The genomic landscape of short insertion and deletion polymorphisms in the chicken (Gallus gallus) genome: A high frequency of deletions in tandem duplicates

Genetics

Volumn 176, Issue 3, 2007, Pages 1691-1701

  Brandström, Mikael ^a   Ellegren, Hans ^a  

^a UPPSALA UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; NUCLEOTIDE; SPACER DNA;

5' UNTRANSLATED REGION; ARTICLE; BREED; CHICKEN; CONTROLLED STUDY; DENSITY; DOMESTIC ANIMAL; GENE DELETION; GENE DUPLICATION; GENE FREQUENCY; GENE INSERTION; GENE MAPPING; GENE REPLICATION; GENE SEQUENCE; GENETIC CORRELATION; GENETIC POLYMORPHISM; GENOME ANALYSIS; INTRON; MICROSATELLITE MARKER; MUTATIONAL ANALYSIS; NONHUMAN; POINT MUTATION; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; TANDEM REPEAT;

5' UNTRANSLATED REGIONS; ANIMALS; CHICKENS; CHROMOSOMES; GENOME; GENOMICS; INTRONS; POINT MUTATION; POLYMORPHISM, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE DELETION; TANDEM REPEAT SEQUENCES; VARIATION (GENETICS);

GALLUS GALLUS;

EID: 34547094391     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.107.070805     Document Type: Article

References (72)

