Analysis of the complete plastid genome of the unicellular red alga Porphyridium purpureum

Journal of Plant Research

Volumn 127, Issue 3, 2014, Pages 389-397

  Tajima, Naoyuki ^a,b   Sato, Shusei ^c   Maruyama, Fumito ^d   Kurokawa, Ken ^b,e   Ohta, Hiroyuki ^b,e   Tabata, Satoshi ^f   Sekine, Kohsuke ^a,b   Moriyama, Takashi ^a,b   Sato, Naoki ^a,b  

^a UNIVERSITY OF TOKYO   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^c TOHOKU UNIVERSITY   (Japan)

^d TOKYO MEDICAL AND DENTAL UNIVERSITY   (Japan)

^e TOKYO INSTITUTE OF TECHNOLOGY   (Japan)

^f KAZUSA DNA RESEARCH INSTITUTE   (Japan)

Author keywords

Genome rearrangement; Plastid genome; Porphyridium purpureum; Rhodophyta; rRNA operon

Indexed keywords

CHROMALVEOLATA; CRYPTOPHYTA; HAPTOPHYCEAE; PORPHYRIDIOPHYCEAE; PORPHYRIDIUM; PORPHYRIDIUM PURPUREUM; RHODOPHYTA;

ANTICODON; RIBOSOME PROTEIN; TRANSFER RNA;

ANTICODON; DNA SEQUENCE; GENETICS; INTRON; MOLECULAR GENETICS; MULTIGENE FAMILY; OPEN READING FRAME; PHYLOGENY; PLANT GENE; PLASTID GENOME; PORPHYRIDIUM;

ANTICODON; GENES, PLANT; GENOME, PLASTID; INTRONS; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; OPEN READING FRAMES; PHYLOGENY; PORPHYRIDIUM; RIBOSOMAL PROTEINS; RNA, TRANSFER; SEQUENCE ANALYSIS, DNA;

EID: 84899979576     PISSN: 09189440     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10265-014-0627-1     Document Type: Article

References (46)

