Detection of genomic variations and DNA polymorphisms and impact on analysis of meiotic recombination and genetic mapping

Proceedings of the National Academy of Sciences of the United States of America

Volumn 111, Issue 27, 2014, Pages 10007-10012

  Qi, Ji ^a,b   Chen, Yamao ^a,b   Copenhaver, Gregory P ^c,d   Ma, Hong ^a,b  

^a Institute of Genetics   (China)

^b FUDAN UNIVERSITY   (China)

^c UNIVERSITY OF NORTH CAROLINA   (United States)

^d UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

Author keywords

Genotyping; High throughput sequencing; Insertions deletions; Structural variation

Indexed keywords

ALLELE; ARABIDOPSIS; ARTICLE; DNA MARKER; GENE MAPPING; GENE SEQUENCE; GENE STRUCTURE; GENETIC ANALYSIS; GENETIC VARIABILITY; GENOTYPE; HIGH THROUGHPUT SEQUENCING; INDEL MUTATION; MEIOTIC RECOMBINATION; NONHUMAN; PLANT GENOME; POLYMORPHIC LOCUS; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; TANDEM REPEAT;

GENOTYPING; HIGH-THROUGHPUT SEQUENCING; INSERTIONS-DELETIONS; STRUCTURAL VARIATION;

ALLELES; ARABIDOPSIS; BASE SEQUENCE; DNA, PLANT; GENOME, PLANT; HUMANS; MEIOSIS; MOLECULAR SEQUENCE DATA; POLYMORPHISM, SINGLE NUCLEOTIDE; RECOMBINATION, GENETIC;

EID: 84903977643     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1321897111     Document Type: Article

References (54)

