Distinct gene number-genome size relationships for eukaryotes and non-eukaryotes: Gene content estimation for dinoflagellate genomes

PLoS ONE

Volumn 4, Issue 9, 2009, Pages

  Hou, Yubo ^a   Lin, Senjie ^a  

^a UNIVERSITY OF CONNECTICUT   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIN; LUCIFERASE; LUCIFERIN; PROTEIN KINASE; PROTEOME; RIBULOSEBISPHOSPHATE CARBOXYLASE; PROTEIN;

ARTICLE; CONTROLLED STUDY; DINOFLAGELLATE; EUKARYOTE; GENE FREQUENCY; GENE NUMBER; GENETIC TRANSFORMATION; GENETIC VARIABILITY; GENOME; GENOME SIZE; MOLECULAR EVOLUTION; NONHUMAN; PHYLOGENY; PROKARYOTE; BIOLOGICAL MODEL; CHLOROPLAST; DNA SEQUENCE; EXPRESSED SEQUENCE TAG; GENE DOSAGE; GENETICS; METABOLISM; METHODOLOGY; MITOCHONDRION; REGRESSION ANALYSIS;

DINOPHYCEAE; EUKARYOTA; PROKARYOTA;

CHLOROPLASTS; DINOFLAGELLIDA; EUKARYOTA; EXPRESSED SEQUENCE TAGS; GENE DOSAGE; GENOME; MITOCHONDRIA; MODELS, GENETIC; PHYLOGENY; PROTEINS; REGRESSION ANALYSIS; SEQUENCE ANALYSIS, DNA;

EID: 70349202709     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0006978     Document Type: Article

References (55)

