View Item 

Show simple item record

Phylogenetic analysis of LSU and SSU r DNA group I introns of lichen photobionts associated with the genera X anthoria and X anthomendoza ( T eloschistaceae, lichenized A scomycetes)

dc.contributor.authorNyati, Shyamen_US
dc.contributor.authorBhattacharya, Debashishen_US
dc.contributor.authorWerth, Silkeen_US
dc.contributor.authorHonegger, Rosmarieen_US
dc.contributor.authorClerck, O.en_US
dc.date.accessioned2014-01-08T20:34:35Z
dc.date.available2015-02-03T16:14:39Zen_US
dc.date.issued2013-12en_US
dc.identifier.citationNyati, Shyam; Bhattacharya, Debashish; Werth, Silke; Honegger, Rosmarie; Clerck, O. (2013). "Phylogenetic analysis of LSU and SSU r DNA group I introns of lichen photobionts associated with the genera X anthoria and X anthomendoza ( T eloschistaceae, lichenized A scomycetes)." Journal of Phycology 49(6): 1154-1166.en_US
dc.identifier.issn0022-3646en_US
dc.identifier.issn1529-8817en_US
dc.identifier.urihttps://hdl.handle.net/2027.42/102100
dc.publisherSchweizerbart science publishersen_US
dc.publisherWiley Periodicals, Inc.en_US
dc.subject.otherTrebouxiaen_US
dc.subject.otherLSU 798 Group I Intronen_US
dc.subject.otherLichenen_US
dc.subject.otherTrebouxiophyceaeen_US
dc.subject.otherPhotobionten_US
dc.subject.otherRbcLen_US
dc.subject.otherSSU 1512 Group I Intronen_US
dc.titlePhylogenetic analysis of LSU and SSU r DNA group I introns of lichen photobionts associated with the genera X anthoria and X anthomendoza ( T eloschistaceae, lichenized A scomycetes)en_US
dc.typeArticleen_US
dc.rights.robotsIndexNoFollowen_US
dc.subject.hlbsecondlevelNatural Resources and Environmenten_US
dc.subject.hlbtoplevelScienceen_US
dc.description.peerreviewedPeer Revieweden_US
dc.description.bitstreamurlhttp://deepblue.lib.umich.edu/bitstream/2027.42/102100/1/jpy12126.pdf
dc.identifier.doi10.1111/jpy.12126en_US
dc.identifier.sourceJournal of Phycologyen_US
dc.identifier.citedreferenceNylander, J. A. A. 2004. MrModeltest v2. Program distributed by the author. Evolutionary Biology Centre, Uppsala University. Available at: http://www.abc.se/~nylander/mrmodeltest2/mrmodeltest2.html (last accessed May 15, 2013)en_US
dc.identifier.citedreferenceNishida, H. & Sugiyama, J. 1995. A common group‐I intron between a plant‐parasitic fungus and its host. Mol. Biol. Evol. 12: 883 – 6.en_US
dc.identifier.citedreferenceNyati, S., Scherrer, S., Werth, S. & Honegger, R. 2014. Green algal photobiont diversity ( Trebouxia spp.) in representatives of Teloschistaceae (Lecanoromycetes, lichen‐forming ascomycetes). The Lichenologist 46, in press. doi: 10.1017/S0024282913000819.en_US
dc.identifier.citedreferencePiercey‐Normore, M. D. & DePriest, P. T. 2001. Algal switching among lichen symbioses. Am. J. Bot. 88: 1490 – 8.en_US
dc.identifier.citedreferencePombert, J. F. & Keeling, P. J. 2010. The mitochondrial genome of the entomoparasitic green alga Helicosporidium. PLoS ONE 5: e8954.en_US
dc.identifier.citedreferencePombert, J. F., Otis, C., Lemieux, C. & Turmel, M. 2005. The chloroplast genome sequence of the green alga Pseudendoclonium akinetum (Ulvophyceae) reveals unusual structural features and new insights into the branching order of chlorophyte lineages. Mol. Biol. Evol. 22: 1903 – 18.en_US