1. Feuk L, Carson AR, Scherer SW (2006) Structural variation in the human genome. Nat Rev Genet 7(2):85-97. (Pubitemid 43128895)
2. Sharp AJ, Cheng Z, Eichler EE (2006) Structural variation of the human genome. Annu Rev Genomics Hum Genet 7:407-442. (Pubitemid 44641878)
3. Mitchell-Olds T, Schmitt J (2006) Genetic mechanisms and evolutionary significance of natural variation in Arabidopsis. Nature 441(7096):947-952. (Pubitemid 43980343)
4. Stankiewicz P, Lupski JR (2002) Genome architecture, rearrangements and genomic disorders. Trends Genet 18(2):74-82. (Pubitemid 34127806)
5. Hurles ME, Dermitzakis ET, Tyler-Smith C (2008) The functional impact of structural variation in humans. Trends Genet 24(5):238-245.
6. Stankiewicz P, Lupski JR (2010) Structural variation in the human genome and its role in disease. Annu Rev Med 61:437-455.
7. Johanson U, et al. (2000) Molecular analysis of FRIGIDA, a major determinant of natural variation in Arabidopsis flowering time. Science 290(5490):344-347.
8. Michaels SD, He Y, Scortecci KC, Amasino RM (2003) Attenuation of FLOWERING LOCUS C activity as a mechanism for the evolution of summer-annual flowering behavior in Arabidopsis. Proc Natl Acad Sci USA 100(17):10102-10107. (Pubitemid 37087074)
9. Koornneef M, Alonso-Blanco C, Vreugdenhil D (2004) Naturally occurring genetic variation in Arabidopsis thaliana. Annu Rev Plant Biol 55:141-172. (Pubitemid 38940929)
10. Krieger U, Lippman ZB, Zamir D (2010) The flowering gene SINGLE FLOWER TRUSS drives heterosis for yield in tomato. Nat Genet 42(5):459-463.
11. Li H, Ruan J, Durbin R (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18(11):1851-1858.
12. Brockman W, et al. (2008) Quality scores and SNP detection in sequencing-by-synthesis systems. Genome Res 18(5):763-770. (Pubitemid 351645066)
13. Li R, Li Y, Kristiansen K, Wang J (2008) SOAP: Short oligonucleotide alignment program. Bioinformatics 24(5):713-714. (Pubitemid 351321217)
14. Qi J, Zhao F, Buboltz A, Schuster SC (2010) inGAP: An integrated next-generation genome analysis pipeline. Bioinformatics 26(1):127-129.
15. Qi J, Zhao F (2011) inGAP-sv: A novel scheme to identify and visualize structural variation from paired end mapping data. Nucleic Acids Res 39(Web Server issue):W567-575.
16. Chen K, et al. (2009) BreakDancer: An algorithm for high-resolution mapping of genomic structural variation. Nat Methods 6(9):677-681.
17. Korbel JO, et al. (2009) PEMer: A computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Genome Biol 10(2):R23.
18. Lee S, Hormozdiari F, Alkan C, Brudno M (2009) MoDIL: Detecting small indels from clone-end sequencing with mixtures of distributions. Nat Methods 6(7):473-474.
19. Hormozdiari F, Alkan C, Eichler EE, Sahinalp SC (2009) Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes. Genome Res 19(7):1270-1278.
20. Hajirasouliha I, et al. (2010) Detection and characterization of novel sequence insertions using paired-end next-generation sequencing. Bioinformatics 26(10):1277-1283.
21. Zeitouni B, et al. (2010) SVDetect: A tool to identify genomic structural variations from paired-end and mate-pair sequencing data. Bioinformatics 26(15):1895-1896.
22. Sindi S, Helman E, Bashir A, Raphael BJ (2009) A geometric approach for classification and comparison of structural variants. Bioinformatics 25(12):i222-i230.
23. Ye K, Schulz MH, Long Q, Apweiler R, Ning Z (2009) Pindel: A pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 25(21):2865-2871.
24. Abel HJ, et al. (2010) SLOPE: A quick and accurate method for locating non-SNP structural variation from targeted next-generation sequence data. Bioinformatics 26(21):2684-2688.
25. Wong K, Keane TM, Stalker J, Adams DJ (2010) Enhanced structural variant and breakpoint detection using SVMerge by integration of multiple detection methods and local assembly. Genome Biol 11(12):R128.
26. Kidd JM, et al. (2008) Mapping and sequencing of structural variation from eight human genomes. Nature 453(7191):56-64. (Pubitemid 351630326)
27. Graubert TA, et al. (2007) A high-resolution map of segmental DNA copy number variation in the mouse genome. PLoS Genet 3(1):e3.
28. Emerson JJ, Cardoso-Moreira M, Borevitz JO, Long M (2008) Natural selection shapes genome-wide patterns of copy-number polymorphism in Drosophila melanogaster. Science 320(5883):1629-1631. (Pubitemid 351931251)
29. Huang X, et al. (2010) Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet 42(11):961-967.
30. Qi J, et al. (2009) Characterization of meiotic crossovers and gene conversion by whole-genome sequencing in Saccharomyces cerevisiae. BMC Genomics 10:475.
31. Lu P, et al. (2012) Analysis of Arabidopsis genome-wide variations before and after meiosis and meiotic recombination by resequencing Landsberg erecta and all four products of a single meiosis. Genome Res 22(3):508-518.
32. Yang S, et al. (2012) Great majority of recombination events in Arabidopsis are gene conversion events. Proc Natl Acad Sci USA 109(51):20992-20997.
33. Mills RE, et al.; 1000 Genomes Project (2011) Mapping copy number variation by population-scale genome sequencing. Nature 470(7332):59-65.
34. Wijnker E, et al. (2013) The genomic landscape of meiotic crossovers and gene conversions in Arabidopsis thaliana. eLife 2:e01426.
35. Lamesch P, et al. (2012) The Arabidopsis Information Resource (TAIR): Improved gene annotation and new tools. Nucleic Acids Res 40(Database issue):D1202-D1210.
36. Schneeberger K, et al. (2011) Reference-guided assembly of four diverse Arabidopsis thaliana genomes. Proc Natl Acad Sci USA 108(25):10249-10254.
37. Cao J, et al. (2011) Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nat Genet 43(10):956-963.
38. Long Q, et al. (2013) Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden. Nat Genet 45(8):884-890.
39. Mercier R, et al. (2005) Two meiotic crossover classes cohabit in Arabidopsis: One is dependent on MER3,whereas the other one is not. Curr Biol 15(8):692-701. (Pubitemid 40599923)
40. Chelysheva L, et al. (2005) AtREC8 and AtSCC3 are essential to the monopolar orientation of the kinetochores during meiosis. J Cell Sci 118(Pt 20):4621-4632. (Pubitemid 41646373)
41. Sanchez-Moran E, Santos JL, Jones GH, Franklin FC (2007) ASY1 mediates AtDMC1-dependent interhomolog recombination during meiosis in Arabidopsis. Genes Dev 21(17):2220-2233. (Pubitemid 47360843)
42. Tsukahara S, et al. (2009) Bursts of retrotransposition reproduced in Arabidopsis. Nature 461(7262):423-426.
43. Initiative TAG; Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408(6814):796-815.
44. Le QH, Wright S, Yu Z, Bureau T (2000) Transposon diversity in Arabidopsis thaliana. Proc Natl Acad Sci USA 97(13):7376-7381. (Pubitemid 30431471)
45. Jiang N, Bao Z, Zhang X, Eddy SR, Wessler SR (2004) Pack-MULE transposable elements mediate gene evolution in plants. Nature 431(7008):569-573. (Pubitemid 39336337)
46. Juretic N, Hoen DR, Huynh ML, Harrison PM, Bureau TE (2005) The evolutionary fate of MULE-mediated duplications of host gene fragments in rice. Genome Res 15(9):1292-1297. (Pubitemid 41247920)
47. Morgante M, et al. (2005) Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize. Nat Genet 37(9):997-1002. (Pubitemid 43086159)
48. Djian P (1998) Evolution of simple repeats in DNA and their relation to human disease. Cell 94(2):155-160.
49. Petruska J, Hartenstine MJ, Goodman MF (1998) Analysis of strand slippage in DNA polymerase expansions of CAG/CTG triplet repeats associated with neurodegenerative disease. J Biol Chem 273(9):5204-5210. (Pubitemid 28108683)
50. Benson G (1999) Tandem repeats finder: A program to analyze DNA sequences. Nucleic Acids Res 27(2):573-580.
51. Loman NJ, et al. (2012) Performance comparison of benchtop high-throughput sequencing platforms. Nat Biotechnol 30(5):434-439.
52. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25(14):1754-1760.
53. Sun Y, et al. (2012) Deep genome-wide measurement of meiotic gene conversion using tetrad analysis in Arabidopsis thaliana. PLoS Genet 8(10):e1002968.
54. Meyer LR, et al. (2013) The UCSC Genome Browser database: Extensions and updates 2013. Nucleic Acids Res 41(Database issue):D64-D69.