The genomic RNA of different isolates of Citrus tristeza virus (CTV) reveals an unusual pattern of sequence diversity: the 3′ halves are highly conserved (homology >90%), while the 5′ halves show much more dissimilarity, with the 5′ nontranslated region (NTR) containing the highest diversity (homology as low as 42%).
We ask what level and pattern of sequence diversity should be expected under this scenario, when both epidemiological and genetic equilibrium between mutation and drift are achieved.
Selection seems to drive EG95 evolution by its secondary structure, since the pattern of sequence change is convergent with regard to protein folding (Fig. 2).
We noticed that different distance measures result in the same pattern of sequence separation and therefore we decided to apply the Blosum62 matrix as the distance measure in other parts of this analysis.
Further evaluation of other normal tissues from patient GA may provide evidence to establish whether the association between recombination in this case was tissue-specific or due to an overall different pattern of sequence evolution within the patient.
After sequencing approximately equal numbers of clones from the shorter (33) and longer (34) cDNA amplicons, a more complex pattern of sequence relationships emerged than was seen with the genomic copies.
The different distance measures result in the same pattern of sequence separation we therefore chose the Blosum62 matrix as the distance measure in all other parts of this analysis.
From the multiple sequence alignment (MSA) of the Tectonin domains, we confirmed a pattern of sequence repeats of 40 to 50 residues in length, which is a unique characteristic of β-propellers [9], [10].
FP was the only sample examined where the frequency of the X-4 fusion is low, so the observed correlation could originate from it having an unusual pattern of sequence diversity along Chromosome 4. Comparison of FP with a previously examined sample from the south [LP from ref. 24] confirms that the finding is not dependent on FP.
Simulations demonstrate the propensity for sexually antagonistic alleles to accumulate as polymorphisms in tightly Y-linked regions of Chromosome 4. The observed pattern of sequence diversity is consistent with this form of intra-locus sexual conflict generating pervasive effects along this transient Y chromosome.
As shown in Figure 10, a similar pattern of sequence composition is observed in positions 7 9 nucleotides before the start position of the mature miRNA for 3' samples, after the 22nd nucleotide of the mature miRNA for 5' samples and symmetrically in both ends of the mature miRNAs for the combined set.
