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Comparative Analysis of Chloroplast Genome of Dysphania ambrosioides (L.) Mosyakin & Clemants Understanding Phylogenetic Relationship in Genus Dysphania R. Br.

박종선|정영재|김용성
한국자원식물학회 (The Plant Resources Society Of Korea)|2019.12|한국자원식물학회지 (Korean Journal of Plant Reources.)|제32권 제6호|pp. 644-668

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참고문헌

키워드

Comparative analysisChloroplastPhylogenetic analysisSimple sequence repeatDysphania ambrosioidesNucleotide diversity

초록

Dysphania ambrosioides (L.) Mosyakin & Clemants which belongs to Chenopodiaceae/Amaranthaceae sensu in APG system has been known as a useful plant in various fields as well as an invasive species spreading all over the world. To understand its phylogenetic relationship with neighbour species, we completed chloroplast genome of D. ambrosioides collected in Korea. Its length is 151,689 bp consisting of four sub-regions: 83,421 bp of large single copy (LSC) and 18,062 bp of small single copy (SSC) regions are separated by 25,103 bp of inverted repeat (IR) regions. 128 genes (84 protein-coding genes, eight rRNAs, and 36 tRNAs) were annotated. The overall GC content of the chloroplast genome is 36.9% and those in the LSC, SSC and IR regions are 34.9%, 30.3%, and 42.7%, respectively. Distribution of simple sequence repeats are similar to those of the other two Dysphania chloroplasts; however, different features can be utilized for population genetics. Nucleotide diversity of Dysphania chloroplast genomes 18 genes including two ribosomal RNAs contains high nucleotide diversity peaks, which may be genus or species-specific manner. Phylogenetic tree presents that D.ambrosioides occupied a basal position in genus Dysphania and phylogenetic relation of tribe level is presented clearly with complete chloroplast genomes.

Abstract

Dysphania ambrosioides (L.) Mosyakin & Clemants which belongs to Chenopodiaceae/Amaranthaceae sensu in APG system has been known as a useful plant in various fields as well as an invasive species spreading all over the world. To understand its phylogenetic relationship with neighbour species, we completed chloroplast genome of D. ambrosioides collected in Korea. Its length is 151,689 bp consisting of four sub-regions: 83,421 bp of large single copy (LSC) and 18,062 bp of small single copy (SSC) regions are separated by 25,103 bp of inverted repeat (IR) regions. 128 genes (84 protein-coding genes, eight rRNAs, and 36 tRNAs) were annotated. The overall GC content of the chloroplast genome is 36.9% and those in the LSC, SSC and IR regions are 34.9%, 30.3%, and 42.7%, respectively. Distribution of simple sequence repeats are similar to those of the other two Dysphania chloroplasts; however, different features can be utilized for population genetics. Nucleotide diversity of Dysphania chloroplast genomes 18 genes including two ribosomal RNAs contains high nucleotide diversity peaks, which may be genus or species-specific manner. Phylogenetic tree presents that D.ambrosioides occupied a basal position in genus Dysphania and phylogenetic relation of tribe level is presented clearly with complete chloroplast genomes.

참고문헌 (85)

