Fig. 4

Comparative analysis of SARS-CoV-2 and non-human coronaviruses. a Maximum likelihood phylogenetic tree of the whole genome sequences of SARS-CoV-2 Wuhan-Hu-1 (MN908947.3) and non-human coronaviruses including Scotophilus bat coronavirus 512(NC_009657.1), Swine enteric alphacoronavirus strain SeACoV-p10(MK977618.1), Bat coronavirus HKU4–1(NC_009019.1), Bat coronavirus HKU5–1(NC_009020.1), Bat coronavirus RaTG13(MN996532.1), Bat SARS-like coronavirus isolate bat-SL-CoVZC45(MG772933.1), Bat SARS-like coronavirus isolate bat-SL-CoVZXC21(MG772934.1), Pangolin coronavirus isolate PCoV_GX-P1E(MT040334.1), Pangolin coronavirus isolate PCoV_GX-P4L(MT040333.1), Avian coronavirus strain H120(MK071267.1), Avian coronavirus strain Ma5(KY626045.1), Bulbul coronavirus HKU11–796(FJ376620.1), Thrush coronavirus HKU12–600(NC_011549.1), Munia coronavirus HKU13–3514(NC_011550.1). b Heat map of RSCU values for the complete coding sequences of SARS-CoV-2 and non-human coronaviruses. The heatmap analysis was performed using CIMminer. Each column represents a codon. Codons with higher RSCU values are highlighted with a red background. c The profiles of the relative synonymous codon usage for complete gene of SARS-CoV-2 and non-human coronaviruses. Over-represented codons (RSCU value > 1.6) and under-represented codons (RSCU value < 0.6) were shown as line graph