18S rDNA phylogeny of Lamproderma and allied genera (Stemonitales, Myxomycetes, Amoebozoa)

PLoS ONE

Volumn 7, Issue 4, 2012, Pages

  Fiore Donno, Anna Maria ^a   Kamono, Akiko ^b   Meyer, Marianne ^c   Schnittler, Martin ^a   Fukui, Manabu ^b   Cavalier Smith, Thomas ^d  

^a UNIVERSITY OF GREIFSWALD   (Germany)

^b HOKKAIDO UNIVERSITY   (Japan)

^c University of Oxford ^*

^d UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 18S;

AMOEBOZOA; ARTICLE; CONTROLLED STUDY; EXON; GENE SEQUENCE; GENETIC VARIABILITY; INTRON; MORPHOSPECIES; MYXOGASTRIA; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE ALIGNMENT; SIBLING; SPECIES IDENTIFICATION; TAXON; TAXONOMIC IDENTIFICATION;

BASE SEQUENCE; DNA, PROTOZOAN; DNA, RIBOSOMAL; INTRONS; MOLECULAR SEQUENCE DATA; MYXOMYCETES; NUCLEIC ACID CONFORMATION; PHYLOGENY; RNA, RIBOSOMAL, 18S;

EID: 84859945805     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0035359     Document Type: Article

References (51)

