The Anolis lizard genome: An amniote genome without isochores

Genome Biology and Evolution

Volumn 3, Issue 1, 2011, Pages 974-984

  Fujita, Matthew K ^a,b   Edwards, Scott V ^a   Ponting, Chris P ^b  

^a HARVARD UNIVERSITY   (United States)

^b UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

Effective population size; GC content; Gene density; Genome structure; Intron; Recombination

Indexed keywords

AMNIOTA; ANOLIS; ANOLIS CAROLINENSIS; ANURA; AVES; MAMMALIA; REPTILIA; SQUAMATA; VERTEBRATA;

ANIMAL; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; CHICKEN; CHROMOSOME MAP; DNA BASE COMPOSITION; EVOLUTION; GENETIC RECOMBINATION; GENETICS; GENOME; HUMAN; HUMAN GENOME; INTRON; ISOCHORE; LIZARD; NUCLEOTIDE SEQUENCE;

ANIMALS; BASE COMPOSITION; BASE SEQUENCE; BAYES THEOREM; BIOLOGICAL EVOLUTION; CHICKENS; CHROMOSOME MAPPING; GENOME; GENOME, HUMAN; HUMANS; INTRONS; ISOCHORES; LIZARDS; MODELS, GENETIC; RECOMBINATION, GENETIC;

EID: 84856296604     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evr072     Document Type: Article

References (60)