dc.identifier.citedreferencePosada, D. & Buckley, T. R. 2004. Model selection and model averaging in phylogenetics: advantages of Akaike Information Criterion and Bayesian approaches over likelihood ratio tests. Syst. Biol. 53: 793 – 808.en_US
dc.identifier.citedreferenceRambaut, A. 2008. FigTree version 1.3. Available at: http://tree.bio.ed.ac.uk/software/figtree/ (last accessed September 28, 2010).en_US
dc.identifier.citedreferenceRambaut, A. & Drummond, A. 2007. Tracer v 1.5. Available at: http://beast.bio.ed.ac.uk/Tracer (last accessed September 27, 2010).en_US
dc.identifier.citedreferenceReeb, V., Haugen, P., Bhattacharya, D. & Lutzoni, F. 2007. Evolution of Pleopsidium (lichenized ascomycota) S943 group I introns and the phylogeography of an intron‐encoded putative homing endonuclease. J. Mol. Evol. 64: 285 – 98.en_US
dc.identifier.citedreferenceRindi, F. & Guiry, M. D. 2003. Composition and distribution of subaerial algal assemblages in Galway City, western Ireland. Cryptogam. Algol. 24: 245 – 67.en_US
dc.identifier.citedreferenceRonquist, F. & Huelsenbeck, J. P. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572 – 4.en_US
dc.identifier.citedreferenceRuoff, B., Johansen, S. & Vogt, V. M. 1992. Characterization of the self‐splicing products of a mobile intron from the nuclear rDNA of Physarum polycephalum. Nucleic Acids Res. 20: 5899 – 906.en_US
dc.identifier.citedreferenceSakamoto, Y., Ishiguro, M. & Kitagawa, G. 1986. Akaike Information Criterion Statistics. D. Reidel, Dordrecht.en_US
dc.identifier.citedreferenceSanchez‐Puerta, M. V., Cho, Y., Mower, J. P., Alverson, A. J. & Palmer, J. D. 2008. Frequent, phylogenetically local horizontal transfer of the cox1 group I Intron in flowering plant mitochondria. Mol. Biol. Evol. 25: 1762 – 77.en_US
dc.identifier.citedreferenceScherrer, S., De Vries, O., Dudler, R., Wessels, J. & Honegger, R. 2000. Interfacial self‐assembly of fungal hydrophobins of the lichen‐forming ascomycetes Xanthoria parietina and X. ectaneoides. Fungal Genet. Biol. 30: 81 – 93.en_US
dc.identifier.citedreferenceSimon, D., Moline, J., Helms, G., Friedl, T. & Bhattacharya, D. 2005. Divergent histories of rDNA group I introns in the lichen family Physciaceae. J. Mol. Evol. 60: 434 – 46.en_US
dc.identifier.citedreferenceSogin, M., Ingold, A., Karlok, M., Nielsen, H. & Engberg, J. 1986. Phylogenetic evidence for the acquisition of ribosomal RNA introns subsequent to the divergence of some of the major Tetrahymena groups. EMBO J. 5: 3625 – 30.en_US
dc.identifier.citedreferenceSwofford, D. L. 2003. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sinauer Associates, Sundarland, MA, USA.en_US
dc.identifier.citedreferenceTamura, K., Dudley, J., Nei, M. & Kumar, S. 2007. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24: 1596 – 9.en_US
dc.identifier.citedreferenceTavaré, S. 1986. Some probabilistic and statistical problems in the analysis of DNA sequences. Lectures on Mathematics in the Life Sciences (American Mathematical Society) 17: 57 – 86.en_US
dc.identifier.citedreferenceThompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. G. 1997. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25: 4876 – 82.en_US
dc.identifier.citedreferenceTurmel, M., Cote, V., Otis, C., Mercier, J. P., Gray, M. W., Lonergan, K. M. & Lemieux, C. 1995. Evolutionary transfer of ORF containing Group‐I introns between different subcellular compartments (chloroplast and mitochondrion). Mol. Biol. Evol. 12: 533 – 45.en_US
