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Given the small number of SNP differences between these three isolates (figure 1B), it was not possible to determine which of these isolates represented the source of the outbreak using genomic data alone.
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As the Hpa genome sequence is derived from isolate Emoy2 [25] and the ESTs isolated here are from isolate Waco9, we searched for possible differences between these two isolates.
Because of the significant temporal separation (45 years) between Schu S4 and NE061598, the sequence conservation between these two isolates was unexpected.
Blast searches against the Emoy2 genome sequence revealed a high level of conservation of several HaCR proteins between these two isolates.
Previous bioinformatic analysis of the FSC198 and Schu S4 genomes demonstrated that there were only eight single nucleotide polymorphisms (SNPs) and three VNTR differences between these two isolates [3].
The evolutionary distance between these two isolates was 0.008 base substitutions per site, lower than the overall average (0.046) for the 38 isolates representative of HPAI H5N1 divergence since 1996.
Between these two isolates, only 39 genes were regulated by at least two-fold (File S3), including CgCDR1 and PUP1, thus suggesting that intrinsic strain variations may mask the real effect of GOF on the C. glabrata transcriptome.
A similar interpretation may be valid for RFLP patterns, which would indicate a close genetic relationship between these eight isolates.
While the evolutionary distance between these six isolates (as compared to E980) is relatively small, there are considerable differences in gene content between strains.
The only significant difference between these two isolates was the presence of an IS5 element upstream of the main flagella regulator, flhDC.
The last gene in this cluster is a recB exonuclease (COK_0801 and COI_0270) which is 100% identical between these two isolates.
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