Additional file 1 of An insight into the gene expression evolution in Gossypium species based on the leaf transcriptomes

Supplementary material 1

CpG Usage in RNA Viruses: Data and Hypotheses

<div><p>CpG repression in RNA viruses has been known for decades, but a reasonable explanation has not yet been proposed to explain this phenomenon. In this study, we calculated the CpG odds ratio of all RNA viruses that have available genome sequences and analyzed the correlation with their genome polarity, base composition, synonymous codon usage, phylogenetic relationship, and host. The results indicated that the viral base composition, synonymous codon usage and host selection were the dominant factors that determined the CpG bias in RNA viruses. CpG usage variation between the different viral groups was caused by different combinations of these pressures, which also differed from each other in strength. The consistent under-representation of CpG usage in −ssRNA viruses is determined predominantly by base composition, which may be a consequence of the U/A preferred mutation bias of −ssRNA viruses, whereas the CpG usage of +ssRNA viruses is affected greatly by their hosts. As a result, most +ssRNA viruses mimic their hosts' CpG usage. Unbiased CpG usage in dsRNA viruses is most likely a result of their dsRNA genome, which allows the viruses to escape from the host-driven CpG elimination pressure. CpG was under-represented in all reverse-transcribing viruses (RT viruses), suggesting that DNA methylation is an important factor affecting the CpG usage of retroviruses. However, vertebrate-infecting RT viruses may also suffer host' CpG elimination pressure that also acts on +ssRNA viruses, which results in further under-representation of CpG in the vertebrate-infecting RT viruses.</p></div

The influence of GC content on viral CpG usage.

<p>(<b>A</b>) Correlation between CpG odds ratios and GC contents of RNA viruses. (B) CpG usage variation between the four groups of RNA viruses. CpG<i>_O/E</i> distribution range of each viral group is shown by yellow dots, and the mean CpG<i>_O/E</i> value of each viral group is indicated by the purple bar. The standard deviations of the mean CpG<i>_O/E</i> values are also indicated. (<b>C</b>) Correlation between the mean CpG<i>_O/E</i> and mean GC content values. (<b>D</b>) Correlation between the CpG<i>_O/E</i> and CpG<i>_O/E</i>_{_CDS} values.</p

CpG usage pattern of RNA viruses within coding region.

<p>(<b>A–D</b>) Distribution of CpG at the three locations in the coding regions of −ssRNA, RT, dsRNA, and +ssRNA viruses, respectively.</p

CpG usage pattern of RNA viruses.

<p>The <i>y</i>-axis depicts the number of viruses with the specific CpG<i>_O/E</i> values given on the <i>x</i>-axis.</p

Schematic representation of the flavonoid biosynthetic pathway modified from [24]–[26].

<p>C4H: Cinnamate-4-hydroxylase; 4CL: 4-Coumarate acyl-COA ligase; CHS: chalcone synthase; CHI: chalcone isomerase; F3′H: flavonoid-3′-hydroxylase; F3′5′H: flavonoid-3′5′-hydroxylase; FLS: flavonol synthase; DFR: dihydroflavonol reductase; ANS: Anthocyanidin synthase; 3GT: 3-O-glucosyltransferase.</p

CpG usages of flaviviruses that infect different types of hosts.

<p>CpG usages of flaviviruses that infect different types of hosts.</p

CpG usage of RNA viruses.

<p>CpG usage of RNA viruses.</p

Pair-wised variance analysis the GC contents between viral groups.

<p>Note: <i>F</i> statistic of one-way ANOVA analysis is 33.343 (<i>P</i><0.001). The pair-wised comparisons were performed based on the GC contents of each viral group and the resulting T values of the independent <i>T</i>-test are shown. * indicates <i>P</i><0.05, ** indicates <i>P</i><0.0001.</p

Pair-wised variance analysis CpG usage between viral groups.

<p>Note: <i>F</i> statistic of one-way ANOVA analysis is 239.252 (<i>P</i><0.001). The pair-wised comparisons were performed based on the CpG<i>_O/E</i> values of each viral group, and the resulting <i>T</i> values of the independent <i>T</i>-test are shown. ** indicates <i>P</i><0.0001. For the detailed analysis procedure, please refer to the Materials and Methods section.</p