Abstract
Utricularia foliosa L., commonly known as leafy bladderwort, is a widespread aquatic carnivorous plant from the Lentibulariaceae family. The species of the Utricularia and Genlisea genera are known to possess the smallest nuclear genomes across angiosperms. This study reveals that U. foliosa have a typical chloroplast genome of 150,851 bp in length, comprised of a large single-copy region (LSC) of 82,720 bp, a small single-copy region (SSC) of 17,481 bp, and inverted repeat regions (IRs) of 25,325 bp. A total of 139 genes, 88 of which are protein coding genes, 37 tRNA genes, eight rRNA genes and six pseudogenes were identified. All plastid NAD(P)H-dehydrogenase genes are present as intact copies. Phylogenetic analyses indicate that U. foliosa is closely related to other suspended or affixed aquatic species belonging to the Utricularia sect. Utricularia.
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References
Adamec L (2006) Respiration and photosynthesis of bladders and leaves of aquatic Utricularia species. Plant Biol 8:765–769. doi:10.1055/s-2006-924540
Albert VA, Jobson RW, Michael TP, Taylor DJ (2010) The carnivorous bladderwort (Utricularia, Lentibulariaceae): a system inflates. J Exp Bot 61:5–9. doi:10.1093/jxb/erp349
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. doi:10.1089/cmb.2012.0021
Darriba D, Taboada GL, Doallo R, Posada D (2012) jModelTest 2: more models, new heuristics and parallel computing. Nat Methods 9:772. doi:10.1038/nmeth.2109
Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15
Hahn C, Bachmann L, Chevreux B (2013) Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads: a baiting and iterative mapping approach. Nucleic Acids Res 41(13):e129. doi:10.1093/nar/gkt371
Kajitani R, Toshimoto K, Noguchi H, Toyoda A, Ogura Y, Okuno M, Yabana M, Harada M, Nagayasu E, Maruyama H, Kohara Y, Fujiyama A, Hayashi T, Itoh T (2014) “Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads”. Genome Res 24(8):1384–1395. doi:10.1101/gr.170720.113
Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30:772–780. doi:10.1093/molbev/mst010
Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359. doi:10.1038/nmeth.1923
Laslett D, Canback B (2004) ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res 32:11–16. doi:10.1093/nar/gkh152
Lohse M, Drechsel O, Kahlau S, Bock R (2013) OrganellarGenomeDRAW–a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets. Nucleic Acids Res 41:575–581. doi:10.1093/nar/gkt289
Müller K, Borsch T, Legendre L, Porembski S, Theisen I, Barthlott W (2004) Evolution of carnivory in Lentibulariaceae and the Lamiales. Plant Biol 6:1–14. doi:10.1055/s-2004-817909
Ronquist F, Huelsenbeck JP (2003) MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574. doi:10.1093/bioinformatics/btg180
Silva SR, Diaz YCA, Penha HA, Pinheiro DG, Fernandes CC, Miranda VFO, Michael TP, Varani, AM (2016) The chloroplast genome of Utricularia reniformis sheds light on the evolution of the ndh gene complex of terrestrial carnivorous plants from the Lentibulariaceae family. Plos ONE 11(10):e0165176. doi:10.1371/journal.pone.0165176
Solís-Parra J, Críales-Hernández M (2016) Capture and selectivity of zooplankton by Utricularia foliosa (Lentibulariaceae) in the Ciénaga de Paredes, Santander, Colombia. J Trop Biol Cons 64:1297–1310. doi:10.15517/rbt.v64i3.21387
Stamatakis A (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–1313. doi:10.1093/bioinformatics/btu033
Taylor P (1989) The genus Utricularia: a taxonomic monograph. Kew bulletin additional series XIV. Kew Royal Botanic Gardens, London
Veleba A, Bureš P, Adamec L, Šmarda P, Lipnerová I, Horová L (2014) Genome size and genomic GC content evolution in the miniature genome-sized family Lentibulariaceae. New Phytol 203:22–28. doi:10.1111/nph.12790
Wyman SK, Jansen RK, Boore JL (2004) Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20:3252–3255. doi:10.1093/bioinformatics/bth352
Acknowledgements
The first author was supported by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES). VFOM thanks for the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) for the fellowship (Bolsa de Produtividade—Proc. # 309040/2014-0).
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Silva, S.R., Pinheiro, D.G., Meer, E.J. et al. The complete chloroplast genome sequence of the leafy bladderwort, Utricularia foliosa L. (Lentibulariaceae). Conservation Genet Resour 9, 213–216 (2017). https://doi.org/10.1007/s12686-016-0653-5
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DOI: https://doi.org/10.1007/s12686-016-0653-5