Evolution of the Chloroplast Genome in Photosynthetic Euglenoids: A Comparison of Eutreptia viridis and Euglena gracilis (Euglenophyta)

Protist

Volumn 163, Issue 6, 2012, Pages 832-843

  Wiegert, Krystle E ^a   Bennett, Matthew S ^a   Triemer, Richard E ^a  

^a MICHIGAN STATE UNIVERSITY   (United States)

Author keywords

Chloroplast; Euglena gracilis; Euglenophyta; Eutreptia viridis; Genome.

Indexed keywords

CHLOROPLAST DNA;

ARTICLE; CHLOROPLAST GENOME; CLUSTER ANALYSIS; COMPARATIVE STUDY; DNA SEQUENCE; EUGLENIDA; GENE ORDER; GENE REARRANGEMENT; GENETICS; MOLECULAR EVOLUTION; MOLECULAR GENETICS; MULTIGENE FAMILY; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE HOMOLOGY;

CLUSTER ANALYSIS; CONSERVED SEQUENCE; DNA, CHLOROPLAST; EUGLENIDA; EVOLUTION, MOLECULAR; GENE ORDER; GENE REARRANGEMENT; GENOME, CHLOROPLAST; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; PHYLOGENY; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY;

ALGAE; EUGLENA GRACILIS; EUGLENIDA; EUTREPTIA VIRIDIS; PYRAMIMONAS;

EID: 84866922366     PISSN: 14344610     EISSN: 16180941     Source Type: Journal    
DOI: 10.1016/j.protis.2012.01.002     Document Type: Article

References (43)

