Insights into the genetic and host adaptability of emerging porcine circovirus 3

Figures & data

Figure 1. (a) The relative and cumulative inertia of the first 35 axes from a COA of the RSCU values; (b) PCA of different genotypes. Green, blue, red and orange refer to PCV3a-1, PCV3a-2, PCV3a-IM and PCV3b, respectively.

Figure 2. ENC values of PCV3 and the different genotypes. Green, blue, red and orange represented PCV3a-1, PCV3a-2, PCV3a-IM and PCV3b, respectively.

Table 1. RSCU analysis of PCV3 genotypes and potential hosts.

			Genotype				Potential host
AA	Codon	PCV3	PCV3a-1	PCV3a-2	PCV3a-IM	PCV3b	Rhinolophus ferrumequinum	Sus scrofa	Homo sapiens	Canis familiaris
Ala	GCA	0.62	0.68	0.69	0.69	0.55	0.64	0.74	0.91	0.79
	GCC	0.93	0.97	0.97	0.9	0.89	2.32	1.8	1.6	1.75
	GCG	1.21	1.14	1.1	1.11	1.31	0.46	0.5	0.42	0.46
	GCT	1.24	1.2	1.24	1.29	1.25	0.58	0.96	1.06	1
Cys	TGC	0.85	0.79	0.86	0.86	0.85	1.20	1.21	1.09	1.15
	TGT	1.15	1.21	1.14	1.14	1.15	0.80	0.79	0.91	0.85
Asp	GAC	0.77	0.78	0.78	0.76	0.77	1.25	1.2	1.07	1.14
	GAT	1.23	1.22	1.22	1.24	1.23	0.75	0.8	0.93	0.86
Glu	GAA	0.90	0.87	0.89	0.91	0.91	0.63	0.72	0.84	0.79
	GAG	1.10	1.13	1.11	1.09	1.09	1.37	1.28	1.16	1.21
Phe	TTC	0.92	0.91	0.92	0.92	0.93	1.05	1.21	1.07	1.18
	TTT	1.08	1.09	1.08	1.08	1.07	0.95	0.79	0.93	0.82
Gly	GGA	1.00	1.04	1.04	1.06	0.95	0.93	0.91	1	0.97
	GGC	0.57	0.57	0.56	0.57	0.58	1.94	1.46	1.35	1.39
	GGG	1.53	1.56	1.53	1.54	1.52	0.51	1.05	1	1
	GGT	0.90	0.83	0.87	0.83	0.96	0.63	0.57	0.65	0.65
His	CAC	1.82	1.82	1.82	1.82	1.82	1.22	1.3	1.16	1.22
	CAT	0.18	0.18	0.18	0.18	0.18	0.78	0.7	0.84	0.78
Ile	ATA	0.87	0.85	1	0.83	0.85	0.10	0.42	0.51	0.45
	ATC	0.14	0.12	0.2	0.16	0.12	1.94	1.67	1.41	1.6
	ATT	1.98	2.03	1.8	2.01	2.03	0.97	0.91	1.08	0.96
Lys	AAA	1.16	1.16	1.16	1.17	1.17	0.63	0.76	0.87	0.79
	AAG	0.84	0.84	0.84	0.83	0.83	1.37	1.24	1.13	1.21
Leu	CTA	0.76	0.8	0.75	0.75	0.76	0.27	0.58	0.43	0.39
	CTC	1.30	1.31	1.27	1.31	1.3	1.38	1.07	1.17	1.3
	CTG	1.44	1.29	1.44	1.47	1.5	2.60	2.4	2.37	2.56
	CTT	0.59	0.59	0.71	0.56	0.55	0.64	0.77	0.79	0.7
	TTA	0.38	0.37	0.36	0.41	0.38	0.42	0.38	0.46	0.35
	TTG	1.53	1.64	1.47	1.5	1.51	0.69	0.79	0.77	0.71
Asn	AAC	1.14	1.06	1.17	1.05	1.18	1.37	1.21	1.06	1.13
	AAT	0.86	0.94	0.83	0.95	0.82	0.63	0.79	0.94	0.87
Pro	CCA	1.21	1.3	1.16	1.23	1.19	0.88	0.94	1.11	1.01
	CCC	0.90	0.89	0.9	0.9	0.9	1.56	1.46	1.29	1.42
	CCG	0.85	0.79	0.89	0.84	0.86	0.44	0.56	0.45	0.48
	CCT	1.04	1.02	1.05	1.03	1.04	1.13	1.05	1.15	1.08
Gln	CAA	1.33	1.33	1.33	1.33	1.32	0.29	0.44	0.53	0.5
	CAG	0.67	0.67	0.67	0.67	0.68	1.71	1.56	1.47	1.5
Arg	AGA	1.66	1.73	1.75	1.68	1.58	1.70	1.12	1.29	1.19
	AGG	1.55	1.51	1.49	1.52	1.59	1.20	1.23	1.27	1.27
	CGA	0.38	0.39	0.39	0.36	0.38	0.60	0.6	0.65	0.64
	CGC	0.77	0.78	0.75	0.78	0.77	1.40	1.31	1.1	1.21
	CGG	0.90	0.88	0.89	0.91	0.91	0.50	1.29	1.21	1.25
	CGT	0.75	0.72	0.73	0.76	0.77	0.60	0.44	0.48	0.44
Ser	AGC	2.20	2.22	2.07	2.18	2.26	2.10	1.62	1.44	1.49
	AGT	0.62	0.61	0.62	0.6	0.63	0.40	0.77	0.9	0.85
	TCA	0.19	0.2	0.21	0.1	0.21	0.35	0.73	0.9	0.77
	TCC	1.24	1.18	1.24	1.31	1.24	1.60	1.5	1.31	1.45
	TCG	0.92	0.98	1.03	1.01	0.83	0.40	0.39	0.33	0.36
	TCT	0.82	0.81	0.83	0.8	0.83	1.15	0.99	1.13	1.08
Thr	ACA	1.04	1.04	1.04	1.04	1.05	1.03	0.92	1.14	1.03
	ACC	1.40	1.32	1.42	1.39	1.42	2.22	1.68	1.42	1.55
	ACG	0.44	0.46	0.42	0.44	0.43	0.27	0.57	0.46	0.52
	ACT	1.13	1.18	1.13	1.13	1.1	0.49	0.83	0.99	0.89
Val	GTA	0.62	0.63	0.63	0.62	0.61	0.23	0.34	0.47	0.41
	GTC	0.44	0.39	0.38	0.44	0.49	1.40	1.07	0.95	1.07
	GTG	0.74	0.74	0.75	0.75	0.73	1.72	2.03	1.85	1.94
	GTT	2.21	2.24	2.25	2.2	2.17	0.65	0.57	0.73	0.58
Tyr	TAC	0.78	0.86	0.77	0.8	0.76	1.58	1.27	1.11	1.21
	TAT	1.22	1.14	1.23	1.2	1.24	0.42	0.73	0.89	0.79

