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Research Article
Phylogenomics, taxonomy and morphological characters of the Microdochiaceae (Xylariales, Sordariomycetes)
expand article infoZhao-Xue Zhang‡, Yu-Xin Shang‡, Meng-Yuan Zhang‡, Jin-Jia Zhang‡, Yun Geng§, Ji-Wen Xia‡, Xiu-Guo Zhang‡
‡ Shandong Agricultural University, Taian, China
§ Shandong Academy of Agricultural Sciences, Jinan, China

Corresponding author: Xiu-Guo Zhang ( zhxg@sdau.edu.cn )

Academic editor: Danushka Sandaruwan Tennakoon
© 2024 Zhao-Xue Zhang, Yu-Xin Shang, Meng-Yuan Zhang, Jin-Jia Zhang, Yun Geng, Ji-Wen Xia, Xiu-Guo Zhang.
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: Zhang Z-X, Shang Y-X, Zhang M-Y, Zhang J-J, Geng Y, Xia J-W, Zhang X-G (2024) Phylogenomics, taxonomy and morphological characters of the Microdochiaceae (Xylariales, Sordariomycetes). MycoKeys 106: 303-325. https://doi.org/10.3897/mycokeys.106.127355
Open Access

Abstract

Species of the family Microdochiaceae (Xylariales, Sordariomycetes) have been reported from worldwide, and collected from different plant hosts. The proposed new genus and two new species, viz., Macroidriella gen. nov., M. bambusae sp. nov. and Microdochium australe sp. nov., are based on multi-locus phylogenies from a combined dataset of ITS rDNA, LSU, RPB2 and TUB2 with morphological characteristics. Microdochium sinense has been collected from diseased leaves of Phragmites australis and this is the first report of the fungus on this host plant. Simultaneously, we annotated 10,372 to 11,863 genes, identified 4,909 single-copy orthologous genes, and conducted phylogenomic analysis based on genomic data. A gene family analysis was performed and it will expand the understanding of the evolutionary history and biodiversity of the Microdochiaceae. The detailed descriptions and illustrations of species are provided.

Key words

Microdochiaceae, multigene phylogeny, new taxa, phylogenomics, taxonomy

Introduction

Microdochium Syd. & P. Syd., is the type genus of the family Microdochiaceae Hern.-Restr., Crous & J.Z. Groenew. This was first described by Syd. & P. Syd. (Sydow 1924). The holotype collection of the type species of Microdochium, M. phragmitis Syd. & P. Syd. was obtained in Germany from the leaves of Phragmites australis (Sydow 1924). Microdochium species were collected as endophytes, plant pathogens, and saprophytes, and were frequently isolated from different plant hosts (Von Arx 1987; Glynn et al. 2005; Jewell and Hsiang 2013; Mandyam et al. 2013; Hiruma et al. 2018; Liang et al. 2019; Lu et al. 2023; Zhang et al. 2023a). Prior research has indicated that the classification of Microdochium within the Amphisphaeriaceae is supported by its morphological similarities (Parkinson et al. 1981; Samuels and Hallett 1983; Von Arx 1984; Jaklitsch and Voglmayr 2012). Hernández‐Restrepo et al. (2016) was proposed that Idriella and Microdochium may be closely related genera. Their phylogenetic analysis revealed that Idriella, Microdochium, and Selenodriella formed a distinct monophyletic group within the Xylariales. Therefore, Hernández‐Restrepo et al. (2016) established the new family Microdochiaceae to encompass this clade.

Currently, there are approximately 68 species of Microdochium listed in the Index Fungorum (2024), with 45 species being accepted. Microdochium has a diverse range of hosts that are widely distributed worldwide (Zhang et al. 2017; Crous et al. 2018, 2019, 2021; Marin-Felix et al. 2019; Huang et al. 2020). However, only a few species of Microdochium have the capability to cause diseases, primarily impacting grasses and cereals. Zhang et al. (2015) identified Microdochium paspali Syd. & P. Syd., which was responsible for causing leaf blight on Paspalum vaginatum Sw. Liang et al. (2019) identified Mi. poae J.M. Liang & Lei Cai, which induced leaf blight disease in turf grasses like Poa pratensis and Agrostis stolonifera L. Stewart et al. (2019) identified Mi. sorghi U. Braun, which was responsible for the development of zonate leaf spots and decay on sorghum species. Mi. albescens (Thüm.) Hern.-Restr. & Crous was the causative agent of leaf scald and grain discoloration in rice, leading to a global decrease in rice yield (Dirchwolf et al. 2023). Mi. bolleyi (R. Sprague) de Hoog & Herm.-Nijh. was cited as the cause of root necrosis and basal rot in creeping bent grass (Hong et al. 2008). In addition to this, some species of Microdochium occur as endophytes or saprophytes. Liu et al. (2022) identified three species, Microdochium miscanthi S.B. Liu, X.Y. Liu, Z. Meng & X.G. Zhang, Mi. sinense S.B. Liu, X.Y. Liu, Z. Meng & X.G. Zhang, and Mi. hainanense S.B. Liu, X.Y. Liu, Z. Meng & X.G. Zhang, isolated from Miscanthus sinensis Anderss. and Phragmites australis (Cav.) Trin. ex Steud in Hainan, China. Zhang et al. (2023a) collected novel species (Mi. bambusae J. Zhang, Z.X. Zhang, & Z. Li, Mi. nannuoshanense J. Zhang, Z.X. Zhang, & Z. Li, and Mi. phyllosaprophyticum J. Zhang, Z.X. Zhang, & Z. Li) from leaves of Bambusaceae plant as a saprobe.

With the advent of the sequencing era, genomics is increasingly being utilized for phylogenetic studies and can offer additional insights into pathogenic mechanisms (Manamgoda et al. 2011; Schoch et al. 2012; Jeewon et al. 2013; David et al. 2016; Mesny et al. 2021; Tsers et al. 2023). However, at present, only the genome information of three species of this taxon (Microdochium) can be retrieved from the NCBI database (https://www.ncbi.nlm.nih.gov/, accessed on 30 April 2024). In this study, we explored the species diversity of Microdochium and described one new species and one new host record based on the molecular phylogenetic analyses and morphological observations. In addition, we conducted genome and transcriptome sequencing of the new species, aiming to conduct phylogenetic analysis, and gene structure annotation at the genomic level. By comparing and analyzing the obtained data with existing species genome information, we aim to reveal the genetic relationship and functional differences between the new species and other species. This will gain a more comprehensive understanding of the biological characteristics and evolutionary history of the new taxa.

