Interspecies hybridization on DNA resequencing microarrays:
efficiency of sequence recovery and accuracy of SNP detection
in human, ape, and codfish mitochondrial DNA genomes
sequenced on a human-specific MitoChip
(
SMC Flynn & SM Carr. BMC Genomics, 8:339)
We investigated
the efficiency of sequence recovery and accuracy of SNP identification
for 15,452 bp of homologous chimpanzee, gorilla, and codfish
mitochondrial (mtDNA) genomes resequenced on a human-specific
microarray. Efficiencies of calls made at high-confidence in both ape
species were 99.59% and 97.89 %, however SNP identification error rates
increased from 0.067 to 0.247 per SNP between the chimpanzee and
gorilla genomes. Resequencing of fish mtDNA correctly called
<4% of the genome, in short inter-ordinally conserved islands.
Differential binding of experimental DNAs to the 25-base SNP-specific
oligonucleotides on the microarray is strongly affected by the density
of mismatches. In ape genomes where 33% and 46% of 25bp regions contain
3 or more interspecific SNPs, efficiency declines log-linearly with
respect to sequence divergence, and accuracy of SNP identification
drops precipitously. The experiments support design of a multi-species
microarray that could sequence homologous but distantly-related mtDNA
genomes simultaneously, without interference from interspecific
cross-hybridization.