Evolution of genome size and genomic GC content in carnivorous holokinetics (Droseraceae)
Jazyk angličtina Země Anglie, Velká Británie Médium print-electronic
Typ dokumentu časopisecké články
PubMed
28025291
PubMed Central
PMC5314647
DOI
10.1093/aob/mcw229
PII: mcw229
Knihovny.cz E-zdroje
- Klíčová slova
- DNA base composition, DNA content, Droseraceae, GC content, carnivorous plants, flow cytometry, genome size evolution, holocentric chromosomes, holokinetic chromosomes,
- MeSH
- biologická evoluce * MeSH
- chromozomy rostlin genetika MeSH
- Droseraceae genetika MeSH
- fylogeneze MeSH
- genetická variace genetika MeSH
- genom rostlinný genetika MeSH
- masožravci MeSH
- zastoupení bazí genetika MeSH
- Publikační typ
- časopisecké články MeSH
BACKGROUND AND AIMS: Studies in the carnivorous family Lentibulariaceae in the last years resulted in the discovery of the smallest plant genomes and an unusual pattern of genomic GC content evolution. However, scarcity of genomic data in other carnivorous clades still prevents a generalization of the observed patterns. Here the aim was to fill this gap by mapping genome evolution in the second largest carnivorous family, Droseraceae, where this evolution may be affected by chromosomal holokinetism in Drosera METHODS: The genome size and genomic GC content of 71 Droseraceae species were measured by flow cytometry. A dated phylogeny was constructed, and the evolution of both genomic parameters and their relationship to species climatic niches were tested using phylogeny-based statistics. KEY RESULTS: The 2C genome size of Droseraceae varied between 488 and 10 927 Mbp, and the GC content ranged between 37·1 and 44·7 %. The genome sizes and genomic GC content of carnivorous and holocentric species did not differ from those of their non-carnivorous and monocentric relatives. The genomic GC content positively correlated with genome size and annual temperature fluctuations. The genome size and chromosome numbers were inversely correlated in the Australian clade of Drosera CONCLUSIONS: Our results indicate that neither carnivory (nutrient scarcity) nor the holokinetism have a prominent effect on size and DNA base composition of Droseraceae genomes. However, the holokinetic drive seems to affect karyotype evolution in one of the major clades of Drosera Our survey confirmed that the evolution of GC content is tightly connected with the evolution of genome size and also with environmental conditions.
Zobrazit více v PubMed
Bennett MD. 1972. Nuclear DNA content and minimum generation time in herbaceous plants. Proceedings of the Royal Society B: Biological Sciences 181: 109–135. PubMed
Bennett MD, Leitch IJ. 2012.
Biro JC. 2008. Correlation between nucleotide composition and folding energy of coding sequences with special attention to wobble bases. Theoretical Biology and Medical Modelling 5: 14. PubMed PMC
Brummitt RK. 2001. World geographical scheme for recording plant distributions, 2nd edm Pittsburgh: Hunt Institute for Botanical Documentation, Carnegie-Mellon University.
Bureš P, Zedek F. 2014. Holokinetic drive: centromere drive in chromosomes without centromeres. Evolution 68: 2412–2420. PubMed
Bureš P, Šmarda P, Hralová I
Bureš P, Zedek F, Marková M. 2013. Holocentric chromosomes In: Wendel J, Greilhuber J, Doležel J, Leitch IJ, eds. Plant genome diversity. Vol. 2. Physical structure of plant genomes. Heidelberg: Springer, 187–208.
