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Light whole genome sequence for SNP discovery across domestic cat breeds

James C Mullikin1*, Nancy F Hansen1, Lei Shen2, Heather Ebling2, William F Donahue2, Wei Tao2, David J Saranga2, Adrianne Brand2, Marc J Rubenfield2, Alice C Young1, Pedro Cruz1, NISC Comparative Sequencing Program1, Carlos Driscoll3, Victor David3, Samer WK Al-Murrani4, Mary F Locniskar4, Mitchell S Abrahamsen4, Stephen J O'Brien3, Douglas R Smith2 and Jeffrey A Brockman4

Author Affiliations

1 Genome Technology Branch and NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA

2 Agencourt Bioscience Corporation, Beverly, Massachusetts 01915, USA

3 Laboratory of Genomic Diversity, National Cancer Institute, Frederick, Maryland 21702, USA

4 Hill's Pet Nutrition Inc., PO Box 1658, Topeka, KS 66601, USA

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BMC Genomics 2010, 11:406  doi:10.1186/1471-2164-11-406

Published: 24 June 2010

Additional files

Additional file 1:

Whole genome assembly statistics. Table S1 comparing the assembly statistics for this assembly and the previously published 1.9X assembly.

Format: DOCX Size: 14KB Download file

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Additional file 2:

Assembly coverage of ENCODE regions. Table S2 listing whole genome shotgun assembly coverage statistics relative to high quality cat BAC clone assemblies of ENCODE regions for this assembly and the previously published 1.9X assembly

Format: DOC Size: 122KB Download file

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Additional file 3:

Order and orientation across ENCODE regions. Plots of assembly order and orientation across all 44 ENCODE regions.

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Additional file 4:

Descriptions of how Additional files 3 and 6 were generated. Methods for generating plots of order and orientation across ENCODE regions and the STRUCTURE analysis of Nancy.

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Additional file 5:

PCR validation results for 94 variants. Table S3 lists the variants by position on the genome assembly, which alleles are expected, and the alleles observed across 8 cats. Pink colored cells indicate the cat(s) from which the alternate allele was discovered in the light whole genome sequence.

Format: DOCX Size: 26KB Download file

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Additional file 6:

STRUCTURE analysis results. Figure S1 shows results of STRUCTURE analysis showing Nancy and representative known-origin wildcat individuals.

Format: DOC Size: 42KB Download file

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