Materials and methods

Morphological study

During a series of field visits in 2023 in Hainan Province, China, plant specimens with necrotic spots were collected. Even though specimens harbor multiple fungi, we managed to obtain pure colonies through the single spore isolation (Senanayake et al. 2020) and tissue isolation techniques (Zhang et al. 2023a). We retrieved small fragments (5 × 5 mm) from the damaged leaf edges, treated them by immersion in a 75% ethanol solution for 60 s, followed by rinsing in sterile distilled water for 45 s and a 10% sodium hypochlorite solution for 45 s. Subsequently, specimens were rinsed three times in sterile deionized water for 30 s. The processed fragments were then placed on sterile filter paper to remove excess moisture before being transferred onto PDA for incubation at 24 °C for 3 days. The hyphal tips from growing colonies were transferred to fresh PDA plates. Images were captured using a Sony Alpha 6400L digital camera (Sony Group Corporation, Tokyo, Japan) on days 7 and 14. Microscopic examination of the fungal structures was conducted using an Olympus SZ61 stereo microscope and an Olympus BX43 microscope (Olympus Corporation, Tokyo, Japan), along with BioHD-A20c color digital camera (FluoCa Scientific, China, Shanghai) for recording. All fungal strains were preserved in 15% sterilized glycerol at 4 °C, with each strain stored in three 2.0 mL tubes for future studies. Structural measurements were carried out using Digimizer software (v5.6.0), with a minimum of 25 measurements taken for each characteristic such as conidiophores, conidiogenous cells, and conidia. Specimens were deposited in the HSAUP (Herbarium of Plant Pathology, Shandong Agricultural University) and HMAS (Herbarium Mycologicum Academiae Sinicae), while living cultures were stored in the SAUCC (Shandong Agricultural University Culture Collection) for preservation and further research purposes. Taxonomic information of the new taxa was submitted to MycoBank (http://www.mycobank.org).

DNA extraction, amplification and sequencing

Fungal DNA was extracted from fresh mycelia grown on PDA using either the CTAB method or a kit method (OGPLF-400, GeneOnBio Corporation, Changchun, China) (Guo et al. 2000; Zhang et al. 2023a). Four gene regions, LSU, ITS, RPB2, and TUB2 were amplified using the primer pairs listed in Suppl. material 1 (Vilgalys et al. 1990; White et al. 1990; Liu et al. 1999; Sung et al. 2007; Jewell et al. 2013). The amplification reaction was conducted in a 25 μL reaction volume, consisting of 12.5 μL 2 × Hieff Canace® Plus PCR Master Mix (Shanghai, China) (with dye) (Yeasen Biotechnology, Cat No. 10154ES03), 0.5 μL each of forward and reverse primer, and 0.5 μL template genomic DNA, with the volume adjusted to 25 μL using distilled deionized water. PCR products were separated and purified using 1% agarose gel and GelRed (TsingKe, Qingdao, China), and UV light was used to visualize the fragments. Gel extraction was performed using a Gel Extraction Kit (Cat: AE0101-C) (Shandong Sparkjade Biotechnology Co., Ltd., Jinan, China). The purified PCR products were subjected to bidirectional sequencing by Biosune Company Limited (Shanghai, China). The raw data (trace data) were analyzed using MEGA v. 7.0 to obtain consistent sequences (Kumar et al. 2016). All sequences generated in this study were deposited in GenBank under the accession numbers provided in Table 1. The abbreviations of the genera names used in our study are as follows: I. = Idriela; S. = Selenodriella; Ma. = Macroidriella; Mi. = Microdochium.

Table 1.
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GenBank accession number of the taxa used in phylogenetic reconstruction.

Species Strain no. GenBank accession number References
ITS LSU RPB2 TUB2
Cryptostroma corticale CBS 218.52 HG934112 MH868531 HG934118 HG934104 Vu et al. (2019)
Idriela lunata CBS 204.56* KP859044 KP858981 – – Hernández‐Restrepo et al. (2016)
CBS 177.57 KP859043 KP858980 – –
I. chlamydospora CGMCC 3.20778* OL897016 OL897058 – ON569069 Zhang et al. (2023b)
GZUIFR 21.922 OL897017 OL897059 – ON569070
I. multiformispora CGMCC 3.20779* OL897018 OL897060 ON568988 ON569071
GZUIFR 21.924 OL897019 OL897061 ON568989 ON569072
GZUIFR 21.925 OL897020 OL897062 ON568990 ON569073
Macroidriella bambusae SAUCC 6792-1* PP716851 PP716512 PP729053 PP729058 This study
SAUCC 6792-2 PP716852 PP716513 PP729054 PP729059
SAUCC 6792-5 PP716853 PP716514 PP729055 PP729060
SAUCC 6113-1 PP716854 PP716515 PP729056 PP729061
SAUCC 6113-3 PP716855 PP716516 PP729057 PP729062
Microdochium albescens CBS 243.83 KP858994 KP858930 KP859103 KP859057 Hernández‐Restrepo et al. (2016)
CBS 291.79 KP858996 KP858932 KP859105 KP859059
Mi. australe SAUCC 6322-5-1* PP695312 PP702043 PP716780 PP716787 This study
SAUCC 6151-1 PP695313 PP702044 PP716779 PP716788
Mi. bambusae SAUCC 1862-1* OR702567 OR702576 OR715785 PP445175 Zhang et al. (2023a)
SAUCC 1866-1 OR702568 OR702577 OR715786 PP445176
Mi. bolleyi CBS 540.92 KP859010 KP858946 KP859119 KP859073 Hernández‐Restrepo et al. (2016)
CPC 25994 KP859018 KP858954 KP859127 KP859074
Mi. chrysanthemoides CGMCC 3.17929* KU746690 KU746736 – KU746781 Zhang et al. (2017)
Mi. chrysopogonis GDMCC 3.683 MT988022 MT988024 MW002442 MW002441 Lu et al. (2023)
LNU-196 MT988020 MT988023 MW002445 MW002442
Mi. chuxiongense YFCC 8794* OK586161 OK586160 OK584019 OK556901 Tang et al. (2022)
Mi. citrinidiscum CBS 109067* KP859003 KP858939 KP859112 KP859066 Hernández‐Restrepo et al. (2016)
Mi. colombiense CBS 624.94* KP858999 KP858935 KP859108 KP859062
Mi. dawsoniorum BRIP 65649* MK966337 – – – Crous et al. (2020)
Mi. fisheri CBS 242.90* KP859015 KP858951 KP859124 KP859078 Hernández‐Restrepo et al. (2016)
Mi. graminearum CGMCC 3.23525* OP103966 OP104016 OP236027 – Gao et al. (2022)
CGMCC 3.23524 OP103965 OP104015 OP236026 –
Mi. hainanense SAUCC 210782 OM956296 OM959324 OM981154 OM981147 Liu et al. (2022)
SAUCC 210781* OM956295 OM959323 OM981153 OM981146
Mi. indocalami SAUCC 1016* MT199884 MT199878 MT510550 MT435653 Huang et al. (2020)
Mi. insulare BRIP 75114a OQ917075 OQ892168 OQ889560 -
Mi. lycopodinum CBS 146.68 KP858993 KP858929 KP859102 KP859056 Hernández-Restrepo et al. (2016)
CBS 122885* KP859016 KP858952 KP859125 KP859080
Mi. maculosum COAD 3358* Ok966954 Ok966953 OL310501 – Crous et al. (2021)
Mi. majus CBS 741.79 KP859001 KP858937 KP859110 KP859064 Hernández-Restrepo et al. (2016)
Mi. miscanthi SAUCC 211092* OM956214 OM957532 OM981148 OM981141 Liu et al. (2022)
SAUCC 211093 OM956215 OM957533 OM981149 OM981142
Mi. musae CBS 143499 MH107894 MH107941 – – Crous et al. (2018)
CBS 143500* MH107895 MH107942 MH108003 –
Mi. nannuoshanense SAUCC 2450-1* OR702569 OR702578 OR715787 PP445177 Zhang et al. (2023a)
SAUCC 2450-3 OR702570 OR702579 OR715788 PP445178
Mi. neoqueenslandicum CBS 445.95 KP858997 KP858933 KP859106 KP859060 Hernández-Restrepo et al. (2016)
CBS 108926* KP859002 KP858938 KP859111 KP859065
Mi. nivale CBS 116205* KP859008 KP858944 KP859117 KP859071
Mi. nivale var. majus CBS 177.29 MH855031 MH866500 – – Vu et al. (2019)
Mi. nivale var. nivales CBS 288.50 – MH868135 – –
Mi. novae-zelandiae CPC 29376* LT990655 – LT990641 LT990608 Marin-Felix et al. (2019)
CPC 29693 LT990656 – LT990642 LT990609
Mi. paspali HK-ML-1371 KJ569509 – – KJ569514 Zhang et al. (2015)
CBS 138620* KJ569513 – – KJ569518
Mi. phyllosaprophyticum SAUCC 3583-1* OR702571 OR702580 OR715789 PP445179 Zhang et al. (2023a)
SAUCC 3583-6 OR702572 OR702581 OR715790 PP445180
Mi. phragmitis CBS 285.71* KP859013 KP858949 KP859122 KP859077 Hernández-Restrepo et al. (2016)
CBS 423.78 KP859012 KP858948 KP859121 KP859076
Mi. poae CGMCC 3.19170* MH740898 – MH740906 MH740914 Liang et al. (2019)
LC 12115 MH740901 – MH740909 MH740917
LC 12116 MH740902 – MH740910 MH740918
Mi. ratticaudae BRIP 68298* MW481661 MW481666 MW626890 – Crous et al. (2021)
Mi. rhopalostylidis CBS 145125* MK442592 MK442532 MK442667 – Crous et al. (2019)
Mi. salmonicolor NC14-294 MK836110 MK836108 – – Das et al. (2020)
Mi. seminicola CBS 139951* KP859038 KP858974 KP859147 KP859101 Hernández-Restrepo et al. (2016)
CPC 26001 KP859025 KP858961 KP859134 KP859088
DAOM 250161 KP859034 KP858970 KP859143 KP859097
Mi. shilinense CGMCC 3.23531* OP103972 OP104022 – OP242834 Gao et al. (2022)
Mi. sinense SAUCC 211097* OM956289 OM959225 OM981151 OM981144 Liu et al. (2022)
SAUCC 211098 OM956290 OM959226 OM981152 OM981145
SAUCC 3922-1 PP695314 PP702045 PP716781 PP716789 This study
SAUCC 3922-3 PP695315 PP702046 PP716782 PP716790
Mi. sorghi CBS 691.96 KP859000 KP858936 KP859109 KP859063 Hernández-Restrepo et al. (2016)
Mi. tainanense CBS 269.76* KP859009 KP858945 KP859118 KP859072
CBS 270.76 KP858995 KP858931 KP859104 KP859058
Mi. trichocladiopsis CBS 623.77* KP858998 KP858934 KP859107 KP859061
Mi. yunnanense SAUCC 1011* MT199881 MT199875 MT510547 MT435650 Huang et al. (2020)
SAUCC 1012 MT199882 MT199876 MT510548 MT435651
Selenodriella cubensis CBS 683.96 KP859053 KP858990 – – Hernández-Restrepo et al. (2016)
S. fertilis CBS 772.83 KP859055 KP858992 – – Hernández-Restrepo et al. (2016)

