Group I introns and associated homing endonuclease genes reveals a clinal structure for Porphyra spiralis var. amplifolia (Bangiales, Rhodophyta) along the Eastern coast of South America

BMC Evolutionary Biology

Volumn 8, Issue 1, 2008, Pages

  Milstein, Daniela ^a   Oliveira, Mariana C ^a   Martins, Felipe M ^a   Matioli, Sergio R ^a  

^a UNIVERSITY OF SÃO PAULO   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

ENDONUCLEASE; RIBOSOME DNA; SELF SPLICING RIBOSOMAL RNA;

ARTICLE; CONTROLLED STUDY; DEMOGRAPHY; GENETIC POLYMORPHISM; GENETIC VARIABILITY; HAPLOTYPE; IN VITRO STUDY; INTRON; MOLECULAR PHYLOGENY; NONHUMAN; NUCLEOTIDE SEQUENCE; POPULATION STRUCTURE; PORPHYRA; RNA TRANSLATION; SOUTH AMERICA; ANIMAL; BIOLOGICAL MODEL; DNA SEQUENCE; GENETIC TRANSCRIPTION; GENETICS; MOLECULAR CLONING; MOLECULAR EVOLUTION; MOLECULAR GENETICS; PHYLOGENY; POPULATION GENETICS; SEQUENCE ALIGNMENT; SMALL RIBOSOMAL SUBUNIT;

BANGIALES; PORPHYRA; PORPHYRA SPIRALIS VAR. AMPLIFOLIA; RHODOPHYTA;

ANIMALS; BASE SEQUENCE; CLONING, MOLECULAR; DNA, RIBOSOMAL; ENDONUCLEASES; EVOLUTION, MOLECULAR; GENETICS, POPULATION; HAPLOTYPES; INTRONS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMORPHISM, GENETIC; PORPHYRA; RIBOSOME SUBUNITS, SMALL; RNA, RIBOSOMAL, SELF-SPLICING; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SOUTH AMERICA; TRANSCRIPTION, GENETIC;

EID: 56549125947     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-8-308     Document Type: Article

References (47)