  1. Albuquerque, U. P., "Medicinal and Aromatic Plants of South America" (2018), Springer
  2. Aravindhan, V., "Diversity of invasive plant species in boluvampatti forest range, the southern Western Ghats, India", Am Eurasian J Agric Environ Sci, 14(8), pp.724~731 (2014)
  3. Asaf, S., "Complete chloroplast genome of Nicotiana otophora and its comparison with related species", Front. Plant Sci, 7, pp.843~ (2016)
  4. Balogh, L., "Plant Invasions: Ecological threats and management solutions", pp.131~146 (2003), Backhuys Publishers
  5. Bammou, L., "Corrosion inhibition of steel in sulfuric acidic solution by the Chenopodium Ambrosioides Extracts", Journal of the Association of Arab Universities for Basic and Applied Sciences, 16(1), pp.83~90 (2014)
  6. Bezerra, J. W. A., "Chemical composition, antimicrobial, modulator and antioxidant activity of essential oil of Dysphania ambrosioides(L. )Mosyakin & Clemants", Comp. Immunol. Microbiol. Infect. Dis, 65, pp.58~64 (2019)
  7. M. Lohse, "Trimmomatic : a flexible trimmer for Illumina sequence data", Bioinformatics, 30(15), pp.2114~2120 (2014)
  8. Brahim, M. A. S., "Chenopodium ambrosioides var. ambrosioides used in Moroccan traditional medicine can enhance the antimicrobial activity of conventional antibiotics", Ind. Crop. Prod, 71, pp.37~43 (2015)
  9. Invasive alien organisms in South West Africa, "Namibia, Foundation for Research Development", Brown, C. J., 1985
  10. Chekem, M. S. G., "Antifungal properties of Chenopodium ambrosioides essential oil against Candida species", Pharmaceuticals, 3(9), pp.2900~2909 (2010)
  11. Chen, J., "The complete chloroplast genome sequence of the relict woody plant Metasequoia glyptostroboides Hu et Cheng", Front. Plant Sci, 6, pp.447~ (2015)
  12. Chen, Y., "Characterization of the complete plastome of Dysphania botrys, a candidate plant for cancer treatment", Mitochondrial DNA B, 3(2), pp.1214~1215 (2018)
  13. Cheng, J., "A comprehensive characterization of simple sequence repeats in pepper genomes provides valuable resources for marker development in Capsicum", Sci. Rep, 6, pp.18919~ (2016)
  14. Chung, H. J., "The complete chloroplast genome sequences of Solanum tuberosum and comparative analysis with Solanaceae species identified the presence of a 241-bp deletion in cultivated potato chloroplast DNA sequence", Plant Cell Rep, 25(12), pp.1369~1379 (2006)
  15. Dillon, S. J., "Dysphania congestiflora(Chenopodiaceae), a new species from Western Australia", Nuytsia, 27, pp.133~138 (2016)
  16. Dogra, K., "An assessment and impact of three invasive species in the Shivalik hills of Himachal Pradesh, India", Int J Biodivers Conserv, 1(1), pp.004~010 (2009)
  17. Dong, W., "Comparative analysis of the complete chloroplast genome sequences in psammophytic Haloxylon species (Amaranthaceae)", PeerJ, 4, pp.e2699~ (2016)
  18. Foxcroft, L. C., "Ornamental plants as invasive aliens : problems and solutions in Kruger National Park, South Africa", Environ Manage, 41(1), pp.32~51 (2008)
  19. Fuentes-Bazan, S., "Towards a species level tree of the globally diverse genus Chenopodium(Chenopodiaceae)", Mol. Phylogenet. Evol, 62(1), pp.359~374 (2012)
  20. Fuentes-Bazan, S., "A novel phylogeny-based generic classification for Chenopodium sensu lato, and a tribal rearrangement of Chenopodioideae(Chenopodiaceae)", Willdenowia, 42(1), pp.5~25 (2012)
