Distribution and evolution of pseudogenes, gene losses, and a gene rearrangement in the plastid genome of the nonphotosynthetic liverwort, Aneura mirabilis (Metzgeriales, Jungermanniopsida)

Journal of Molecular Evolution

Volumn 67, Issue 1, 2008, Pages 111-122

  Wickett, Norman J ^a   Fan, Yu ^a   Lewis, Paul O ^a   Goffinet, Bernard ^a  

^a UNIVERSITY OF CONNECTICUT   (United States)

Author keywords

Aneura mirabilis; Bryophytes; Chloroplast; Cryptothallus; Liverworts; Parasitic plants; Pseudogenes; Selective constraints

Indexed keywords

CHLOROPHYLL;

ARTICLE; CONTROLLED STUDY; DNA EXTRACTION; EVOLUTION; FUNCTIONAL GENOMICS; GENE AMPLIFICATION; GENE LOSS; GENE REARRANGEMENT; LIVERWORT; NDH GENE; NONHUMAN; PLASTID; POLYMERASE CHAIN REACTION; PSEUDOGENE;

EVOLUTION, MOLECULAR; GENE DELETION; GENE REARRANGEMENT; GENES, PLANT; GENOME, PLASTID; HEPATOPHYTA; PHYLOGENY; PSEUDOGENES;

ANEURA; BRYOPHYTES; CRYPTOTHALLUS; JUNGERMANNIOPSIDA; MARCHANTIA POLYMORPHA; MARCHANTIOPHYTA; METZGERIALES; MIRABILIS;

EID: 48449093225     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-008-9133-1     Document Type: Article

References (60)

