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Full genome re-sequencing reveals a novel circadian clock mutation in Arabidopsis

Kevin Ashelford1, Maria E Eriksson2, Christopher M Allen3, Rosalinda D'Amore1, Mikael Johansson2, Peter Gould1, Suzanne Kay1, Andrew J Millar4, Neil Hall1* and Anthony Hall1*

Author Affiliations

1 School of Biological Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK

2 Department of Plant Physiology, Umea Plant Science Centre, Umea University, SE-901 87 Umea, Sweden

3 Applied Biosystems, 120 Birchwood Boulevard, Warrington WA3 7QH, UK

4 Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Mayfield Road, Edinburgh EH9 3JH, UK

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Genome Biology 2011, 12:R28  doi:10.1186/gb-2011-12-3-r28

Published: 23 March 2011

Additional files

Additional file 1:

Figure S1 - plant to plant variation in clock function is greater in Col-0 than in Ws-2. Seedlings were entrained under 12-h light/12-h dark cycles for 12 days, after which they were transferred to constant light where rhythms of leaf movement were assayed. Ws-2, filled squares; Col-0, empty squares. Period estimates for individual seedlings are plotted against their relative amplitude errors (R.A.E.).

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Additional file 2:

Table S1 - sequence tag counts available at various stages of the analysis, as reported by the different matching schema employed.

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Additional file 3:

Table S2 - SNP counts before and after filtering as reported by the various matching schema. a Unfiltered SNPs were all those reported by the Corona lite SNP detection pipeline. bFiltering involved retaining only those SNP loci where tag coverage exceeded 5× in both ebi-1 and Ws-2, the SOLiD score was 0.7 or greater, and SNPs were homozygous. (c) 'Schema screened' SNPs were those filtered SNPs reported by all five schema.

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Additional file 4:

Table S3 - dCAPS and CAPS marker design and use to validate SNP discovery. SNP marker denotes the chromosome position of the SNP based on the TAIR 8 Arabidopsis genome build. In the primer sequence the underlined base is the mismatched base in the primer sequence. ^Borderline SNP; aSNP in the clock gene PRR7; bSNP in At5g05660, EBI.

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Additional file 5:

Table S4 - EMS-induced SNPs on chromosome 5.

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Additional file 6:

Table S5 - EMS-induced SNPs on chromosome 1.

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Additional file 7:

Figure S2 - the presence or absence of EMS-induced mutations on chromosome 1 do not affect the phenotype of ebi-1. Transgenic seedlings carrying the LUC reporter gene fused to the CAB2 promoter were entrained under 12-h light/12-h dark cycles for 7 days, after which luminescence was monitored in constant red light. WT, open squares; ebi-1, closed squares; ebi-1 with no EMS-induced SNP on chromosome 1, red triangles.

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Additional file 8:

Table S6 - analysis of temporal expression patterns of non-synonymous SNPs on chromosome 5 using Diurnal to fit temporal expression data to expression pattern models consistent with circadian regulation.

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Additional file 9:

Figure S3 - identification of a SNP in PRR7. Top: A schematic representation of the PRR7 protein in Arabidopsis ecotype Columbia is shown in green. Gray boxes represent the two conserved region Receiver (REC) domain and CCT motif. The amino acids were aligned using the ClustalW program. Bottom: identical and similar amino acid residues are highlighted with black and gray backgrounds, respectively. The SNP leads to a change from arginine (R) to histidine (H) at position 329. The frame shows the residue in the Pseudo Response Regulator protein from Arabidopsis ecotype Columbia (BAB13742, PRR7), Hordeum vulgare subsp. vulgare (AAY17586, PRR), Arabidopsis thaliana (AAY62604, PRR3), Triticum aestivum (ABL09464, PRR), Oryza sativa Indica (BAD38858, PRR 37), Oryza sativa Indica (BAD38859, PRR73), Lemna paucicostata (BAE72697, PRR37), Lemna gibba (BAE72700, PRR37), obtained from NCBI database, and Gossypium raimondii (TC272), Brassica napus (TC71410), Brassica napus (TC78134), Gossypium raimondii (TC82653), and Citrus clementina (TC8380) obtained from TGI databases.

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