1. Alföldi et al. 2011. The genome of the green anole lizard and a comparative analysis with birds and mammals. Nature. doi:10.1038/nature10390
2. Balakrishnan CN, Edwards SV. 2009. Nucleotide variation, linkage disequilibrium and founder-facilitated speciation in wild populations of the zebra finch (Taeniopygia guttata). Genetics 181:645-660.
3. Belle EM, Duret L, Galtier N, Eyre-Walker A. 2004. The decline of isochores in mammals: an assessment of the GC content variation along the mammalian phylogeny. J Mol Evol. 58:653-660.
4. Belle EM, Smith N, Eyre-Walker A. 2002. Analysis of the phylogenetic distribution of isochores in vertebrates and a test of the thermal stability hypothesis. J Mol Evol. 55:356-363. (Pubitemid 34913546)
5. Bernardi G. 2000. Isochores and the evolutionary genomics of vertebrates. Gene 241:3-17.
6. Bernardi G. 2001. Misunderstandings about isochores. Part 1. Gene 276:3-13. (Pubitemid 32925254)
7. Bernardi G. 2007. The neoselectionist theory of genome evolution. Proc Natl Acad Sci U S A. 104:8385-8390. (Pubitemid 47175497)
8. Bernardi G, Bernardi G. 1986. Compositional constraints and genome evolution. J Mol Evol. 24:1-11. (Pubitemid 17013869)
9. Birdsell JA. 2002. Integrating genomics, bioinformatics, and classical genetics to study the effects of recombination on genome evolution. Mol Biol Evol. 19:1181-1197. (Pubitemid 34743242)
10. Brown TC, Jiricny J. 1987. A specific mismatch repair event protects mammalian cells from loss of 5-methylcytosine. Cell 50:945-950.
11. Chojnowski J, Braun E. 2008. Turtle isochore structure is intermediate between amphibians and other amniotes. Integr Comp Biol. 48:454-462.
12. Chojnowski JL, et al. 2007. Patterns of vertebrate isochore evolution revealed by comparison of expressed mammalian, avian, and crocodilian genes. J Mol Evol. 65:259-266. (Pubitemid 47561682)
13. Clay OK, Bernardi G. 2011. GC3 of genes can be used as a proxy for isochore base composition: a reply to Elhaik et al. Mol Biol Evol. 28:21-23.
14. Cohen N, Dagan T, Stone L, Graur D. 2005. GC composition of the human genome: in search of isochores. Mol Biol Evol. 22:1260-1272. (Pubitemid 40577764)
15. Comeron J, Kreitman M. 2000. The correlation between intron length and recombination in Drosophila. Dynamic equilibrium between mutational and selective forces. Genetics 156:1175-1190.
16. Comeron J, Williford A, Kliman R. 2008. The Hill-Robertson effect: evolutionary consequences of weak selection and linkage in finite populations. Heredity 100:19-31. (Pubitemid 350293641)
17. Costantini M, Bernardi G. 2008. Replication timing, chromosomal bands, and isochores. Proc Natl Acad Sci U S A. 105:3433-3437. (Pubitemid 351723570)
18. Costantini M, Cammarano R, Bernardi G. 2009. The evolution of isochore patterns in vertebrate genomes. BMC Genomics 10:146.
19. Costantini M, Clay O, Auletta F, Bernardi G. 2006. An isochore map of human chromosomes. Genome Res. 16:536-541.
20. Cuny G, Soriano P, Macaya G, Bernardi G. 1981. The major components of the mouse and human genomes. 1. Preparation, basic properties and compositional heterogeneity. Eur J Biochem. 115:227-233. (Pubitemid 11103627)
21. D'Onofrio G. 2002. Expression patterns and gene distribution in the human genome. Gene 300:155-160. (Pubitemid 35441170)
22. Duret L, Eyre-Walker A, Galtier N. 2006. A new perspective on isochore evolution. Gene 385:71-74. (Pubitemid 44834574)
23. Duret L, Galtier N. 2009. Biased gene conversion and the evolution of mammalian genomic landscapes. Annu Rev Genomics Hum Genet. 10:285-311.
24. Duret L, Mouchiroud D, Gautier C. 1995. Statistical analysis of vertebrate sequences reveals that long genes are scarce in GC-rich isochores. J Mol Evol. 40:308-317.
25. Duret L, Semon M, Piganeau G, Mouchiroud D, Galtier N. 2002. Vanishing GC-rich isochores in mammalian genomes. Genetics 162:1837-1847. (Pubitemid 36114667)
26. Elhaik E, Landan G, Graur D. 2009. Can GC content at third-codon positions be used as a proxy for isochore composition? Mol Biol Evol. 26:1829-1833.
27. Ellegren H. 2007. Molecular evolutionary genomics of birds. Cytogenet Genome Res. 117:120-130. (Pubitemid 47202672)
28. Eyre-Walker A. 1999. Evidence of selection on silent site base composition in mammals: potential implications for the evolution of isochores and junk DNA. Genetics 152:675-683. (Pubitemid 29272719)
29. Eyre-Walker A, Hurst LD. 2001. The evolution of isochores. Nat Rev Genet. 2:549-555. (Pubitemid 33674028)
30. Fearnhead P, Vasileiou D. 2009. Bayesian analysis of isochores. J Am Stat Assoc. 104:132-141.