1. ALTSCHUL, S. F., T. L. MADDEN, A. A. SCHAFFER, J. ZHANG, Z. ZHANG et al., 1997 Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402.
2. AXELSSON, E., M. T. WEBSTER, N. G. SMITH, D. W. BURT and H. ELLEGREN, 2005 Comparison of the chicken and turkey genomes reveals a higher rate of nucleotide divergence on microchromosomes than macrochromosomes. Genome Res. 15: 120-125.
3. BENSON, G., 1999 Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27: 573-580.
4. BHANGALE, T. R., M. J. RIEDER, R. J. LIVINGSTON and D. A. NICKERSON, 2005 Comprehensive identification and characterization of diallelic insertion-deletion polymorphisms in 330 human candidate genes. Hum. Mol. Genet. 14: 59-69.
5. BOIS, P. R., 2003 Hypermutable minisatellites, a human affair? Genomics 81: 349-355.
6. BRAY, N., and L. PACHTER, 2004 MAVID: constrained ancestral alignment of multiple sequences. Genome Res. 14: 693-699.
7. BRITTEN, R. J., 2002 Divergence between samples of chimpanzee and human DNA sequences is 5%, counting indels. Proc. Natl. Acad. Sci. USA 99: 13633-13635.
8. BRITTEN, R. J., L. ROWEN, J. WILLIAMS and R. A. CAMERON, 2003 Majority of divergence between closely related DNA samples is due to indels. Proc. Natl. Acad. Sci. USA 100: 4661-4665.
9. CHAMARY, J. V., and L. D. HURST, 2004 Similar rates but different modes of sequence evolution in introns and at exonic silent sites in rodents: evidence for selectively driven codon usage. Mol. Biol. Evol. 21: 1014-1023.
10. CHEN, J. M., N. CHUZHANOVA, P. D. STENSON, C. FEREC and D. N. COOPER, 2005a Meta-analysis of gross insertions causing human genetic disease: novel mutational mechanisms and the role of replication slippage. Hum. Mutat. 25: 207-221.
11. CHEN, J. M., P. D. STENSON, D. N. COOPER and C. FEREC, 2005b A systematic analysis of LINE-1 endonuclease-dependent retrotranspositional events causing human genetic disease. Hum. Genet. 117: 411-427.
12. CHIMPANZEE SEQUENCING and ANALYSIS CONSORTIUM, 2005 Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437: 69-87.
13. COMERON, J. M., and M. KREITMAN, 2000 The correlation between intron length and recombination in Drosophila: dynamic equilibrium between mutational and selective forces. Genetics 156: 1175-1190.
14. COOPER, G. M., M. BRUDNO, E. A. STONE, I. DUBCHAK, S. BATZOGLOU et al., 2004 Characterization of evolutionary rates and constraints in three mammalian genomes. Genome Res. 14: 539-548.
15. ELLEGREN, H., 2004 Microsatellites: simple sequences with complex evolution. Nat. Rev. Genet. 5: 435-445.
16. ELLEGREN, H., N. G. SMITH and M. T. WEBSTER, 2003 Mutation rate variation in the mammalian genome. Curr. Opin. Genet. Dev. 13: 562-568.
17. FAIN, M. G., and P. HOUDE, 2004 Parallel radiations in the primary clades of birds. Evolution 58: 2558-2573.
18. GAFFNEY, D. J., and P. D. KEIGHTLEY, 2005 The scale of mutational variation in the murid genome. Genome Res. 15: 1086-1094.
19. GREGORY, T. R., 2004 Insertion-deletion biases and the evolution of genome size. Gene 324: 15-34.
20. GREGORY, T. R., 2005 Synergy between sequence and size in large-scale genomics. Nat. Rev. Genet. 6: 699-708.
21. HAMILTON, M. B., J. M. BRAVERMAN and D. F. SORIA-HERNANZ, 2003 Patterns and relative rates of nucleotide and insertion/deletion evolution at six chloroplast intergenic regions in New World species of the Lecythidaceae. Mol. Biol. Evol. 20: 1710-1721.
22. HARDISON, R. C., K. M. ROSKIN, S. YANG, M. DIEKHANS, W. J. KENT et al., 2003 Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. Genome Res. 13: 13-26.
23. HELLMANN, I., I. EBERSBERGER, S. E. PTAK, S. PAABO and M. PRZEWORSKI, 2003 A neutral explanation for the correlation of diversity with recombination rates in humans. Am. J. Hum. Genet. 72: 1527-1535.
24. HOLM, S, 1979 A simple sequentially rejective multiple test procedure. Scand. J. Stat. 6: 65-70.
25. HOLMES, I., 2005 Using evolutionary expectation maximization to estimate indel rates. Bioinformatics 21: 2294-2300.
26. HUANG, S. W., R. FRIEDMAN, N. YU, A. YU and W. H. LI, 2005 How strong is the mutagenicity of recombination in mammals? Mol. Biol. Evol. 22: 426-431.
27. HUGHES, A. L., and M. K. HUGHES, 1995 Small genomes for better flyers. Nature 377: 391.
28. HUGHES, A. L., and H. PIONTKIVSKA, 2005 DNA repeat arrays in chicken and human genomes and the adaptive evolution of avian genome size. BMC Evol. Biol. 5: 12.
29. INTERNATIONAL CHICKEN GENOME SEQUENCING CONSORTIUM, 2004 Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432: 695-716.
30. INTERNATIONAL CHICKEN POLYMORPHISM MAP CONSORTIUM, 2004 A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature 432: 717-722.
31. JOHNSON, K. P., 2004 Deletion bias in avian introns over evolutionary timescales. Mol. Biol. Evol. 21: 599-602.
32. KAWAKITA, A., T. SOTA, J. S. ASCHER, M. Ito, H. TANAKA et al., 2003 Evolution and phylogenetic utility of alignment gaps within intron sequences of three nuclear genes in bumble bees (Bombus). Mol. Biol. Evol. 20: 87-92.
33. KEIGHTLEY, P. D., and T. JOHNSON, 2004 MCALIGN: stochastic alignment of noncoding DNA sequences based on an evolutionary model of sequence evolution. Genome Res. 14: 442-450.
34. KONDRASHOV, A. S., and I. B. ROGOZIN, 2004 Context of deletions and insertions in human coding sequences. Hum. Mutat. 23: 177-185.
35. KOZLOWSKI, J., M. KONARZEWSKI and A. T. GAWELCZYK, 2003 Cell size as a link between noncoding DNA and metabolic rate scaling. Proc. Natl. Acad. Sci. USA 100: 14080-14085.
36. LERCHER, M. J., and L. D. HURST, 2002 Human SNP variability and mutation rate are higher in regions of high recombination. Trends Genet. 18: 337-340.
