@ARTICLE{TreeBASE2Ref31676,
author = {Wu Zhang and Johannes (Ewald) Zacharias Groenewald and Lorenzo Lombard and Rene K. Schumacher and Alan John Lander Phillips and Pedro W. Crous},
title = {Evaluating species in Botryosphaeriales},
year = {2021},
keywords = {Multi-Locus Sequence Typing (MLST); canker and leaf spot pathogens; new taxa; systematics},
doi = {10.3767/persoonia.2021.46.03},
url = {http://doi.org/10.3767/persoonia.2021.46.03},
pmid = {},
journal = {Persoonia},
volume = {46},
number = {},
pages = {63--115},
abstract = {The Botryosphaeriales (Dothideomycetes) includes numerous endophytic, saprobic, and plant pathogenic species associated with a wide range of symptoms, most commonly on woody plants. In a recent phylogenetic treatment of 499 isolates in the culture collection (CBS) of the Westerdijk Institute, we evaluated the families and genera accommodated in this order of important fungi. The present study presents multigene phylogenetic analyses for an additional 230 isolates, using ITS, tef1, tub2, LSU and rpb2 loci, in combination with morphological data. Based on these data, 58 species are reduced to synonymy, and eight novel species are described. They include Diplodia afrocarpi (Afrocarpus, South Africa), Dothiorella diospyricola (Diospyros, South Africa), Lasiodiplodia acaciae (Acacia, Indonesia), Neofusicoccum podocarpi (Podocarpus, South Africa), N. rapaneae (Rapanea, South Africa), Phaeobotryon ulmi (Ulmus, Germany), Saccharata grevilleae (Grevillea, Australia) and S. hakeiphila (Hakea, Australia). The results have clarified the identity of numerous isolates that lacked Latin binomials or had been deposited under incorrect names in the CBS collection in the past. They also provide a solid foundation for more in-depth future studies on taxa in the order. Sequences of the tef1, tub2 and rpb2 genes proved to be the most reliable markers. At the species level, results showed that the most informative genes were inconsistent, but that a combination of four candidate barcodes (ITS, tef1, tub2 and rpb2) provided reliable resolution. Furthermore, given the large number of additional isolates included in this study, and newly generated multigene DNA datasets, several species could also be reduced to synonymy. The study illustrates the value of reassessing the identity of older collections in culture collections utilising modern taxonomic frameworks and methods.}
}
Analyses for Study 27596
Citation title:
"Evaluating species in Botryosphaeriales" .
Study name:
"Evaluating species in Botryosphaeriales" .
This study is part of submission 27596
(Status: Published).
Analyses
Analysis 1
Analysis details
Input data
43 Input object(s)
Output data
43 Output object(s)
Fig. 1. Bayesian phylogeny of Botryosphaeria multigene alignment.
Fig. 10. Bayesian phylogeny of Saccharata multigene alignment.
Fig. 2. Bayesian phylogeny of Diplodia multigene alignment.
Fig. 3. Bayesian phylogeny of Dothiorella multigene alignment.
Fig. 4. Bayesian phylogeny of Lasiodiplodia multigene alignment.
Fig. 5. Bayesian phylogeny of Neofusicoccum multigene alignment.
Fig. 6. Bayesian phylogeny of Neofusicoccum parvum species complex multigene alignment.
Fig. 7. Bayesian phylogeny of Neoscytalidium multigene alignment.
Fig. 8. Bayesian phylogeny of several genera multigene alignment.
Fig. 9. Bayesian phylogeny of Pseudofusicoccum multigene alignment.
Fig. S10A. Bayesian phylogeny of the Saccharata ITS alignment.
Fig. S10B. Bayesian phylogeny of the Saccharata rpb2 alignment.
Fig. S10C. Bayesian phylogeny of the Saccharata tef1 alignment.
Fig. S1A. Bayesian phylogeny of the Botryosphaeria ITS alignment.
Fig. S1B. Bayesian phylogeny of the Botryosphaeria tef1 alignment.