dc.identifier.citedreferenceVaughn, J. C., Mason, M. T., Sperwhitis, G. L., Kuhlman, P. & Palmer, J. D. 1995. Fungal origin by horizontal transfer of a plant mitochondrial Group‐I intron in the chimeric CoxI gene of Peperomia. J. Mol. Evol. 41: 563 – 72.en_US
dc.identifier.citedreferenceZuker, M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31: 3406 – 15.en_US
dc.identifier.citedreferenceAhmadjian, V. 1988. The lichen alga Trebouxia ‐ does it occur free‐living. Plant Syst. Evol. 158: 243 – 7.en_US
dc.identifier.citedreferenceAimi, T., Yamada, T., Yamashita, M. & Murooka, Y. 1994. Characterization of the nuclear large subunit ribosomal RNA encoding gene and the group‐I self splicing intron from Chlorella ellipsoidea C‐87. Gene 145: 139 – 44.en_US
dc.identifier.citedreferenceAltschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. 1997. Gapped BLAST and PSI‐BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389 – 402.en_US
dc.identifier.citedreferenceBachar, D., Guillou, L. & Christen, R. 2013. Detection of introns in eukaryotic small subunit ribosomal RNA gene sequences. Dataset Papers Biol. 2013: 12.en_US
dc.identifier.citedreferenceBeck, A., Friedl, T. & Rambold, G. 1998. Selectivity of photobiont choice in a defined lichen community: inferences from cultural and molecular studies. New Phytol. 139: 709 – 20.en_US
dc.identifier.citedreferenceBeck, A., Kasalicky, T. & Rambold, G. 2002. Myco‐photobiontal selection in a Mediterranean cryptogam community with Fulgensia fulgida. New Phytologist 153: 317 – 26.en_US
dc.identifier.citedreferenceBhattacharya, D., Cannone, J. J. & Gutell, R. R. 2001. Group I intron lateral transfer between red and brown algal ribosomal RNA. Curr. Genet. 40: 82 – 90.en_US
dc.identifier.citedreferenceBhattacharya, D., Damberger, S., Surek, B. & Melkonian, M. 1996a. Primary and secondary structure analyses of the rDNA group‐I introns of the Zygnematales (Charophyta). Curr. Genet. 29: 282 – 6.en_US
dc.identifier.citedreferenceBhattacharya, D., Friedl, T. & Damberger, S. 1996b. Nuclear‐encoded rDNA group I introns: origin and phylogenetic relationships of insertion site lineages in the green algae. Mol. Biol. Evol. 13: 978 – 89.en_US
dc.identifier.citedreferenceBhattacharya, D., Friedl, T. & Helms, G. 2002. Vertical evolution and intragenic spread of lichen‐fungal group I introns. J. Mol. Evol. 55: 74 – 84.en_US
dc.identifier.citedreferenceBhattacharya, D., Surek, B., Rusing, M., Damberger, S. & Melkonian, M. 1994. Group I introns are inherited through common ancestry in the nuclear encoded ribosomal RNA of Zygnematales (Charophyceae). Proc. Nat. Acad. Sci. USA 91: 9916 – 20.en_US
dc.identifier.citedreferenceBhattacharya, D., Weber, K., An, S. S. & Berning‐Koch, W. 1998. Actin phylogeny identifies Mesostigma viride as a flagellate ancestor of the land plants. J. Mol. Evol. 47: 544 – 50.en_US
dc.identifier.citedreferenceBoch, S., Prati, D., Werth, S., Rüetschi, J. & Fischer, M. 2011. Lichen endozoochory by snails. PLoS ONE 6: e18770.en_US
dc.identifier.citedreferenceBurke, J. M., Belfort, M., Cech, T. R., Davies, R. W., Scweyen, R. J., Shub, D. A., Szostak, J. W. & Tabak, H. F. 1987. Structural conventions for group I introns. Nucleic Acids Res. 15: 7217 – 21.en_US
