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Chapter 13 : Alignments and Comparative Profiles of Picornavirus Genera

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Alignments and Comparative Profiles of Picornavirus Genera, Page 1 of 2

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Abstract:

Genome connoisseurs are always looking for new methods to tweak the data, especially in sequence regions where good fits are harder to achieve or recognize. The previous capsid alignments were based on superimposition of virion crystal structure hydrogen-bonding maps, then extended by multiple, reiterative pairwise comparisons to include similar related sequences. With the HMMER program suite full-length picornavirus genome hidden Markov model (HMM)-profiles (lengths of 8,000 to 9,000 bases) were calculated from the previous alignments. The alignments were checked for consistency, and then refined mathematically and heuristically to (i) maximize the number of matched bases and encoded amino acids, (ii) minimize the location and frequency of indels (insertions/deletions), and (iii) emphasize the conservation of homologous features such as catalytic sites and proteolytic cleavage sites. The current iterations now include genome-length alignments for the seven most populous picornaviral genera (, , , , , , and ) and extend over 173 different strains, providing formats for about 1,000,000 bases. The correlate polyprotein alignments, derived by translation of the aligned RNAs, include about 291,000 amino acids. For eukaryotes, there is very little information about the specific pressures that might shape a given lineage. Certainly, the symmetrical methylation of CG dinucleotides has a unique structural significance in many higher DNA genomes, reducing the value and frequency of this sequence in coding regions.

Citation: Palmenberg A, Sgro J. 2002. Alignments and Comparative Profiles of Picornavirus Genera, p 149-155. In Semler B, Wimmer E (ed), Molecular Biology of Picornavirus. ASM Press, Washington, DC. doi: 10.1128/9781555817916.ch13

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Figures

Image of FIGURE 1a
FIGURE 1a

Polyprotein similarity plots. The protein alignments for picornaviral genera were culled to include only full-length sequences. The GCG program PLOTSIMILARITY calculated the average shared identity (window = 20) along the length of each alignment. The data for each genus and for separately calculated select species were plotted relative to a polyprotein map showing the cleavage site divisions and numbered according to the parental alignment columns. The dashed horizontal line and the “average” value on each plot refer to the overall identity shared among included sequences (calculated with window =1). The “identities” value gives the percentage of alignment columns where all (n) sequences were the same. This value (occasionally) includes some locations with shared gaps, in addition to locations with identical amino acids. The plot is partial (1ABC only), because a full-length sequence of Ljungan vims, the type member of the LV species (GenBank: AF020521), and the only non-HPeV strain in this genus, was not available.

Citation: Palmenberg A, Sgro J. 2002. Alignments and Comparative Profiles of Picornavirus Genera, p 149-155. In Semler B, Wimmer E (ed), Molecular Biology of Picornavirus. ASM Press, Washington, DC. doi: 10.1128/9781555817916.ch13
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Image of FIGURE 1b
FIGURE 1b

Polyprotein similarity plots. The protein alignments for picornaviral genera were culled to include only full-length sequences. The GCG program PLOTSIMILARITY calculated the average shared identity (window = 20) along the length of each alignment. The data for each genus and for separately calculated select species were plotted relative to a polyprotein map showing the cleavage site divisions and numbered according to the parental alignment columns. The dashed horizontal line and the “average” value on each plot refer to the overall identity shared among included sequences (calculated with window =1). The “identities” value gives the percentage of alignment columns where all (n) sequences were the same. This value (occasionally) includes some locations with shared gaps, in addition to locations with identical amino acids. The plot is partial (1ABC only), because a full-length sequence of Ljungan vims, the type member of the LV species (GenBank: AF020521), and the only non-HPeV strain in this genus, was not available.

Citation: Palmenberg A, Sgro J. 2002. Alignments and Comparative Profiles of Picornavirus Genera, p 149-155. In Semler B, Wimmer E (ed), Molecular Biology of Picornavirus. ASM Press, Washington, DC. doi: 10.1128/9781555817916.ch13
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Download as Powerpoint
Image of FIGURE 2
FIGURE 2

Codon and genome base compositions. Base compositions for 19 picornavirus species were summed separately, then averaged for (i) the whole genome, (ii) 1st codon base, (iii) 2nd codon base, and (iv) 3rd codon base. Each concentric ring represents an individual species, subdivided according to the averaged observed frequency (percent) of A:G:C:U. The data were sorted in ascending order by A content in the 3rd codon position, and maintain the same order in each plot: (inside ring) AiV, ThV, FMDV, ERBV, BEV, AEV, ERAV, HEV-A, EMCV, PTV, HEV-B, PV, PEV-B, HEV-C, HAV, HPeV, HEV-D, HRV-B, HRV-A (outside ring).

Citation: Palmenberg A, Sgro J. 2002. Alignments and Comparative Profiles of Picornavirus Genera, p 149-155. In Semler B, Wimmer E (ed), Molecular Biology of Picornavirus. ASM Press, Washington, DC. doi: 10.1128/9781555817916.ch13
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