Bock, D.G., N.C. Kane, D.P. Ebert and L.H. Rieseberg. 2014. Genome skimming reveals the origin of the Jerusalem Artichoke tuber crop species: neither from Jerusalem nor an artichoke. New Phytol. 201(3):1021-1030. https://doi.org/10.1111/nph.12560
  3. Conant, G.C. and K.H. Wolfe. 2008. GenomeVx: simple webbased creation of editable circular chromosome maps. Bioinformatics 24:861-862. https://doi.org/10.1093/bioinformatics/btm598
  4. Dempewolf, H., N.C. Kane, K.L. Ostevik, M. Geleta, M.S. Barker, Z. Lai, M.L. Stewart, E. Bekele, J.M.M. Engels, Q. Cronk and L.H. Rieseberrg. 2010. 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):1048-1058. https://doi.org/10.1111/j.1755-0998.2010.02859.x
  5. 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. https://doi.org/10.1038/srep08348
  6. Doorduin, L., B. Gravendeel, Y. Lammers, Y. Ariyurek, T. Chin-A-Woeng and K. Vrieling. 2011. 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):93-105. https://doi.org/10.1093/dnares/dsr002
  7. 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. https://doi.org/10.1093/nar/gkh458
  8. Hwang, Y.-J., A. Younis, K.B. Ryu, K.-B. Lim, C.-H. Eun, J. Lee, S.-H. Sohn and S.-J. Kwon. 2014. Karyomorphological Analysis of Wild Chrysanthemum boreale Collected from Four Natural Habitats in Korea. Flower Res. J. 21(4):182-189.
  9. Jeong, H., J.M. Lim, J. Park, Y.M. Sim, H.G. Choi, J. Lee and W.J. Jeong. 2014. Plastid and mitochondrion genomic sequences from Arctic Chlorella sp. ArM0029B. BMC Genomics 15:286-299. https://doi.org/10.1186/1471-2164-15-286
  10. 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. https://doi.org/10.1093/nar/gkh152
  11. Lee, J. 1997. Gene clusters and introns of Spirogyra maxima chloroplast and other charophytes and their phylogenetic implications in green plants. Texas A&M University Ph.D. Thesis.
  12. 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. https://doi.org/10.4490/ALGAE.2002.17.1.053
  13. 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. https://doi.org/10.4490/ALGAE.2002.17.1.059
  14. 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. https://doi.org/10.1111/brv.12104
  15. Liu, P.-L., Q. Wan, Y.-P. Guo, J. Yang and G.-Y. Rao. 2012. Phylogeny of the Genus Chrysanthemum L.: Evidence from Single-Copy Nuclear Gene and Chloroplast DNA Sequences. PLoS One 7(11):e48970. https://doi.org/10.1371/journal.pone.0048970
  16. Liu, Y., N. Huo, L. Dong, Y. Wang, S. Zhang, H.A. Young, X. Feng and Y.Q. Gu. 2013. Complete Chloroplast Genome Sequences of Mongolia Medicine Artemisia frigida and Phylogenetic Relationships with Other Plants. PLoS One 8(2):e57533. https://doi.org/10.1371/journal.pone.0057533
  17. 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. https://doi.org/10.1093/nar/25.5.0955
  18. Nie, X., S. Lv, Y. Zhang, X. Du, L. Wang, S.S. Biradar, X. Tan, F. Wan and S. Weining. 2012. Complete chloroplast genome sequence of a major invasive species, crofton weed (Ageratina adenophora). PLoS One 7(5):e36869. https://doi.org/10.1371/journal.pone.0036869
  19. Nock, C.J., D.L. Waters, M.A. Edward, S.G. Bowen, N. Rice, G.M. Cordeiro and R.J. Henry. 2011. Chloroplast genome sequences from total DNA for plant identification. Plant Biotechnol. J. 9(3):328-333. https://doi.org/10.1111/j.1467-7652.2010.00558.x
  20. Park, C.-W. 2007. The Genera of Vascular Plants of Korea. Academy Publishing Co., Seoul.
  21. Park, J.-H. 2007. Dendranthema (DC.) Des Moul., Actes. Linn. Bordeaux 20: 561, 1855. In: C.-W. Park (ed.), The Genera of Vascular Plants of Korea. Academy Publishing Co., Seoul. pp. 1024-1026.
  22. Shaw, J., B.L. Edgar, E.S. Edward and L.S. Randall. 2007. 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):275-288. https://doi.org/10.3732/ajb.94.3.275
  23. 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. https://doi.org/10.3732/ajb.94.3.302
  24. Walker, J.F., M.J. Zanis and N.C. Emery. 2014. Comparative analysis of complete chloroplast genome sequence and inversion variation in Lasthenia burkei (Madieae, Asteraceae). Am. J. Bot. 101(4):722-729. https://doi.org/10.3732/ajb.1400049
  25. Wyman, S.K., R.K. Jansen and J.L. Boore. 2004. Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20:3252-3255. https://doi.org/10.1093/bioinformatics/bth352