1. Adl S.M., Simpson A.G.B., Farmer M.A., Andersen R.A., Anderson O.R., Barta J.R., Bowser S.S., Brugerolle G., Fensome R.A., Fredericq S., James R.Y., Karpov S., Kugrens P., Krug J., Lane C.E., Lewis L.A., Lodge J., Lynn D.H., Mann D.G., McCourt R.M., Mendoza L., Moestrup Ø., Mozley-Stadridge S.E., Nerad R.A., Shearer C.A., Smirnov A.V., Spiegel F.W., Taylor M.F.J.R. The new higher level classification of eukaryotes with emphasis on the taxonomy of protists. J Eukaryot Microbiol 2005, 52:399-451.
2. Benson D.A., Karsch-Mizrachi I., Lipman D.J., Ostell J., Sayers E.W. GenBank. Nucleic Acids Res 2011, 39:D32-D37.
3. Burger G., Lavrov D.V., Forget L., Lang B.F. Sequencing complete mitochondrial and plastid genomes. Nature Protocols 2007, 2:603-614.
4. Cavalier-Smith T. A revised six-kingdom system of life. Biol Rev 1998, 73:203-266.
5. Christopher D.A., Hallick R.B. Euglena gracilis chloroplast ribosomal protein operon: A new chloroplast gene for ribosomal protein L5 and description of a novel organelle intron category designated group III. Nucleic Acids Res 1989, 17:7591-7608.
6. Christopher D.A., Hallick R.B. Complex RNA maturation pathway for a chloroplast ribosomal protein operon with an internal tRNA cistron. Plant Cell 1990, 2:659-671.
7. Copertino D.W., Hallick R.B. Group II twintron: An intron within an intron in a chloroplast cytochrome b-559 gene. EMBO J 1991, 10:433-442.
8. Copertino D.W., Christopher D.A., Hallick R.B. A mixed Group-II Group-III Twintron in the Euglena gracilis chloroplast ribosomal protein S3-gene - Evidence for intron insertion during gene evolution. Nucleic Acids Res 1991, 19:6491-6497.
9. Copertino D.W., Hall E.T., Van Hook F.W., Jenkins K.P., Hallick R.B. A group III twintron encoding a maturase-like gene excises through lariat intermediates. Nucleic Acids Res 1994, 22:1029-1036.
10. Darling A.C.E., Mau B., Blattner F.R., Perna N.T. Mauve: Multiple alignment of conserved genomic sequence with rearrangements. Genome Res 2004, 14:1394-1403.
11. Doetsch N.A., Thompson M.D., Hallick R.B. A maturase-ecoding group III twintron is conserved in deeply rooted euglenoid species: Are group III introns the chicken or the egg?. Mol Biol Evol 1998, 15:76-86.
12. Gibbs S.P. The chloroplasts of Euglena may have evolved from symbiotic green algae. Can J Bot 1978, 56:2883-2889.
13. Gibbs S.P. The chloroplasts of some algal groups may have evolved from endosymbiotic eukaryotic algae. Ann NY Acad Sci 1981, 361:193-208.
14. Hallick R.B., Hong L., Drager R.G., Favreau M.R., Monfort A., Orsat B., Spielmann A., Stutz E. Complete sequence of Euglena gracilis chloroplast DNA. Nucleic Acids Res 1993, 21:3537-3544.
15. Huber-Pestalozzi G (1955) Die Binnengewässer. Das Phytoplankton des Süsswassers. Volume 16(4), E. Schweizerbart'sche Verlagsbuchhandlung, Stuttgart, Germany, 410 pp.
16. Jenkins K.P., Hong L., Hallick R.B. Alternative splicing of the Euglena gracilis chloroplast roaA transcript. RNA (NY) 1995, 1:624-633.
17. Koller B., Delius H. A chloroplast DNA of Euglena gracilis with five complete rRNA operons and two extra 16S rRNA genes. Mol Gen Genet 1982, 188:305-308.
18. Lambowitz A.M., Belfort M. Introns as mobile genetic elements. Annu Rev Biochem 1993, 62:587-622.
19. Lane C.E., Archibald J.M. The eukaryotic tree of life: endosymbiosis takes its TOL. Trends Ecol Evol 2008, 23:268-275.
20. Linton E.W., Karnkowska-Ishikawa A., Kim J.I., Shin W., Bennett M.S., Kwiatowski J., ZakryŚ B., Triemer R.E. Reconstructing euglenoid evolutionary relationships using three genes: Nuclear SSU and LSU, and chloroplast SSU rDNA sequences and the description of Euglenaria gen. nov. (Euglenophyta). Protist 2010, 161:603-619.
21. Lowe T.M., Eddy S.R. tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997, 25:955-964.
22. Manhart J.R., Palmer J.D. The gain of two chloroplast tRNA introns marks the green algal ancestors of land plants. Nature 1990, 345:268-270.
23. Marin B., Palm A., Klingberg M., Melkonian M. Phylogeny and taxonomic revision of plastid-containing euglenophytes based on SSU rDNA sequence comparisons and synapomorphic signatures in the SSU rRNA secondary structure. Protist 2003, 154:99-145.
24. Mohr G., Perlman P.S., Lambowitz A.M. Evolutionary relationships among group II intron-encoded proteins and identification of a conserved domain that may be related to maturase function. Nucleic Acids Res 1993, 22:4991-4997.
25. Moreira D., von der Heyden S., Bass D., López-García P., Chao E., Cavalier-Smith T. Global eukaryote phylogeny: Combined small- and large-subunit ribosomal DNA trees support monophyly of Rhizaria, Retaria and Excavata. Mol Phylogenet Evol 2007, 44:255-266.
26. Nock C.J., Waters D.L.E., Edwards M.A., Bowen S.G., Rice N., Cordeiro G.M., Henry R.J. Chloroplast genome sequences from total DNA for plant identification. Plant Biotechnol J 2011, 9:328-333.
27. Noe L., Kucherov G. YASS: Enhancing the sensitivity of DNA similarity search. Nucleic Acids Res 2005, 33:W540-W543.
28. Parfrey L.W., Grant J., Tekle Y.I., Lasek-Nesselquist E., Morrison H.G., Sogin M.L., Patterson D.J., Katz L.A. Broadly sampled multigene analyses yield a well-resolved eukaryotic tree of life. Syst Biol 2010, 59:518-533.
29. Parks M., Cronn R., Liston A. Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes. BMC Biol 2009, 7:84.
30. Qiu Y.-L., Li L., Wang B., Chen Z., Knoop V., Groth-Malonek M., Dombrovska O., Lee J., Kent L., Rest J., Estabrook G.F., Hendry T.A., Taylor D.W., Testa C.M., Ambros M., Crandall-Stotler B., Duff R.J., Stech M., Frey W., Quandt D., Davis C.C. The deepest divergences in land plants inferred from phylogenomic evidence. Proc Natl Acad Sci USA 2006, 103:15511-15516.
31. Schattner P., Brooks A.N., Lowe T.M. The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res 2005, 33:W686-W689.
32. Sheveleva E.V., Hallick R.B. Recent horizontal intron transfer to a chloroplast genome. Nucleic Acids Res 2004, 32:803-810.
33. Simpson A.G.B., Roger A.J. Protein phylogenies robustly resolve the deep-level relationships within Euglenozoa. Mol Phylogenet Evol 2004, 30:201-212.
34. Smith S.W., Overbeek R., Woese C.R., Gilbert W., Gillevet P.M. The genetic data environment an expandable GUI for multiple sequence analysis. Bioinformatics 1994, 10:671-675.
35. Thompson M.D., Copertino D.W., Thompson E., Favreau M.R., Hallick R.B. Evidence for the late origin of introns in chloroplast genes from an evolutionary analysis of the genus Euglena. Nucleic Acids Res 1995, 23:4745-4752.
36. Triemer R.E., Linton E., Shin W., Nudelman A., Brosnan S., Monfils A., Bennett M. Phylogeny of the Euglenales based upon combined SSU and LSU rDNA sequence comparisons and description of Discoplastis gen nov (Euglenophyta). J Phycol 2006, 42:731-740.
37. Turmel M., Gagnon M.-C., O'Kelly C.J., Otis C., Lemieux C. The chloroplast genomes of the green algae Pyramimonas, Monomastix, and Pycnococcus shed new light on the evolutionary history of prasinophytes and the origin of the secondary chloroplasts of euglenids. Mol Biol Evol 2009, 26:631-648.
38. Untergasser A., Nijveen H., Rao X., Bisseling T., Geurts R., Leunissen J.A.M. Primer3Plus, an enhanced web interface to Primer3. Nucleic Acids Res 2007, 35:W71-W74.
39. Watanabe M.M., Hiroki M. NIES - Collection List of Strains 1997, National Institute for Environmental Studies, Tsukuba, 127 pp. 5th ed.
40. Wurtz E.A., Buetow D.E. Intraspecific variation in the structural organization and redundancy of chloroplast ribosomal DNA cistrons in Euglena gracilis. Curr Genet 1981, 3:181-187.
41. Wyman S.K., Jansen R.K., Boore J.L. Automatic annotation of organellar genomes with DOGMA. Bioinformatics 2004, 20:3252-3255.
42. Yepiz-Plascencia G.M., Rodebaugh C.A., Hallick R.B. The Euglena gracilis chloroplast rpoB gene: Novel gene organization and transcription of the RNA polymerase subunit operon. Nucleic Acids Res 1990, 18:1869-1878.
43. Zhang L., Jenkins K.P., Stutz E., Hallick R. The Euglena gracilis intron-encoded mat2 locus is interrupted by three additional group II introns. RNA (NY) 1995, 1:1079-1088.