Unfortunately, so far, there are practically no other "functional" data concerning the HyPRP family (reviewed in Introduction), so we can only speculate on possible functional differences on the basis of HyPRP sequence analyses.
HCV strains are classified into seven recognized genotypes (1-7) on the basis of phylogenetic and sequence analyses of whole viral genomes.
On the basis of sequence alignments and phylogenetic analyses, which included a number of known stress-related NAC TFs from Arabidopsis and rice, we identified 50 new putative stress-related GmNAC genes.
In planta studies in Arabidopsis have provided strong evidence that the non-ethylene receptor AHK1 is involved with osmotic stress responses by functioning as a positive regulator of drought and salt-stress responses in ABA signalling., On the basis of sequence alignments and phylogenetic analyses, we identified three GmHKs which share over 60% high identity with AHK1 (Fig. 1; Table 1).
While all homologs were initially collected, representative species for each taxonomic major group were selected for phylogenetic analyses on the basis of sequence completeness which was not consistent across all genomes sequences.
Gene models were refined on the basis of sequence homology and EST support, and the subfamily assignment confirmed by protein BLAST analyses on the National Center for Biotechnology Information website.
The concept of patterns is the basis of sequence analysis.
rRNA loci were identified on the basis of sequence similarity.
Only the seven wPip-V-infected specimens found associated with the mtDNA-1 group on the basis of cytb sequence were analysed since not enough DNA was available from the five remaining specimens.
However, on the basis of the spike and nucleocapsid protein sequence analyses, it is highly likely that the entire genome of the Minnesota strain is genetically identical to that of the other 8 strains (Technical Appendix Figure, panels B, C).
