Sequence-based detection and breakpoint assembly of polymorphic inversions

Genetics

Volumn 192, Issue 1, 2012, Pages 131-137

  Corbett Detig, Russell B ^a   Cardeno, Charis ^b   Langley, Charles H ^b  

^a HARVARD UNIVERSITY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHROMOSOME ABERRATION; CHROMOSOME INVERSION; CHROMOSOME POLYMORPHISM; CYTOLOGY; DROSOPHILA MELANOGASTER; GENE SEQUENCE; GENOTYPING TECHNIQUE; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL;

ANIMALS; BASE SEQUENCE; CHROMOSOME BREAKPOINTS; CHROMOSOME INVERSION; CHROMOSOMES, INSECT; DROSOPHILA MELANOGASTER; FEMALE; GENOMICS; GENOTYPE; POLYMERASE CHAIN REACTION;

DROSOPHILA MELANOGASTER;

EID: 84866127755     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.112.141622     Document Type: Article

References (44)

1. Adams, M. D., S. E. Celniker, R. A. Holt, C. A. Evans, J. D. Gocayne et al., 2000 The genome sequence of Drosophila melanogaster. Science 287: 2185-2195.
2. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, 1990 Basic local alignment search tool. J. Mol. Biol. 3: 403-410.
3. Anderson, A. R., A. A. Hoffmann, S. W. McKechnie, P. A. Umina, and A. R. Weeks, 2005 The latitudinal cline in the In(3R)Payne inversion polymorphism has shifted in the last 20 years in Australian Drosophila melanogaster populations. Mol. Ecol. 14: 851-858.
4. Andolfatto, P., J. D. Wall, and M. Kreitman, 1999 Unusual haplotype structure at the proximal breakpoint of In(2L)t in a natural population of Drosophila melanogaster. Genetics 153: 1297-1311.
5. Ashburner, M., and F. Lemeunier, 1976 Relationships within the melanogaster species subgroup of the genus Drosophila (Sophophora). 1. Inversion polymorphisms in Drosophila melanogaster and Drosophila simulans. Proc. R. Soc. Lond. 193: 137-157.
6. Aulard S., J. R. David, and F. Lemeunier, 2002 Chromosomal inversion polymorphism in Afrotropical populations of Drosophila melanogaster. Genet. Res. 79: 49-63.
7. Aulard, S., L. Monti, N. Chaminade, and F. Lemeunier, 2004 Mitotic and polytene chromosomes: comparisons between Drosophila melanogaster and Drosophila simulans. Genetica 120: 137-150.
8. Bansal, V., A. Bashir, and V. Bafna, 2007 Evidence for large inversion polymorphisms in the human genome from HapMap data. Genome Res. 17: 219-230.
9. Caceres, M., J. M. Ranz, A. Barbadilla, M. Long, and A. Ruiz, 1999 Generation of a widespread Drosophila inversion by a transposable element. Science 285: 415-418.
10. Charlesworth, D., B. Charlesworth, and G. Marais, 2005 Steps in the evolution of heteromorphic sex chromosomes. Heredity 95: 118-128.
11. Cridland, J., and K. Thornton, 2010 Validation of rearrangement breakpoints identified by paired-end sequencing in natural populations of Drosophila melanogaster. Genome Biol. Evol. 2: 83-101.
12. Dobzhansky, T., 1951 Genetics and the Origin of Species, Ed. 3. Columbia University Press, New York.
13. Dubinin, N. P., N. N. Sokolov, and G. G. Tiniakov, 1937 Intraspecific chromosomal variability. Biol Zh. 6: 1007.
14. Frydenberg, J., A. A. Hoffmann, and V. Loeschcke, 2003 DNA sequence variation and latitudinal associations in hsp23, hsp26 and hsp27 from natural populations of Drosophila melanogaster. Mol. Ecol. 12: 2025-2032.
15. Gordon, D., C. Abajian, and P. Green, 1998 Consed: a graphical tool for sequence finishing. Genome Res. 8: 195-202.
16. Green, P., 1996 Phrap documentation. Available at: http://www. phrap.org/phredphrap/phrap.html
17. Hoffmann, A. A., and L. H. Rieseberg, 2008 Revisiting the impact of inversions in evolution: From population genetic markers to drivers of adaptive shifts and speciation? Annu. Rev. Ecol. Evol. Syst. 39: 21-42.
18. Hudson, R. R., M. Slatkin, and W. P. Maddison, 1992 Estimation of levels of gene flow from DNA-sequence data. Genetics 132: 583-589.
19. Jaenike, J., 2001 Sex chromosome meiotic drive. Annu. Rev. Ecol. Syst. 32: 25-49.
20. Kennington, W. J., A. A. Hoffmann, and L. Partridge, 2007 Mapping regions within cosmopolitan inversion In(3R)Payne associated with natural variation in body size in Drosophila melanogaster. Genetics 177: 549-556.
