Structural analysis of the common ragweed (Ambrosia artemisiifolia L.) chloroplast genome

Authors

  • Erzsébet Nagy University of Pannonia, Department of Plant Science and Biotechnology, e-mail: nagy.erzsebet@georgikon.hu (correspondence)
  • János Taller University of Pannonia, Department of Plant Science and Biotechnology https://orcid.org/0000-0002-1972-9040

Keywords:

common ragweed, chloroplast genome, plastome genes, repeats, microsatellites

Abstract

Chloroplast is an essential organelle in plants. Besides its key role in photosynthesis fatty acids and many amino acids are synthesized in chloroplasts. Due to the endosymbiotic origin chloroplasts have their own DNA, the cpDNA that called also plastome. The chloroplast genome has well defined structure and due to its conservative nature slow evolution is characteristic for it. In the present study we analyzed the plastome structure of common ragweed (Ambrosia artemisiifolia), the most widespread and highly allergenic weed in many parts in the world. Compared to other chloroplast genomes, the analysis indicates the differences in start codon of some genes, in gene content and structure, in intron content, as well as the repeated sequence motifs are identified, with special attention on the potential microsatellites. Results of this study can be utilized in future phylogenetic analyses and genotyping.

References

Alberts, B., Johnson, A., Lewis, J. et al. 2015. Molecular Biology of the Cell. 6th edition. New York, Garland Science. Energy Conversion: Mitochondria and Chloroplasts. 753–812.

Benson, G. 1999. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Research. 27. (2). 573–580. https://doi.org/10.1093/nar/27.2.573

Birky, C. W. 2001. The Inheritance of Genes in Mitochondria and Chloroplasts: Laws, Mechanisms, and Models. Annu. Rev. Genet. 35. 125–148. https://doi.org/10.1146/annurev.genet.35.102401.090231

Chen, X., Zhou, J., Ciu, Y., Wang, Y., Duan, B., Yao, H. 2018. Identification of Ligularia herbs using the complete chloroplast genome as a super-barcode. Front. Pharmacol. 9. 695. https://doi.org/10.3389/fphar.2018.00695

Curci, P.L., De Paola, D., Danzi, D., Vendramin, G.G., Sonnate, G. 2015. Complete chloroplast genome of the multifunctional crop globe artichoke and comparison with other Asteraceae. Plos One. 10. (3). e0120589. https://doi.org/10.1371/journal.pone.0120589

Délye, C., Jasieniuk, M., Le Corre, V. 2013. Deciphering the evolution of herbicide resistance in weeds. Trends Genet. 29. 649–658. https://doi.org/10.1016/j.tig.2013.06.001

Doorduin, L., Gravendeel, B., Lammers, Y., Ariyurek, Y., Chin-A-Woeng, T., Vrieling, K. 2011. The complete chloroplast genome of 17 individuals of pest species Jacobaea vulgaris: SNPs, micrsatellites and barcoding markers for population and phylogenetic studies. DNA Research. 18. 93–105. https://doi.org/10.1093/dnares/dsr002

Faircloth, B. 2008. Msatcommander: detection of microsatellite repeat arrays and automated, locus-specific primer design. Molecular Ecology Resources. 8. 92–94. https://doi.org/10.1111/j.1471-8286.2007.01884.x

Kim, H. T., Chung, M. G., Kim, K.-J. 2014. Chloroplast genome evolution in early diverged Leptosporangiate ferns. Mol. Cells. 37. (5). 372–382. https://doi.org/10.14348/molcells.2014.2296

Kim, K.-J., Lee, H.-L. 2004. Complete chloroplast genome sequence from Korean ginseng (Panax schinseng Nees) and comparative analysis of sequence evolution among 17 vascular plants. DNA Research. 11. 247–261. https://doi.org/10.1093/dnares/11.4.247

Kim, I., Park, J. Y., Lee, Y. S., Lee, H. O., Park, H.-S., Jayakodi, M., Waminal, N. E., Kang, J. H., Lee, T. J., Sung, H. S., Kim, K. Y., Yang, T.-J. 2017. Discrimination and authentication of Eclipta prostrata and E. alba based on the complete chloroplast genomes. Plant Breed. Biotech. 5. (4). 334–343. https://doi.org/10.9787/PBB.2017.5.4.334

Kurtz, S., Choudhuri, J. V., Ohlebusch, E., Schleiermacher, C., Stoye, J., Giergerich, R. 2001. REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Research. 29. (22). 4633–4642. https://doi.org/10.1093/nar/29.22.4633

Liu, Y., Huo, N., Wang, Y., Zhang, S., Young, H. A., Feng, X., Gu, Y. Q. 2013. Complete chloroplast genome sequences of mongolian medicine Artemisia frigida and phylogenetic relationships with other plants. Plos One. 8. (2). e575333. https://doi.org/10.1371/journal.pone.0057533

Martins, W. S., Lucas, D. C. S., de Sousa Neves, K. F., Bertioli, D. J. 2009. WebSat- a web software for microsatellite marker development. Bioinformation. 3. (6). 282–283. https://doi.org/10.6026/97320630003282

Nagy, E., Hegedűs, G., Taller, J., Kutasy, B., Virág, E. 2017. Illumina sequencing of the chloroplast genome of common ragweed (Ambrosia artemisiifolia L.). Data in Brief. 15. 606–611. https://doi.org/10.1016/j.dib.2017.10.009

Sakamoto, W., Takami, T. 2018. Chloroplast DNA Dynamics: Copy Number, Quality Control and Degradation. Plant & Cell Physiology. 59. (6). 1120–1127. Sato, S., Nakamura, Y., https://doi.org/10.1093/pcp/pcy084

Kaneko, T., Asamizu, E., Tabata, S. 1999. Complete structure of thechloroplast genome of Arabidopsis thaliana. DNA Reasearch. 6. 283–290. https://doi.org/10.1093/dnares/6.5.283

Shimada, H., Fukuta, M., Ishikawa, M., Sugiura, M. 1990. Rice chloroplast RNA polymerase genes: the absence og an intron in rpoC1 and the presence of an extra sequence in rpoC2. Molecular and General Genetics MGG. 221. (3). 395–402. https://doi.org/10.1007/BF00259404

Timme, R. E., Kuehl, J. L., Boore, J. L., Jansen, R. K. 2007. A comparative analysis of the Lactuca and Heliathus (Asteracea) plastid genomes: identification of divergent regions and categorization 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

Wang, X.-Y., Zhou, Z.-S., Liu, G., Quian, Z.-Q. 2018. Characteritation of the complete chloroplast genome of the invasive weed Galinsoga quadriradiata (Asterales: Asteraceae). Consevation Genet. Resour. 10. 89–92. https://doi.org/10.1007/s12686-017-0771-8

Wiegert, K. E., Benett, M. S., Triemer, R. E. 2012. Evolution of the chloroplast genome in photosynthetic euglenoids: a comparison of Eutreptia viridis and Euglena gracilis (Eugleniphyta). Protist. 163. 832–843. https://doi.org/10.1016/j.protis.2012.01.002

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Published

2020-12-31

Issue

Vol. 24 No. 4 (2020)

Section

Articles

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Copyright (c) 2020 Nagy Erzsébet, Taller János

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