Hyphodermella zixishanensis (Polyporales, Basidiomycota), a new species with reddish hymenial surface
Wang, Hui; Gu, Zi-Rui; Zhao, Chang-Lin (2021), Hyphodermella zixishanensis (Polyporales, Basidiomycota), a new species with reddish hymenial surface, Dryad, Dataset, https://doi.org/10.5061/dryad.8sf7m0cnq
A new corticioid fungal species, Hyphodermella zixishanensis, is described based on combination of morphological features and molecular evidence. The species is characterized by an annual growth habit, resupinate basidiomata with reddish, a monomitic hyphal system with generative hyphae bearing simple septa, IKI–, CB– and ellipsoid, colorless, thin-walled, smooth basidiospores. Sequences of ITS and nLSU gene regions were generated, and phylogenetic analyses were performed with maximum likelihood, maximum parsimony and Bayesian inference methods. The phylogenetic analyses showed that the species belongs to Hyphodermella and placed as sister taxon to H. aurantiaca.
The studied specimens were deposited at the herbarium of Southwest Forestry University (SWFC), Kunming, Yunnan Province, P.R. China. Macromorphological descriptions are based on field notes. Colour terms follow Petersen (1996). Micromorphological data were obtained from dried specimens, and observed under a light microscope following Dai (2012). The following abbreviations were used: KOH = 5% potassium hydroxide, CB = Cotton Blue, CB– = acyanophilous, IKI = Melzer’s reagent, IKI– = both inamyloid and indextrinoid, L = mean spore length (arithmetic average of all spores), W = mean spore width (arithmetic average of all spores), Q = variation in the L/W ratios between the specimens studied, n (a/b) = number of spores (a) measured from given number (b) of specimens.
Molecular techniques and phylogenetic analyses
CTAB rapid plant genome extraction kit-DN14 (Aidlab Biotechnologies Co., Ltd, Beijing) was used to obtain genomic DNA from dried specimens. A small piece of dried fungal specimen (about 30 mg) was ground to powder with liquid nitrogen. The powder was transferred to a 1.5 ml centrifuge tube, suspended in 0.4 ml of lysis buffer, and incubated in a 65 °C water bath for 60 min. After that, 0.4 ml phenol-chloroform (24:1) was added and the suspension was shaken vigorously. After centrifugation at 13,000 rpm for 5 min, 0.3 ml supernatant was transferred to a new tube and mixed with 0.45 ml binding buffer. The mixture was then transferred to an adsorbing column (AC) for centrifugation at 13,000 rpm for 0.5 min. Then, 0.5 ml inhibitor removal fluid was added in AC for a centrifugation at 12,000 rpm for 0.5 min. After washing twice with 0.5 ml washing buffer, the AC was transferred to a clean centrifuge tube, and 100 ml elution buffer was added to the middle of the adsorbed film to elute the DNA. ITS region was amplified with primer pair ITS5 and ITS4 (White et al. 1990). Nuclear LSU region was amplified with primer pair LR0R and LR7 (http://www.biology.duke.edu/fungi/mycolab/primers.htm). The PCR procedure for ITS was as follows: initial denaturation at 95°C for 3 min, followed by 35 cycles at 94°C for 40 s, 58°C for 45 s and 72°C for 1 min, and a final extension of 72°C for 10 min. The PCR procedure for nLSU was as follows: initial denaturation at 94°C for 1 min, followed by 35 cycles at 94°C for 30 s, 48°C 1 min and 72°C for 1.5 min, and a final extension of 72°C for 10 min. The PCR products were purified and directly sequenced at Kunming Tsingke Biological Technology Limited Company, Kunming, Yunnan Province, P.R. China. All newly generated sequences were deposited at GenBank (Table 1).
Sequences were aligned in MAFFT 6 (Katoh and Toh 2008; http://mafft.cbrc.jp/alignment/ server/) using the “G-INS-I” strategy for nLSU, the “E-INS-I” strategy for ITS+nLSU, and manually adjusted in BioEdit (Hall 1999). Alignment datasets were deposited in TreeBase (submission ID 28053). Candelabrochaete africana Boidin obtained from GenBank was used as an outgroup to root the LSU tree (Fig. 1.) following Justo et al. (2017) and Pirex concentricus was selected as an outgroup for phylogenetic analyses of the ITS+nLSU region (Fig. 2) following Zhao et al. (2017).
Maximum parsimony analyses were applied to the ITS+nLSU and nLSU dataset sequences. Approaches to phylogenetic analysis followed Chen et al. (2016), and the tree construction procedure was performed in PAUP* version 4.0b10 (Swofford 2002). All characters were equally weighted and gaps were treated as missing data. Trees were inferred using the heuristic search option with TBR branch swapping and 1000 random sequence additions. Max-trees was set to 5000, branches of zero length were collapsed and all parsimonious trees were saved. Clade robustness was assessed using a bootstrap (BT) analysis with 1000 replicates (Felsenstein 1985). Descriptive tree statistics tree length (TL), consistency index (CI), retention index (RI), rescaled consistency index (RC), and homoplasy index (HI) were calculated for each maximum parsimonious tree generated. Sequences were also analyzed using Maximum Likelihood (ML) with RAxML-HPC2 through the Cipres Science Gateway (http://www.phylo.org/sub_sections/portal). Branch support (BS) for ML analysis was determined by 1000 bootstrap replicate. MrModeltest 2.3 (Nylander 2004) was used to determine the best-fit evolution model for each data set for Bayesian inference (BI). Bayesian inference was calculated with
MrBayes3.1.2 (Ronquist and Huelsenbeck 2003). Four Markov chains were run for 2 runs from random starting trees for 250 thousand generations for nLSU (Fig. 1) and 100 thousand generations for ITS+nLSU (Fig. 2), and trees were sampled every 100 generations. The first one-fourth generations were discarded as burn-in. A majority rule consensus tree of all remaining trees was calculated. Branches were considered as significantly supported if they received ML bootstrap value >75%, maximum parsimony bootstrap value (MP) >75%, or Bayesian posterior probabilities (PP) >0.95.
Yunnan Provincial Department of Education Science Research Fund Project, Award: 202001AS070043
Yunnan Provincial Department of Education Science Research Fund Project, Award: 2021Y275