1. The natural history of group I introns. P Haugen DM Simon D Bhattacharya, Trends Genet 2005 21 2 111 119 10.1016/j.tig.2004.12.007 15661357
2. Variant forms of a group I intron in nuclear small-subunit rRNA genes of the marine red alga Porphyra spiralis var. amplifolia. MC Oliveira MA Ragan, Mol Biol Evol 1994 11 195 207 8170361
3. Nucleolar introns from Physarum flavicomum contain insertion elements that may explain how mobile group-I introns gained their open reading frames. A Vader J Naess K Haugli F Haugli S Johansen, Nucleic Acids Res 1994 22 4553 4559 7984404 10.1093/nar/22.22.4553
4. Complex group-I introns in nuclear SSU rDNA of red and green algae: evidence of homing-endonuclease pseudogenes in the Bangiophyceae. P Haugen VAR Huss H Nielsen S Johansen, Curr Genet 1999 36 345 353 10.1007/s002940050509 10654088
5. A Structural and Phylogenetic Analysis of the Group IC1 Introns in the Order Bangiales (Rhodophyta). KM Müller JJ Cannone RR Gutell RG Sheath, Mol Biol Evol 2001 18 1654 1667 11504846
6. Homing endonucleases: keeping the house in order. M Belfort RJ Roberts, Nucleic Acids Res 1997 25 3379 3388 9254693 10.1093/nar/25.17.3379
7. Mechanisms of intron mobility. M Belfort PS Perlman, J Biol Chem 1995 270 51 30237 30240 10.1074/jbc.270.51.30237 8530436
8. Homing endonucleases: structural and functional insight into the catalysts of intron/intein mobility. BS Chevalier L Stoddard, Nucleic Acids Res 2001 29 3757 3774 11557808 10.1093/nar/29.18.3757
9. The restriction fold turns to the dark side: a bacterial homing endonuclease with a PD-(D/E)-XK motif. L Zhao RP Bonocora DA Shub BL Stoddard, EMBO J 2007 26 2432 2442 17410205 10.1038/sj.emboj.7601672
10. A family of nuclear homing endonucleases. S Johansen TM Embley NP Willassen, Nucleic Acids Res 1993 21 18 4405 8415009 10.1093/nar/21.18.4405
11. The nuclear 18S ribosomal RNA gene of the red alga Hildenbrandia rubra contains a group I intron. MA Ragan CJ Bird EL Rice RK Singh, Nucleic Acids Res 1993 21 16 3898 8367310 10.1093/nar/21.16.3898
12. Biogeography and systematics of Hildenbrandia (Rhodophyta, Hildenbrandiales) in North America: inferences from morphometrics and rbcL and 18S rRNA gene sequence analyses. AR Sherwood RG Sheath, Eur J Phycol 1999 34 523 532
13. Molecular phylogeny of Bangiales (Rhodophyta) based on small subunit rDNA sequencing: Emphasis on Brazilian Porphyra species. D Milstein MC Oliveira, Phycologia 2005 44 2 212 221 10.2216/0031-8884(2005)44[212:MPOBRB]2.0.CO;2
14. A preliminary investigation of the order Bangiales (Bangiophycidae, Rhdophyta) based on sequences of the nuclear small-subunit ribossomal RNA genes. MC Oliveira J Kurniawan CJ Bird EL Rice CA Murphy RK Singh RR Gutell MA Ragan, Phycol Res 1995 43 71 79 10.1111/j.1440-1835.1995.tb00007.x
15. A reassessment of the taxonomic status of Porphyra suborbiculata, Porphyra carolinensis and Porphyra lilliputiana (Bangiales, Rhodophyta) based on molecular and morphological data. JE Broom WA Nelson C Yarish WA Jones R Aguilar Rosas LE Aguilar Rosas, Eur J Phycol 2002 37 227 235 10.1017/S0967026202003566
16. Molecular divergence of the SSU rRNA gene and internal transcribed spacer 1 in Porphyra yezoensis (Rhodophyta). M Kunimoto H Kito Y Kaminishi Y Mizukami N Murase, J Appl Phycol 1999 11 211 216 10.1023/A:1008023525847
17. Molecular features of a defined genetic marker for the determination of the Porphyra tenera lineage. M Kunimoto H Kito Y Mizukami N Murase I Levine, J Appl Phycol 2003 15 337 343 10.1023/A:1025182508440
18. A molecular and morphological investigation of the relationship between Batrachospermum spermatoinvolucrum and B. gelatinosum (Batrachospermales, Rhodophyta). ML Vis RG Sheath, Eur J Phycol 1998 33 231 239 10.1080/ 09670269810001736733
19. Genetic variability and potential sources of Grateloupia doryphora (Halymeniaceae, Rhodophyta), an invasive species in Rhode Island waters (USA). M Marston MV Bohnsack, J Phycol 2002 38 649 658 10.1046/j.1529-8817.2002.01063.x
20. Hybridization studies in Bostrychia. 2: Correlation of crossing data and plastid DNA sequence data within B. radicans and B. moritziana (Rhodophyta, Ceramiales). GC Zuccarello JA West, Phycologia 1997 36 293 304
21. Phylogeography of the Bostrychia calliptera-B. pinnata complex (Rhodomelacea, Rhodophyta) and divergence rates based on nuclear, mitochondrial and plastid DNA markers. GC Zuccarello JA West, Phycologia 2002 41 1 49 60