dc.identifier.citedreferencedel Campo, E. M., Casano, L. M., Gasulla, F. & Barreno, E. 2009. Presence of multiple group I introns closely related to bacteria and fungi in plastid 23S rRNAs of lichen‐forming Trebouxia. Int. microbiol. J. Spanish Soc. Microbiol. 12: 59 – 67.en_US
dc.identifier.citedreferenceCech, T. R. 1988. Conserved sequences and structures of Group‐I introns ‐ building an active‐site for RNA catalysis ‐ a review. Gene 73: 259 – 71.en_US
dc.identifier.citedreferenceCech, T. R., Damberger, S. H. & Gutell, R. R. 1994. Representation of the secondary and tertiary structure of Group‐I Introns. Nat. Struct. Biol. 1: 273 – 80.en_US
dc.identifier.citedreferenceCurtis, B. A. & Archibald, J. M. 2010. A spliceosomal intron of mitochondrial DNA origin. Curr. Biol. 20: R919 – 20.en_US
dc.identifier.citedreferenceDel Campo, E. M., Casano, L. M., Gasulla, F. & Barreno, E. 2010a. Suitability of chloroplast LSU rDNA and its diverse group I introns for species recognition and phylogenetic analyses of lichen‐forming Trebouxia algae. Mol. Phylogenet. Evol. 54: 437 – 44.en_US
dc.identifier.citedreferenceDel Campo, E. M., Gimeno, J., De Nova, J. P. G., Casano, L. M., Gasulla, F., García‐Breijo, F., Reig‐Armiñana, J. & Barreno, E. 2010b. South European populations of Ramalina farinacea (L.) Ach. share different Trebouxia algae. In Thomas Nash III; Linda Geiser; Bruce McCune; Dagmar Triebel; Alexandru M. Tomescu; William Sanders [Ed.] Biology of Lichens – Symbiosis, Ecology, Environm. Monitoring, Systematics, Cyber Applications. Schweizerbart science publishers, Stuttgart, Germany, pp. 247 – 56.en_US
dc.identifier.citedreferenceDePriest, P. T. 1993. Small subunit rDNA variation in a population of lichen fungi due to optional group I introns. Gene 134: 67 – 74.en_US
dc.identifier.citedreferenceDePriest, P. T. 2004. Early molecular investigations of lichen‐forming symbionts: 1986–2001. Annu. Rev. Microbiol. 58: 273 – 301.en_US
dc.identifier.citedreferenceDePriest, P. T. & Been, M. D. 1992. Numerous group I introns with variable distributions in the ribosomal DNA of a lichen fungus. J. Mol. Biol. 228: 315 – 21.en_US
dc.identifier.citedreferenceDrummond, A., Suchard, M. A., Xie, D. & Rambaut, A. 2012. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol. 29: 1969 – 73.en_US
dc.identifier.citedreferenceDujon, B. 1989. Group I introns as mobile genetic elements: facts and mechanistic speculations ‐ a review. Gene 82: 91‐&.en_US
dc.identifier.citedreferenceEinvik, C., Elde, M. & Johansen, S. 1998. Group I twintrons: genetic elements in myxomycete and schizopyrenid amoeboflagellate ribosomal DNAs. J. Biotechnol. 64: 63 – 74.en_US
dc.identifier.citedreferenceEttl, H. & Gärtner, G. 1995. Syllabus der Boden‐, Luft‐und Flechtenalgen. Gustav Fischer, Stuttgart, Germany.en_US
dc.identifier.citedreferenceFarris, J. S., Källersjö, M., Kluge, A. G. & Bult, C. 1995. Testing significance of incongruence. Cladistics 10: 315 – 9.en_US
dc.identifier.citedreferenceFriedl, T., Besendahl, A., Pfeiffer, P. & Bhattacharya, D. 2000. The distribution of group I introns in lichen algae suggests that lichenization facilitates intron lateral transfer. Mol. Phylogenet. Evol. 14: 342 – 52.en_US
