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Strains described so far have shown restricted sequence diversity within their host-specific clusters.
However, the highly restricted sequence diversity of circulating variants of PARV4 also suggests that the virus has emerged and spread in the human population relatively recently.
In fact, Viridiplantae and Thaumarchaeota did not cluster together, which was confirmed by a second analysis based on a more restricted sequence sampling.
The presence of five putative MITEs in such a restricted sequence analysis led to the hypothesis that these elements are abundant components of epichloae genomes.
As pointed out by Floyd and Bowman, the restricted sequence conservation of 14 amino acids hampers phylogenetic analysis in case of the CLE family [ 56].
Most of these sequences were conserved miRNAs based on computational similarity searches with restricted sequence datasets, with very few novel miRNAs identified [ 38- 40].
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The restricted sequencing depth will thus affect the statistical power of detecting less abundant resistance genes as well as assessing the frequencies of chromosomal mutations known to cause resistance.
Other types of photosynthetic symbiont may occur, as this study restricted sequencing to representatives of the major groups.
Multi-species transcriptome comparison may be used in order to identify orthologous gene groups, measure changes in the size of protein-coding gene families, study gene family evolution and detect taxonomically restricted sequences (i.e. species-specific or genus-specific sequences).
We excluded data from studies that profiled only specific exons or mutation hotspots in these two genes, as restricted sequencing might not detect recently characterized oncogenic mutations such as those in exon 20 of EGFR and codon 61 of KRAS or changes in codons not associated with gene activation.
Options are included for further restricting sequence retrieval according to sequence length.
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