1. Lynch M, Conery JS (2003) The origins of genome complexity. Science 302: 1401-1404.
2. Konstantinidis KT, Tiedje JM (2004) Trends between gene content and genome size in prokaryotic species with larger genomes. Proc Natl Acad Sci U S A 101: 3160-3165.
3. Gregory TR (2005) Synergy between sequence and size in large-scale genomics. Nature Rev Genet 6: 699-708.
4. Hackett JD, Anderson DM, Erdner DL, Bhattacharya D (2004) Dinoflagellates: a remarkable evolutionary experiment. Am J Bot 91: 1523-1534.
5. Lin S (2006) The smallest dinoflagellate genome is yet to be found: a comment on LaJeunesse, et al. "Symbiodinium (Pyrrhophyta) genome sizes (DNA content) are smallest among dinoflagellates". J Phycol 42: 746-748.
6. LaJeunesse TC, Lambert G, Andersen RA, Coffroth MA, Galbraith DW (2005) Symbiodinium (Pyrrhophyta) genome sizes (DNA content) are smallest among dinoflagellates. J Phycol 41: 880-886.
7. Veldhuis MJW, Cucci TL, Sieracki ME (1997) Cellular DNA content of marine phytoplankton using two new fluorochromes: taxonomic and ecological implications. J Phycol 33: 527-541.
8. Holm-Hansen O (1969) Algae: amounts of DNA and organic carbon in single cells. Science 163: 87-88.
9. Rizzo PJ (1987) Biochemistry of the dinoflagellate nucleus. In: Taylor FJR, ed. The biology of dinoflagellates. Oxford: Blackwell Science Inc. pp 143-173.
10. Gregory TR, Nicol JA, Tamm H, Kullman B, Kullman K, et al. (2007) Eukaryotic genome size databases. Nucleic Acids Res 35: D332-D338.
11. Allen JR, Roberts TM, Loeblich I, Alfred R, Klotz LC (1975) Characterization of the DNA from the dinoflagellate Crypthecodinium cohnii and implications for nuclear organization. Cell 6: 161-169.
12. Hinnebusch AG, Klotz LC, Immergut E, Loeblich ARI (1980) Deoxyribonucleic acid sequence organization in the genome of the dinoflagellate Crypthecodinium cohnii. Biochem 19: 1744-1755.
13. Steel RE (1980) Aspects of the composition and organization of dinoflagellate DNA [Ph.D. thesis]. New Haven: Yale University.
14. Anderson DM, Grabher A, Herzog M (1992) Separation of coding sequences from structural DNA in the dinoflagellate Crypthecodinium cohnii. Mol Mar Biol Biotechnol 2: 89-96.
15. Moreau H, Geraud ML, Bhaud Y, Soyer-Gobillard MO (1998) Cloning, characterization and chromosomal localization of a repeated sequence in Crypthecodinium cohnii, a marine dinoflagellate. Int Microbiol 1: 35-43.
16. Zhang H, Lin S (2003) Complex gene structure of the form II RUBISCO in the dinoflagellate Prorocentrum minimum (Dinophyceae). J Phycol 39: 1160-1171.
17. Zhang H, Hou Y, Lin S (2006) Isolation and characterization of proliferating cell nuclear antigen from the dinoflagellate Pfiesteria piscicida. J Euk Microbiol 53: 142-150.
18. Xu L, Chen H, Hu X, Zhang R, Zhang Z, et al. (2006) Average gene length is highly conserved in prokaryotes and eukaryotes and diverges only between the two kingdoms. Mol Biol Evol 23: 1107-1108.
19. Archibald J (2007) Nucleomorph genomes: structure, function, origin and evolution. BioEssays 29: 392-402.
20. Spector DL (1984) Dinoflagellate nuclei. In: Spector DL, ed. Dinoflagellates. New York: Academic Press. pp 107-147.
21. Bouligand Y, Norris V (2001) Chromosome separation and segregation in dinoflagellates and bacteria may depend on liquid crystalline states. Biochimie 83: 187-192.
22. Chan YH, Wong JTY (2007) Concentration-dependent organization of DNA by the dinoflagellate histone-like protein HCc3. Nucleic Acids Res 35: 2573-2583.
23. Sigee DC (1984) Structural DNA and genetically active DNA in dinoflagellate chromosomes. Biosystems 16: 203-210.
24. Bhaud Y, Guillebault D, Lennon JF, Defacque H, Soyer-Gobillard MO, et al. (2000) Morphology and behaviour of dinoflagellate chromosomes during the cell cycle and mitosis. J Cell Sci 113: 1231-1239.
25. Lin S, Zhang H, Gray MW (2008) RNA editing in dinoflagellates and its implications for the evolutionary history of the editing machinery. In: Smith H, ed. RNA and DNA editing: molecular mechanisms and their integration into biological systems. Hoboken, NJ: John Wiley & Sons, Inc. pp 280-309.
26. Zhang H, Campbell DA, Sturm NR, Lin S (2009) Dinoflagellate spliced leader RNA genes display a variety of sequences and genomic arrangements. Mol Biol Evol 26: 1757-1771.
27. Lukes J, Leander BS, Keeling PJ (2009) Cascades of convergent evolution: the corresponding evolutionary histories of euglenozoans and dinoflagellates. Proc Natl Acad Sci U S A 106: 9963-9970.