Notes: Ex-type or ex-epitype strains are marked with “*” and the new species described in this study was marked in bold.

Library construction, quality control and whole-genome sequencing

Library construction and sequencing were carried out by Novogene Co., Ltd. (Beijing, China). Obtain FASTQ format data, which included sequence information and corresponding sequencing quality information (Cock et al. 2010). Preprocess the raw data that were obtained from the sequencing platform using fastp (https://github.com/OpenGene/fastp) to obtain clean data for subsequent analysis (Chen et al. 2018). Clean data were deposited in the National Center for Biotechnology Information (NCBI) under BioProject PRJNA1105317.

Genome assembly and annotation

Genome data were assembled using the software SPAdes v 3.12.0 (Bankevich et al. 2012). Genome annotation mainly included three aspects: a. Masking of repetitive sequences (RepeatMasker version v4.1.4; RepeatModeler v2.0.3, https://www.repeatmasker.org/); b. Annotation of non-coding RNA (RNAmmer v1.2; tRNAscan-SE v2.0); c. Annotation of gene structure (RNA-seq prediction: Trinity v2.14.0, HISAT2 v2.2.1, StringTie v2.2.0; Ab inito prediction: BRAKER2; Homology protein prediction: GeMoMa v1.9) (Grabherr et al. 2011; Pertea et al. 2015; Keilwagen et al. 2016, 2018; Bruna et al. 2021). The final genome and annotation files were integrated using EVM and PASA (Haas et al. 2008, 2011).

Phylogeny

The generated consensus sequences were subjected to Megablast searches to identify closely related sequences in the NCBI’s GenBank nucleotide database (Zhang et al. 2000). Newly generated sequences in this study were aligned with related sequences retrieved from GenBank (Table 1) using MAFFT 7 (Katoh et al. 2019; http://mafft.cbrc.jp/alignment/server/) online service with the default strategy and corrected manually used MEGA 7. For phylogenetic analyses, we operated following the methods by Zhang et al. (2023a), single and concatenated ITS rDNA, LSU, RPB2 and TUB2 sequence alignments were subjected to analysis by maximum likelihood (ML) and Bayesian Inference (BI) algorithms, respectively. ML and BI were run on the CIPRES Science Gateway portal (https://www.phylo.org/, accessed on 30 April 2023) or offline software (ML was operated in RaxML-HPC2 on XSEDE v8.2.12, and BI analysis was operated in MrBayes v3.2.7a with 64 threads on Linux). For ML analyses, the default parameters were used and 1,000 rapid bootstrap replicates were run with the GTR+G+I model of nucleotide evolution; BI analysis was performed using a fast bootstrap algorithm with an automatic stop option (Zhang et al. 2023a). The GTR+I+G model was recommended for LSU, RPB2, and TUB2, while SYM+I+G was suggested for ITS. The Markov chain Monte Carlo (MCMC) analysis of the five concatenated genes was conducted over 1,130,000 generations, yielding 22,602 trees. Following the discard of the initial 5,650 trees generated during the burn-in phase, the remaining trees were used to compute posterior probabilities in the majority rule consensus trees.

For phylogenomic analyses, the genome sequences were submitted to GenBank under the accession numbers in Table 2. The final annotated data were processed to retain the coding protein genes and the longest transcript. Extracted all coding protein genes to identify gene families and single copy orthologous genes using OrthoFinder v2.5.5 (https://github.com/davidemms/OrthoFinder), according to the method by Emms and Kelly (2015, 2019). Multiple sequence alignment was used ParaAT v1.0 (https://ngdc.cncb.ac.cn/tools/paraat) and merged into supergene using seqkit v2.7.0 (https://github.com/shenwei356/seqkit) (Zhang et al. 2012; Shen et al. 2016). Phylogenomic analysis was carried out following the methods by Stamatakis et al. (2014), using RAxML-NG v1.2.1 (https://github.com/amkozlov/raxml-ng) with the LG+G8+F model and 100 bootstrap replications. All resulted trees were plotted using FigTree v. 1.4.4 (http://tree.bio.ed.ac.uk/software/figtree) or ITOL: Interactive Tree of Life (https://itol.embl.de/, accessed on 20 October 2023) (Letunic and Bork 2021) and the layout of the trees was edited in Adobe Illustrator CC 2019.

