Interactions among genomic structure, function, and evolution revealed by comprehensive analysis of the Arabidopsis thaliana genome

Genomics

Volumn 88, Issue 4, 2006, Pages 394-406

  Wu, Chengcang ^a   Wang, Suojin ^a   Zhang, Hong Bin ^a  

^a TEXAS A AND M UNIVERSITY   (United States)

Author keywords

arabidopsis thaliana; DNA molecule structure and organization; genetic recombination; genome evolution; genome function; genomic components

Indexed keywords

ARABIDOPSIS; ARTICLE; CONTROLLED STUDY; CORRELATION ANALYSIS; EVOLUTION; GENE DELETION; GENE INSERTION; GENETIC RECOMBINATION; GENOME; NONHUMAN; PHENOTYPE; PLANT CHROMOSOME; PRIORITY JOURNAL; RETROPOSON; STATISTICAL SIGNIFICANCE;

ARABIDOPSIS; BIOLOGICAL EVOLUTION; CHROMOSOME MAPPING; CHROMOSOMES, PLANT; DNA TRANSPOSABLE ELEMENTS; EVOLUTION; GENE ORDER; GENETIC VARIATION; GENOME, PLANT; RECOMBINATION, GENETIC; RETROELEMENTS; VARIATION (GENETICS);

ARABIDOPSIS; ARABIDOPSIS THALIANA;

EID: 33748698238     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2006.05.003     Document Type: Article

References (35)

1. Hodgkin J., Plasterk R.H.A., and Waterston R.H. The nematode Caenorhabditis elegans and its genome. Science 270 (1995) 410-414
2. Adams M.D., et al. The genome sequence of Drosophila melanogaster. Science 287 (2000) 2185-2195
3. Arabidopsis Genome Initiative, Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408 (2000) 796-815
4. International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 409 (2001) 860-921
5. Goff S.A., et al. A draft sequence of the rice genome (Oryza sativa L. spp. japonica). Science 296 (2002) 92-100
6. Holt R.A., et al. The genome sequence of the malaria mosquito Anopheles gambiae. Science 298 (2002) 129-149
7. International Chicken Genome Sequencing Consortium. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432 (2004) 695-716
8. Xia Q., et al. A draft sequence for the genome of the domesticated silkworm (Bombyx mori). Science 306 (2004) 1937-1940
9. International Rice Genome Sequencing Project. The map-based sequence of the rice genome. Nature 436 (2005) 793-800
10. Chen M., et al. Microcolinearity in sh2-homologous regions of the maize, rice, and sorghum genomes. Proc. Natl. Acad. Sci. USA 94 (1997) 3431-3435
11. Gale M.D., and Devos K.M. Comparative genetics in the grasses. Proc. Natl. Acad. Sci. USA 95 (1998) 1971-1974
12. Feuillet C., and Keller B. High gene density is conserved at syntenic loci of small and large grass genomes. Proc. Natl. Acad. Sci. USA 96 (1999) 8265-8270
13. International SNP Map Working Group. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409 (2001) 928-933
14. Jander G., et al. Arabidopsis map-based cloning in the post-genome era. Plant Physiol. 129 (2002) 440-450
15. Schoof H., et al. MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource based on the first complete plant genome. Nucleic Acids Res. 30 (2002) 91-93
16. Bortoluzzi S., et al. A comprehensive, high-resolution genomic transcript map of human skeletal muscle. Genome Res. 8 (1998) 817-825
17. Duret L., Marais G., and Biémont C. Transposons but not retrotransposons are located preferentially in regions of high recombination rate in Caenorhabditis elegans. Genetics 156 (2000) 1661-1669
18. Fullerton S.M., Carvalho A.B., and Clark A.G. Local rates of recombination are positively correlated with GC content in the human genome. Mol. Biol. Evol. 18 (2001) 1139-1142
19. Lercher M.J., Urrutia A.O., and Hurst L.D. Clustering of housekeeping genes provides a unified model of gene order in the human genome. Nat. Genet. 31 (2002) 180-183
20. Rizzon C., Marais G., Gouy M., and Biemont C. Recombination rate and the distribution of transposable elements in the Drosophila melanogaster genome. Genome Res. 12 (2002) 400-407
21. Hardison R.C., et al. Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. Genome Res. 13 (2003) 13-26
22. Pal C., and Hurst L.D. Evidence for co-evolution of gene order and recombination rate. Nat. Genet. 33 (2003) 392-395
23. Wright S.I., Agrawal N., and Bureau T.E. Effects of recombination rate and gene density on transposable element distributions in Arabidopsis thaliana. Genome Res. 13 (2003) 1897-1903
24. Meunier J., and Duret L. Recombination drives the evolution of GC-content in the human genome. Mol. Biol. Evol. 21 (2004) 984-990
25. Huang S.-W., Friedman R., Yu N., Yu A., and Li W.-H. How strong is the mutagenicity of recombination in mammals?. Mol. Biol. Evol. 22 (2005) 426-431
26. Djian P. Evolution of simple repeats in DNA and their relation to human disease. Cell 94 (1998) 155-160
27. Flavell R.B., and Moore G. Plant genome constituents and their organization. In: Foster G., and Twell D. (Eds). Plant Gene Isolation: Principles and Practice (1996), Wiley, England 1-25
28. Pelissier T., et al. Athila, a new retroelement from Arabidopsis thaliana. Plant Mol. Biol. 29 (1995) 441-452
29. Lin X., et al. Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana. Nature 402 (1999) 761-768
30. Chen M., et al. An integrated physical and genetic map of the rice genome. Plant Cell 14 (2002) 537-545
31. Copley R.R., Schultz J., Ponting C.P., and Bork P. Protein families in multicellular organisms. Curr. Opin. Struct. Biol. 9 (1999) 408-415
32. Teichmann S.A., and Babu M.M. Conservation of gene co-regulation in prokaryotes and eukaryotes. Trends Biotechnol. 20 (2002) 407-410
33. Snel B., Van Noort V., and Huynen M.A. Gene co-regulation is highly conserved in the evolution of eukaryotes and prokaryotes. Nucleic Acids Res. 32 (2004) 4725-4731
34. Carroll S.B. Genetics and the making of Homo sapiens. Nature 422 (2003) 849-857
35. Copenhaver G.P., et al. Genetic definition and sequence analysis of Arabidopsis centromeres. Science 286 (1999) 2468-2474