  21. Goia, I., "Geographic origins of invasive alien species in"Iron Gates"Natural Park(Banat, Romania)", Transylv. Rev. Syst. Ecol. Res, 16(3), pp.115~130 (2014)
  22. 한병우, "진도(전라남도 진도군)의 관속식물상", 한국자원식물학회지, 31(2), pp.162~194 (2018), 한국자원식물학회[DOI]
  23. Hegazy, A., "Invasive plant communities in the Nile Delta coast", Global J. Environ. Res, 2(1), pp.53~61 (2008)
  24. Hong, S. Y., "Complete chloroplast genome sequences and comparative analysis of Chenopodium quinoa and C. album", Front. Plant Sci, 8, pp.1696~ (2017)
  25. Ibironke, G., "Studies on the antiinflammatory and analgesic properties of Chenopodium ambrosioides leaf extract in rats", Int. J. Pharmacol, 3(1), pp.111~115 (2007)
  26. Jardim, C. M., "Composition and antifungal activity of the essential oil of the Brazilian Chenopodium ambrosioides L", J. Chem. Ecol, 34(9), pp.1213~1218 (2008)
  27. Jeon, J. H., "Comparative Analysis of the Complete Chloroplast Genome Sequences of Three Closely Related East-Asian Wild Roses(Rosa sect. Synstylae;Rosaceae)", Genes, 10(1), pp.23~ (2019)
  28. Kadereit, G., "Phylogeny of Amaranthaceae and Chenopodiaceae and the evolution of C4 photosynthesis", Int. J. Plant Sci, 164(6), pp.959~986 (2003)
  29. Kadereit, G., "Molecular phylogeny of Atripliceae(Chenopodioideae, Chenopodiaceae) : implications for systematics, biogeography, flower and fruit evolution, and the origin of C4 photosynthesis", Am. J. Bot, 97(10), pp.1664~1687 (2010)
  30. Katoh, K., "MAFFT multiple sequence alignment software version 7 : improvements in performance and usability", Mol. Biol. Evol, 30(4), pp.772~780 (2013)
  31. Kim, S. H., "Comparison of Whole Plastome Sequences between Thermogenic Skunk Cabbage Symplocarpus renifolius and Nonthermogenic S. nipponicus(Orontioideae; Araceae)in East Asia", Int. J. Mol. Sci, 20(19), pp.4678~ (2019)
  32. Kim, Y., "The complete chloroplast genome sequence of Dysphania pumilio(R. Br. )Mosyakin & Clemants(Amaranthaceae)", Mitochondrial DNA B, 4(1), pp.403~404 (2019)
  33. Kiuchi, F., "Monoterpene hydroperoxides with trypanocidal activity from Chenopodium ambrosioides", J. Nat. Prod, 65(4), pp.509~512 (2002)
  34. Kumar, R., "Evaluation of Chenopodium ambrosioides oil as a potential source of antifungal, antiaflatoxigenic and antioxidant activity", Int. J. Food Microbiol, 115(2), pp.159~164 (2007)
  35. 이유미, "한국내 귀화식물의 현황과 고찰", 식물분류학회지, 41(1), pp.87~101 (2011), 한국식물분류학회
  36. Li, H, "Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM", arXiv preprint arXiv:1303.3997, ~ (2013)
  37. Li, H, "The sequence alignment", map format and SAMtools, 2009, pp.25(16), 2078~2079
  38. Li, W., "Interspecific chloroplast genome sequence diversity and genomic resources in Diospyros", BMC plant Biol, 18(1), pp.210~ (2018)
  39. Li, W., "Complete chloroplast genome of Camellia japonica genome structures, comparative and phylogenetic analysis", PLOS ONE, 14(5), pp.e0216645~ (2019)
  40. Li, Z. Z., "Comparative genomics of the balsaminaceae sister genera Hydrocera triflora and Impatiens pinfanensis", Int. J. Mol. Sci, 19(1), pp.319~ (2018)
  41. Liu, J., "Invasive alien plants in China : role of clonality and geographical origin", Biol. Invasions, 8(7), pp.1461~1470 (2006)
  42. Lohse, M., "Organellar GenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes", Curr. Genet, 52(5-6), pp.267~274 (2007)[DOI]
  43. Lowe, T. M., "tRNAscan-SE : a program for improved detection of transfer RNA genes in genomic sequence", Nucleic Acids Res, 25(5), pp.955~964 (1997)