1. Abascal F, Zardoya R, Posada D (2005) ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21: 2104-2105.
2. Alkatib S, Fleischmann TT, Scharff LB, Bock R (2012) Evolutionary constraints on the plastid tRNA set decoding methionine and isoleucine. Nucleic Acids Res 40: 6713-6724.
3. Bernard C, Thomas JC, Mazel D, Mousseau A, Castets AM, Tandeau de Marsac N, Dubacq JP (1992) Characterization of the genes encoding phycoerythrin in the red alga Rhodella violacea: evidence for a splitting of the rpeB gene by an intron. Proc Natl Acad Sci USA 89: 9564-9568.
4. Bhattacharya D, Price DC, Chan CX, Qiu H, Rose N, Ball S, Weber APM, Arias MC, Henrissat B, Coutinho PM, Krishnan A, Zäuner S, Morath S, Hilliou F, Egizi A, Perrineau MM, Yoon HS (2013) Genome of the red alga Porphyridium purpureum. Nat Commun 4: 1941.
5. Burki F, Okamoto N, Pombert JF, Keeling PJ (2012) The evolutionary history of haptophytes and cryptophytes: phylogenomic evidence for separate origins. Proc Biol Sci 279: 2246-2254.
6. Cavalier-Smith T (1998) A revised six-kingdom system of life. Biol Rev 73: 203-266.
7. Cech TR (1988) Conserved sequences and structures of group I introns: building an active site for RNA catalysis--a review. Gene 73: 259-271.
8. Chan CX, Yang EC, Banerjee T, Yoon HS, Martone PT, Estevez JM, Bhattacharya D (2011) Red and green algal monophyly and extensive gene sharing found in a rich repertoire of red algal genes. Curr Biol 21: 328-333.
9. DePriest MS, Bhattacharya D, López-Bautista JM (2013) The plastid genome of the red macroalga Grateloupia taiwanensis (Halymeniaceae). PLoS One 8: e68246.
10. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
11. Francis MA, Dudock BS (1982) Nucleotide sequence of a spinach chloroplast isoleucine tRNA. J Biol Chem 257: 1195-1198.
12. Glöckner G, Rosenthal A, Valentin K (2000) The structure and gene repertoire of an ancient red algal plastid genome. J Mol Evol 51: 382-390.
13. Hagopian JC, Reis M, Kitajima JP, Bhattacharya D, Oliveria MC (2004) Comparative analysis of the complete plastid genome sequence of the red alga Gracilaria tenuistipitata var. liui provides insights into the evolution of Rhodoplasts and their relationship to other plastids. J Mol Evol 59: 464-477.
14. Harper JT, Keeling PJ (2003) Nucleus-encoded, plastid-targeted glyceraldehyde-3-phosphate dehydrogenase (GAPDH) indicates a single origin for chromalveolate plastids. Mol Biol Evol 20: 1730-1735.
15. Janouškovec J, Liu SL, Martone PT, Carré W, Leblanc C, Collén J, Keeling PJ (2013) Evolution of red algal plastid genomes: ancient architectures, introns, horizontal gene transfer, and taxonomic utility of plastid markers. PLoS One 8: e59001.
16. Jobb G, von Haeseier A, Strimmer K (2004) TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics. BMC Evol Biol 4: 18.
17. Kim E, Archibald JM (2009) Diversity and evolution of plastids and their genomes. The chloroplast--interactions with the environment. In: Aronsson H, Sandelius AS (eds) Plant cell monographs, vol 13. Springer, Berlin, pp 1-39.
18. Konishi T, Shinohara K, Yamada K, Sasaki Y (1996) Acetyl-CoA carboxylase in higher plants: most plants other than gramineae have both the prokaryotic and the eukaryotic forms of this enzyme. Plant Cell Physiol 37: 117-122.
19. Lang BF, Laforest MJ, Burger G (2007) Mitochondrial introns: a critical view. Trends Genet 23: 119-125.
20. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and Clustal X version 2. 0. Bioinformatics 23: 2947-2948.
21. Livne A, Sukenik A (1990) Acetyl-coenzyme-A carboxylase from the marine prymnesiophyte Isochrysis galbana. Plant Cell Physiol 31: 851-858.
22. Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25: 955-964.
23. Nakanishi K, Bonnefond L, Kimura S, Suzuki T, Ishitani R, Nureki O (2009) Structural basis for translational fidelity ensured by transfer RNA lysidine synthetase. Nature 461: 1144-1148.
24. Lys(UUU) gene from mustard (Sinapis alba) contains a class II intron potentially coding for a maturase-related polypeptide. Curr Genet 11: 251-257.
25. Noguchi H, Taniguchi T, Itoh T (2008) MetaGeneAnnotator: detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes. DNA Res 15: 387-396.
26. O'Brien EA, Zhang Y, Wang E, Marie V, Badejoko W, Lang BF, Burger G (2009) GOBASE: an organelle genome database. Nucleic Acids Res 37: D946-D950.
27. Ohta N, Sato N, Nozaki H, Kuroiwa T (1997) Analysis of the cluster of ribosomal protein genes in the plastid genome of a unicellular red alga Cyanidioschyzon merolae: translocation of the str cluster as an early event in the Rhodophyte-Chromophyte lineage of plastid evolution. J Mol Evol 45: 688-695.
28. Ohta N, Matsuzaki M, Misumi O, Miyagishima S, Nozaki H, Tanaka K, Shin-I T, Kohara Y, Kuroiwa T (2003) Complete sequence and analysis of the plastid genome of the unicellular red alga Cyanidioschyzon merolae. DNA Res 10: 67-77.
29. Okaichi T, Nishio S, Imatomi Y (1982) Collection and mass culture. In: Jpn Fish Soc (ed) In toxic phytoplankton--occurrence, mode of action, and toxins. Koseisya-Koseikaku, Tokyo, pp 22-34.
30. Qiu H, Yang EC, Bhattacharya D, Yoon HS (2012) Ancient gene paralogy may mislead inference of plastid phylogeny. Mol Biol Evol 29: 3333-3343.
31. Reith M, Munholland J (1995) Complete nucleotide sequence of the Porphyra purpurea chloroplast genome. Plant Mol Biol Rep 13: 333-335.
32. Roessler PG, Ohlrogge JB (1993) Cloning and characterization of the gene that encodes acetyl-coenzyme A carboxylase in the alga Cyclotella cryptica. J Biol Chem 268: 19254-19259.
33. Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
34. Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream MA, Barrell B (2000) Artemis: sequence visualization and annotation. Bioinformatics 16: 944-945.
35. Sasaki NV, Sato N (2010) CyanoClust: comparative genome resources of cyanobacteria and plastids. Database 2010: bap025.
36. Sato N (2000) SISEQ: manipulation of multiple sequence and large database files for common platforms. Bioinformatics 16: 180-181.
37. Sato N (2009) Gclust: trans-kingdom classification of proteins using automatic individual threshold setting. Bioinformatics 25: 599-605.
38. Soma A, Ikeuchi Y, Kanemasa S, Kobayashi K, Ogasawara N, Ote T, Kato J, Watanabe K, Sekine Y, Suzuki T (2003) An RNA-modifying enzyme that governs both the codon and amino acid specificities of isoleucine tRNA. Mol Cell 12: 689-698.
39. Stirewalt VL, Michalowski CB, Löffelhardt W, Bohnert HJ, Bryant DA (1995) Nucleotide sequence of the cyanelle genome from Cyanophora paradoxa. Plant Mol Biol Rep 13: 327-332.
40. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731-2739.
41. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680.
42. Verbruggen H, Maggs CA, Saunders GW, Le Gall L, Yoon HS, De Clerck O (2010) Data mining approach identifies research priorities and data requirements for resolving the red algal tree of life. BMC Evol Biol 10: 16.
43. Wang L, Mao Y, Kong F, Li G, Ma F, Zhang B, Sun P, Bi G, Zhang F, Xue H, Cao M (2013) Complete sequence and analysis of plastid genomes of two economically important red algae: Pyropia haitanensis and Pyropia yezoensis. PLoS One 8: e65902.
44. Yoon HS, Hackett JD, Pinto G, Bhattacharya D (2002) The single, ancient origin of chromist plastids. Proc Natl Acad Sci USA 99: 15507-15512.
45. Yoon HS, Müller KM, Sheath RG, Ott FD, Bhattacharya D (2006) Defining the major lineages of red algae (Rhodophyta). J Phycol 42: 482-492.
46. Zimmerly S, Hausner G, Wu XC (2001) Phylogenetic relationships among group II intron ORFs. Nucleic Acids Res 29: 1238-1250.