Table 2.
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BioSample and SRA NCBI number of the taxa used in phylogenomic reconstruction in this study.

Species Strains BioSample SRA NCBI* References
Asterophora parasitica AP01 SAMN09737569 SRS3956156
Cryphonectria parasitica EP155 SAMN02744051 SRS6915724 Crouch et al. 2020
Diaporthe eres CBS 160.32 SAMN21449118 SRS10459569 Hilário et al. 2022
Macroidriella bambusae SAUCC 6792-1 SAMN41099213 SRR28834790 This study
Microdochium australe SAUCC 6322-5-1 SAMN41099214 SRR28834789 This study
Mi. bambusae SAUCC 1862-1 SAMN41099215 SRR28834788 This study
Mi. bolleyi J235TASD1 SAMN04386150 SRS1667728 David et al. 2016
Mi. nannuoshanense SAUCC 2450-1 SAMN41099216 SRR28834787 This study
Mi. nivale F00608 SAMN26062287 SRS14642463 Tsers et al. 2023
Mi. phyllosaprophyticum SAUCC 3583-1 SAMN41099217 SRR28834786 This study
Mi. trichocladiopsis MPI-CAGE-CH-0230 SAMN06297163 SRS2394902 Mesny et al. 2021
Pestalotiopsis fici W106-1 SAMN02369365 Wang et al. 2015
Xylaria flabelliformis G536 SAMN11912834 SRS4852315

Species information described in this study is marked in bold.

Results

Phylogenetic and phylogenomic analyses

A total of 80 isolates representing species within the Microdochiaceae family used for phylogenetic analysis. One strain of Cryptostroma corticale (CBS 218 52) was used as an outgroup taxon. The final alignment comprised 3,386 concatenated characters, spanning from positions 1 to 553 (ITS), 554 to 1,827 (LSU), 1,828 to 2,676 (RPB2), and 2,677 to 3,386 (TUB2). The maximum likelihood (ML) optimization likelihood was calculated to be -23041.844775. The matrix exhibited 1,071 distinct alignment patterns, with 25.57% of characters or gaps remaining undetermined. MrModelTest suggested that Dirichlet base frequencies be utilized for the ITS, LSU, RPB2, and TUB2 data partitions. The alignment exhibited a total of 876 unique site patterns (ITS: 287, LSU: 186, RPB2: 386, TUB2: 213). The topology of the ML tree corroborated that of the tree obtained from Bayesian inference; therefore, only the ML tree is depicted (Fig. 1). Based on the four-gene phylogeny (Fig. 1), the 80 strains were classified into 47 species. To enhance the visual appeal and conciseness of the phylogenetic tree, 39 strains were collapsed within it (The complete ML phylogenetic tree is available in the Suppl. material 5). Among them, five strains (SAUCC 6792-1, SAUCC 6792-2, SAUCC 6792-5, SAUCC 6113-1 and SAUCC 6113-3) identified a new genus, Macroidriella gen. nov., with solid support (98% MLBV and 1.0 BIPP), and M. bambusae sp. nov. (SAUCC 6792-1) as the type species. Two strains (SAUCC 6322-5-1 and SAUCC 6151-1) identified as Microdochium australe sp. nov.

Figure 1. 

A maximum likelihood tree was constructed using a combined dataset of ITS, LSU, RPB2, and TUB2 sequence data. Branch support values, shown as ML/BIPP, are indicated above the nodes: MLBV ≥ 70% on the left and BIPP ≥ 0.90 on the right. Ex-type cultures are denoted in bold and marked with an asterisk (*). Strains from the current study are highlighted in red. The tree was rooted with Cryptostroma corticale (CBS 218.52). The scale bar at the bottom center represents 0.05 substitutions per site.

We sequenced the genomes of six species in Microdochiaceae for phylogenomic analyses, and downloaded the published genomes of four species from in NCBI Datasets (https://www.ncbi.nlm.nih.gov/datasets/). Xylaria flabelliformis G536 was used as an outgroup taxon. Based on 4,909 clusters of orthologous proteins, the ML tree is depicted (Fig. 2). The phylogenomic tree was divided into two clades (excepted outgroup), viz, clade 1 (Microdochium nannuoshanense SAUCC 2450-1, Mi. phyllosaprophyticum SAUCC 3583-1, Mi. australe SAUCC 6322-5-1 and Mi. bambusae SAUCC 1862-1) and clade 2 (Mi. nivale F00608, Mi. bolleyi J235TASD1, Mi. trichocladiopsis MPI-CAGE-CH-0230 and Macroidriella bambusae SAUCC 6792-1). The branch length of all four strains was < 0.1 in clade 1, indicating that their evolutionary distance was relatively close compared to clade 2 (each strain’s branch was > 0.1). Due to limited genomic data, Macroidriella bambusae (SAUCC 6792-1) was not individually clustered, but the evolutionary distance of Macroidriella bambusae is relatively far compared to other species.

Figure 2. 

A Maximum Likelihood phylogenomic tree was constructed using a combined 4,909 clusters of orthologous proteins. Maximum Likelihood bootstrap values (≥ 70%) are indicated along branches. Genera are highlighted in different colors. The scale bar at the bottom represents 0.1 substitutions per site.

Annotations and comparative analysis

After structural annotation of the genomic data, we conducted a statistical summary, including, number of genes, total number of cds, total number of exons, total number of introns, total cds length, total exon length and total intron length (Suppl. material 2). Due to the limited genomic data available for Microdochiaceae, we will conduct gene family analysis by comparing the self-tested data of the new genus (Macroidriella) with genomic data from the orders of Diaporthales (Cryphonectria parasitica EP155 and Diaporthe eres CBS 160.32), Xylariales (Pestalotiopsis fici W106-1 and Xylaria flabelliformis G536), and the Basidiomycota (Asterophora parasitica AP01). The intersections of gene family among the six representative strains (≤ 6) are 3431, the maximum number (508) of gene family intersections between Macroidriella bambusae and Microdochium trichocladiopsis, and the minimum number (4) of gene family intersections between Macroidriella bambusae and Asterophora parasitica (Fig. 3a). The intersections of gene family among the seven representative strains are 3,291, the unique number of genes in Asterophora parasitica was 513 (maximum), the unique number of genes in Macroidriella bambusae was 42 (minimum) (Fig. 3b). We have presented the number of single-copy genes, multi-copy genes and so on for the seven representative strains (Fig. 3c).

Figure 3. 

Gene family analysis of Macroidriella a UpSet plot of six strains, showing the intersection counts between different strains in the form of a bar graph b petal plot of seven strains, the center of the petal represents the number of shared genes c bar chart of homologous genes for each strain.

Taxonomy

Macroidriella Z.X. Zhang, J. W. Xia & X.G. Zhang, gen. nov.

MycoBank No: 853699

Type species

Macroidriella bambusae Z. X. Zhang, J. W. Xia & X. G. Zhang.

Etymology

Referring to the composed of “Macro-” and “-idriella” (Similar in morphology to Idriella and bigger than Idriella in conidia).

Description

Genus of Microdochiaceae. Endogenic on diseased leaves of Bambusaceae sp. Sporodochia yellowish brown, slimy. Conidiophores are indistinct and often reduced to conidiogenous cells. Conidiogenous cells are straight or slightly branched, smooth, curved, mono- or polyblastic, terminal, hyaline, septate, cylindrical and ampulliform. Conidia are solitary, hyaline, lunate, curved, mooned, multi-guttulate, apex rounded, base usually flattened. Sexual morphs were not observed, chlamydospores were not observed.