Notes: optimal codons are displayed in bold. Over-represented (RSCU > 1.6) codons are marked in bold and italics.

Table 2. Correlation analysis among codon composition, ENC value, nucleic acid composition, Gravy, Aroma and axis 1, axis2.

	A%	C%	G%	T%	T3s	C3s	A3s	G3s	GC	GC3s	ENC	Gravy	Aromo	axis1
C%	−0.149
G%	−0.733**	−0.362**
T%	−0.071	−0.801**	0.170
T3s	−0.174	−0.765**	0.333*	0.873**
C3s	−0.336*	0.677**	−0.108	−0.436**	−0.316*
A3s	0.833**	0.077	−0.682**	−0.256	−0.494**	−0.432**
G3s	−0.764**	−0.221	0.881**	0.147	0.362**	−0.022	−0.788**
GC	−0.731**	0.668**	0.452**	−0.627**	−0.465**	0.567**	−0.475**	0.491**
GC3s	−0.796**	0.441**	0.515**	−0.312*	−0.102	0.739**	−0.810**	0.641**	0.837**
ENC	0.079	0.563**	−0.358**	−0.461**	−0.503**	0.070	0.324*	−0.182	0.248	−0.012
Gravy	−0.426**	−0.263	0.356*	0.424**	0.418**	0.320*	−0.620**	0.343*	0.046	0.417**	−0.366**
Aromo	0.078	0.165	−0.042	−0.267	−0.051	−0.079	0.098	0.006	0.115	−0.047	0.105	−0.627**
axis1	−0.469**	−0.279*	0.514**	0.321*	0.624**	0.291*	−0.777**	0.530**	0.144	0.495**	−0.485**	0.491**	0.208
axis2	0.461**	−0.615**	−0.107	0.461**	0.311*	−0.388**	0.267	−0.242	−0.676**	−0.514**	−0.520**	−0.074	0.013	0.000

The **p < 0.01, * 0.05 < p < 0.01.

Figure 3. ENC-plot analysis (ENC plotted against GC_3s). The black curve represents the expected curve derived from the positions of strains when the codon usage was only determined by the GC3s composition. PCV3a-1, PCV3a-2, PCV3a-IM and PCV3b are represented in green, blue, red and orange, respectively.

Figure 4. PR2 analysis of PCV3 and specific genes. Red, green and blue refer to complete coding sequences, ORF1 and ORF2, respectively.

Figure 5. Neutrality plot analysis (GC_12s plotted against GC_3s) for all the coding sequences of PCV3 and the different genotypes.

Figure 6. (a) CAI and (b) SiD analysis of different genotypes of PCV3 coding sequences in relation to potential host species, including Sus scrofa (purple), Homo sapiens (green), Canis familiaris (blue) and Rhinclophus ferrumequinum (brown).