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Homologous recombination is a force in the evolution of canine distemper virus

Fig 3

Analysis of recombination breakpoints in the CDV genome strain HLJ1-06 using the SimPlot program and MEGA 5.0 software package.

(A) A similarity Plot analysis of the genome sequences of JX681125/HLJ1-06 and its putative parents (KC427278/HeBei and HM046486/ Phoca/Caspian/2007). The JX681125/HLJ1-06 was used as the query. The y-axis presented the percentage of identity with a window size of 600 bp and a step size of 20 bp. The vertical line indicated the breakpoint regions. (B) Boot Scan analysis of JX681125/HLJ1-06 and its parent sequences. The y-axis presented the percentage of permutated trees using a sliding window. (E) Similarity Plot analysis of the L gene sequences of JX681125/HLJ1-06 and its putative parents (KC427278/HeBei and HM046486/Phoca/Caspian/2007). (F) Boot Scan analysis of JX681125/HLJ1-06 and its parent sequences in L gene. The remaining are identical as in panels A and B. A PDV isolate, KC80222/PDV/Wadden_Sea.NLD/1998 was used as an outgroup. (C and D) The phylogenetic tree of the segment in different regions in the CDV genome from 12922–14259 and 1–12921 + 14260–15690 bp. (G and H) The phylogenetic tree of the segment in different regions in the L gene from 3749–5255 and 1–3748 + 5256–6555 bp. The recombinant strain and their major and minor putative parents are indicated with “●”, “▲”, and “▼”, respectively. The PDV isolates are marked with a “■”.

Fig 3

doi: https://doi.org/10.1371/journal.pone.0175416.g003