dc.identifier.citedreferenceGargas, A., Depriest, P. T., Grube, M. & Tehler, A. 1995a. Multiple origins of lichen symbioses in fungi suggested by SSU rDNA phylogeny. Science 268: 1492 – 5.en_US
dc.identifier.citedreferenceGargas, A., Depriest, P. T. & Taylor, J. W. 1995b. Positions of multiple insertions in SSU rDNA of lichen‐forming fungi. Mol. Biol. Evol. 12: 208 – 18.en_US
dc.identifier.citedreferenceGutierrez, G., Blanco, O., Divakar, P. K., Lumbsch, H. T. & Crespo, A. 2007. Patterns of group I intron presence in nuclear SSU rDNA of the lichen family Parmeliaceae. J. Mol. Evol. 64: 181 – 95.en_US
dc.identifier.citedreferenceHarris, L. B. & Rogers, S. O. 2011. Evolution of small putative group I introns in the SSU rRNA gene locus of Phialophora species. BMC Res. Notes 4: 258.en_US
dc.identifier.citedreferenceHaugen, P., Simon, D. M. & Bhattacharya, D. 2005a. The natural history of group I introns. Trends Genet. 21: 111 – 9.en_US
dc.identifier.citedreferenceHaugen, P., Wikmark, O.‐G., Vader, A., Coucheron, D. H., Sjøttem, E. & Johansen, S. D. 2005b. The recent transfer of a homing endonuclease gene. Nucleic Acids Res. 33: 2734 – 41.en_US
dc.identifier.citedreferenceHelms, G. 2003. Taxonomy and symbiosis in associations of Physciaceae and Trebouxia. PhD thesis, University of Göttingen, Göttingen, Germany, 156 pp.en_US
dc.identifier.citedreferenceHonegger, R. 1991. Functional aspects of the lichen symbiosis. Ann. Rev. Plant Physiol. Mol. Biol. 42: 553 – 78.en_US
dc.identifier.citedreferenceHonegger, R. 2001. The symbiotic phenotype of lichen‐forming ascomycetes. In Hock, B. [Ed.] Fungal Associations. Springer, Berlin, pp. 165 – 88.en_US
dc.identifier.citedreferenceHonegger, R. 2003. The impact of different long‐term storage conditions on the viability of lichen‐forming ascomycetes and their green algal photobiont. Trebouxia spp. Plant Biol. 5: 324 – 30.en_US
dc.identifier.citedreferenceHonegger, R. 2012. Differential gene expression within the cyanobacterial cell population of a lichen thallus. New Phytol. 196: 657 – 60.en_US
dc.identifier.citedreferenceHonegger, R., Edwards, D. & Axe, L. 2013a. The earliest records of internally stratified cyanobacterial and algal lichens from the Lower Devonian of the Welsh Borderland. New Phytol. 197: 264 – 75.en_US
dc.identifier.citedreferenceHonegger, R., Axe, L. & Edwards, D. 2013b. Bacterial epibionts and endolichenic actinobacteria and fungi in the Lower Devonian lichen. Chlorolichenomycites salopensis. Fungal Biology 117: 512 – 8.en_US
dc.identifier.citedreferenceHoshina, R. & Imamura, N. 2009. Phylogenetically close group I introns with different positions among Paramecium bursaria photobionts imply a primitive stage of intron diversification. Mol. Biol. Evol. 26: 1309 – 19.en_US
dc.identifier.citedreferenceHuelsenbeck, J. P. & Ronquist, F. 2001. MrBayes: Bayesian inference of phylogeny. Bioinformatics 17: 754 – 5.en_US
dc.identifier.citedreferenceItten, B. & Honegger, R. 2010. Population genetics in the homothallic lichen‐forming ascomycete Xanthoria parietina. Lichenologist 42: 751 – 61.en_US
dc.identifier.citedreferenceJohansen, S., Muscarella, D. E. & Vogt, V. M. 1996. Insertion Elements in Ribosomal DNA Ribosomal RNA: Structure, evolution, processing, and function in biosynthesis. CRC Press, Boca Raton, FL, pp. 89 – 110.en_US