Fig. S1C. Bayesian phylogeny of the Botryosphaeria tub2 alignment.
Fig. S2A. Bayesian phylogeny of the Diplodia ITS alignment.
Fig. S2B. Bayesian phylogeny of the Diplodia tef1 alignment.
Fig. S2C. Bayesian phylogeny of the Diplodia tub2 alignment.
Fig. S3A. Bayesian phylogeny of the Dothiorella ITS alignment.
Fig. S3B. Bayesian phylogeny of the Dothiorella tef1 alignment.
Fig. S3C. Bayesian phylogeny of the Dothiorella tub2 alignment.
Fig. S4A. Bayesian phylogeny of the Lasiodiplodia ITS alignment.
Fig. S4B. Bayesian phylogeny of the Lasiodiplodia rpb2 alignment.
Fig. S4C. Bayesian phylogeny of the Lasiodiplodia tef1 alignment.
Fig. S4D. Bayesian phylogeny of the Lasiodiplodia tub2 alignment.
Fig. S5A. Bayesian phylogeny of the Neofusicoccum ITS alignment.
Fig. S5B. Bayesian phylogeny of the Neofusicoccum rpb2 alignment.
Fig. S5C. Bayesian phylogeny of the Neofusicoccum tef1 alignment.
Fig. S5D. Bayesian phylogeny of the Neofusicoccum tub2 alignment.
Fig. S6A. Bayesian phylogeny of the Neofusicoccum parvum complex ITS alignment.
Fig. S6B. Bayesian phylogeny of the Neofusicoccum parvum complex rpb2 alignment.
Fig. S6C. Bayesian phylogeny of the Neofusicoccum parvum complex tef1 alignment.
Fig. S6D. Bayesian phylogeny of the Neofusicoccum parvum complex tub2 alignment.
Fig. S7A. Bayesian phylogeny of the Neoscytalidium ITS alignment.
Fig. S7B. Bayesian phylogeny of the Neoscytalidium tef1 alignment.
Fig. S7C. Bayesian phylogeny of the Neoscytalidium tub2 alignment.
Fig. S8A. Bayesian phylogeny of the different genera ITS alignment.
Fig. S8B. Bayesian phylogeny of the different genera LSU alignment.
Fig. S8C. Bayesian phylogeny of the different genera tef1 alignment.
Fig. S9A. Bayesian phylogeny of the Pseudofusicoccum ITS alignment.
Fig. S9B. Bayesian phylogeny of the Pseudofusicoccum tef1 alignment.
Fig. S9C. Bayesian phylogeny of the Pseudofusicoccum tub2 alignment.
Analysis 2
Analysis details
Input data
10 Input object(s)
Output data
8 Output object(s)
Fig. 1 (support values overlayed). RAxML phylogeny of Botryosphaeria multigene alignment.
Fig. 10 (support values overlayed). RAxML phylogeny of Saccharata multigene alignment.
Fig. 2 (support values overlayed). RAxML phylogeny of Diplodia multigene alignment.
Fig. 3 (support values overlayed). RAxML phylogeny of Dothiorella multigene alignment.
Fig. 4 (support values overlayed). RAxML phylogeny of Lasiodiplodia multigene alignment.
Fig. 5 (support values overlayed). RAxML phylogeny of Neofusicoccum multigene alignment.
Fig. 8 (support values overlayed). RAxML phylogeny of several genera multigene alignment.
Fig. 9 (support values overlayed). RAxML phylogeny of Pseudofusicoccum multigene alignment.
Analysis 3
Analysis details
Input data
33 Input object(s)
Output data
33 Output object(s)
Fig. S10A (bootstrap support values overlayed). First of four equally most parsimonious trees of the Saccharata ITS alignment.
Fig. S10B (bootstrap support values overlayed). First of ten equally most parsimonious trees of the Saccharata rpb2 alignment.
Fig. S10C (bootstrap support values overlayed). First of twenty equally most parsimonious trees of the Saccharata tef1 alignment.
Fig. S1A (bootstrap support values overlayed). First of two equally most parsimonious trees of the Botryosphaeria ITS alignment.