  44. Mardis, E. R, "The impact of next-generation sequencing technology on genetics", Trends Genet, 24(3), pp.133~141 (2008)
  45. Maslo, S, "Preliminary list of invasive alien plant species(IAS)in Bosnia and Herzegovina", Herbologia, 16(1), pp.1~14 (2016)
  46. Metzker, M. L, "Sequencing technologies-the next generation", Nat. Rev. Genet, 11(1), pp.31~ (2010)
  47. Mito, T., "Invasive alien species in Japan : the status quo and the new regulation for prevention of their adverse effects", Global Environmental Research, 8(2), pp.171~193 (2004)
  48. Monzote, L., "Activity of the essential oil from Chenopodium ambrosioides grown in Cuba against Leishmania amazonensis", Chemotherapy, 52(3), pp.130~136 (2006)
  49. Monzote, L., "Essential oil from Chenopodium ambrosioides and main components : activity against Leishmania, their mitochondria and other microorganisms", Exp. Parasitol, 136, pp.20~26 (2014)
  50. Mosyakin, S. L., "New nomenclatural combinations in Dysphania R. Br. (Chenopodiaceae) : taxa occurring in North America", Ukr. Bot. Zhur, 59(4), pp.380~385 (2002)
  51. Mosyakin, S. L., "Further transfers of glandularpubescent species from Chenopodium subg. Ambrosia to Dysphania(Chenopodiaceae)", J Bot Res Inst Tex, 2(1), pp.425~431 (2008)
  52. Nei, M., "Mathematical model for studying genetic variation in terms of restriction endonucleases", PNASU, 76(10), pp.5269~5273 (1979)
  53. Nguyen, L. T., "IQ-TREE : a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies", Mol Biol Evol, 32(1), pp.268~274 (2014)
  54. Pace, L., "Global Change and Protected Areas", pp.495~504 (2001), Springer
  55. Pandey, A. K., "Repellent activity of some essential oils against two stored product beetles Callosobruchus chinensis L. and C. maculatus F. (Coleoptera : Bruchidae)with reference to Chenopodium ambrosioides L. oil for the safety of pigeon pea seeds", J. Food Sci. Technol, 51(12), pp.4066~4071 (2014)
  56. Park, J., "The second complete chloroplast genome of Dysphania pumilio (R. Br.) mosyakin & clemants (Amranthaceae): intraspecies variation of invasive weeds", Mitochondrial DNA Part B, 4(1), pp.1428~1429 (2019)
  57. Pavela, R., "Clausena anisata and Dysphania ambrosioides essential oils : from ethno-medicine to modern uses as effective insecticides", Environ. Sci. Pollut. R, 25(11), pp.10493~10503 (2018)
  58. Perth, U, "Dysphania sect. Botryoides(Amaranthaceae s. lat. )in Asia", Willdenowia, 43(1), pp.65~80 (2011)
  59. Prasad, C. S., "In vitro and in vivo antifungal activity of essential oils of Cymbopogon martini and Chenopodium ambrosioides and their synergism against dermatophytes", Mycoses, 53(2), pp.123~129 (2010)
  60. Rastogi, J., "Diversity of invasive alien species in Pantnagar flora", Tropical Plant Research, 2(3), pp.282~287 (2015)
  61. Reyes-Becerril, M., "Antioxidant, intestinal immune status and anti-inflammatory potential of Chenopodium ambrosioides L. in fish : In vitro and in vivo studies", Fish Shellfish Immunol, 86, pp.420~428 (2019)
  62. Rossi-Bergamann, B., "Brazilian medicinal plants : a rich source of immunomodulatory substances, Ciênc", Ciênc. Cult, 49(5, pp.6) (1997), 395~401
  63. Sekar, K. C, "Invasive alien plants of Indian Himalayan region-diversity and implication", Am J Plant Sci, 3(02), pp.177~ (2012)
  64. Shukla, N., "Mining and analysis of simple sequence repeats in the chloroplast genomes of genus Vigna", Biotechnology Research and Innovation, 2(1), pp.9~18 (2018)
