Sequencing of natural strains of Arabidopsis thaliana with short reads

Genome Research

Volumn 18, Issue 12, 2008, Pages 2024-2033

  Ossowski, Stephan ^a   Schneeberger, Korbinian ^a   Clark, Richard M ^a,b   Lanz, Christa ^a   Warthmann, Norman ^a   Weigel, Detlef ^a  

^a MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY   (Germany)

^b UNIVERSITY OF UTAH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; ARTICLE; DNA POLYMORPHISM; GENE DELETION; GENE DUPLICATION; GENE LOCUS; GENE SEQUENCE; GENETIC VARIABILITY; GENOME; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

ARABIDOPSIS; BASE SEQUENCE; CHROMOSOME MAPPING; CHROMOSOMES, PLANT; DNA, PLANT; FRAMESHIFT MUTATION; GENE DUPLICATION; GENOME, PLANT; MOLECULAR SEQUENCE DATA; POLYMORPHISM, GENETIC; SEQUENCE ANALYSIS, DNA; SEQUENCE DELETION; SEQUENCE HOMOLOGY, NUCLEIC ACID;

ARABIDOPSIS THALIANA;

EID: 57149099394     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.080200.108     Document Type: Article

References (24)

1. The Arabidopsis Genome Initiative. 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815.
2. Bomblies, K., Lempe, J., Epple, P., Warthmann, N., Lanz, C., Dangl, J.L., and Weigel, D. 2007. Autoimmune response as a mechanism for a Dobzhansky-Muller-type incompatibility syndrome in plants. PLoS Biol. 5: e236. doi: 10.1371/journal.pbio.0050236.
3. Borevitz, J., Liang, D., Plouffe, D., Chang, H., Zhu, T., Weigel, D., Berry, C., Winzeler, E., and Chory, J. 2003. Large-scale identification of single-feature polymorphisms in complex genomes. Genome Res. 13: 513-523.
4. Borevitz, J.O., Hazen, S.P., Michael, T.P., Morris, G.P., Baxter, I.R., Hu, T.T., Chen, H., Werner, J.D., Nordborg, M., Salt, D.E., et al. 2007. Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana. Proc. Natl. Acad. Sci. 104: 12057-12062.
5. Butler, J., MacCallum, I., Kleber, M., Shlyakhter, I., Belmonte, M., Lander, E., Nusbaum, C., and Jaffe, D. 2008. ALLPATHS: De novo assembly of whole-genome shotgun microreads. Genome Res. 18: 810-820.
6. Chaisson, M. and Pevzner, P. 2008. Short read fragment assembly of bacterial genomes. Genome Res. 18: 324-330.
7. Clark, R.M., Schweikert, G., Toomajian, C., Ossowski, S., Zeller, G., Shinn, P., Warthmann, N., Hu, T.T., Fu, G., Hinds, D.A., et al. 2007. Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana. Science 317: 338-342.
8. Emrich, S.J., Li, L., Wen, T.J., Yandeau-Nelson, M.D., Fu, Y., Guo, L., Chou, H.H., Aluru, S., Ashlock, D.A., and Schnable, P.S. 2007. Nearly identical paralogs: Implications for maize (Zea mays L.) genome evolution. Genetics 175: 429-439.
9. Hernandez, D., Francois, P., Farinelli, L., Osteras, M., and Schrenzel, J. 2008. De novo bacterial genome sequencing: Millions of very short reads assembled on a desktop computer. Genome Res. 18: 802-809.
10. Hillier, L.W., Marth, G.T., Quinlan, A.R., Dooling, D., Fewell, G., Barnett, D., Fox, P., Glasscock, J.I., Hickenbotham, M., Huang, W., et al. 2008. Whole-genome sequencing and variant discovery in C. elegans. Nat. Methods 5: 183-188.
11. Kim, S., Plagnol, V., Hu, T.T., Toomajian, C., Clark, R.M., Ossowski, S., Ecker, J.R., Weigel, D., and Nordborg, M. 2007. Recombination and linkage disequilibrium in Arabidopsis thaliana. Nat. Genet. 39: 1151-1155.
12. Koornneef, M., Alonso-Blanco, C., and Vreugdenhil, D. 2004. Naturally occurring genetic variation in Arabidopsis thaliana. Annu. Rev. Plant Physiol. Plant Mol. Biol. 55: 141-172.
13. Korbel, J.O., Urban, A.E., Affourtit, J.P., Godwin, B., Grubert, F., Simons, J.F., Kim, P.M., Palejev, D., Carriero, N.J., Du, L., et al. 2007. Paired-end mapping reveals extensive structural variation in the human genome. Science 318: 420-426.
14. Kroymann, J., Donnerhacke, S., Schnabelrauch, D., and Mitchell-Olds, T. 2003. Evolutionary dynamics of an Arabidopsis insect resistance quantitative trait locus. Proc. Natl. Acad. Sci. 100 (Suppl. 2): 14587-14592.
15. Li, H., Ruan, J., and Durbin, R. 2008. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 18: 1851-1858.
16. Mitchell-Olds, T. and Schmitt, J. 2006. Genetic mechanisms and evolutionary significance of natural variation in Arabidopsis. Nature 441: 947-952.
17. Noël, L., Moores, T.L., van der Biezen, E.A., Parniske, M., Daniels, M.J., Parker, J.E., and Jones, J.D. 1999. Pronounced intraspecific haplotype divergence at the RPP5 complex disease resistance locus of Arabidopsis. Plant Cell 11: 2099-2112.
18. Nordborg, M., Hu, T.T., Ishino, Y., Jhaveri, J., Toomajian, C., Zheng, H., Bakker, E., Calabrese, P., Gladstone, J., Goyal, R., et al. 2005. The pattern of polymorphism in Arabidopsis thaliana. PLoS Biol. 3: e196. doi: 10.1371/journal.pbio.0030196.
19. Rice, P., Longden, I., and Bleasby, A. 2000. EMBOSS: The European Molecular Biology Open Software Suite. Trends Genet. 16: 276-277.
20. Simon, M., Loudet, O., Durand, S., Bérard, A., Brunel, D., Sennesal, F.X., Durand-Tardif, M., Pelletier, G., and Camilleri, C. 2008. Quantitative trait loci mapping in five new large recombinant inbred line populations of Arabidopsis thaliana genotyped with consensus single-nucleotide polymorphism markers. Genetics 178: 2253-2264.
21. Warthmann, N., Fitz, J., and Weigel, D. 2007. MSQT for choosing SNP assays from multiple DNA alignments. Bioinformatics 23: 2784-2787.
22. Wright, S.I. and Gaut, B.S. 2005. Molecular population genetics and the search for adaptive evolution in plants. Mol. Biol. Evol. 22: 506-519.
23. Zeller, G., Clark, R.M., Schneeberger, K., Bohlen, A., Weigel, D., and Rätsch, G. 2008. Detecting polymorphic regions in the Arabidopsis thaliana genome with resequencing microarrays. Genome Res. 18: 918-929.
24. Zerbino, D. and Birney, E. 2008. Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18: 821-829.