Notes

In the phylogenetic tree (Fig. 1), Macroidriella is allied to Idriella, Microdochium and Selenodriella, but forms a separate lineage with good statistical support (98% MLBV and 1.0 BIPP). In morphology, the conidia of Macroidriella are predominantly lunate and curved, unlike the elliptical conidia of Microdocium, suggesting a genus of its own, because it is similar to Idriella in morphology (but the conidia of Macroidriella are longer than Idriella), both being lunate conidia, it is named Macroidriella gen. nov.

Macroidriella bambusae Z.X. Zhang & X.G. Zhang, sp. nov.

MycoBank No: 853712
Fig. 4

Type

China, Hainan Province, Danzhou City: Hainan tropical botanical garden, on diseased leaves of Bambusaceae sp., 15 October 2023, Z. X. Zhang (HMAS 352974, holotype), ex-holotype living culture SAUCC 6792-1.

Figure 4. 

Macroidriella bambusae (HMAS 352974, holotype) a a leaf of Bambusaceae sp. b, c colonies on PDA from above and below after 14 days d colony overview e, f conidiogenous cells and conidia g, h conidia. Scale bars: 10 μm (e–h).

Etymology

Referring to the species name of the host plant Bambusaceae sp.

Description

Endogenic on diseased leaves of Bambusaceae sp. Mycelia are superficial and immersed, 2–3.5 µm wide, branched, membranous and hyaline. Sporodochia yellowish brown, slimy. Conidiophores are indistinct and often reduced to conidiogenous cells. Conidiogenous cells are straight or slightly curved, 10.4–15 × 1.7–2.8 µm, mono- or polyblastic, terminal, hyaline, septate, cylindrical and smooth. Conidia are solitary, hyaline, lunate, curved, mooned, 16.5–21.7 × 2–2.8 µm, multi-guttulate, apex rounded, base usually flattened. Sexual morphs were not observed, chlamydospores were not observed, see Fig. 4.

Culture characteristics

Cultures incubated on PDA at 25 °C in darkness, reaching 63–70 mm diam., had a growth rate of 4.5–5.0 mm/day after 14 days, with moderate aerial mycelia, the center and edges are milky white, with a yellow-brown color in the middle, and sporodochia are observed.

Additional material studied

China, Hainan Province, Danzhou City, Hainan tropical botanical garden, on diseased leaves of Bambusaceae sp., 15 October 2023, Z. X. Zhang (HSAUP 6792-2), living culture SAUCC 6792-2; ibid, (HSAUP 6792-5), living culture SAUCC 6792-5; on dead leaves, 15 October 2023, Z. X. Zhang (HSAUP 6113-1), living culture SAUCC 6113-1; ibid., (HSAUP 6113-3), living culture SAUCC 6113-3.

Notes

Phylogenetic analyses showed that Macroidriella bambusae formed an independent clade (Fig. 1), and closely related to Idriella multiformispora (lunate, curved-shaped conidia) and Microdochium bolleyi. The Ma. bambusae was distinguished from I. multiformispora (CGMCC 3.20779) by 60/520, 22/1222, 74/848 and 57/710 base-pair differences, from Mi. bolleyi (CBS 540.92) by 40/514, 19/765, 138/850 and 51/710 base pairs in ITS, LSU, RPB2 and TUB2 sequences, respectively. Morphologically, Ma. bambusae (16.5–21.7 × 2–2.8 µm) longer than I. multiformispora (8.5–13.5 × 1.0–2 µm) and Mi. bolleyi (5–8.7 × 1.6–2.3 µm) in conidia. Therefore, we describe this fungus as a novel species.

Microdochium australe Z.X. Zhang, & X.G. Zhang, sp. nov.

MycoBank No: 853695
Fig. 5

Type

China, Hainan Province, Jianfengling National Forest Park, on diseased leaves of Phragmites australis, 13 October 2023, Z. X. Zhang (HMAS 352973, holotype), ex-holotype culture SAUCC 6322-5-1.

Etymology

Referring to the species name of the host plant Phragmites australis.

Description

Endogenic on diseased leaves of Phragmites australis. Mycelia are superficial and immersed, 3–3.3 µm wide, branched, membranous and hyaline. Sporodochia black, aggregative or solitary. Conidiophores are indistinct and often reduced to conidiogenous cells. Conidiogenous cells are straight or slightly curved, 15.4–23.5 × 2.8–4 µm, terminal, hyaline, septate, ampulliform or obpyriform, smooth. Conidia are solitary, hyaline, straight to slight curved, oblong to ellipsoid, 11.3–16.1 × 2.5–3.7 µm, multi-guttulate, (2)3-septate, apex rounded, base usually flattened. Sexual morphs were not observed, chlamydospores were not observed, see Fig. 5.

Figure 5. 

Microdochium australe (HMAS 352973, holotype) a a leaf of Phragmites australis b, c colonies on PDA from above and below after 14 days d colony overview e, f conidiogenous cells and conidia g, h conidia. Scale bars: 10 μm (e–h).

Culture characteristics

Cultures incubated on PDA at 25 °C in darkness, reaching 73–76 mm diam., had a growth rate of 5.2–5.4 mm/day after 14 days, with moderate aerial mycelia, milky white to grey‐white, with regular margin, and sporodochia are observed, reverses black to brown in the centre, with grey‐white and regular margin.

Additional material studied

China, Hainan Province, Jianfengling National Forest Park, on saprophytic leaves, 13 October 2023, Z. X. Zhang (HSAUP 6151-1), living culture SAUCC 6151-1.

Notes

Phylogenetic analyses showed that Microdochium australe sp. nov. formed an independent clade closely related to Microdochium bambusae and Microdochium indocalami (Fig. 1). Mi. australe was distinguished from Mi. bambusae (SAUCC 1862-1) by 47/503, 2/836, 56/848 and 17/710 base pair differences, from Mi. bambusae and Mi. indocalami (SAUCC 1016) by 52/503, 2/848, 44/840 and 17/708 base pairs in ITS, LSU, RPB2 and TUB2 sequences, respectively. Morphologically, Mi. australe (11.3–16.1 × 2.5–3.7 µm, (2)3-septate) differs from Mi. bambusae (13.0–17 × 2.5–3.5 μm, aseptate) and Mi. indocalami in conidia (13–15.5 × 3.5–5.5 μm, 3-septate), and, therefore, we described this fungus as a novel species.

Microdochium sinense S.B. Liu, X.Y. Liu, Z. Meng & X.G. Zhang, J. Fungi 2022, 8, 577.

Fig. 6

Material examined

China, Hainan Province, Jianfengling National Forest Park, on diseased leaves of Phragmites australis, 12 April 2023, Z. X. Zhang (HSAUP 3922-1), living culture SAUCC 3922-1; ibid., (HSAUP 3922-3), living culture SAUCC 3922-3.

Description

Endogenic on diseased leaves of Phragmites australis. Mycelia are superficial and immersed, 2.1–2.9 µm wide, branched, membranous and hyaline. Conidia are solitary, hyaline, straight, oblong to ellipsoid, 12.3–15 × 3.5–5.6 µm, multi-guttulate, apex rounded, base usually flattened. Conidiophores were not observed, chlamydospores were not observed, sexual morphs were not observed, see Fig. 6.

Figure 6. 

