The complete chloroplast genome sequence of the folk medicinal and vegetable plant purslane (Portulaca oleracea L.)

References

• Abdel Moneim, A.E., Dkhil, M.A., &Al-Quraishy, S. (2013). The potential role of Portulaca oleracea as a neuroprotective agent in rotenone-induced neurotoxicity and apoptosis in the brain of rats. Pesticide Biochemistry and Physiology, 105, 203–212. doi:10.1016/j.pestbp.2013.02.004
   Web of Science ®Google Scholar
• Allen, G.C., Flores-Vergara, M.A., Krasynanski, S., Kumar, S., &Thompson, W.F. (2006). A modified protocol for rapid DNA isolation from plant tissues using cetyltrimethylammonium bromide. Nature Protocols, 1, 2320–2325. doi:10.1038/nprot.2006.384
   PubMed Web of Science ®Google Scholar
• Bl, N., &Louis, B. (1987). Taxonomic studies in the genus Portulaca L. (Portulacaceae). Feddes Repertorium, 98, 399–402.
   Google Scholar
• Bremer, B., Bremer, K., Chase, M.W., Fay, M.F., Reveal, J.L., Soltis, D.E., … Zmarzty, S. (2009). An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III. Botanical Journal of the Linnean Society, 161, 105–121. doi:10.1111/j.1095-8339.2009.00996.x
   Web of Science ®Google Scholar
• Byng, J.W., Chase, M.W., Christenhusz, M.J.M., Fay, M.F., Judd, W.S., Mabberley, D.J., … Weber, A. (2016). An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV. Botanical Journal of the Linnean Society, 181, 1–20. doi:10.1111/boj.12385
   Web of Science ®Google Scholar
• Chen, T., Zhu, L., Liu, X., Li, Y., Zhao, C., Xu, Z., … Zhang, H. (2011). Synthesis and antioxidant activity of phosphorylated polysaccharide from Portulaca oleracea L. with H3PW12O40 immobilized on polyamine functionalized polystyrene bead as catalyst. Journal of Molecular Catalysis A: Chemical, 342–343, 74–82. doi:10.1016/j.molcata.2011.04.014
   Web of Science ®Google Scholar
• Choi, K.S., &Park, S. (2015). The complete chloroplast genome sequence of Aster spathulifolius (Asteraceae); genomic features and relationship with Asteraceae. Gene, 572, 214–221. doi:10.1016/j.gene.2015.07.020
   PubMed Web of Science ®Google Scholar
• Clegg, M.T., Gaut, B.S., Learn, G.H., &Morton, B.R. (1994). Rates and patterns of chloroplast DNA evolution. Proceedings of the National Academy of Sciences, 91, 6795–6801. doi:10.1073/pnas.91.15.6795
   PubMed Web of Science ®Google Scholar
• D’Andrea, R.M., Triassi, A., Casas, M.I., Andreo, C.S., &Lara, M.V. (2015). Identification of genes involved in the drought adaptation and recovery in Portulaca oleracea by differential display. Plant Physiology and Biochemistry, 90, 38–49. doi:10.1016/j.plaphy.2015.02.023
   PubMed Web of Science ®Google Scholar
• Daniell, H., Lin, C., Yu, M., &Chang, W. (2016). Chloroplast genomes: Diversity, evolution, and applications in genetic engineering. Genome Biology, 17. doi:10.1186/s13059-016-1004-2
   PubMed Web of Science ®Google Scholar
• Frazer, K.A., Pachter, L., Poliakov, A., Rubin, E.M., &Dubchak, I. (2004). VISTA: Computational tools for comparative genomics. Nucleic Acids Research, 32, W273–W279. doi:10.1093/nar/gkh458
   PubMed Web of Science ®Google Scholar
• Kamal Uddin, M., Juraimi, A.S., Anwar, F., Hossain, M.A., &Alam, M.A. (2012). Effect of salinity on proximate mineral composition of purslane (Portulca oleracea L.). Australian Journal of Crop Science, 6, 1732–1736.
