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The remaining structural and non-structural proteins are derived from an indigenous strain of EHDV-2 (Alberta), making it difficult to distinguish this strain from other American strains of EHDV using group specific serological or RNA sequence based assays (RT-PCR) that target these more conserved genome segments and proteins.
However, in phi1, surprisingly only two (ORFans 84.1 and 263.1) of the seven unique ORFs are in the HPRs; the others are located in more conserved genome regions.
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Such events are remarkable from the evolutionary point of view, because they demonstrate an unexpected plasticity of the mitochondrial genomes of basal Metazoa compared to the more conserved genomes of Bilateria.
Put simply, as genome ends become more conserved, recombination events between corresponding genome ends will just swap similar genome regions for one another.
Likewise, sequence divergence will usually be low in recent radiations, with the result that targeting more conserved portions of the genome may waste sequencing effort.
Sequence alignment algorithms 1 have substantially facilitated comparative genomics/proteomics research by showing conservation pattern along orthologous sequences, and biologically functional segments are likely to be those more conserved regions along the genome.
The identification of single GATA123 and single GATA456 orthologs in the more conserved hemichordate and cephalochordate genomes highlights how these basal deuterostomes may provide useful model systems for investigating conserved GATA factor requirements without the functional redundancies observed in vertebrates.
Interestingly, all three of the transcription factors with significantly more conserved binding sites within the postwhole genome duplicated compared with prewhole genome duplicated species have been associated with the regulation of glycolytic genes and may be related to the shift in metabolism from respiration to fermentation in the presence of oxygen (Piskur et al. 2006).
Based on the number of conserved and specific genes, BLASTN results indicate that Psg genomes contain more conserved and less specific genes compared to those members in the same genomospecies than to members of other genomospecies with the exception of Psy FF5 (Fig. 7AC), and this trend is basically consistent with their phylogenetic relationship using housekeeping genes (Fig. 4).
There is little reason to think that genomic repeats like transposons should be more conserved than the rest of the genome, on the contrary transposons are used in the study of closely related species or intra-species strains [ 23, 24] as they evolve more quickly.
While Figure 8 can provide some hints as to viral regions that are more or less constrained based on mean polymorphism levels, genome scans of FST provide stronger evidence of sites that are either more conserved or more divergent than the genome average.
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