Microdochium sinense a diseased symptoms on a leaf of Phragmites australis b, c colonies on PDA from above and below after 14 days d conidiomata on PDA e, f conidia. Scale bars: 10 μm (e–f).

Culture characteristics

Cultures incubated on PDA at 25 °C in darkness, reach-ing 72–76 mm diam., had a growth rate of 5.1–5.4 mm/day after 14 days, with moder-ate aerial mycelia, milky white to grey‐white, with irregular margin, reverses light brown in the centre, with grey‐white and regular margin.

Notes

Phylogenetic analyses of four combined genes (ITS, LSU, RPB2 and TUB2) showed that SAUCC 3922-1 and SAUCC 3922-3 clustered with the type collection of Microdochium sinense with strong support (Fig. 1). We, therefore, identified the isolated strains (SAUCC 3922-1 and SAUCC 3922-3) as Mi. sinense. Morphologically, the conidia of the both (newly isolated and type) were similar (12.3–15 × 3.5–5.6 vs. 11.5–19.34 × 2.8–5.4 µm).

Discussion

The establishment of the family Microdochiaceae by Hernández‐Restrepo et al. (2016) to encompass the clade consisting of Idriella, Microdochium, and Selenodriella within the Xylariales highlights the importance of phylogenetic analysis in understanding the evolutionary relationships among fungi. This new classification helps to better organize and categorize fungal species based on their genetic relatedness and morphological characteristics (Hernández‐Restrepo et al. 2016; Liang et al. 2019; Huang et al. 2020; Liu et al. 2022; Lu et al. 2023; Zhang et al. 2023a). In the recent study, nine strains isolated from two host plants, Phragmites australis and Bambusaceae sp., were introduced into a new genus, Macroidriella and two new species, Macroidriella bambusae and Microdochium australe. The Global Biodiversity Information Facility (GBIF) currently hosts 1,594 georeferenced records of Microdochiaceae species worldwide (https://www.gbif.org/, accessed on April 30, 2024). The distribution of this family is predominantly in the United States, Europe, and Oceania, with fewer occurrences in Asia.

In the recent study of the family, Microdochium emerged as a prominent research focus, with 12 species of this genus documented across five Provinces (Guizhou, Hainan, Henan, Shandong, and Yunnan) since the beginning of the 21st century in China (Zhang et al. 2015; Liang et al. 2019; Huang et al. 2020; Gao et al. 2022; Liu et al. 2022; Tang et al. 2022). Microdochium species have been identified on a variety of host families (10 families), with over half of the fungi associated with Poaceae plants. In contrast, Idriella and Selenodriella have been less extensively studied, with Idriella having only two reported species since the turn of the 21st century. Through the joint analysis of multiple gene fragments and genomes, the position of new taxa can be better determined, especially through phylogenomic analyses, which was provided with more robust support values. Comparative analysis will help us determine the position of the Macroidriella genus on the evolutionary tree and its relationship with other fungi. By comparing the genomic data of different fungi, we can identify common gene families and infer their evolutionary relationships. Through comparative genomic analysis, it can be observed that Macroidriella has 42 unique single-copy orthologous genes. Asterophora shares only 4 single-copy orthologous genes with Macroidriella, which also indicates that their relationship is very distant (belonging to different fungal phyla).

This study represents a pioneering effort in Microdochiaceae as it integrates multi-gene fragments with genomic data to unveil the phylogenetic relationships within the family. By combining these diverse datasets, a comprehensive understanding of the evolutionary history of Microdochiaceae is achieved, shedding new light on its genetic landscape and evolutionary dynamics.

Acknowledgements

We would like to express our gratitude to Jie Zhang, a master’s student at Shandong Agricultural University, for her assistance in this study.

Additional information

Conflict of interest

The authors have declared that no competing interests exist.

Ethical statement

No ethical statement was reported.

Funding

This research was supported by National Natural Science Foundation of China (nos. 32100016, 32270024, U2002203 and 32370001).

Author contributions

Sampling, molecular biology analysis: Zhao-Xue Zhang and Yu-Xin Shang; fungal isolation: Yu-Xin Shang and Jin-Jia Zhang; description and phylogenetic analysis: Meng-Yuan Zhang; microscopy: Yun Geng; writing—original draft preparation: Zhao-Xue Zhang; writing—review and editing, Ji-Wen Xia and Xiu-Guo Zhang. All authors read and approved the final manuscript.

Author ORCIDs

Zhao-Xue Zhang https://orcid.org/0000-0002-4824-9716

Ji-Wen Xia https://orcid.org/0000-0002-7436-7249

Data availability

All of the data that support the findings of this study are available in the main text or Supplementary Information.