dc.identifier.citedreferenceJohn, D. M., Whitton, B. A. & Brook, A. J. 2002. The Freshwater Algal Flora of the British Isles: An Identification Guide to Freshwater and Terrestrial Algae. Cambridge University Press, Cambridge, UK.en_US
dc.identifier.citedreferenceKroken, S. & Taylor, J. W. 2000. Phylogenetic species, reproductive mode, and specificity of the green alga Trebouxia forming lichens with the fungal genus Letharia. Bryologist 103: 645 – 60.en_US
dc.identifier.citedreferenceKuhsel, M. G., Strickland, R. & Palmer, J. D. 1990. An ancient Group‐I intron shared by eubacteria and chloroplasts. Science 250: 1570 – 3.en_US
dc.identifier.citedreferenceLindstrom, S. C. & Pistolic, J. 2005. Detection of a Group I (IE) fungal intron in the green algal genus Urospora (Ulvophyceae). J. Phycol. 41: 359 – 65.en_US
dc.identifier.citedreferenceMaddison, W. P. & Maddison, D. R. 2002. MacClade. Sinauer Associates, Sundarland, MA, USA.en_US
dc.identifier.citedreferenceMcManus, H. A., Lewis, L. A., Fucikova, K. & Haugen, P. 2012. Invasion of protein coding genes by green algal ribosomal group I introns. Mol. Phylogenet. Evol. 62: 109 – 16.en_US
dc.identifier.citedreferenceMeier, F. A., Scherrer, S. & Honegger, R. 2002. Faecal pellets of lichenivorous mites contain viable cells of the lichen‐forming ascomycete Xanthoria parietina and its green algal photobiont, Trebouxia arboricola. Biol. J. Linnean Soc. 76: 259 – 68.en_US
dc.identifier.citedreferenceMichel, F. & Westhof, E. 1990. Modeling of the 3 dimensional architecture of group I catalytic introns based on comparative sequence analysis. J. Mol. Biol. 216: 585 – 610.en_US
dc.identifier.citedreferenceMüller, K. M., Ellenor, D. W., Sherwood, A. R., Sheath, R. G., Cannone, J. J. & Gutell, R. R. 2005. Evidence for lateral transfer of an IE intron between fungal and red algal small subunit rRNA genes. J. Phycol. 41: 380 – 90.en_US
dc.identifier.citedreferenceMyllys, L., Kallersjo, M. & Tehler, A. 1999. Variable sizes of introns in the SSU rDNA in three species of Roccella (Arthoniales, Euascomycetes). Curr. Genet. 36: 79 – 85.en_US
dc.identifier.citedreferenceNelsen, M. P. & Gargas, A. 2008. Dissociation and horizontal transmission of codispersing lichen symbionts in the genus Lepraria (Lecanorales: Stereocaulaceae). New Phytol. 177: 264 – 75.en_US
dc.identifier.citedreferenceNelsen, M. P. & Gargas, A. 2009. Symbiont flexibility in Thamnolia vermicularis (Pertusariales: Icmadophilaceae). Bryologist 112: 404 – 17.en_US
dc.identifier.citedreferenceNielsen, H. & Johansen, S. D. 2009. Group I introns: moving in new directions. RNA Biol. 6: 375 – 83.en_US
dc.owningcollnameInterdisciplinary and Peer-Reviewed


Files in this item

Name:
jpy12126.pdf
Size:
343.4KB
Format:
PDF
View/Open

Show simple item record

Remediation of Harmful Language

The University of Michigan Library aims to describe library materials in a way that respects the people and communities who create, use, and are represented in our collections. Report harmful or offensive language in catalog records, finding aids, or elsewhere in our collections anonymously through our metadata feedback form. More information at Remediation of Harmful Language.

Accessibility

If you are unable to use this file in its current format, please select the Contact Us link and we can modify it to make it more accessible to you.