The random nature of genome architecture: Predicting open reading frame distributions

PLoS ONE

Volumn 4, Issue 7, 2009, Pages

  McCoy, Michael W ^a   Allen, Andrew P ^b   Gillooly, James F ^c  

^a Boston University   (United States)

^b MACQUARIE UNIVERSITY   (Australia)

^c UNIVERSITY OF FLORIDA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; DNA CONTENT; DROSOPHILA MELANOGASTER; EUKARYOTE; GENE SEQUENCE; GENE STRUCTURE; GENOME ANALYSIS; GENOME SIZE; GEOBACILLUS; GEOBACILLUS KAUSTOPHILUS; NONHUMAN; OPEN READING FRAME; PROKARYOTE; PROTEIN LOCALIZATION; START CODON; STOCHASTIC MODEL; STOP CODON; BIOLOGICAL MODEL; GENOME; STATISTICS;

EUKARYOTA; PROKARYOTA;

GENOME; MODELS, GENETIC; OPEN READING FRAMES; STOCHASTIC PROCESSES;

EID: 68149092101     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0006456     Document Type: Article

References (40)

1. Daubin V, Moran NA (2004) Comment on "The origins of genome complexity". Science 306(5698): 978a.
2. Lynch M, Conery JS (2003) The origins of genome complexity. Science 302(5649): 1401-1404.
3. Lynch M, Conery JS (2004) Response to comment on "The origins of genome complexity". Science 306(5698): 978.
4. Vinogradov AE, Lynch M, Conery JS (2004) Testing genome complexity. Science 304(5669): 389b-390.
5. Carpena P, Bernaola-Galván P, Román-Roldán R, Oliver JL (2002) A simple and species-independent coding measure. Gene 300(1-2): 97-104.
6. Lynch M (2006) The origins of eukaryotic gene structure. Molecular Biology and Evolution 23(2): 450-468.
7. Lynch M (2007) The Origins of Genome Architecture. Sunderland, MA: Sinauer.
8. Yi SV, Streelman JT (2005) Genome size is negatively correlated with effective population size in ray-finned fish. Trends in Genetics 21(12): 643-646.
9. Carroll SB (2008) Evo-Devo and an expanding evolutionary synthesis: A genetic theory of morphological evolution. Cell 134(1): 25-36.
10. Pagel M, Johnstone RA (1992) Variation across species in the size of the nuclear genome supports the junk-DNA explanation for the C-value paradox. Proceedings of the Royal society of London Series B: Biological Sciences 249(1325): 119-124.
11. Vinogradov AE (1998) Buffering: a possible passive-homeostasis rule for redundant DNA. Journal of Theoretical Biology 193(2): 197-199.
12. Vinogradov AE (2004) Evolution of genome size: multilevel selection, mutation bias or dynamical chaos. Current Opinions in Genetics and Development 14: 620-626.
13. Yi SV (2006) Non-adaptive evolution of genome complexity. Bioessays 28(10): 979-982.
14. Cavalier-Smith T (1978) Nuclear volume control by nucleoskeletal DNA, selection for cell volume and cell growth rate, and the solution of the DNA C-value paradox. Journal of Cell Science 34(1): 247-278.
15. Skovgaard M, Jensen LJ, Brunak S, Ussery D, Krogh A (2001) On the total number of genes and their length distribution in complete microbial genomes. Trends in Genetics 17(8): 425-428.
16. Zhang J (2000) Protein-length distributions for the three domains of life. Trends in Genetics 16(3): 107-109.
17. Bolker BM (2008) Ecological Models and Data in R. Princeton: Princeton University Press.
18. Todinov M (2005) Reliability and Risk Models: Setting Reliability Requirements: Wiley. 340 p.
19. Barlow RE, Proschan F (1965) Mathematical theory of reliability: Society for Industrial Mathematics. 274 p.
20. Loewe L, Charlesworth B (2006) Inferring the distribution of mutational effects on fitness in Drosophila. Biology Letters 2(3): 426-430.
21. Engen S, Lande R (1996) Population dynamic models generating species abundance distributions of the gamma type. Journal of Theoretical Biology 178(3): 325-331.
22. Engen S, Lande R (1996) Population dynamic models generating the lognormal species abundance distribution. Mathematical Biosciences 132(2): 169-183.
23. Senapathy P (1986) Origin of eukaryotic introns: A hypothesis, based on codon distribution statistics in genes, and its implications. Proceedings of the National Academy of Sciences 83(7): 2133-2137.
24. Oliver JL, Marín A (1996) A relationship between GC content and coding-sequence length. Journal of Molecular Evolution 43(3): 216-223.
25. Cottret L, Lucas A, Marrakchi E, Rogier O, Lefort V, et al. (2008) GeneR: R for genes and sequences analysis. R Package Version 2.12.0. ed: R Foundation for Statistical Computing.
26. Charif D, Lobry JR (2007) SeqinR 1.0-2: a contributed package to the R-project for statistical computing devoted to biological sequences retrieval and analysis. In: Bastolla U, Porto MERH, Vendruscolo M, eds. Structural approaches to sequence evolution: Molecules, networks, populations. New York: Springer Verlag. pp 207-232.
27. Team RDC (2007) R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing.
28. Bolker BM (2008) bbmle: Tools for general maximum likelihood estimation. R package version 0.8.9 ed: R Foundation for Statistical Computing.
29. Burnham KP, Anderson DR (2001) Model Selection and Multimodel Inference: A Practical-Theoretic Approach: Springer Verlag. .
30. Bernardi G, Bernardi G (1990) Compositional patterns in the nuclear genome of cold-blooded vertebrates. Journal of Molecular Evolution 31(4): 265-281.
31. Vinogradov AE (1994) Measurement by flow cytometry of genomic AT/GC ratio and genome size. Cytometry 16(1): 34.
32. Wood SN (2004) Stable and efficient multiple smoothing parameter estimation for generalized additive models. Journal of the American Statistical Association 99: 673-686.
33. Cavalier-Smith T (1985) Cell volume and the evolution of eukaryotic genome size. In: Cavalier-Smith T, ed. The evolution of Genome Size. Chichester: John Wiley & Sons. pp 104-184.
34. Gregory TR (2001) Coincidence, coevolution, or causation? DNA content, cell size, and the C-value enigma. Biological Reviews 76(01): 65-101.
35. Hawkins JS, Kim H, Nason JD, Wing RA, Wendel JF (2006) Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium. Genome Research 16(10): 1252-1261.
36. Kidwell MG (2002) Transposable elements and the evolution of genome size in eukaryotes. Genetica 115(1): 49-63.
37. Wessler SR (2006) Transposable elements and the evolution of eukaryotic genomes. Proceedings of the National Academy of Sciences 103(47): 17600-17601.
38. Basrai MA, Hieter P, Boeke JD (1997) Small open reading frames: Beautiful needles in the haystack. Genome Research 7(8): 768-771.
39. Kastenmayer JP, Ni L, Chu A, Kitchen LE, Au WC, et al. (2006) Functional genomics of genes with small open reading frames (sORFs) in S. cerevisiae. Genome Research 16(3): 365-373.
40. Siew N, Azaria Y, Fischer D (2004) The ORFanage: an ORFan database. Nucleic Acids Research 32(Database Issue): D281.