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Recombination analysis

PL Peixun Li
YS Yesheng Shen
TW Tailong Wang
JL Jing Li
YL Yan Li
YZ Yiran Zhao
SL Sidang Liu
BL Baoquan Li
ML Mengda Liu
FM Fanliang Meng
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In this study, the full-length genome of SDHY-DZ037 was sequenced for recombination analysis. Alignment was screened using RDP4, implementing the RDP (28), GENECONV (29), Bootscan (30), Chimaera (31), SiScan (32), MaxChi (33), and 3Seq (34) algorithms. At least four of the above methods can identify a recombination event. In addition, if the breakpoint region of the recombination event is larger than 100 nt, the region can be regarded as a recombination region. To confirm these presumed recombinant events, we generated a series of phylogenetic trees for each sequence region identified during the analysis (35). For each region, evolutionary analysis of maximum likelihood was performed in MEGA X. To visualize the recombinant signal and inferred breakpoint locations, a similarity analysis between the presumptive recombinant sequences and the parental lineages was implemented in SIMPLOT v3.5.1 (36). The window size was set to 200 nt and the step size to 20 nt.

Copyright and License information:  ©2022 Li, Shen, Wang, Li, Li, Zhao, Liu, Li, Liu and Meng.
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