21. Kidd, J. M., G. M. Cooper, W. F. Donahue, H. S. Hayden, N. Sampas et al., 2008 Mapping and sequencing of structural variation from eight human genomes. Nature 453: 56-64.
22. Kirkpatrick, M., and N. Barton, 2006 Chromosome inversions, local adaptation and speciation. Genetics 173: 419-434.
23. Knibb, W. R., J. G. Oakenshot, and J. B. Gibson, 1981 Chromosome inversion polymorphism in Drosophila melanogaster.I. Latitudinal clines and associations between inversions in Australasian populations. Genetics 98: 833-847.
24. Krimbas, C. B., and J. R. Powell, 1992 Drosophila Inversion Polymorphism. CRC Press, Boca Raton, FL.
25. Kusano, A., C. Staber, H. Y. E. Chan, and B. Ganetzky, 2003 Closing the (Ran)GAP on segregation distortion in Drosophila. Bioessays 25: 108-115.
26. Langley, C. H., M. Crepeau, C. Cardeno, R. Corbett-Detig, and K. Stevens, 2011 Circumventing heterozygosity: sequencing the amplified genome of a single haploid Drosophila melanogster embryo. Genetics 188: 239-246.
27. Langley, C. H., K. Stevens, C. Cardeno, Y. C. G. Lee, D. R. Schrider et al. 2012 Genomic variation in natural populations of Drosophila melanogaster. Genetics (in press)
28. Li, H., J. Ruan, and R. Durbin, 2008 Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 18: 1851-1858.
29. Li, R., W. Fan, G. Tian, H. Zhu, L. He et al., 2009 The sequence and de novo assembly of the giant panda genome. Nature 463: 311-317.
30. Lucchesi, J. C., and D. T. Suzuki, 1968 The interchromosomal control of recombination. Annu. Rev. Genet. 2: 53-86.
31. Lyon, M. F., 2003 Transmission ratio distortion in mice. Annu. Rev. Genet. 37: 393-408.
32. Mathiopoulos, K. D., A. della Torre, V. Predazzi, V. Petrarca, and M. Coluzzi, 1998 Cloning of inversion breakpoints in the Anopheles gambiae complex traces a transposable element at the inversion junction. Proc. Natl. Acad. Sci. USA 95: 12444-12449.
33. Matzkin, L. M., T. J. S. Merritt, C. T. Zhu, and W. F. Eanes, 2005 The structure and population genetics of the breakpoints associated with the cosmopolitan chromosomal inversion In(3R) Payne in Drosophila melanogaster. Genetics 170: 1143-1152.
34. Medvedev, P., M. Stanciu, and M. Brudno, 2009 Computational methods for discovering structural variation with next-generation sequencing. Nat. Methods 6: S13-S20.
35. Novitski, E., and G. Braver, 1954 An analysis of crossing-over within a heterozygous inversion in Drosophila melanogaster. Genetics 39: 197-209.
36. Ranz, J. M., D. Maurin, Y. S. Chan, M. V. Grotthuss, L. W. Hillier et al., 2007 Principles of genome evolution in the Drosophila melanogaster species group. PLoS Biol. 5: 1366-1381.
37. Sindi, S. S., and B. J. Raphael, 2010 Identification and frequency estimation of inversion polymorphisms from haplotype data. J. Comput. Biol. 17(3): 517-531.
38. Sturtevant, A. H., 1917 Genetic factors affecting the strength of linkage in Drosophila. Proc. Natl. Acad. Sci. USA 3: 555-558.
39. Sturtevant, A. H., 1926 A crossover reducer in Drosophila melanogaster due to inversion of a section of the third chromosome. Biol. Zentralbl. 46: 697-702.
40. Sturtevant, A. H., 1931 Known and probable inverted sections of the autosomes of Drosophila melanogaster. Carnegie Inst. Washington Publ. 421: 1-27.
41. Sturtevant, A. H., and G. W. Beadle, 1936 The relations of inversions in the X chromosome of Drosophila melanogaster to crossing over and disjunction. Genetics 21: 544-604.
42. Tuzun, E., A. J. Sharp, J. A. Bailey, R. Kaul, V. A. Morrison et al., 2005 Fine-scale structural variation of the human genome. Nat. Genet. 37: 727-732.
43. Van Delden, W., and A. Kamping, 1991 Changes in relative fitness with temperature among second chromosome arrangements in Drosophila melanogaster. Genetics 127: 507-514.
44. Wesley, C. S., and W. F. Eanes, 1994 Isolation and analysis of the breakpoint sequences of chromosome inversion In(3L)Payne in Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 91: 3132-3136.