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Independent evolution of tetraloop in enterovirus oriL replicative element and its putative binding partners in protein 3C

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95 days ago
Independent evolution of tetraloop in enterovirus oriL replicative element and its putative binding partners in… https://t.co/1fa6ZT0OM5
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Supplemental Information

Multiple sequence alignment of Enterovirus A full genomes

DOI: 10.7287/peerj.preprints.3153v2/supp-1

Multiple sequence alignment of filtered set Enterovirus A full genomes

Sequences that differed from any other sequence in the dataset by less than 1% of the nucleotide sequence were omitted.

DOI: 10.7287/peerj.preprints.3153v2/supp-2

Multiple sequence alignment of Enterovirus B full genomes

DOI: 10.7287/peerj.preprints.3153v2/supp-3

Multiple sequence alignment of filtered set Enterovirus B full genomes

Sequences that differed from any other sequence in the dataset by less than 1% of the nucleotide sequence were omitted.

DOI: 10.7287/peerj.preprints.3153v2/supp-4

Multiple sequence alignment of Enterovirus C full genomes

DOI: 10.7287/peerj.preprints.3153v2/supp-5

Multiple sequence alignment of filtered set Enterovirus C full genomes

Sequences that differed from any other sequence in the dataset by less than 1% of the nucleotide sequence were omitted.

DOI: 10.7287/peerj.preprints.3153v2/supp-6

Multiple sequence alignment of Enterovirus D full genomes

DOI: 10.7287/peerj.preprints.3153v2/supp-7

Multiple sequence alignment of filtered set Enterovirus D full genomes

Sequences that differed from any other sequence in the dataset by less than 1% of the nucleotide sequence were omitted.

DOI: 10.7287/peerj.preprints.3153v2/supp-8

Multiple sequence alignment of Enterovirus E full genomes

DOI: 10.7287/peerj.preprints.3153v2/supp-9

Multiple sequence alignment of filtered set Enterovirus E full genomes

Sequences that differed from any other sequence in the dataset by less than 1% of the nucleotide sequence were omitted.

DOI: 10.7287/peerj.preprints.3153v2/supp-10

Multiple sequence alignment of Enterovirus F full genomes

DOI: 10.7287/peerj.preprints.3153v2/supp-11

Multiple sequence alignment of filtered set Enterovirus F full genomes

Sequences that differed from any other sequence in the dataset by less than 1% of the nucleotide sequence were omitted.

DOI: 10.7287/peerj.preprints.3153v2/supp-12

Multiple sequence alignment of Enterovirus G full genomes

DOI: 10.7287/peerj.preprints.3153v2/supp-13

Multiple sequence alignment of filtered set Enterovirus G full genomes

Sequences that differed from any other sequence in the dataset by less than 1% of the nucleotide sequence were omitted.

DOI: 10.7287/peerj.preprints.3153v2/supp-14

Multiple sequence alignment of Enterovirus H full genomes

DOI: 10.7287/peerj.preprints.3153v2/supp-15

Multiple sequence alignment of filtered set Enterovirus H full genomes

Sequences that differed from any other sequence in the dataset by less than 1% of the nucleotide sequence were omitted.

DOI: 10.7287/peerj.preprints.3153v2/supp-16

Multiple sequence alignment of Enterovirus J full genome

DOI: 10.7287/peerj.preprints.3153v2/supp-17

Multiple sequence alignment of filtered set Enterovirus J full genomes

Sequences that differed from any other sequence in the dataset by less than 1% of the nucleotide sequence were omitted.

DOI: 10.7287/peerj.preprints.3153v2/supp-18

Multiple sequence alignment of Rhinovirs A full genomes

DOI: 10.7287/peerj.preprints.3153v2/supp-19

Multiple sequence alignment of filtered set Rhinovirus A full genomes

Sequences that differed from any other sequence in the dataset by less than 1% of the nucleotide sequence were omitted.

DOI: 10.7287/peerj.preprints.3153v2/supp-20

Multiple sequence alignment of Rhinovirus B full genomes

DOI: 10.7287/peerj.preprints.3153v2/supp-21

Multiple sequence alignment of filtered set Rhinovirus B full genomes

Sequences that differed from any other sequence in the dataset by less than 1% of the nucleotide sequence were omitted.

DOI: 10.7287/peerj.preprints.3153v2/supp-22

Multiple sequence alignment of Rhinovirus C full genomes

DOI: 10.7287/peerj.preprints.3153v2/supp-23

Multiple sequence alignment of filtered set Rhinovirus C full genomes

Sequences that differed from any other sequence in the dataset by less than 1% of the nucleotide sequence were omitted.

DOI: 10.7287/peerj.preprints.3153v2/supp-24

Occurrence of domain d apical sequences in filtered sets of full genomes of different enterovirus species and serotypes

Tetraloops CCCG, UGUG, CAUG and UUGG that were unique for species Enterovirus A, B, C and D and were lost upon filtration, were added and are shown in blue. The gradient coloring from red to green represents abundance heat map for the genomes with different domain d sequence.

DOI: 10.7287/peerj.preprints.3153v2/supp-25

Variety of domain d apical loop sequence in genomes of Enterovirus A species

DOI: 10.7287/peerj.preprints.3153v2/supp-26

Variety of domain d apical loop sequence in genomes of Enterovirus B species

DOI: 10.7287/peerj.preprints.3153v2/supp-27

Variety of domain d apical loop sequence in genomes of Enterovirus C species

DOI: 10.7287/peerj.preprints.3153v2/supp-28

Variety of domain d apical loop sequence in genomes of Enterovirus D species

DOI: 10.7287/peerj.preprints.3153v2/supp-29

Variety of domain d apical loop sequence in genomes of Enterovirus E and F species

DOI: 10.7287/peerj.preprints.3153v2/supp-30

Variety of domain d apical loop sequence in genomes of Enterovirus G, H and J species

DOI: 10.7287/peerj.preprints.3153v2/supp-31

Variety of domain d apical loop sequence in genomes of Rhinovirus A, B and C species

DOI: 10.7287/peerj.preprints.3153v2/supp-32

Variety of putative RNA-binding tripeptide of protein 3C in genomes of Enterovirus A species

DOI: 10.7287/peerj.preprints.3153v2/supp-33

Variety of putative RNA-binding tripeptide of protein 3C in genomes of Enterovirus C species

DOI: 10.7287/peerj.preprints.3153v2/supp-34

Variety of putative RNA-binding tripeptide and preceding residue of protein 3C in genomes of Rhinovirus A species

DOI: 10.7287/peerj.preprints.3153v2/supp-35

Variety of putative RNA-binding tripeptide of protein 3C in genomes of Rhinovirus C species

DOI: 10.7287/peerj.preprints.3153v2/supp-36

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Maria A Prostova conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Andrei A Deviatkin conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Irina O Tcelykh performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Alexander N Lukashev conceived and designed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.

Anatoly P Gmyl conceived and designed the experiments, wrote the paper, reviewed drafts of the paper.

Funding

This work was supported by Russian Science Foundation (No. 15-15-00147). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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