31. Fortes G, Bouza C, Martínez P, Sánchez L. 2007. Diversity in isochore structure among cold-blooded vertebrates based on GC content of coding and non-coding sequences. Genetica 129:281-289. (Pubitemid 46233130)
32. Fullerton SM, Bernardo Carvalho A, Clark AG. 2001. Local rates of recombination are positively correlated with GC content in the human genome. Mol Biol Evol. 18:1139-1142. (Pubitemid 32520487)
33. Galtier N, Gouy M. 1998. Inferring pattern and process: maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis. Mol Biol Evol. 15:871-879. (Pubitemid 28321885)
34. Glor RE, Losos JB, Larson A. 2005. Out of cuba: overwater dispersal and speciation among lizards in the Anolis carolinensis subgroup. Mol Ecol. 14:2419-2432. (Pubitemid 40886040)
35. GoldmanN,YangZ.1994.Acodon-based modelofnucleotidesubstitution for protein-coding DNA sequences. Mol Biol Evol. 11:725-736.
36. Hardison RC, et al. 2003. Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. Genome Res. 13:13-26.
37. Heger A, Ponting C. 2007a. OPTIC: orthologous and paralogous transcripts in clades. Nucleic Acids Res. 36:D267-D270.
38. Heger A, Ponting CP. 2007b. Evolutionary rate analyses of orthologs and paralogs from 12 Drosophila genomes. Genome Res. 17:1837-1849. (Pubitemid 351360007)
39. Hill WG, Robertson A. 1966. The effect of linkage on limits to artificial selection. Genet Res. 89:311-336.
40. Hillis DM, Moritz C, Porter CA, Baker RJ. 1991. Evidence for biased gene conversion in concerted evolution of ribosomal DNA. Science 251:308-310. (Pubitemid 21916880)
41. Hughes S, Clay O, Bernardi G. 2002. Compositional patterns in reptilian genomes. Gene 295:323-329. (Pubitemid 35279264)
42. Hughes S, Zelus D, Mouchiroud D. 1999. Warm-blooded isochore structure in Nile crocodile and turtle. Mol Biol Evol. 16:1521-1527. (Pubitemid 29510895)
43. International Chicken Genome Sequencing Consortium (ICGSC). 2004. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432:695-716.
44. Janes DE, Organ CL, Fujita MK, Shedlock AM, Edwards SV. 2010. Genome evolution in Reptilia, the sister group of mammals. Annu Rev Genomics Hum Genet. 11:239-264.
45. Janes DE, Organ CL, Valenzuela N. 2008. New resources inform study of genome size, content, and organization in nonavian reptiles. Integr Comp Biol. 48:447-453.
46. Lander ES, et al. 2001. Initial sequencing and analysis of the human genome. Nature 409:860-921. (Pubitemid 32165345)
47. Li W, Bernaola-Galván P, Carpena P, Oliver JL. 2003. Isochores merit the prefix 'iso'. Comput Biol Chem. 27:5-10.
48. Madsen O. 2009. Mammals (Mammalia). In: Hedges SB, Kumar S, editors. The timetree of life. Oxford: Oxford University Press. p. 459-461.
49. Mancera E, Bourgon R, Brozzi A, Huber W, Steinmetz L. 2008. Highresolution mapping of meiotic crossovers and non-crossovers in yeast. Nature 454:479-485.
50. Meunier J, Duret L. 2004. Recombination drives the evolution of GC-content in the human genome. Mol Biol Evol. 21:984-990. (Pubitemid 38658206)
51. Montoya-Burgos JI, Boursot P, Galtier N. 2003. Recombination explains isochores in mammalian genomes. Trends Genet. 19:128-130. (Pubitemid 36279177)
52. Mouchiroud D, et al. 1991. The distribution of genes in the human genome. Gene. 100:181-187.
53. Olmo E. 1981. Evolution of genome size and DNA base composition in reptiles. Genetica 57:39-50.
54. Olmo E. 1984. Reptilia. In: John B, Bauer H, Kayano H, Levan A, editors. Animal cytogenetics. Berlin (Germany): Gebrü der Borntrager. p. 1-100.
55. Peterson DG, Stack SM, Healy JL, Donohoe BS, Anderson LK. 1994. The relationship between synaptonemal complex length and genome size in four vertebrate classes (Osteicthyes, Reptilia, Aves, Mammalia). Chromosome Res. 2:153-162. (Pubitemid 24110425)
56. Ream RA, Johns GC, Somero GN. 2003. Base compositions of genes encoding alpha-actin and lactate dehydrogenase-a from differently adapted vertebrates show no temperature-adaptive variation in G + C content. Mol Biol Evol. 20:105-110. (Pubitemid 36077904)
57. Romiguier J, Ranwez V, Douzery EJ, Galtier N. 2010. Contrasting GC-content dynamics across 33 mammalian genomes: relationship with life-history traits and chromosome sizes. Genome Res. 20:1001-1009.
58. Shedlock A, Edwards SV. 2009. Amniotes (Amniota). In: Hedges SB, Kumar S, editors. The timetree of life. Oxford: Oxford University Press. p. 375-379.
59. Watanabe Y, et al. 2002. Chromosome-wide assessment of replication timing for human chromosomes 11q and 21q: disease-related genes in timing-switch regions. Hum Mol Genet. 11:13-21. (Pubitemid 34100764)
60. Yang Z. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 24:1586-1591. (Pubitemid 47236688)