1. LA Allison LD Simon P Maliga 1996 Deletion of rpoB reveals a second distinct transcription system in plastids of higher plants EMBO J 15 2802 2809
2. S Berg K Krupinska K Krause 2003 Plastids of three Cuscuta species differing in plastid coding capacity have a common parasite-specific RNA composition Planta 218 135 142
3. MI Bidartondo 2005 The evolutionary ecology of myco-heterotrophy New Phytol 167 335 352
4. MI Bidartondo TD Bruns M Weiss C Sergio DJ Read 2003 Specialized cheating of the ectomycorrhizal symbiosis by an epiparasitic liverwort Proc Roy Soc Lond B Biol Sci 270 835 842
5. MC Brundrett 2002 Coevolution of roots and mycorrhizas of land plants New Phytol 154 275 304
6. RA Bungard 2004 Photosynthetic evolution in parasitic plants: insight from the chloroplast genome BioEssays 26 235 247
7. CJ Cox B Goffinet AJ Shaw SB Boles 2004 Phylogenetic relationships among the mosses based on heterogeneous Bayesian analysis of multiple genes from multiple genomic compartments Syst Bot 29 234 250
8. Crandall-Stotler B, Stotler RE (2000) Morphology and classification of Marchantiophyta. Cambridge University Press, Cambridge
9. Davis EC (2004) A molecular phylogeny of leafy liverworts (Jungermanniidae: Marchantiophyta). Missouri Botanical Garden Press, St. Louis
10. P Delavault P Thalouarn 2002 The obligate root parasite Orobanche cumana exhibits several rbcL sequences Gene 297 85 92
11. PM Delavault NM Russo NA Lusson PA Thalouarn 1996 Organization of the reduced plastid genome of Lathraea clandestina, an achlorophyllous parasitic plant Physiol Plantarum 96 674 682
12. CW dePamphilis JD Palmer 1990 Loss of photosynthetic and chlororespiratory genes from the plastid genome of a parasitic flowering plant Nature 348 337 339
13. TS Feild TJ Brodribb 2005 A unique mode of parasitism in the conifer coral tree Parasitaxus ustus (Podocarpaceae) Plant Cell Environ 28 1316 1325
14. LL Forrest EC Davis DG Long BJ Crandall-Stotler A Clark ML Hollingsworth 2006 Unraveling the evolutionary history of the liverworts (Marchantiophyta): multiple taxa, genomes and analyses Bryologist 109 303 334
15. HT Funk S Berg K Krupinska UG Maier K Krause 2007 Complete DNA sequences of the plastid genomes of two parasitic flowering plant species, Cuscuta reflexa and Cuscuta gronovii BMC Plant Biol 7 45
16. B Goffinet RJ Bayer DH Vitt 1998 Circumscription and phylogeny of the Orthotrichales (Bryopsida) inferred from rbcL sequence analyses Am J Bot 85 1324 1337
17. B Goffinet NJ Wickett AJ Shaw CJ Cox 2005 Phylogenetic significance of the rpoA loss in the chloroplast genome of mosses Taxon 54 353 360
18. G Haberhausen K Zetsche 1994 Functional loss of all ndh genes in an otherwise relatively unaltered plastid genome of the holoparasitic flowering plant Cuscuta reflexa Plant Mol Biol 24 217 222
19. M Hager M Hermann A Biehler A Krieger-Liszkay R Bock 2002 Lack of the small plastid-encoded psbJ polypeptide results in a defective water-splitting apparatus of photosystem II, reduced photosystem I levels, and hypersensitivity to light J Biol Chem 277 14031 14039
20. PTJ Hajdukiewicz LA Allison P Maliga 1997 The two RNA polymerases encoded by the nuclear and the plastid compartments transcribe distinct groups of genes in tobacco plastids EMBO J 16 4041 4048
21. DM Hillis JJ Bull 1993 An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis Syst Biol 42 182 192
22. EA Kellogg ND Juliano 1997 The structure and function of RuBisCO and their implications for systematic studies Am J Bot 84 413 428
23. P Korall KA Pryer JS Metzgar H Schneider DS Conant 2006 Tree ferns: monophyletic groups and their relationships as revealed by four protein-coding plastid loci Mol Phylogenet Evol 39 830 845
24. SL Kosakovsky Pond SDW Frost 2005 A genetic algorithm approach to detecting lineage-specific variation in selection pressure Mol Biol Evol 22 478 485
25. SL Kosakovsky Pond SDW Frost SV Muse 2005 HyPhy: hypothesis testing using phylogenies Bioinformatics 21 676 679
26. K Krause S Berg K Krupinska 2003 Plastid transcription in the holoparasitic plant genus Cuscuta: parallel loss of the rrn16 PEP-promoter and of the rpoA and rpoB genes coding for the plastid-encoded RNA polymerase Planta 216 815 823
27. K Krause RM Maier W Kofer K Krupinska RG Herrmann 2000 Disruption of plastid-encoded RNA polymerase genes in tobacco: expression of only a distinct set of genes is not based on selective transcription of the plastid chromosome Mol Gen Genet 263 1022 1030
28. Kuijt J (1969) The biology of parasitic flowering plants. University of California Press, Berkeley
29. Maddison DR, Maddison WP (2000) MacClade version 4: analysis of phylogeny and character evolution. Sinauer Associates, Sunderland, MA
30. J McNeal J Kuehl J Boore C de Pamphilis 2007 Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus Cuscuta BMC Plant Biol 7 57
