Intra-specific variability and biological relevance of P3N-PIPO protein length in potyviruses

Table 1 Viruses showing alternative stop codons in the pipo ORF

GenBank accession	Virus	PIPO size	# Isolates	Alternative stop codons	Frequency of functional
NC_001445	Plum pox virus	99	69	100 (1)	0.014
				103 (59)	0.87
				106 (68)	0.116
NC_001616	Potato virus Y	75	80	62 (1)	0.0125
				65 (1)	0.0125
				73 (21)	0.26
				74 (1)	0.0125
				76 (58)	0.64
				77 (79)	0.05
				93 (80)	0.0125
NC_001671	Pea seed-borne mosaic virus	79	3	80 (2)	0.67
NC_001671	Pea seed-borne mosaic virus	79	3	169 (1)	0.33
NC_001785	Papaya ringspot virus	72	9	69 (1)	0.11
				73 (8)	0.78
				80 (4)	0.11
NC_003224	Zucchini yellow mosaic virus	76	12	76 (1)	0.083
NC_003224	Zucchini yellow mosaic virus	76	12	77 (12)	0.917
NC_003398	Sugarcane mosaic virus	80	13	81 (9)	0.69
NC_003398	Sugarcane mosaic virus	80	13	82 (8)	0.31
NC_004039	Potato virus A	83	7	84 (6)	0.857
NC_004039	Potato virus A	83	7	95 (7)	0.143
NC_002509	Turnip mosaic virus	60	101	61 (87)	0.861
				70 (87)	0.139

For each virus, the GenBank accession number of the reference sequence and its estimated PIPO size is given. The last three columns indicate the number of available isolates for each virus, the observed alternative stop codons (the number of isolates showing each stop codon is indicated within parenthesis) and the frequency at which a stop codon is the functional one for each virus, respectively. In the last column, frequencies are obtained for each virus by dividing the number of times a given stop codon appears first in the P3N-PIPO sequence by the total number of isolates.

ISSN: 2730-7182