   Google Scholar
• Khakhlova, O., &Bock, R. (2006). Elimination of deleterious mutations in plastid genomes by gene conversion. The Plant Journal, 46, 85–94. doi:10.1111/j.1365-313X.2006.02673.x
   PubMed Web of Science ®Google Scholar
• Kikuchi, S., Bedard, J., Hirano, M., Hirabayashi, Y., Oishi, M., Imai, M., … Nakai, M. (2013). Uncovering the protein translocon at the chloroplast inner envelope membrane. Science, 339, 571–574. doi:10.1126/science.1229262
   PubMed Web of Science ®Google Scholar
• Kurtz, S., Choudhuri, J.V., Ohlebusch, E., Schleiermacher, C., Stoye, J., &Giegerich, R. (2001). REPuter: The manifold applications of repeat analysis on a genomic scale. Nucleic Acids Research, 29, 4633–4642. doi:10.1093/nar/29.22.4633
   PubMed Web of Science ®Google Scholar
• Kurtz, S., Phillippy, A., Delcher, A.L., Smoot, M., Shumway, M., Antonescu, C., &Salzberg, S.L. (2004). Versatile and open software for comparing large genomes. Genome Biology, 5, R12. doi:10.1186/gb-2004-5-2-r12
   PubMed Web of Science ®Google Scholar
• Lohse, M., Drechsel, O., &Bock, R. (2007). OrganellarGenomeDRAW (OGDRAW): A tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes. Current Genetics, 52, 267–274. doi:10.1007/s00294-007-0161-y
   PubMed Web of Science ®Google Scholar
• Ma, J., Yang, B., Zhu, W., Sun, L., Tian, J., &Wang, X. (2013). The complete chloroplast genome sequence of Mahonia bealei (Berberidaceae) reveals a significant expansion of the inverted repeat and phylogenetic relationship with other angiosperms. Gene, 528, 120–131. doi:10.1016/j.gene.2013.07.037
   PubMed Web of Science ®Google Scholar
• Ma, P.-F., Zhang, Y.-X., Zeng, C.-X., Guo, Z.-H., &Li, D.-Z. (2014). Chloroplast phylogenomic analyses resolve deep-level relationships of an intractable bamboo tribe Arundinarieae (poaceae). Systematic Biology, 63, 933–950. doi:10.1093/sysbio/syu054
   PubMed Web of Science ®Google Scholar
• Ni, L., Zhao, Z., Xu, H., Chen, S., &Dorje, G. (2016). The complete chloroplast genome of Gentiana straminea (Gentianaceae), an endemic species to the Sino-Himalayan subregion. Gene, 577, 281–288. doi:10.1016/j.gene.2015.12.005
   PubMed Web of Science ®Google Scholar
• Nie, X., Lv, S., Zhang, Y., Du, X., Wang, L., Biradar, S.S., … Weining, S. (2012). Complete chloroplast genome sequence of a major invasive species, crofton weed (Ageratina adenophora). PLoS One, 7, e36869. doi:10.1371/journal.pone.0036869
   PubMed Web of Science ®Google Scholar
• Nyffeler, R. (2007). The closest relatives of cacti: Insights from phylogenetic analyses of chloroplast and mitochondrial sequences with special emphasis on relationships in the tribe Anacampseroteae. American Journal of Botany, 94, 89–101. doi:10.3732/ajb.94.1.89
   PubMed Web of Science ®Google Scholar
• Nyffeler, R., &Eggli, U. (2010). Disintegrating Portulacaceae: A new familial classification of the suborder portulacineae (Caryophyllales) based on molecular and morphological data. Taxon, 59, 227–240.
   Web of Science ®Google Scholar
• Ocampo, G., &Columbus, J.T. (2012). Molecular phylogenetics, historical biogeography, and chromosome number evolution of Portulaca (Portulacaceae). Molecular Phylogenetics and Evolution, 63, 97–112. doi:10.1016/j.ympev.2011.12.017
   PubMed Web of Science ®Google Scholar
• Powell, W., Morgante, M., McDevitt, R., Vendramin, G.G., &Rafalski, J.A. (1995). Polymorphic simple sequence repeat regions in chloroplast genomes: Applications to the population genetics of pines. Proceedings of the National Academy of Sciences, 92, 7759–7763. doi:10.1073/pnas.92.17.7759
   PubMed Web of Science ®Google Scholar
• Raubeson, L.A., &Jansen, R.K. (2005). Chloroplast genomes of plants, plant diversity and evolution: Genotypic and phenotypic variation in higher plants.  London: CABI.
   Google Scholar
• Ren, S., Weeda, S., Akande, O., &Guo, Y. (2011). Drought tolerance and AFLP-based genetic diversity in purslane (Portulaca oleracea L.). Journal of Biotech Research, 3, 51–61.
   Google Scholar
• Sanderson, M.J., Copetti, D., Burquez, A., Bustamante, E., Charboneau, J.L., Eguiarte, L.E., … Wojciechowski, M.F. (2015). Exceptional reduction of the plastid genome of saguaro cactus (Carnegiea gigantea): Loss of the ndh gene suite and inverted repeat. American Journal of Botany, 102, 1115–1127. doi:10.3732/ajb.1500184
   PubMed Web of Science ®Google Scholar
• Schäferhoff, B., Fleischmann, A., Fischer, E., Albach, D.C., Borsch, T., Heubl, G., &Müller, K.F. (2010). Towards resolving Lamiales relationships: Insights from rapidly evolving chloroplast sequences. BMC Evolutionary Biology, 10, 352. doi:10.1186/1471-2148-10-352
   PubMed Web of Science ®Google Scholar
• Schattner, P., Brooks, A.N., &Lowe, T.M. (2005). The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Research, 33, W686–W689. doi:10.1093/nar/gki366
   PubMed Web of Science ®Google Scholar
• Shaw, J., Lickey, E.B., Schilling, E.E., &Small, R.L. (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, 275–288. doi:10.3732/ajb.94.3.275
   PubMed Web of Science ®Google Scholar
• Shinozaki, K., Ohme, M., Tanaka, M., Wakasugi, T., Hayashida, N., Matsubayashi, T., … Sugiura, M. (1986). The complete nucleotide sequence of the tobacco chloroplast genome: Its gene organization and expression. EMBO Journal, 5, 2043–2049.
