Variable site plots for nucleotide (a) and amino acid (b) sequence of 37 CSFVs.

<p>The number of differences at each site represents the number of variable isolates estimated with multiple sequence alignment. Each color indicates a different genomic region.</p

Information of the isolates used in this study.

<p>Information of the isolates used in this study.</p

Pairwise dN/dS (ω) values of the protein coding gene sequences of 37 CSFVs.

<p>Pairwise dN/dS (ω) values of the protein coding gene sequences of 37 CSFVs.</p

The best fit evolutionary models estimated for CSFV genomic regions with Modeltest 3.7.

<p>The best fit evolutionary models estimated for CSFV genomic regions with Modeltest 3.7.</p

Bayesian skyline plot based on the entire genome sequences of 37 CSFV isolate.

<p>The plot depicts changes in the effective population size (<i>N</i>_<i>e</i>). The dark line shows the effective population size estimated through time. The upper and lower lines indicate the 95% HPD range of BSP.</p

Bayesian maximum clade credibility phylogenetic tree based on the whole genome sequences of 37 CSFVs.

<p>With the BI and ML methods, identical topology was produced. Divergence times (in years) are positioned below the nodes; the 95% HPD intervals are indicated in brackets. The confidence of the phylogenetic analysis is presented above the nodes: left numbers represent Bayesian posterior probabilities (≥ 0.80) and right ones represent ML bootstrap values (≥ 60%). Subgenotypes and groups are indicated above the corresponding nodes using squares and circles.</p

The BI tree based on NS4B sequences of 37 CSFVs.

<p>The robustness of the phylogenetic analysis is showed above the nodes: left numbers are Bayesian posterior probabilities (≥0.80) and right ones are ML bootstrap values (≥60%). Subgenotypes and groups are marked above the corresponding nodes using squares and circles.</p

Time-Calibrated Phylogenomics of the Classical Swine Fever Viruses: Genome-Wide Bayesian Coalescent Approach

<div><p>The phylogeny of classical swine fever virus (CSFV), the causative agent of classical swine fever (CSF), has been investigated extensively. However, no evolutionary research has been performed using the whole CSFV genome. In this study, we used 37 published genome sequences to investigate the time-calibrated phylogenomics of CSFV. In phylogenomic trees based on Bayesian inference (BI) and Maximum likelihood (ML), the 37 isolates were categorized into five genetic types (1.1, 1.2, 2.1, 2.3, and 3.4). Subgenotype 1.1 is divided into 3 groups and 1 unclassified isolate, 2.1 into 4 groups, 2.3 into 2 groups and 1 unclassified isolate, and subgenotype 1.2 and 3.4 consisted of one isolate each. We did not observe an apparent temporal or geographical relationship between isolates. Of the 14 genomic regions, NS4B showed the most powerful phylogenetic signal. Results of this evolutionary study using Bayesian coalescent approach indicate that CSFV has evolved at a rate of 13×.010^-4 substitutions per site per year. The most recent common ancestor of CSFV appeared 2770.2 years ago, which was about 8000 years after pig domestication. The effective population size of CSFV underwent a slow increase until the 1950s, after which it has remained constant.</p></div

Additional file 4: of Genome sequencing and protein domain annotations of Korean Hanwoo cattle identify Hanwoo-specific immunity-related and other novel genes

Protein sequences which have locations with depth > 10×. (XLSX 101 kb

Additional file 3: of Genome sequencing and protein domain annotations of Korean Hanwoo cattle identify Hanwoo-specific immunity-related and other novel genes

FASTA sequences for scaffolds which have locations with depth > 10×. (XLSX 9907 kb