28. Ivens AC, Peacock CS, Worthey EA, Murphy L, Aggarwal G, et al. (2005) The genome of the kinetoplastid parasite, Leishmania major. Science 309: 436-442.
29. Berriman M, Ghedin E, Hertz-Fowler C, Blandin G, Renauld H, et al. (2005) The genome of the African trypanosome Trypanosoma brucei. Science 309: 416-422.
30. Rizzo PJ, Nooden LD (1973) Isolation and chemical composition of dinoflagellate nuclei. J Euk Microbiol 20: 666-672.
31. Roberts TM, Tuttle RC, Allen JR, Loeblich AR, Klotz LC (1974) New genetic and physicochemical data on structure of dinoflagellate chromosomes. Nature 248: 446-447.
32. Blank RJ (1987) Cell architecture of the dinoflagellate Symbiodinium sp. inhabiting the Hawaiian stony coral Montipora verrucosa. Mar Bio 94: 143-155.
33. Pfiester L, Anderson DM (1987) Dinoflagellate reproduction. In: Taylor FJR, ed. The Biology of dinoflagellates. Oxford: Blackwell Scientific Inc. pp 611-648.
34. Coats DW (2002) Dinoflagellate life-cycle complexities. J Phycol 38: 417-419.
35. Santos SR, Coffroth MA (2003) Molecular genetic evidence that dinoflagellates belonging to the genus Symbiodinium Freudenthal are haploid. Biol Bull 204: 10-20.
36. McEwan M, Humayun R, Slamovits CH, Keeling PJ (2008) Nuclear genome sequence survey of the dinoflagellate Heterocapsa triquetra. J Euk Microbiol 55: 530-535.
37. Hackett JD, Scheetz TE, Yoon HS, Soares MB, Bonaldo MF, et al. (2005) Insights into a dinoflagellate genome through expressed sequence tag analysis. BMC Genomics 6.
38. Patron NJ, Waller RF, Archibald JM, Keeling PJ (2005) Complex protein targeting to dinoflagellate plastids. J Mol Biol 348: 1015-1024.
39. Van Dolah FM, Lidie KB, Monroe EA, Bhattacharya D, Campbell L, et al. (2009) The Florida red tide dinoflagellate Karenia brevis: new insights into cellular and molecular processes underlying bloom dynamics. Harmful Algae 8: 562-572.
40. Patron NJ, Waller RF, Keeling PJ (2006) A tertiary plastid uses genes from two endosymbionts. J Mol Biol 357: 1373-1382.
41. Slamovits CH, Keeling PJ (2008) Plastid-derived genes in the nonphotosynthetic alveolate Oxyrrhis marina. Mol Biol Evol 25: 1297-1306.
42. Slamovits CH, Keeling PJ (2008) Widespread recycling of processed cDNAs in dinoflagellates. Curr Biol 18: R550-R552.
43. Lynch M (2007) Genomic expansion by gene duplication. In: Lynch M, ed. The origins of genome architecture. Sunderland, MA: Sinauer Associates. pp 193-235.
44. Wolfe KH, Shields DC (1997) Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387: 708-713.
45. Ramsey J, Schemske DW (1998) Pathways, mechanisms, and rates of polyploid formation in flowering plants. Annu Rev Ecol Syst 29: 467-501.
46. Aury JM, Jaillon O, Duret L, Noel B, Jubin C, et al. (2006) Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia. Nature 444: 171-178.
47. Gregory TR, Mable BK (2005) Polyploidy in animals. In: Gregory TR, ed. The evolution of the genome. San Diego, CA: Elsevier. pp 427-517.
48. Loeblich AR, III, Schmidt RJ, Sherley JL (1981) Scanning electron microscopy of Heterocapsa pygmaea sp. nov., and evidence for polyploidy as a speciation mechanism in dinoflagellates. J Plankton Res 3: 67-79.
49. Bachvaroff TR, Place AR (2008) From stop to start: tandem gene arrangement, copy number and trans-splicing sites in the dinoflagellate Amphidinium carterae. PLoS ONE 3: e2929.
50. Salois P, Morse D (1997) Characterization and molecular phylogeny of a protein kinase cDNA from the dinoflagellate gonyaulax (Dinophyceae). J Phycol 33: 1063-1072.
51. Liu LY, Hastings JW (2006) Novel and rapidly diverging intergenic sequences between tandem repeats of the luciferase genes in seven dinoflagellate species. J Phycol 42: 96-103.
52. Lee D, Mittag M, Sczekan S, Morse D, Hastings JW (1993) Molecular cloning and genomic organization of a gene for luciferin-binding protein from the dinoflagellate Gonyaulax polyedra. J Biol Chem 268: 8842-8850.
53. Bertomeu T, Morse D (2004) Isolation of a dinoflagellate mitotic cyclin by functional complementation in yeast. Biochem Biophys Res Commun 323: 1172-1183.
54. Le QH, Markovic P, Hastings JW, Jovine RVM, Morse D (1997) Structure and organization of the peridinin chlorophyll a binding protein gene in Gonyaulax polyedra. Mol General Genet 255: 595-604.
55. Reichman J, Wilcox T, Vize P (2003) PCP gene family in Symbiodinium from Hippopus hippopus: low level of concerted evolution, isoform diversity and spectral tuning of chromophores. Mol Biol Evol 20: 2143-2154.