1. Cavalier-Smith T, Chao EE, Oates B, (2004) Molecular phylogeny of Amoebozoa and the evolutionary significance of the unikont Phalansterium. Eur J Protistol 40: 21-48.
2. Smirnov A, Chao EE, Nassonova E, Cavalier-Smith T, (2011) A revised classification of naked lobose amoebae (Amoebozoa: Lobosa). Protist 162: 545-570.
3. Lado C, (2001) Nomenmyx. A nomenclatural taxabase of Myxomycetes. Cuad Trab Flora Micol Iber 16: 1-221.
4. Andersen RA, Anderson RO, Banner FT, Barta JR, Boltovskoy D, et al. (2000) The illustrated guide to the Protozoa; Lee JJ, Leedale GF, Bradbury P, editors. Lawrence, Kansas, USA Society of Protozoologists.
5. Dyková I, Lom J, Dvořáková H, Pecková H, Fiala I, (2007) Didymium-like myxogastrids (class Mycetozoa) as endocommensals of sea urchins (Sphaerechinus granularis). Folia Parasitologica 54: 1-12.
6. Fiore-Donno AM, Kamono A, Chao EE, Fukui M, Cavalier-Smith T, (2010) Invalidation of Hyperamoeba by transferring its species to other genera of Myxogastria J Euk Microbiol 57: 189-196.
7. Karpov SA, Mylnikov AP, (1997) Ultrastructure of the colourless flagellate Hyperamoeba flagellata with specifical reference to the flagellar apparatus. Eur J Protistol 33: 349-355.
8. Walochnik J, Michel R, Aspock H, (2004) A molecular biological approach to the phylogenetic position of the genus Hyperamoeba. J Euk Microbiol 51: 433-440.
9. Zaman V, Zaki M, Howe J, Ng M, Leipe DD, et al. (1999) Hyperamoeba isolated from human feces: description and phylogenetic affinity. Eur J Protistol 35: 197-207.
10. Urich T, Lanzén A, Qi J, Huson DH, Schleper C, et al. (2008) Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome. PLoS ONE 3: e2527.
11. ElHage N, Little C, Clark J, (2000) Biosystematics of the Didymium squamulosum complex. Mycologia 92: 54-64.
12. Schnittler M, Mitchell DW, (2000) Species diversity in Myxomycetes based on morphological species concept-a critical examination. Stapfia 73: 55-62.
13. Fiore-Donno AM, Novozhilov Y, Meyer M, Schnittler M, (2011) Genetic structure of two protist species (Myxogastria, Amoebozoa) suggests asexual reproduction in sexual amoebae. PLoS ONE 6: e22872.
14. Olive LS, (1975) The Mycetozoans. New York Academic Press.
15. Clark J, (1997) Myxomycete reproductive systems: Stemonitis species. Mycologia 89: 241-243.
16. Collins ONR, (1981) Myxomycete genetics, 1960-1981. J Elisha Mitchell Sci Soc 97: 101-125.
17. Clark J, Haskins EF, (2010) Reproductive systems in the myxomycetes: a review. Mycosphere 1: 337-353.
18. Schnittler M, Unterseher M, Pfeiffer T, Novozhilov Y, Fiore-Donno AM, (2010) Ecology of sandstone ravine myxomycetes from Saxonian Switzerland (Germany). Nova Hedwigia 90: 277-302.
19. Moreno G, Sanchez A, Singer H, Illana C, Castillo A, (2002) A study on nivicolous Myxomycetes. The genus Lamproderma I. Fungi non Delineati raro vel haud perspecte et explorate descripti aut definite picti, Pars XIX Alassio, Italy Edizioni Candusso pp. 1-65.
20. Poulain M, Meyer M, Bozonnet J, (2011) Les Myxomycètes; Fédération Mycologique et Botanique Dauphiné-Savoie, editor. Sevrier, France.
21. Ronikier A, Ronikier M, (2009) How 'alpine' are nivicolous myxomycetes? A worldwide assessment of altitudinal distribution. Mycologia 101: 1-16.
22. Kalyanasundaram I, Mubarak A, (1989) Taxonomic note on the myxomycete genus Diachea. Mycol Res 93: 233-235.
23. Kalyanasundaram I, (1973) Capillitial development in Stemonitis. Taxonomy of Fungi I. Subramanian C, editor: University of Madras, India pp. 9-13.
24. Haskins EF, Kerr NS, (1978) Vergleich der Plasmodien-Typen und der Sporulation bei Myxomyceten (Film C 1220 des IWF, Göttingen 1976). Publikationen zu Wissenschaftlichen Filmen, Sektion Biologie, 11: 1-34.
25. Fiore-Donno AM, Nikolaev SI, Nelson M, Pawlowski J, Cavalier-Smith T, et al. (2010) Deep phylogeny and evolution of slime moulds (Mycetozoa). Protist 161: 55-70.
26. Shadwick LL, Spiegel FW, Shadwick JDL, Brown MW, Silberman JD, (2009) Eumycetozoa = Amoebozoa?: SSUrDNA phylogeny of protosteloid slime molds and its significance for the amoebozoan supergroup. PLoS ONE 4: e6754.
27. Fiore-Donno AM, Meyer M, Baldauf SL, Pawlowski J, (2008) Evolution of dark-spored Myxomycetes (slime-molds): molecules versus morphology. Mol Phyl Evol 46: 878-889.
28. Dennison ML, (1945) The genus Lamproderma and its relationships. I. Mycologia 37: 80-108.
29. Dennison ML, (1945) The genus Lamproderma and its relationships. II. Mycologia 37: 197-204.
30. Kowalski DT, (1970) The species of Lamproderma. Mycologia 62: 621-672.
31. Meylan C, (1931) Les espèces nivales du genre Lamproderma. Bull Soc Vaud Sci Nat 57: 359-373.
32. Stephenson SL, Novozhilov Y, Schnittler M, (2000) Distribution and ecology of Myxomycetes in high-latitude regions of the Northern Hemisphere. J Biogeogr 27: 741-754.
33. Ing B, (1983) A ravine association of myxomycetes. J Biogeogr 10: 299-306.
34. Alexopoulos CJ, (1973) Myxomycetes. In: The fungi: an advanced treatise. Ainsworth GC, Sparrow FK, Sussman AS, editors. New York: Academic Press pp. 39-60.
35. Ing B, (1999) The Myxomycetes of Britain and Ireland-an identification handbook. Slough, England The Richmond Publishing Co. Ltd.
36. Lado C, Pando F, (1997) Myxomycetes, I. Ceratiomyxales, Echinosteliales, Liceales, Trichiales; Real Jardìn Botanìco de Madrid, editor. Madrid, Espana Cramer, J.
37. Neubert H, Nowotny W, Baumann K, (2000) Die Myxomyceten Deutchlands und des angrenzenden Alpenraumes. Band 3 Stemonitales. Gomaringen (D): K. Baumann Verlag.
38. Hall TA, (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium 41: 95-98.
39. Johansen T, Johansen S, Haugli FB, (1988) Nucleotide sequence of Physarum polycephalum small subunit ribosomal RNA as inferred from the gene sequence: secondary structure and evolutionary implications. Curr Genet 14: 265-273.
40. Guindon S, Gascuel O, (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52: 696-704.
41. Lanave C, Preparata G, Saccone C, Serio G, (1984) A new method for calculating evolutionary substitution rates. J Mol Evol 20: 86-93.
42. Rodriguez F, Oliver JL, Marin A, Medina JR, (1990) The general stochastic model of nucleotide substitution. J Theor Biol 142: 485-501.
43. Stamatakis A, Ludwig T, Meier H, (2005) RAxML-III: A fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 21: 456-463.
44. Huelsenbeck JP, Ronquist F, (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755.
45. Wuyts J, De Rijk P, Van de Peer Y, Pison G, Rousseeuw P, et al. (2000) Comparative analysis of more than 3000 sequences reveals the existence of two pseudoknots in area V4 of eukaryotic small subunit ribosomal RNA. Nuc Ac Res 28: 4698-4708.
46. Lundblad EW, Einvik C, Ronning S, Haugli K, Johansen S, (2004) Twelve group I introns in the same pre-rRNA transcript of the myxomycete Fuligo septica: RNA processing and evolution. Mol Biol Evol 21: 1283-1293.
47. Meylan C, (1930) Note sur un nouveau genre de myxomycètes. Bull Soc Vaud Sci Nat 57: 147-149.
48. Clark J, Stephenson SE, (1990) Didymium iridis reproductive systems: new additions. Mycologia 82: 274-276.
49. Alexopoulos CJ, Brooks TE, (1971) Taxonomic studies in the myxomycetes. III. Clastodermataceae: a new family of the Echinosteliales. Mycologia 63: 925-928.
50. Fiore-Donno AM, Haskins EF, Pawlowski J, Cavalier-Smith T, (2009) Semimorula liquescens is a modified echinostelid myxomycete (Mycetozoa) Mycologia 101: 773-776.
51. Wuyts J, Van de Peer1 Y, Winkelmans T, De Wachter R, (2002) The European database on small subunit ribosomal RNA. Nuc Ac Res 30: 183-185.