SupplementarytableS3. The possible recombination and reassortment events in MDV isolates detected by RDP4.56a

Segment / Event / Recombinant / Major parent / Minor parent / RDPRCS / Toolsb / p-value
individual componentanalysis about recombination
U2 / recombination / MDV-N / Unknownc / MDV-BDP1 / 0.612 / BMCST / 7.990×10-12
U2 / recombination / MDV-VU / FBNYV-[ES;Mu29D] / Unknownc / 0.479 / MCS / 2.605×10-03
U2 / recombination / MDV-VF / MDV-BDM1 / Unknownc / 0.537 / RMCT / 4.835×10-08
the concatenated (CON) dataset analysis about recombination and reasortment
N / reassortment / MDV-VF / MDV-BDP1 / MDV-VU / 0.427 / GBMCST / 7.046×10-48
R / reassortment / MDV-VF / MDV-N / MDV-VU / 0.448 / RGBMCS / 4.004×10-20
U4 / reassortment / MDV-N / MDV-BD1 / MDV-VF / 0.410 / GBMCST / 2.534×10-30
U4 / recombination / MDV-BD1 / PNYDV-[AT;1] / Unknownc / 0.557 / RGBMCS / 3.899×10-26
U2 / recombination / MDV-VF / FBNYV-[ES;Mu29D] / Unknownc / 0.497 / RGBMCS / 1.813×10-21

athe separate genomic components of all viruses in genus Nanovirus were alignedindividually (DNA-R, DNA-S,DNA-C, DNA-M, DNA-N,DNA-U1, DNA-U2,DNA-U4).Moreover,the concatenated(CON) cognate genome components sequence in the order DNA- R, -S, -C, -M, -N, -U1, -U2 and -U4 was aligned among all reported MDV isolates, a SCSV isolate with six components and all other nanoviruses with eight components. All sequences used were listed in the Suppl. Table S4. Each component started with the virion-strand origin hairpin-loopsequence TATTACC.

bThe recombinationdetection methods that detected the illustrated recombination events are indicated by a single letter: R, RDP; G, GENECONV; B,BOOTSCAN; M, MACHI; C, CHIMAERA; S, SISCAN; T, 3SEQ. The p-valuelisted is for the method yielding the greatest support foroccurrence of recombination (indicated in bold italic type in the detection methods)

cindicates that the potential parental sequence was detected with low confidence.