Short Communication |
Corresponding author: Javier Fernández-López ( jflopez@rjb.csic.es ) Academic editor: Thorsten Lumbsch
© 2018 Javier Fernández-López, María P. Martín, Margarita Dueñas, M. Teresa Telleria.
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Fernández-López J, Martín MP, Dueñas M, Telleria MT (2018) Multilocus phylogeny reveals taxonomic misidentification of the Schizopora paradoxa (KUC8140) representative genome. MycoKeys 38: 121-127. https://doi.org/10.3897/mycokeys.38.28497
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Schizopora paradoxa, current name Xylodon paradoxus, is a white-rot fungus with certain useful biotechnological properties. The representative genome of Schizopora paradoxa strain KUC8140 was published in 2015 as part of the 1000 Fungal Genomes Project. Multilocus phylogenetic analyses, based on three nuclear regions (ITS, LSU and rpb2), confirmed a misidentification of S. paradoxa strain KUC8140 which should be identified as Xylodon ovisporus. This wrong identification explains the unexpected geographical distribution of S. paradoxa, since this species has a European distribution, whereas the strain KUC8140 was recorded from Korea, Eastern Asia.
Hymenochaetales , phylogenetic analyses, taxonomy, white-rot fungi, Xylodon
The genus Schizopora Velen., currently synonymous with Xylodon (Pers.) Fr. (
The representative genome of Schizopora paradoxa strain KUC8140, current name Xylodon paradoxus (Schrad.) Chevall., was sequenced in 2015 as part of the 1000 Fungal Genomes Project (http://jgi.doe.gov/fungi) (
In order to infer the taxonomic position of the strain KUC8140, phylogenetic relationships of six Xylodon species were addressed. DNA from specimens of X. paradoxus, X. quercinus (Pers.) Gray, X. nothofagi (G. Cunn.) Hjorstam & Ryvarden, X. raduloides Riebesehl & E. Langer, X. flaviporus (Ber. & M.A. Curtis ex Cooke) Riebesehl & E. Langer and X. ovisporus (Corner) Riebesehl & E. Langer was extracted from herbaria specimens and culture collections (Table
Specimen information, GenBank accession numbers and genome BLAST searches (ID) used in this study. New sequences generated in this study are indicated in bold. n.d.: no data.
Species | Specimen voucher | Country | GenBank accession number | ||
---|---|---|---|---|---|
ITS | LSU | rpb2 | |||
Lyomyces crustosus | HHB 10401 | USA | MH260068 | MH260061 | MH259316 |
HHB 13100 | USA | MH260069 | MH260062 | MH259317 | |
UC 2022841 | USA | KP814310 | n.d. | n.d. | |
Xylodon flaviporus | ICMP 13836 | Taiwan | AF145585 | n.d. | n.d. |
MA-Fungi 79440, 12094IS | Germany | MH260071 | MH260066 | MH259319 | |
Xylodon nothofagi | ICMP 13839 | New Zealand | AF145582 | MH260064 | MH259322 |
PDD 91630, BCP 3306 | New Zealand | GQ411524 | n.d. | n.d. | |
Xylodon ovisporus | ICMP 13835 | Taiwan | AF145586 | MH260063 | MH259320 |
ICMP 13837 | Taiwan | AF145587 | n.d. | n.d. | |
Xylodon paradoxus | FCUG 2425 | Russia | AF145577 | n.d. | n.d. |
MA-Fungi 70444, 11060MD | France | MH260070 | MH260065 | n.d. | |
MA-Fungi 81294, 13833MD | France | MH260072 | n.d. | MH259318 | |
Xylodon quercinus | H 6013352 | Finland | KT361632 | n.d. | n.d. |
MA-Fungi 91311, 1JFL | Spain | MH260073 | MH260067 | MH259321 | |
Xylodon raduloides | ICMP 13833 | Australia | AF145580 | KY962853 | n.d. |
MA-Fungi 75310, GP2291 | Spain | KY962825 | KY962864 | KY967055 | |
Schizopora paradoxa | KUC8140 | Korea | ID14957398 | ID14957349 | ID1495735 |
Using the BLAST tool from the JGI portal, ITS, LSU and rpb2 sequences were extracted from the KUC8140 strain genome (https://genome.jgi.doe.gov/pages/blast-query.jsf?db=Schpa1). The same regions from X. paradoxus specimens FCUG-2425, MA-Fungi 70444 and MA-Fungi 81294 were used as reference sequences for BLAST searches, respectively (Table
Raw sequence data were processed and assembled with Geneious version 9.0.2. (
Phylogenetic tree estimation for each alignment was performed using Maximum Likelihood (ML) and Bayesian Inference (BI). ML and bootstrapping analyses were conducted in RAxML (
The ITS+LSU dataset was 1193 characters long (ITS = 594; LSU = 599) and the rpb2 dataset was 647 characters long. The results of phylogenetic analyses of ITS+LSU and rpb2 datasets are summarised in Fig.
Maximum likelihood trees for ITS+LSU (left) and rpb2 (right) regions of Xylodon species. In order to assess genealogical concordance, dotted lines link the position of the same specimen in both trees. Grey boxes indicate the position of KUC8140 strain with Xylodon ovisporus and the position of X. paradoxus. Numbers over branches are maximum likelihood bootstrap (MLB) values and posterior probabilities (BPP). Voucher numbers and species names are indicated in Table
Our phylogenetic analyses confirmed the misidentification of S. paradoxa strain KUC8140, since sequences of this strain grouped in the X. ovisporus clade, showing a different evolutionary history from X. paradoxus. Therefore, S. paradoxa strain KUC8140, from Korea, must be identified as Xylodon ovisporus, reported from Asia and West Pacific areas (
According to our phylogenetic analyses, Xylodon ovisporus is the sister species of X. flaviporus and morphological characters confirm this relationship. The species can be discriminated by the spore size, shorter in the first one (
This work was supported by the Plan Nacional I+D+i projects n° CGL2012-35559, CGL2015-67459-P.
J.F.L. was supported by a Predoctoral Grant from the Ministerio de Economía y Competitividad (Spain) (BES-2013-066429). Karl-Henrik Larsson provided comments and suggestions that improved this manuscript. Thanks to M. Glenn (Seton Hall University, US) for the English revision. Also to the staff of ICMP, PDD and the Madison Forest Products Laboratory (USDA) for their invaluable assistance.