31. A Melis HC Chen 2005 Chloroplast sulfate transport in green algae-genes, proteins and effects Photosynth Res 86 299 307
32. DL Nickrent OY Yan RJ Duff CW dePamphilis 1997 Do nonasterid holoparasitic flowering plants have plastid genomes? Plant Mol Biol 34 717 729
33. Nickrent DL, Duff RJ ECA, Wolfe AD, Young ND, Steiner KE, dePamphilis CW (1998) Molecular phylogenetic and evolutionary studies of parasitic plants. Kluwer, Boston
34. Nylander JAA (2004) MrModeltest v2. Program distributed by the author, Evolutionary Biology Centre, Uppsala University
35. N Ohta PR Galsworthy AB Pardee 1971 Genetics of sulfate transport by Salmonella typhimurium J Bacteriol 105 1053 1062
36. K Ohyama H Fukuzawa T Kohchi H Shirai T Sano S Sano K Umesono Y Shiki M Takeuchi Z Chang Aota S-i H Inokuchi H Ozeki 1986 Chloroplast gene organization deduced from complete sequence of liverwort Marchantia polymorpha chloroplast DNA Nature 322 572 574
37. SM Perold 2001 Studies in the liverwort family Aneuraceae (Metzgeriales) from southern Africa. 1. The genus Aneura and its local representative Bothalia 31 167 173
38. YL Qiu LB Li B Wang ZD Chen V Knoop M Groth-Malonek O Dombrovska J Lee L Kent J Rest GF Estabrook TA Hendry DW Taylor CM Testa M Ambros B Crandall-Stotler RJ Duff M Stech W Frey D Quandt CC Davis 2006 The deepest divergences in land plants inferred from phylogenomic evidence Proc Natl Acad Sci USA 103 15511 15516
39. MJ Quiles 2006 Stimulation of chlororespiration by heat and high light intensity in oat plants Plant Cell Environ 29 1463 1470
40. Rambaut A, Drummond AJ (2007) Tracer v1.4. Program distributed by the authors
41. CP Randle AD Wolfe 2005 The evolution and expression of rbcL in holoparasitic sister-genera Harveya and Hyobanche (Orobanchaceae) Am J Bot 92 1575 1585
42. DJ Read JG Duckett R Francis R Ligrone A Russell 2000 Symbiotic fungal associations in 'lower' land plants Phil Trans Roy Soc Lond B 355 815 830
43. Rochaix JD (2006) The role of nucleus- and chloroplast-encoded factors in the synthesis of the photosynthetic apparatus. Springer, Dordrecht
44. JD Rochaix K Perron D Dauvillee F Laroche Y Takahashi M Goldschmidt-Clermont 2004 Post-transcriptional steps involved in the assembly of photosystem I in Chlamydomonas Biochem Soc Trans 32 567 570
45. F Ronquist JP Huelsenbeck 2003 MRBAYES 3: Bayesian phylogenetic inference under mixed models Bioinformatics 19 1572 1574
46. Schuster RM (1992) The Hepaticae and Anthocerotae of North America, vol V. Field Museum of Natural History, Chicago, IL
47. A Sirko M Hryniewicz D Hulanicka A Bock 1990 Sulfate and thiosulfate transport in Escherichia coli K-12: nucleotide sequence and expression of the cysTWAM gene cluster J Bacteriol 172 3351 3357
48. B Stoebe W Martin KV Kowallik 1998 Distribution and nomenclature of protein-coding genes in 12 sequenced chloroplast genomes Plant Mol Biol Rep 16 243 255
49. C Sugiura Y Kobayashi S Aoki C Sugita M Sugita 2003 Complete chloroplast DNA sequence of the moss Physcomitrella patens: evidence for the loss and relocation of rpoA from the chloroplast to the nucleus Nucleic Acids Res 31 5324 5331
50. Swofford DL (2002) PAUP*: Phylogenetic Analyses Using Parsimony (*and other methods). Version 4. Sinauer, Sunderland, MA
51. P Thalouarn C Theodet N Russo P Delavault 1994 The reduced plastid genome of a nonphotosynthetic angiosperm Orobanche Hederae has retained the rbcL gene Plant Physiol Biochem 32 233 242
52. M Tillich P Lehwark BR Morton UG Maier 2006 The evolution of chloroplast RNA editing Mol Biol Evol 23 1912 1921
53. NJ Wickett B Goffinet 2008 Origin and relationships of the myco-heterotrophic liverwort Cryptothallus mirabilis Malmb. (Metzgeriales, Marchantiophyta) Bot J Linn Soc 156 1 12
54. NJ Wickett Y Zhang SK Hansen JM Roper JV Kuehl SA Plock PG Wolf CW dePamphilis JL Boore B Goffinet 2008 Functional gene losses occur with minimal size reduction in the plastid genome of the parasitic liverwort Aneura mirabilis Mol Biol Evol 25 393 401
55. CF Wimpee RL Wrobel DK Garvin 1991 A divergent plastid genome in Conopholis americana, an achlorophyllous parasitic plant Plant Mol Biol 17 161 166
56. AD Wolfe CW dePamphilis 1997 Alternate paths of evolution for the photosynthetic gene rbcL in four nonphotosynthetic species of Orobanche Plant Mol Biol 33 965 977
57. AD Wolfe CW dePamphilis 1998 The effect of relaxed functional constraints on the photosynthetic gene rbcL in photosynthetic and nonphotosynthetic parasitic plants Mol Biol Evol 15 1243 1258
58. KH Wolfe CW Morden JD Palmer 1992 Function and evolution of a minimal plastid genome from a nonphotosynthetic parasitic plant Proc Natl Acad Sci USA 89 10648 10652
59. ND Young CW dePamphilis 2005 Rate variation in parasitic plants: correlated and uncorrelated patterns among plastid genes of different function BMC Evol Biol 5 16
60. Zwickl DJ (2006) Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. University of Texas at Austin, Austin