Fig. S1B (bootstrap support values overlayed). First of 36 equally most parsimonious trees of the Botryosphaeria tef1 alignment.
Fig. S1C (bootstrap support values overlayed). First of 35 equally most parsimonious trees of the Botryosphaeria tub2 alignment.
Fig. S2A (bootstrap support values overlayed). First of 1000 equally most parsimonious trees of the Diplodia ITS alignment.
Fig. S2B (bootstrap support values overlayed). First of 1000 equally most parsimonious trees of the Diplodia tef1 alignment.
Fig. S2C (bootstrap support values overlayed). First of 1000 equally most parsimonious trees of the Diplodia tub2 alignment.
Fig. S3A (bootstrap support values overlayed). First of 1000 equally most parsimonious trees of the Dothiorella ITS alignment.
Fig. S3B (bootstrap support values overlayed). First of 1000 equally most parsimonious trees of the Dothiorella tef1 alignment.
Fig. S3C (bootstrap support values overlayed). First of 1000 equally most parsimonious trees of the Dothiorella tub2 alignment.
Fig. S4A (bootstrap support values overlayed). First of 1000 equally most parsimonious trees of the Lasiodiplodia ITS alignment.
Fig. S4B (bootstrap support values overlayed). First of 1000 equally most parsimonious trees of the Lasiodiplodia rpb2 alignment.
Fig. S4C (bootstrap support values overlayed). First of 486 equally most parsimonious trees of the Lasiodiplodia tef1 alignment.
Fig. S4D (bootstrap support values overlayed). First of 1000 equally most parsimonious trees of the Lasiodiplodia tub2 alignment.
Fig. S5A (bootstrap support values overlayed). First of 1000 equally most parsimonious trees of the Neofusicoccum ITS alignment.
Fig. S5B (bootstrap support values overlayed). First of 640 equally most parsimonious trees of the Neofusicoccum rpb2 alignment.
Fig. S5C (bootstrap support values overlayed). First of 1000 equally most parsimonious trees of the Neofusicoccum tef1 alignment.
Fig. S5D (bootstrap support values overlayed). First of 1000 equally most parsimonious trees of the Neofusicoccum tub2 alignment.
Fig. S6A (bootstrap support values overlayed). First of 1000 equally most parsimonious trees of the Neofusicoccum parvum complex ITS alignment.
Fig. S6B (bootstrap support values overlayed). First of eight equally most parsimonious trees of the Neofusicoccum parvum complex rpb2 alignment.
Fig. S6C (bootstrap support values overlayed). First of eighteen equally most parsimonious trees of the Neofusicoccum parvum complex tef1 alignment.
Fig. S6D (bootstrap support values overlayed). First of six equally most parsimonious trees of the Neofusicoccum parvum complex tub2 alignment.
Fig. S7A (bootstrap support values overlayed). First of 1000 equally most parsimonious trees of the Neoscytalidium ITS alignment.
Fig. S7B (bootstrap support values overlayed). Single most parsimonious tree of the Neoscytalidium tef1 alignment.
Fig. S7C (bootstrap support values overlayed). First of three equally most parsimonious trees of the Neoscytalidium tub2 alignment.
Fig. S8A (bootstrap support values overlayed). First of 1000 equally most parsimonious trees of the different genera ITS alignment.
Fig. S8B (bootstrap support values overlayed). First of 84 equally most parsimonious trees of the different genera LSU alignment.
Fig. S8C (bootstrap support values overlayed). First of six equally most parsimonious trees of the different genera tef1 alignment.
Fig. S9A (bootstrap support values overlayed). First of 30 equally most parsimonious trees of the Pseudofusicoccum ITS alignment.
Fig. S9B (bootstrap support values overlayed). First of 72 equally most parsimonious trees of the Pseudofusicoccum tef1 alignment.
Fig. S9B (bootstrap support values overlayed). First of five equally most parsimonious trees of the Pseudofusicoccum tef1 alignment.
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Citation title: "Evaluating species in Botryosphaeriales".