Chung KS, Hipp AL, Roalson EH. 2012. Chromosome number evolves independently of genome size in a clade with nonlocalized centromeres ( PubMed
Cuacos M, H Franklin FC, Heckmann S. 2015. Atypical centromeres in plants – what they can tell us. Frontiers in Plant Sciences 6: 913. PubMed PMC
Demidov D, Schubert V, Kumke K PubMed
Escudero M, Hipp AL., Hansen TF, Voje KL., Luceño M. 2012. Selection and inertia in the evolution of holocentric chromosomes in sedges (Carex, Cyperaceae). New Phytologist 195: 237–247. PubMed
Escudero M, Maguilla E, Loureiro J, Castro M, Castro S, Luceño M. 2015. Genome size stability despite high chromosome number variation in PubMed
Fleischmann A, Michael TP, Rivadavia F PubMed PMC
Foerstner KU, von Mering C, Hooper SD, Bork P. 2005. Environments shape the nucleotide composition of genomes. EMBO Reports 6: 1208–1213. PubMed PMC
Givnish TJ, Burkhardt EL, Happel RE, Weintraub JE. 1984. Carnivory in the bromeliad
Gonella PM, Rivadavia F, Fleischmann A. 2015.
Govaerts R, Cheek M. 2014.
Greilhuber J, Borsch T, Müller K, Worberg A, Porembski S, Barthlott W. 2006. Smallest angiosperm genomes found in Lentibulariaceae, with chromosomes of bacterial size. Plant Biology 8: 770–777. PubMed
Greilhuber J, Doležel J, Lysák MA, Bennet MD. 2005. The origin, evolution and proposed stabilization of the terms ‘Genome Size’ and ‘C-Value’ to describe nuclear DNA contents. Annals of Botany 95: 255–260. PubMed PMC
Harmon L, Weir J, Brock C
Heckmann S, Houben A. 2013. Holokinetic centromeres In: Jiang J, Birchler JA, eds. Plant centromere biology. Oxford: Wiley-Blackwell, 83–94.
Heubl G, Bringmann G, Meimberg H. 2006. Molecular phylogeny and character evolution of carnivorous plant families in Caryophyllales – revisited. Plant Biology 8: 821–830. PubMed
Hijmans RJ, Cameron SE, Parra JL, Jones PG, Jarvis A. 2005. Very high resolution interpolated climate surfaces for global land areas. International Journal of Climatology 25: 1965–1978.
Ibarra-Laclette E, Albert VA, Herrera-Estrella A, Herrera-Estrella L. 2011a. Is GC bias in the nuclear genome of the carnivorous plant PubMed PMC
Ibarra-Laclette E, Albert VA, Perez-Torres CA PubMed PMC
Ibarra-Laclette E, Lyons E, Hernández-Guzmán G PubMed PMC
International Rice Genome Sequencing Project. 2005. The map-based sequence of the rice genome. Nature 436: 793–800. PubMed
Jensen MK, Vogt JK, Bressendorff S PubMed PMC
Jobson RW, Albert VA. 2002. Molecular rates parallel diversification contrasts between carnivorous plant sister lineages. Cladistics 18: 127–136. PubMed
Kondo K, Nontachaiyapoom S. 2008. An evidence on diffused centromeres in
Leitch AR, Leitch IJ. 2008. Genomic plasticity and the diversity of polyploid plants. Science 320: 481–483. PubMed
Leushkin EV, Sutormin RA, Nabieva ER, Penin AA, Kondrashov AS, Logacheva MD. 2013. The miniature genome of a carnivorous plant PubMed PMC
Lipnerová I, Bureš P, Horová L, Šmarda P. 2013. Evolution of genome size in PubMed PMC
Lukhtanov VA, Shapoval NA, Anokhin BA, Saifitdinova AF, Kuznetsova VG. 2015. Homoploid hybrid speciation and genome evolution via chromosome sorting. Proceedings of the Royal Society B: Biological Sciences 282: 20150157. PubMed PMC
Mann S, Phoebe-Chen YP. 2010 PubMed
McPherson S. 2008. Glistening carnivores the sticky-leaved insect-eating plants. Poole, UK: Redfern Natural History Productions.
McPherson S. 2010. Carnivorous plants and their habitats, vol. 2. Poole, UK: Redfern Natural History Productions.
