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Genetics/ Molecular Biology

Intragenomic nuclear RNA variation in a cryptic Amanita taxon

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Pages 93-103 | Received 13 May 2017, Accepted 10 Jan 2018, Published online: 04 Jun 2018

LITERATURE CITED

  • Adams KL, Wendel JF. 2005. Polyploidy and genome evolution in plants. Current Opinion in Plant Biology 8:135–141.
  • Aldrovandi MSP, Johnson JE, O’Meara BC, Petersen RH, Hughes KW. 2015. The Xeromphalina campanella/kauffmanii complex: species delineation and biogeographical patterns of speciation. Mycologia 107:1270–1284.
  • Alvarez I, Wendel JF. 2003. Ribosomal ITS sequences and plant phylogenetic inference. Molecular Phylogenetics and Evolution 29:417–434.
  • Bennett RJ, Smith AG. 1991. Use of a genomic clone for ribosomal RNA from Brassica oleraceae. RFLP analysis of Brassica Species. Plant Molecular Biology 16:685–688.
  • Chen ZJ, Ni Z. 2006. Mechanisms of genomic rearrangements and gene expression changes in plant polyploids. Bioessays 28:240–252.
  • Coen E, Strachan T, Dover G. 1982. Dynamics of concerted evolution of ribosomal DNA and histone gene families in the melanogaster species subgroup of Drosophila. Journal of Molecular Biology 158:17–35.
  • Dakai TC, Giudici P, Solieri L. 2016. Contrasting patterns of rDNA homogenization within the Zygosaccharomyces rouxii species complex. PLoS ONE 11(8): e0160744. DOI:10.1371/journal.pone.0160744
  • Dover GA. 1989. Linkage disequilibrium and molecular drive in the rDNA gene family. Genetics 122:249–252.
  • Eickbush TH, Eickbush DG. 2007. Finely orchestrated movements: evolution of the ribosomal RNA genes. Genetics 175:477–485.
  • Fuertes-Aguilar J, Rosello JA, Nieto-Feliner G. 1999. Nuclear ribosomal DNA (nrDNA) concerted evolution in natural and artificial hybrids of Arneria (Plumbaginaceae). Molecular Ecology 8:1341–1346.
  • Ganley ARD, Kobayashi T. 2007. Highly efficient concerted evolution in the ribosomal DNA repeats: total rDNA repeat variation revealed by whole-genome shotgun sequence data. Genome Research 17:184–191.
  • GCG. 2000.Wisconsin Package of sequence analysis programs, Version 10.3 Accelrys Inc., San Diego, California.
  • Geneious. 2015. Geneious version 8.1.8 created by Biomatters. Available from: http://www.geneious.com/
  • Graur D, Li W-H. 2000. Fundamentals of molecular evolution. Sunderland, Massachusetts: Sinauer Associates. 439 p.
  • Guindon S, Gascuel O. 2008. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology 52:696–704.
  • Hughes KW, Petersen RH. 2001. Apparent recombination or gene conversion in the ribosomal ITS region of a Flammulina (Fungi, Agaricales) hybrid. Molecular Biology and Evolution. 18:94–96.
  • Hughes KW, Petersen RH, Lickey EB. 2009. Using heterozygosity to estimate a percentage DNA sequence similarity for environmental species delimitation across basidiomycete fungi. New Phytologist 182:795–798.
  • Hughes KW, Petersen RH, Lodge DJ, Bergemann S, Baumgartner K, Tulloss RET, Lickey EB, Cifuentes Blanco J. 2013. Evolutionary consequences of putative intra- and interspecific hybridization in agaric fungi. Mycologia 105:1577–1594.
  • Hughes KW, Reboredo-Segovia A, Morris SD. 2015. Cloning of ribosomal ITS PCR products creates frequent, non-random chimeric sequences—a test involving a heterozygotes between Gymnopus dichrous taxa I and II. Mycokeys 10:45–56.
  • James SA, O’Kelly MJT, Carter DM, Davey RP, van Oudenaarden A, Roberts IN. 2009. Repetitive sequence variation and dynamics in the ribosomal DNA array of Saccharomyces cerevisiae as revealed by whole-genome resequencing. Genome Research 19:626–635.
  • Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, Thierer T, Ashton B, Mentjies P, Drummond A. 2012. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647–1649.
  • Kovarik A, Dadejova M, Lim YK, Chase MW, Clarkson JJ, Knapp S, Leitch AR. 2008. Evolution of rDNA in Nicotiana Allopolyploids: a potential link between rDNA homogenization and epigenetics. Annals of Botany 101:815–823.
  • Liao D. 2000. Gene conversion drives within genic sequences: concerted evolution of ribosomal RNA genes in bacteria and archaea. Journal of Molecular Evolution 51:305–317.
  • Lindner DL, Banik MT. 2011. Intragenomic variation in the ITS rDNA region obscures phylogenetic relationships and inflates estimates of operational taxonomic units in genus Laetiporus. Mycologia 103:731–740.
  • Lindner DL, Carlsen T, Henrik Nilsson R, Davey M, Schumacher T, Kauserud H. 2013. Employing 454 amplicon pyrosequencing to reveal intragenomic divergence in the internal transcribed spacer rDNA region in fungi. Ecology and Evolution 3:1751–1764.
  • Liu YL, Whelen S, Hall BD. 1999. Phylogenetic relationships among ascomycetes: evidence from an RNA polymerase II subunit. Molecular Biology and Evolution 16:1799–1808.
  • Long EO, Dawid IB. 1980. Repeated genes in eukaryotes. Annual Review of Biochemistry 49:727–764.
  • Matheny PB. 2005. Improving phylogenetic inference of mushrooms with RPB1 and RPB2 nucleotide sequences (Inocybe, Agaricales). Molecular Phylogenetics and Evolution 37:1–23.
  • Naidoo K, Steenkamp ET, Coetzee MPA, Wingfield MJ, Wingfield BD. 2013. Concerted evolution in the ribosomal RNA cistron. PLoS ONE 8:e59355.
  • Nei M. 1987. Molecular evolutionary genetics. New York: Columbia University Press. 512 p.
  • O’Donnell K, Cigelnik E. 1997. Two divergent intragenomic rDNA ITS2 types within a monophyletic lineage of the fungus Fusarium are nonorthologous. Molecular Phylogenetics and Evolution 7:103–116.
  • O’Kane SL, Schaal BA, Al-Shehbaz IA. 1996. The origins of Arabidopsis suecica as indicated by nuclear rDNA sequences. Systematic Botany 21:559–566.
  • Prokopowich CD, Gregory TR, Crease TJ. 2003. The correlation between rDNA copy number and genome size in eukaryotes. Genome 46:48–50.
  • Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, Levesque CA, Chen W, Consortium FB. 2012. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proceedings of the National Academy of Sciences of the United States of America 109:6241–6246.
  • Simon UK, Weiß M. 2008. Intragenomic variation of fungal ribosomal genes is higher than previously thought. Molecular Biology and Evolution 25:2251–2254.
  • Tulloss RE, Rodríguez-Caycedo C, Hughes KW, Geml J, Kudzma LV, Wolfe BE, Arora D. 2015. Nomenclatural changes in Amanita. II. Amanitaceae 1:1–6.
  • White TJ, Bruns T, Lee S, Taylor J. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ, eds. PCR protocols: a guide to methods and applications. San Diego, California: Academic Press. p. 315–322.
  • Xu J, Wang P. 2015. Mitochondrial inheritance in basidiomycete fungi. Fungal Biology Reviews 29:209–219.

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