The pattern of insertion/deletion polymorphism in Arabidopsis thaliana

Molecular Genetics and Genomics

Volumn 280, Issue 4, 2008, Pages 351-361

  Zhang, Wen ^a   Sun, Xiaoqin ^a   Yuan, Huizhong ^a   Araki, Hitoshi ^b   Wang, Jue ^a   Tian, Dacheng ^a  

^a NANJING UNIVERSITY   (China)

^b SWISS FEDERAL INSTITUTE OF AQUATIC SCIENCE AND TECHNOLOGY   (Switzerland)

Author keywords

Arabidopsis; GC content; Insertion deletion; Polymorphism; SNP

Indexed keywords

ARABIDOPSIS; ARTICLE; DNA POLYMORPHISM; GENE DELETION; GENE FREQUENCY; GENE IDENTIFICATION; GENE INSERTION; GENE LOCATION; GENE LOCUS; GENE SEQUENCE; GENETIC VARIABILITY; PRIORITY JOURNAL;

ARABIDOPSIS; BASE COMPOSITION; GENOME, PLANT; INDEL MUTATION; POLYMORPHISM, GENETIC; QUANTITATIVE TRAIT LOCI;

ARABIDOPSIS; ARABIDOPSIS THALIANA;

EID: 51349160932     PISSN: 16174615     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00438-008-0370-1     Document Type: Article

References (32)

1. MD Barker 1989 High-frequency homologous recombination between duplicate chromosomal immunoglobulin mu heavy-chain constant regions Mol Cell Biol 9 5500 5507
2. J Batley G Barker H O'Sullivan KJ Edwards D Edwards 2003 Mining for single nucleotide polymorphisms and insertions/deletions in maize expressed sequence Plant Physiol 132 84 91
3. J Berger T Suzuki K Senti J Stubbs G Schaffner BJ Dickson 2001 Genetic mapping with SNP markers in Drosophila Nat Genet 29 475 481
4. TR Bhangale MJ Rieder RJ Livingston DA Nickerson 2005 Comprehensive identification and characterization of diallelic insertion-deletion polymorphisms in 330 human candidate genes Hum Mol Genet 14 59 69
5. RJ Britten L Rowen J Williams RA Cameron 2003 Majority of divergence between closely related DNA samples is due to InDels Proc Natl Acad Sci USA 100 4661 4665
6. SK Chan M Hsing F Hormozdiari A Cherkasov 2007 Relationship between insertion/deletion (indel) frequency of proteins and essentiality BMC Bioinformatics 8 227
7. A Crombach P Hogeweg 2007 Chromosome rearrangements and the evolution of genome structuring and adaptability Mol Biol Evol 24 5 1130 1139
8. RJ DeBerardinis JL Goodier EM Ostertag HH Kazazian Jr 1998 Rapid amplification of a retrotransposon subfamily is evolving the mouse genome Nat Genet 20 3 288 290
9. J Ding H Araki Q Wang P Zhang D Tian 2007 Highly asymmetric rice genomes BMC Genomics 8 154
10. M Garcia-Diaz TA Kunkel 2006 Mechanism of a genetic glissando*: structural biology of InDel mutations Trends Biochem Sci 31 206 214
11. TR Gregory 2004 Insertion-deletion biases and the evolution of genome size Gene 324 15 34
12. M Hammarlund MW Davis H Nguyen D Dayton EM Jorgensen 2005 Heterozygous insertions alter crossover distribution but allow crossover interference in Caenorhabditis elegans Genetics 171 1047 1056
13. RC Hardison KM Roskin S Yang M Diekhans D Kolbe 2003 Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution Genome Res 131 13 26
14. DA Hinds AP Kloek M Jen X Chen KA Frazer 2006 Common deletions and SNPs are in linkage disequilibrium in the human genome Nat Genet 38 82 85
15. G Jander SR Norris SD Rounsley DF Bush RL Last 2002 Arabidopsis map-based cloning in the post-genome era Plant Physiol 129 440 450
16. AS Kondrashov 2003 Direct estimates of human per nucleotide mutation rates at 20 loci causing Mendelian diseases Hum Mutat 21 12 27
17. Kondrashov FA, Rogozin IB, Wolf YI, Koonin EV (2002) Selection in the evolution of gene duplication. Genome Biol 3:research0008.1-0008.9
18. Levin I (1999) Relating statistics and experimental design: an introduction. Sage Publications, Thousand Oaks
19. S Levy G Sutton PC Ng L Feuk JC Venter 2007 The diploid genome sequence of an individual human PLoS Biol 5 e254
20. RE Mills CT Luttig CE Larkins A Beauchamp SE Devine 2006 An initial map of insertion and deletion (INDEL) variation in the human genome Genome Res 16 9 1182 1190
21. T Mitchell-Olds J Schmitt 2006 Genetic mechanisms and evolutionary significance of natural variation in Arabidopsis Nature 441 947 952
22. M Nordborg TT Hu Y Ishino J Jhaveri H Zheng 2005 The pattern of polymorphism in Arabidopsis thaliana PLoS Biol 3 e196
23. CE Pearson KN Edamura JD Cleary 2005 Repeat instability: mechanisms of dynamic mutations Nat Rev Genet 6 729 742
24. DA Petrov TA Sangster JS Johnston DL Hartl KL Shaw 2000 Evidence for DNA loss as a determinant of genome size Science 287 1060 1062
25. SO Rogers AJ Bendich 1985 Extraction of DNA from milligram amounts of fresh, herbarium and mummified plant tissues Plant Mol Biol 5 69 76
26. S Schwartz WJ Kent A Smit Z Zhang W Miller 2003 Human-mouse alignments with BLASTZ Genome Res 13 103 107
27. T Sun Y Gao W Tan S Ma D Lin 2007 A six-nucleotide insertion-deletion polymorphism in the CASP8 promoter is associated with susceptibility to multiple cancers Nat Genet 39 605 613
28. F Tajima 1989 Statistical method for testing the neutral mutation hypothesis by DNA polymorphism Genetics 123 585 595
29. MI Tenaillon MC Sawkins AD Long RL Gaut BS Gaut 2001 Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.) Proc Natl Acad Sci USA 98 9161 9166
30. The Chimpanzee Sequencing and Analysis Consortium 2005 Initial sequence of the chimpanzee genome and comparison with the human genome Nature 437 69 87
31. SR Wicks RT Yeh WR Gish RH Waterston RHA Plasterk 2001 Rapid gene mapping in Caenorhabditis elegans using a high density polymorphism map Nat Genet 28 160 164
32. S Yang K Jiang H Araki J Ding D Tian 2007 A molecular isolation mechanism associated with high intra-specific diversity in rice Gene 394 87 95