37. LEVINSON, G., and G. A. GUTMAN, 1987 Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Mol. Biol. Evol. 4: 203-221.
38. LONGMAN-JACOBSEN, N., J. F. WILLIAMSON, R. L. DAWKINS and S. GAUDIERI, 2003 In polymorphic genomic regions indels cluster with nucleotide polymorphism: Quantum Genomics. Gene 312: 257-261.
39. LUDWIG, M. Z., N. H. PATEL and M. KREITMAN, 1998 Functional analysis of eve stripe 2 enhancer evolution in Drosophila: rules governing conservation and change. Development 125: 949-958.
40. MAKOVA, K. D., S. YANG and F. CHIAROMONTE, 2004 Insertions and deletions are male biased too: a whole-genome analysis in rodents. Genome Res. 14: 567-573.
41. MESSIER, W., S. H. LI and C. B. STEWART, 1996 The birth of microsatellites. Nature 381: 483.
42. MILLS, R. E., C. T. LUTTIG, C. E. LARKINS, A. BEAUCHAMP, C. TSUI et al., 2006 An initial map of insertion and deletion (INDEL) variation in the human genome. Genome Res. 16: 1182-1190.
43. MOUSE GENOME SEQUENCING CONSORTIUM, 2002 Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562.
44. MÜLLER, K., 2006 Incorporating information fromlength-mutational events into phylogenetic analysis. Mol. Phylogenet. Evol. 38: 667-676.
45. NEAFSEY, D. E., and S. R. PALUMBI, 2003 Genome size evolution in pufferfish: a comparative analysis of diodontid and tetraodontid pufferfish genomes. Genome Res. 13: 821-830.
46. OGURTSOV, A. Y., S. SUNYAEV and A. S. KONDRASHOV, 2004 Indel-based evolutionary distance and mouse-human divergence. Genome Res. 14: 1610-1616.
47. OMETTO, L., W. STEPHAN and D. DE LORENZO, 2005 Insertion/deletion and nucleotide polymorphism data reveal constraints in Drosophila melanogaster introns and intergenic regions. Genetics 169: 1521-1527.
48. OPHIR, R., and D. GRAUR, 1997 Patterns and rates of indel evolution in processed pseudogenes from humans and murids. Gene 205: 191-202.
49. PEREIRA, S. L., and A. J. BAKER, 2006 A molecular timescale for galliform birds accounting for uncertainty in time estimates and heterogeneity of rates of DNA substitutions across lineages and sites. Mol. Phylogenet. Evol. 38: 499-509.
50. PETROV, D. A., 2002a DNA loss and evolution of genome size in Drosophila. Genetica 115: 81-91.
51. PETROV, D. A., 2002b Mutational equilibrium model of genome size evolution. Theor. Popul. Biol. 61: 531-544.
52. PETROV, D. A., T. A. SANGSTER, J. S. JOHNSTON, D. L. HARTL and K. L. SHAW, 2000 Evidence for DNA loss as a determinant of genome size. Science 287: 1060-1062.
53. PODLAHA, O., and J. ZHANG, 2003 Positive selection on protein-length in the evolution of a primate sperm ion channel. Proc. Natl. Acad. Sci. USA 100: 12241-12246.
54. PRICE, A. L., E. ESKIN and P. A. PEVZNER, 2004 Whole-genome analysis of Alu repeat elements reveals complex evolutionary history. Genome Res. 14: 2245-2252.
55. PRIMMER, C. R., and H. ELLEGREN, 1998 Patterns of molecular evolution in avian microsatellites. Mol. Biol. Evol. 15: 997-1008.
56. RDevelopment Core Team, 2006 R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna.
57. SAMONTE, R. V., and E. E. EICHLER, 2002 Segmental duplications and the evolution of the primate genome. Nat. Rev. Genet. 3: 65-72.
58. SUNDSTRÖM, H., and H. ELLEGREN, 2004 Reduced variation on the chicken Z chromosome. Genetics 164: 377-385.
59. TAYLOR, M. S., C. P. PONTING and R. R. Copley, 2004 Occurrence and consequences of coding sequence insertions and deletions in mammalain genomes. Genome Res. 14: 555-566.
60. TSUNODA, T., G. M. LATHROP, A. Sekine, R. Yamada, A. Takahashi et al., 2004 Variation of gene-based SNPs and linkage disequilibrium patterns in the human genome. Hum. Mol. Genet. 13: 1623-1632.
61. VAN TUINEN, M., and G. J. DYKE, 2004 Calibration of galliform molecular clocks using multiple fossils and genetic partitions. Mol. Phylogenet. Evol. 30: 74-86.
62. WALTARI, E, and S. V. EDWARDS, 2002 Evolutionary dynamics of intron size, genome size, and physiological correlates in archosaurs. Am. Nat. 160: 539-552.
63. WEBER, J. L., D. DAVID, J. HEIL, Y. FAN, C. ZHAO et al., 2002 Human diallelic insertion/deletion polymorphisms. Am. J. Hum. Genet. 71: 854-862.
64. WEBSTER, M. T., E. AXELSSON and H. ELLEGREN, 2006 Strong regional biases in nucleotide substitution in the chicken genome. Mol. Biol. Evol. 23: 1203-1216.
65. VINOGRADOV, A. E., 1997 Nucleotypic effect in homeotherms: bodymass independent resting metabolic rate of passerine birds is related to genome size. Evolution 51: 220-225.
66. VINOGRADOV, A. E., 2002 Growth and decline of introns. Trends Genet. 18: 232-236.
67. VINOGRADOV, A. E., and O. V. ANATSKAYA, 2006 Genome size and metabolic intensity in tetrapods: a tale of two lines. Proc. Biol. Sci. 273: 27-32.
68. XIE, X., J. LU, E. J. KULBOKAS, T. R. GOLUB, V. MOOTHA et al., 2005 Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals. Nature 434: 338-345.
69. YANG, S., A. F. SMIT, S. SCHWARTZ, F. CHIAROMONTE, K. M. ROSKIN et al., 2004 Patterns of insertions and their covariation with substitutions in the rat, mouse, and human genomes. Genome Res. 14: 517-527.
70. ZHANG, Z., and M. GERSTEIN, 2003 Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes. Nucleic Acids Res. 31: 5338-5348.
71. ZHAO, Z., Y. X. FU, D. HEWETT-EMMETT and E. BOERWINKLE, 2003 Investigating single nucleotide polymorphism (SNP) density in the human genome and its implications for molecular evolution. Gene 312: 207-213.
72. ZHU, Y., J. E. STRASSMANN and D. C. QUELLER, 2000 Insertions, substitutions, and the origin of microsatellites. Genet Res. 76: 227-236.