Table 1.
Bayesian inference of phylogeny and structure reconstruction analysis for brown rot strains from phylotypes IIB-1 and IIB-2
| Strain | Phylotypea | Sequevara | Country | Host | Phylogenyb | Structurec |
|
|---|---|---|---|---|---|---|---|
| Major cluster | Subcluster | ||||||
| CFBP4787 | IIB | 1 | Portugal | Potato | AIO | 1 | A |
| UW551 | IIB | 1 | Kenya | Pelargonium | AIO | 1 | A |
| CMR34 | IIB | 1 | Cameroon | Tomato | AIO | 1 | A |
| JT516 | IIB | 1 | Réunion | Potato | AIO | 1 | A |
| CFBP3870 | IIB | 1 | South Africa | Potato | AIO | 1 | A |
| JT646 | IIB | 1 | Sri Lanka | Potato | AIO | 1 | A |
| LNPV28.23 | IIB | 1 | Réunion | Potato | AIO | 1 | A |
| JQ1051 | IIB | 1 | Réunion | Tomato | AIO | 1 | A |
| CFBP3865 | IIB | 1 | France | Potato | EuMr | 1 | A |
| CFBP3785 | IIB | 1 | Portugal | Potato | EuMr | 1 | B |
| CFBP4812 | IIB | 1 | France | Tomato | EuMr | 1 | B |
| JQ1006 | IIB | 1 | Réunion | Potato | EuMr | 1 | B |
| CFBP3579 | IIB | 1 | France | Tomato | EuMr | 1 | B |
| CFBP4578 | IIB | 1 | Egypt | Tomato | EuMr | 1 | B |
| PSS525 | IIB | 1 | Taiwan | Potato | EuMr | 1 | B |
| LNPV19.66 | IIB | 1 | France | Potato | EuMr | 1 | C |
| RM | IIB | 1 | Uruguay | Potato | EuMr | 1 | C |
| CFBP3927 | IIB | 1 | Greece | Potato | EuMr | 1 | C |
| CFBP3884 | IIB | 1 | Sweden | Potato | North | 1 | D |
| IPO1609 | IIB | 1 | Netherlands | Potato | North | 1 | D |
| AP31H | IIB | 1 | Uruguay | Potato | Andean | 2 | |
| CFBP3784 | IIB | 1 | Portugal | Potato | Andean | 2 | |
| CFBP3873 | IIB | 1 | Belgium | Potato | Andean | 2 | |
| CFBP7103 | IIB | 1 | Spain | Potato | Andean | 2 | |
| ETAC | IIB | 1 | Uruguay | Potato | Andean | 2 | |
| CFBP3107 | IIB | 1 | Peru | Potato | Andean | 2 | |
| CFBP4808 | IIB | 1 | Israel | Potato | EuMr | 2 | |
| CFBP1410 | IIB | 2 | Colombia | Banana, plantain | 2 | ||
| CFBP3879 | IIB | 2 | Colombia | Potato | 2 | ||
| CFBP4611 | IIB | 2 | Colombia | Potato | 2 | ||
| CFBP3858 | IIB | 1 | Netherlands | Potato | Out | ND | |
Determined by sequencing of the partial endoglucanase (egl) gene (13).
Cluster determined from the phylogenetic reconstruction performed using MrBayes, version 3.2 (Fig. 2). Designations reflect the main origin of strains within each cluster: AIO, African–Indian Ocean regions; EuMr, European and Mediterranean regions; North, Northern European region; Andean, Latin American region. “Out” refers to the outer phylogenetic position of the strain compared to its sequevar.
Statistical groups were obtained by a Bayesian population structure assessment analysis with STRUCTURE software for numbers of clusters (K) ranging from 1 to 10. The major population was assessed as having 2 clusters, according to the likelihood of assignment decreasing from a ΔK value of 74 for 1 cluster to 1.44 for 6 clusters. Cluster 1 was assigned with an average inference of 0.872, and cluster 2 was assigned with an average inference of 0.799. The subpopulation was assessed as having 4 clusters, according to the likelihood of assignment increasing from a ΔK value of 11.210 for 1 cluster to 25.814 for 3 clusters, and then decreasing until K reached a value of 10. Subcluster A was assigned with an average inference of 0.837; subcluster B, with an average inference of 0.576; subcluster C, with an average inference of 0.554; and subcluster D, with an average inference of 0.693. ND, not done.