   PubMed Web of Science ®Google Scholar
• Sloan, D.B., Triant, D.A., Forrester, N.J., Bergner, L.M., Wu, M., &Taylor, D.R. (2014). A recurring syndrome of accelerated plastid genome evolution in the angiosperm tribe Sileneae (Caryophyllaceae). Molecular Phylogenetics and Evolution, 72, 82–89. doi:10.1016/j.ympev.2013.12.004
   PubMed Web of Science ®Google Scholar
• Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., &Kumar, S. (2011). MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution, 28, 2731–2739. doi:10.1093/molbev/msr121
   PubMed Web of Science ®Google Scholar
• Tangphatsornruang, S., Sangsrakru, D., Chanprasert, J., Uthaipaisanwong, P., Yoocha, T., Jomchai, N., &Tragoonrung, S. (2010). The chloroplast genome sequence of mungbean (Vigna radiata) determined by high-throughput pyrosequencing: Structural organization and phylogenetic relationships. DNA Research, 17, 11–22. doi:10.1093/dnares/dsp025
   PubMed Web of Science ®Google Scholar
• Uddin, M.K., Juraimi, A.S., Ali, M.E., &Ismail, M.R. (2012). Evaluation of antioxidant properties and mineral composition of Purslane (Portulaca oleracea L.) at different growth stages. International Journal of Molecular Sciences, 13, 10257–10267. doi:10.3390/ijms130810257
   PubMed Web of Science ®Google Scholar
• Uddin, M.K., Juraimi, A.S., Hossain, M.S., Nahar, M.A., Ali, M.E., &Rahman, M.M. (2014). Purslane weed (Portulaca oleracea): A prospective plant source of nutrition, omega-3 fatty acid, and antioxidant attributes. The Scientific World Journal, 2014, 1–6. doi:10.1155/2014/951019
   Web of Science ®Google Scholar
• Wicke, S., Schneeweiss, G.M., DePamphilis, C.W., Müller, K.F., &Quandt, D. (2011). The evolution of the plastid chromosome in land plants: Gene content, gene order, gene function. Plant Molecular Biology, 76, 273–297. doi:10.1007/s11103-011-9762-4
   PubMed Web of Science ®Google Scholar
• Wolfe, K.H., Morden, C.W., Ems, S.C., &Palmer, J.D. (1992). Rapid evolution of the plastid translational apparatus in a nonphotosynthetic plant: Loss or accelerated sequence evolution of tRNA and ribosomal protein genes. Journal of Molecular Evolution, 35, 304–317. doi:10.1007/BF00161168
   PubMed Web of Science ®Google Scholar
• Wu, C.-S., &Chaw, S.-M. (2014). Highly rearranged and size-variable chloroplast genomes in conifers II clade (cupressophytes): Evolution towards shorter intergenic spacers. Plant Biotechnology Journal, 12, 344–353. doi:10.1111/pbi.12141
   PubMed Web of Science ®Google Scholar
• Wyman, S.K., Jansen, R.K., &Boore, J.L. (2004). Automatic annotation of organellar genomes with DOGMA. Bioinformatics, 20, 3252–3255. doi:10.1093/bioinformatics/bth352
   PubMed Web of Science ®Google Scholar
• Xiang, B., Li, X., Qian, J., Wang, L., Ma, L., Tian, X., &Wang, Y. (2016). The complete chloroplast genome sequence of the medicinal plant Swertia mussotii using the PacBio RS II platform. Molecules, 21. doi:10.3390/molecules21081029
   Web of Science ®Google Scholar
• Xiang, L., Xing, D., Wang, W., Wang, R., Ding, Y., &Du, L. (2005). Alkaloids from Portulaca oleracea L. Phytochemistry, 66, 2595–2601. doi:10.1016/j.phytochem.2005.08.011
   PubMed Web of Science ®Google Scholar
• Yang, M., Zhang, X., Liu, G., Yin, Y., Chen, K., Yun, Q., … Yu, J. (2010). The complete chloroplast genome sequence of date palm (Phoenix dactylifera L.). PLoS One, 5, e12762. doi:10.1371/journal.pone.0012762
   PubMed Web of Science ®Google Scholar
• Yao, X., Tang, P., Li, Z., Li, D., Liu, Y., &Huang, H. (2015). The first complete chloroplast genome sequences in actinidiaceae: Genome structure and comparative analysis. PLoS One, 10, e129347. doi:10.1371/journal.pone.0129347
   PubMed Web of Science ®Google Scholar
• Zhao, R., Gao, X., Cai, Y., Shao, X., Jia, G., Huang, Y., … Zheng, X. (2013). Antitumor activity of Portulaca oleracea L. polysaccharides against cervical carcinoma in vitro and in vivo. Carbohydrate Polymers, 96, 376–383. doi:10.1016/j.carbpol.2013.04.023
   PubMed Web of Science ®Google Scholar