22. Phylogeography of a freshwater red algae Batrachospermum helminthosum in North America. WB Chiasson NJ Machesky ML Vis, Phycologia 2003 42 6 654 660
23. Molecular identification of two sibling species under the name Gracilaria chilensis (Rhodophyta, Gracilariales). S Cohen S Faugeron EA Martinez JA Correa F Viard C Destombe M Valero, J Phycol 2004 40 742 747 10.1111/j.1529-8817.2004. 03203.x
24. The genus Porphyra C. Ag. (Rhodophyta-Bangiales) in the American South Atlantic. I. Brazilian species. EC Oliveira J Coll, Bot Mar 1975 18 191 197
25. Phylogenetic evidence for horizontal transmission of group I introns in the nuclear ribosomal DNA of mushroom-forming fungi. DS Hibbett, Mol Biol Evol 1996 13 903 917 8751999
26. The ITS region of nuclear ribosomal DNA: a valuable source of evidence on angiosperm phylogeny. BG Baldwin MJ Sanderson JM Porter MF Wojciechowski CS Campbell MJ Donoghue, Ann Missouri Bot Gard 1995 82 247 277 10.2307/2399880
27. BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. TA Hall, Nucleic Acids Symp Ser 1999 41 95 98
28. DNAsp, DNA polymorphism analyses using the coalescent and other methods. J Rozas JC Sanchez-Delbarrio X Messeguer R Rozas, Bioinformatics 2003 19 2496 2497 10.1093/bioinformatics/btg359 14668244
29. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. F Tajima, Genetics 1989 123 3 585 595 2513255
30. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. YX Fu, Genetics 1997 147 915 925 9335623
31. Fluxus-engineering.com. http://www.fluxus-engineering.com
32. Arlequin (version 3.0): an integrated software package for population genetics data analysis. L Excoffier G Laval S Schneider, Evolutionary Bioinformatics Online 2005 1 47 50
33. A new nomenclature of group I introns in ribosomal DNA. S Johansen P Haugen, RNA 2001 7 935 936 11453066 10.1017/S1355838201010500
34. A self-splicing intron in the small subunit rRNA gene of Pneumocystis carinii. ML Sogin JC Edman, Nucleic Acids Res 1989 17 5349 59 2788266 10.1093/nar/17.13.5349
35. J Sambrook EF Fritsch T Maniatis, Molecular Cloning: A Laboratory Manual Cold Spring Harbour Laboratories press 1989
36. Basic local alignment search tool. SF Altschul W Gish W Miller EW Myers DJ Lipman, J Mol Biol 215 403 410 2231712
37. Intraspecific gene genealogies: trees grafting into networks. D Posada KA Crandall, Trends Ecol Evol 2001 16 1 37 45 10.1016/S0169-5347(00)02026-7 11146143
38. Recurrent invasion and extinction of a selfish gene. MR Goddard A Burt, Proc Natl Acad Sci USA 1999 96 13880 13885 10570167 10.1073/pnas.96.24.13880
39. DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-Ppo I. KE Flick MS Jurica RJ Monnat BL Stoddard, Nature 1998 394 96 101 10.1038/27952 9665136
40. Genetic populations structure of the Hawaiian alien invasive seaweed Acanthophora spicifera (Rhodophyta) as revealed by DNA sequencing and ISSR analyses. DC O' Doherty AR Sherwood, Pac Science 2007 61 2 223 233 10.2984/1534-6188(2007)61[223:GPSOTH]2.0.CO;2
41. Rubisco spacer sequence divergence in the rhodophyte alga: a technique for discrimination of closely related species. C Destombe SE Douglas, Curr Genet 1991 19 395 8 10.1007/BF00309601 1680570
42. A molecular and morphological analysis of the Gymnogongrus devoniensis (Rhodophyta) complex in the North Atlantic. CA Maggs SE Douglas J Fenety CJ Bird, J Phycol 1992 28 214 232 10.1111/j.0022-3646.1992.00214.x
43. A mitochondrial marker for red algal intraspecific relationships. GC Zuccarello G Burger JA West RJ King, Mol Ecol 1999 8 1443 1447 10.1046/j.1365-294x.1999.00710.x 10564449
44. A preorganized active site in the crystal structure of the Tetrahymena ribozyme. BL Golden AR Gooding ER Podell TR Cech, Science 1998 282 259 264 10.1126/science.282.5387.259 9841391
45. Self-splicing of group I introns. TR Cech, Annu Rev Biochem 1990 59 543 568 10.1146/annurev.bi.59.070190.002551 2197983
46. A gene phylogeny of the red algae (Rhodophyta) based on plastid rbc L. DW Freshwater S Fredericq BS Butler MH Hommersand MW Chase, Proc Natl Acad Sci USA 1994 91 7281 7285 8041781 10.1073/pnas.91.15.7281
47. Autocatalytic cyclization of an excised intervening sequence RNA is a cleavage-ligation reaction. AJ Zaug PJ Grabowski TR Cech, Nature 1983 301 578 83 10.1038/301578a0 6186917