  65. Song, Z., "Genetic diversity in the northernmost Oryza rufipogon populations estimated by SSR markers", Theor. Appl. Genet, 107(8), pp.1492~1499 (2003)
  66. Stohlgren, T. J., "Plant Invasions in Protected Areas: Patterns, problems and challenges", pp.267~283 (2013), Springer
  67. Sukhorukov, A. P, "Taxonomic notes on Dysphania and Atriplex (Chenopodiaceae)", Willdenowia, 42(2), pp.169~181 (2012)
  68. Sukhorukov, A.P, "Molecular phylogenetic data and seed coat anatomy resolve the generic position of some critical Chenopodioideae(Chenopodiaceae-Amaranthaceae)with reduced perianth segments", PhytoKeys, 109, pp.103~128 (2018)
  69. Sukhorukov, A.P, "A new species of Dysphania(Chenopodioideae, Chenopodiaceae)from South-West Tibet and East Himalaya", Phytotaxa, 203(2), pp.138~146 (2015)
  70. Thomson, A. M., "Comparative analysis of 24 chloroplast genomes yields highly informative genetic markers for the Brazil nut family (Lecythidaceae)", bioRxiv:192112, ~ (2017)
  71. Verloove, F, "New xenophytes from Gran Canaria(Canary Islands, Spain), with emphasis on naturalized and(potentially)invasive species", Collect Bot, 32, pp.59~82 (2013)
  72. Verloove, F., "The non-native vascular flora of Belgium: a new nothospecies and three new combinations", Syst. Geogr. Plants, pp.217~220 (2006)
  73. Wang, J., "Allelopathy of volatile oil from Chenopodium ambrosioides L. on receptors", Southwest China Journal of Agricultural Sciences, 22(3), pp.777~780 (2009)
  74. Wang, M. L., "Microsatellite markers in plants and insects. Part I:Applications of biotechnology", Genes, Genomes and Genomics, 3(1), pp.54~67 (2009)
  75. Wang, W., "Whole-genome comparison reveals divergent IR borders and mutation hotspots in chloroplast genomes of herbaceous bamboos(Bambusoideae : Olyreae)", Molecules, 23(7), pp.1537~ (2018)
  76. Weber, E., "Assessing the risk of potentially invasive plant species in central Europe", J. Nat. Conserv, 12(3), pp.171~179 (2004)
  77. Wei, H., "The toxicity and physiological effect of essential oil from Chenopodium ambrosioides against the diamondback moth, Plutella xylostella(Lepidoptera : Plutellidae)", Crop. Prot, 76, pp.68~74 (2015)
  78. Wilson, H. D., "Loss of duplicate gene expression in tetraploid Chenopodium", Syst. Ecol, 11(1), pp.7~13 (1983)
  79. Würschum, T., "Population structure, genetic diversity and linkage disequilibrium in elite winter wheat assessed with SNP and SSR markers", Theor. Appl. Genet, 6(6), pp.1477~1486 (2013)
  80. Xie, D. F., "Comparative analysis of the chloroplast genomes of the Chinese endemic genus Urophysa and their contribution to chloroplast phylogeny and adaptive evolution", Int. J. Mol. Sci, 19(7), pp.1847~ (2018)
  81. Xu, H., "An inventory of invasive alien species in China", NeoBiota, 15, pp.1~26 (2012)
  82. Yang, Y., "Comparative analysis of the complete chloroplast genomes of five Quercus species", Front. Plant Sci, 7, pp.959~ (2016)
  83. Zerbino, D. R., "Velvet : algorithms for de novo short read assembly using de Bruijn graphs", Genome Res, 8(5), pp.821~829 (2008)
  84. Zhao, Q. Y., "Optimizing de novo transcriptome assembly from short-read RNA-Seq data : a comparative study", BMC Bioinformatics, 12(14), pp.S2~ (2011)
  85. Zhu, G., "Flora of China. Vol. 5 (Ulmaceae through Basellaceae)", pp.351~414 (2003), Science Press, Missouri Botanical Garden Press

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