Musto H, Naya H, Zavala A PubMed
Nishikawa K, Furuta Y, Ishitobi K. 1984. Chromosomal evolution in genus
Nishio Y, Nakamura Y, Kawarabayasi Y PubMed PMC
Orme D, Freckleton R, Thomas G
Paradis E, Claude J, Strimmer K. 2004. APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20: 289–290. PubMed
R Core Team
Revell LJ. 2012. Phytools: an R package for phylogenetic comparative biology (and other things). Methods in Ecology and Evolution 3: 217–223.
Rivadavia F, de Miranda VFO, Hoogenstrijd G, Pinheiro F, Heubl G, Fleichmann A. 2012. Is PubMed PMC
Roalson E, McCubbin AG, Whitkus R. 2007. Chromosome evolution in Cyperales In: Columbus JT, Friar EA, Porter JM, Prince LM, Simpson MG, eds. Monocots: comparative biology and evolution of Poales. Claremont, CA: Allen, 62–71.
Rothfels K, Heimburg M. 1968. Chromosome size and DNA values in sundews (Droseraceae). Chromosoma 25: 96–103.
Sheikh SA, Kondo K, Hoshi Y. 1995. Study of diffused centromeric nature of
Shirakawa J, Hoshi Y, Kondo K. 2011a. Chromosome differentiation and genome organization in carnivorous plant family Droseraceae. Chromosome Botany 6: 111–119.
Shirakawa J, Nagano K, Hoshi Y. 2011b. A chromosome study of two centromere differentiating
Šíchová J., Ohno M, Dincă V, Watanabe M, Sahara K, Marec F. 2016. Fissions, fusions, and translocations shaped the karyotype and multiple sex chromosome constitution of the northeast-Asian wood white butterfly,
Šmarda P, Bureš P. 2012. The variation of base composition in plant genomes In: Wendel JF, Greilhuber J, Doležel J, Leitch IJ, eds. Plant genome diversity, vol. 1 Vienna: Springer, 209–235.
Šmarda P, Bureš P, Horová L, Foggi B, Rossi G. 2008. Genome size and GC content evolution of PubMed PMC
Šmarda P, Bureš P, Horová L, et al. 2014. Ecological and evolutionary significance of genomic GC content diversity in monocots. Proceedings of the National Academy of Sciences, USA 111: E4096–E4102. PubMed PMC
Sterner RW, Elser JJ. 2002. Ecological stoichiometry. The biology of elements from molecules to biosphere. Princeston and Oxford: Princeston University Press.
Veleba A, Bureš P, Adamec L, Šmarda P, Lipnerová I, Horová I. 2014. Genome size and genomic GC content evolution in the miniature genome-sized family Lentibulariaceae. New Phytologist 203: 22–28. PubMed
Veselý P, Bureš P, Šmarda P, Pavlíček T. 2012. Genome size and DNA base composition of geophytes: the mirror of phenology and ecology? Annals of Botany 109: 65–75. PubMed PMC
Vu GTH, Schmutzer T, Bull F PubMed
Wendel J, Greilhuber J, Doležel J, Leitch IJ. 2013. Plant genome diversity. Vol. 2. Physical structure of plant genomes. Heidelberg: Springer.
Záveská Drábková L, Vlček C. 2010. Molecular phylogeny of the genus PubMed
Zedek F, Bureš P. 2016. Absence of positive selection on CenH3 in PubMed PMC
Zedek F, Šmerda J, Šmarda P, Bureš P. 2010. Correlated evolution of LTR retrotransposons and genome size in the genus PubMed PMC
Zedek F, Veselý P, Horová L, Bureš P. 2016. Flow cytometry may allow microscope-independent detection of holocentric chromosomes in plants. Scientific Reports 6: 27161. doi: 10.1038/srep27161. PubMed PMC
Centromere drive may propel the evolution of chromosome and genome size in plants
The smallest angiosperm genomes may be the price for effective traps of bladderworts
Chromosome size matters: genome evolution in the cyperid clade
Reference standards for flow cytometric estimation of absolute nuclear DNA content in plants
Recent ecophysiological, biochemical and evolutional insights into plant carnivory
Super-Resolution Microscopy Reveals Diversity of Plant Centromere Architecture