References

  • Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA (2012) SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. Journal of Computational Biology 19(5): 455–477. https://doi.org/10.1089/cmb.2012.0021
  • Bruna T, Hoff KJ, Stanke M, Lomsadze A, Borodovsky M (2021) BRAKER2: Automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database. NAR Genomics and Bioinformatics 3(1): lqaa108. https://doi.org/10.1093/nargab/lqaa108
  • Cock PJA, Fields CJ, Goto N, Heuer ML, Rice PM (2010) The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Research 38(6): 1767–1771. https://doi.org/10.1093/nar/gkp1137
  • Crouch JA, Dawe A, Aerts A, Barry K, Churchill ACL, Grimwood J, Hillman BI, Milgroom MG, Pangilinan J, Smith M, Salamov A, Schmutz J, Yadav JS, Grigoriev IV, Nuss DL (2020) Genome Sequence of the Chestnut Blight Fungus Cryphonectria parasitica EP155: A Fundamental Resource for an Archetypical Invasive Plant Pathogen. Phytopathology 110(6): 1180–1188. https://doi.org/10.1094/PHYTO-12-19-0478-A
  • Crous PW, Schumacher RK, Wingfield MJ, Akulov A, Denman S, Roux J, Braun U, Burgess TI, Carnegie AJ, Váczy KZ, Guatimosim E, Schwartsburd PB, Barreto RW, Hernández-Restrepo M, Lombard L, Groenewald JZ (2018) New and interesting fungi 1. Fungal Systematics and Evolution 1(1): 169–215. https://doi.org/10.3114/fuse.2018.01.08
  • Crous PW, Schumacher RK, Akulov A, Thangavel R, Hernández-Restrepo M, Carnegie AJ, Cheewangkoon R, Wingfield MJ, Summerell BA, Quaedvlieg W, Coutinho TA, Roux J, Wood AR, Giraldo A, Groenewald JZ (2019) New and interesting fungi 2. Fungal Systematics and Evolution 3(1): 57–134. https://doi.org/10.3114/fuse.2019.03.06
  • Crous PW, Wingfield MJ, Chooi YH, Gilchrist CLM, Lacey E, Pitt JI, Roets F, Swart WJ, Cano-Lira JF, Valenzuela-Lopez N, Hubka V, Shivas RG, Stchigel AM, Holdom DG, Jurjević Ž, Kachalkin AV, Lebel T, Lock C, Martín MP, Tan YP, Tomashevskaya MA, Vitelli JS, Baseia IG, Bhatt VK, Brandrud TE, De Souza JT, Dima B, Lacey HJ, Lombard L, Johnston PR, Morte A, Papp V, Rodríguez A, Rodríguez-Andrade E, Semwal KC, Tegart L, Abad ZG, Akulov A, Alvarado P, Alves A, Andrade JP, Arenas F, Asenjo C, Ballarà J, Barrett MD, Berná LM, Berraf-Tebbal A, Bianchinotti MV, Bransgrove K, Burgess TI, Carmo FS, Chávez R, Čmoková A, Dearnaley JDW, Santiago ALCMA, Freitas-Neto JF, Denman S, Douglas B, Dovana F, Eichmeier A, Esteve-Raventós F, Farid A, Fedosova AG, Ferisin G, Ferreira RJ, Ferrer A, Figueiredo CN, Figueiredo YF, Reinoso-Fuentealba CG, Garrido-Benavent I, Cañete-Gibas CF, Gil-Durán C, Glushakova AM, Gonçalves MFM, González M, Gorczak M, Gorton C, Guard FE, Guarnizo AL, Guarro J, Gutiérrez M, Hamal P, Hien LT, Hocking AD, Houbraken J, Hunter GC, Inácio CA, Jourdan M, Kapitonov VI, Kelly L, Khanh TN, Kisło K, Kiss L, Kiyashko A, Kolařík M, Kruse J, Kubátová A, Kučera V, Kučerová I, Kušan I, Lee HB, Levicán G, Lewis A, Liem NV, Liimatainen K, Lim HJ, Lyons MN, Maciá-Vicente JG, Magaña-Dueñas V, Mahiques R, Malysheva EF, Marbach PAS, Marinho P, Matočec N, McTaggart AR, Mešić A, Morin L, Muñoz-Mohedano JM, Navarro-Ródenas A, Nicolli CP, Oliveira RL, Otsing E, Ovrebo CL, Pankratov TA, Paños A, Paz-Conde A, Pérez-Sierra A, Phosri C, Pintos Á, Pošta A, Prencipe S, Rubio E, Saitta A, Sales LS, Sanhueza L, Shuttleworth LA, Smith J, Smith ME, Spadaro D, Spetik M, Sochor M, Sochorová Z, Sousa JO, Suwannasai N, Tedersoo L, Thanh HM, Thao LD, Tkalčec Z, Vaghefi N, Venzhik AS, Verbeken A, Vizzini A, Voyron S, Wainhouse M, Whalley AJS, Wrzosek M, Zapata M, Zeil-Rolfe I, Groenewald JZ (2020) Fungal Planet description sheets: 1042–1111. Persoonia 44(1): 301–459. https://doi.org/10.3767/persoonia.2020.44.11
  • Crous PW, Cowan DA, Maggs‐Kölling G, Yilmaz N, Thangavel R, Wingfield MJ, Noordeloos ME, Dima B, Brandrud TE, Jansen GM, Morozova OV, Vila J, Shivas RG, Tan YP, Bishop-Hurley S, Lacey E, Marney TS, Larsson E, Le Floch G, Lombard L, Nodet P, Hubka V, Alvarado P, Berraf-Tebbal A, Reyes JD, Delgado G, Eichmeier A, Jordal JB, Kachalkin AV, Kubátová A, Maciá-Vicente JG, Malysheva EF, Papp V, Rajeshkumar KC, Sharma A, Spetik M, Szabóová D, Tomashevskaya MA, Abad JA, Abad ZG, Alexandrova AV, Anand G, Arenas F, Ashtekar N, Balashov S, Bañares Á, Baroncelli R, Bera I, Biketova AY, Blomquist CL, Boekhout T, Boertmann D, Bulyonkova TM, Burgess TI, Carnegie AJ, Cobo-Diaz JF, Corriol G, Cunnington JH, da Cruz MO, Damm U, Davoodian N, de A Santiago ALCM, Dearnaley J, de Freitas LWS, Dhileepan K, Dimitrov R, Di Piazza S, Fatima S, Fuljer F, Galera H, Ghosh A, Giraldo A, Glushakova AM, Gorczak M, Gouliamova DE, Gramaje D, Groenewald M, Gunsch CK, Gutiérrez A, Holdom D, Houbraken J, Ismailov AB, Istel Ł, Iturriaga T, Jeppson M, Jurjević Ž, Kalinina LB, Kapitonov VI, Kautmanová I, Khalid AN, Kiran M, Kiss L, Kovács Á, Kurose D, Kušan I, Lad S, Læssøe T, Lee HB, Luangsa-Ard JJ, Lynch M, Mahamedi AE, Malysheva VF, Mateos A, Matočec N, Mešić A, Miller AN, Mongkolsamrit S, Moreno G, Morte A, Mostowfizadeh-Ghalamfarsa R, Naseer A, Navarro-Ródenas A, Nguyen TTT, Noisripoom W, Ntandu JE, Nuytinck J, Ostrý V, Pankratov TA, Pawłowska J, Pecenka J, Pham THG, Polhorský A, Pošta A, Raudabaugh DB, Reschke K, Rodríguez A, Romero M, Rooney-Latham S, Roux J, Sandoval-Denis M, Smith MT, Steinrucken TV, Svetasheva TY, Tkalčec Z, van der Linde EJ, Vegte VDM, Vauras J, Verbeken A, Visagie CM, Vitelli JS, Volobuev SV, Weill A, Wrzosek M, Zmitrovich IV, Zvyagina EA, Groenewald JZ (2021) Fungal Planet description sheets: 1182–1283. Pers. Mol. Phylogeny Evol. Fungi. 46: 313–528. https://doi.org/10.3767/persoonia.2021.46.11
  • David AS, Haridas S, LaButti K, Lim J, Lipzen A, Wang M, Barry K, Grigoriev IV, Spatafora JW, May G (2016) Draft Genome Sequence of Microdochium bolleyi, a Dark Septate Fungal Endophyte of Beach Grass. Genome Announcements 4(2): e00270–e16. https://doi.org/10.1128/genomeA.00270-16
  • Dirchwolf PM, Moschini RC, Gutiérrez SA, Carmona MA (2023) Modelling of the effects of environmental factors on rice grain discoloration incidence in Corrientes province, Argentina. Journal of Phytopathology 171(1): 12–22. https://doi.org/10.1111/jph.13150
  • Emms DM, Kelly S (2015) OrthoFinder: Solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biology 16(1): 157. https://doi.org/10.1186/s13059-015-0721-2
  • Gao Y, Ren G, Wanasinghe DN, Xu J, Gomes De Farias AR, Gui H (2022) Two New Species and a New Record of Microdochium from Grasses in Yunnan Province, South-West China. Journal of Fungi (Basel, Switzerland) 8(12): 1297. https://doi.org/10.3390/jof8121297
  • Glynn NC, Hare MC, Parry DW, Edwards SG (2005) Phylogenetic analysis of EF‐1 alpha gene sequences from isolates of Microdochium nivale leads to elevation of varieties Majus and Nivale to species status. Fungal Biology 109: 872–880. https://doi.org/10.1017/S0953756205003370
  • Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A (2011) Full-length transcriptome assembly from RNA-seq data without a reference genome. Nature Biotechnology 29(7): 644–652. https://doi.org/10.1038/nbt.1883
  • Haas BJ, Salzberg SL, Zhu W, Pertea M, Allen JE, Orvis J, White O, Buell CR, Wortman JR (2008) Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biology 9(1): R7. https://doi.org/10.1186/gb-2008-9-1-r7
  • Hernández‐Restrepo M, Groenewald JZ, Crous PW (2016) Taxonomic and phylogenetic re‐evaluation of Microdochium, Monographella and Idriella. Persoonia 36(1): 57–82. https://doi.org/10.3767/003158516X688676
  • Hilário S, Gonçalves MFM, Fidalgo C, Tacão M, Alves A (2022) Genome Analyses of Two Blueberry Pathogens: Diaportheamygdali CAA958 and Diaporthe eres CBS 160.32. Journal of Fungi (Basel, Switzerland) 8(8): 804. https://doi.org/10.3390/jof8080804
  • Hiruma K, Kobae Y, Toju H (2018) Beneficial associations between Brassicaceae plants and fungal endophytes under nutrient-limiting conditions: Evolutionary origins and host–symbiont molecular mechanisms. Current Opinion in Plant Biology 44: 145–154. https://doi.org/10.1016/j.pbi.2018.04.009
  • Hong SK, Kim WG, Choi HW, Lee SY (2008) Identification of Microdochium bolleyi associated with basal rot of creeping bent grass in Korea. Mycobiology 36(2): 77–80. https://doi.org/10.4489/MYCO.2008.36.2.077
  • Jaklitsch WM, Voglmayr H (2012) Phylogenetic relationships of five genera of Xylariales and Rosasphaeria gen. nov. (Hypocreales). Fungal Diversity 52(1): 75–98. https://doi.org/10.1007/s13225-011-0104-2
  • Jeewon R, Ittoo J, Mahadeb D, Jaufeerally-Fakim Y, Wang HK, Liu AR (2013) DNA based identification and phylogenetic characterisation of endophytic and saprobic fungi from Antidesma madagascariense, a medicinal plant in Mauritius. Journal of Mycology 781914: 10. https://doi.org/10.1155/2013/781914
  • Katoh K, Rozewicki J, Yamada KD (2019) MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Briefings in Bioinformatics 20: 1160–1166. https://doi.org/10.1093/bib/bbx108
  • Keilwagen J, Wenk M, Erickson JL, Schattat MH, Grau J, Hartung F (2016) Using intron position conservation for homology-based gene prediction. Nucleic Acids Research 44(9): e89. https://doi.org/10.1093/nar/gkw092
  • Keilwagen J, Hartung F, Paulini M, Twardziok SO, Grau J (2018) Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi. BMC Bioinformatics 19(1): 189. https://doi.org/10.1186/s12859-018-2203-5
  • Kumar S, Stecher G, Tamura K (2016) MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Molecular Biology and Evolution 33(7): 1870–1874. https://doi.org/10.1093/molbev/msw054
  • Letunic I, Bork P (2021) Interactive Tree of Life (iTOL) v5: An online tool for phylogenetic tree display and annotation. Nucleic Acids Research 49(W1): 293–296. https://doi.org/10.1093/nar/gkab301
  • Liu SB, Liu XY, Zhang ZX, Xia JW, Zhang XG, Meng Z (2022) Three new species of Microdochium (Sordariomycetes, Amphisphaeriales) on Miscanthus sinensis and Phragmites australis from Hainan, China. Journal of Fungi (Basel, Switzerland) 8(6): 577. https://doi.org/10.3390/jof8060577
  • Lu X, Mai M, Tan W, Zhang M, Xie J, Lu Y, Niu XL, Zhang W (2023) Identification and fungicide sensitivity of Microdochium chrysopogonis (Ascomycota, Amphisphaeriaceae), a new species causing tar spot of Chrysopogon zizanioides in southern China. MycoKeys 100: 205–232. https://doi.org/10.3897/mycokeys.100.112128
  • Marin-Felix Y, Hernández-Restrepo M, Wingfield MJ, Akulov A, Carnegie AJ, Cheewangkoon R, Gramaje D, Groe-newald JZ, Guarnaccia V, Halleen F, Lombard L, Luangsa-ard J, Marincowitz S, Moslemi A, Mostert L, Quaedvlieg W, Schumacher RK, Spies CFJ, Thangavel R, Taylor PWJ, Wilson AM, Wingfield BD, Wood AR, Crous PW (2019) Genera of phytopathogenic fungi: GOPHY 2. Studies in Mycology 92(1): 47–133. https://doi.org/10.1016/j.simyco.2018.04.002
  • Mesny F, Miyauchi S, Thiergart T, Pickel B, Atanasova L, Karlsson M, Hüttel B, Barry KW, Haridas S, Chen C, Bauer D, Andreopoulos W, Pangilinan J, LaButti K, Riley R, Lipzen A, Clum A, Drula E, Henrissat B, Kohler A, Grigoriev IV, Martin FM, Hacquard S (2021) Genetic determinants of endophytism in the Arabidopsis root mycobiome. Nature Communications 12(1): 7227. https://doi.org/10.1038/s41467-021-27479-y
  • Parkinson VO, Sivanesan A, Booth C (1981) The perfect state of the rice leaf-scald fungus and the taxonomy of both the perfect and imperfect states. Transactions of the British Mycological Society 76(1): 59–69. https://doi.org/10.1016/S0007-1536(81)80009-5
  • Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL (2015) StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nature Biotechnology 33(3): 290–295. https://doi.org/10.1038/nbt.3122
  • Samuels GJ, Hallett IC (1983) Microdochium stoveri and Monographella stoveri, new combinations for Fusarium stoveri and Micronectriella stoveri. Transactions of the British Mycological Society 81(3): 473–483. https://doi.org/10.1016/S0007-1536(83)80115-6
  • Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, André Levesque C, Chen W et al. (2012) Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proceedings of the National Academy of Sciences of the United States of America 109(16): 6241–6246. https://doi.org/10.1073/pnas.1117018109
  • Senanayake IC, Rathnayaka AR, Marasinghe DS, Calabon MS, Gentekaki E, Lee HB, Hurdeal VG, Pem D, Dissanayake LS, Wijesinghe SN, Bundhun D, Nguyen TT, Goonasekara ID, Abeywickrama PD, Bhunjun CS, Jayawardena RS, Wanasinghe DN, Jeewon R, Bhat DJ, Xiang MM (2020) Morphological approaches in studying fungi: Collection, examination, isolation, sporulation and preservation. Mycosphere 11(1): 2678–2754. https://doi.org/10.5943/mycosphere/11/1/20
  • Stewart S, Rodríguez M, Mattos N, Abreo E, Stewart S, Rodríguez M, Mattos N, Abreo E (2019) First report of zonate leaf spot in sorghum caused by Microdochium sorghi in Uruguay. Agrociencia (Montevideo) 23(2): 94–98. https://doi.org/10.31285/AGRO.23.74
  • Sung GH, Sung JM, Hywel-Jones NL, Spatafora JW (2007) A multi-gene phylogeny of Clavicipitaceae (Ascomycota, Fungi): identification of localized incongruence using a combinational bootstrap approach. Molecular Phylogenetics and Evolution 44(3): 1204–1223. https://doi.org/10.1016/J.YMPEV.2007.03.011
  • Sydow H (1924) Mycotheca germanic. Fasc. XLII–XLV (No. 2051–2250). Annls Mycol 22: 257–268.
  • Tang D, Zou W, Wang Y, Huang OU, Yu H (2022) Morphology and phylogeny of Microdochium chuxiongense sp. nov., a fungus from Southwest China. Phytotaxa 555(2): 147–158. https://doi.org/10.11646/phytotaxa.555.2.3
  • Tsers I, Marenina E, Meshcherov A, Petrova O, Gogoleva O, Tkachenko A, Gogoleva N, Gogolev Y, Potapenko E, Muraeva O, Ponomareva M, Korzun V, Gorshkov V (2023) First genome-scale insights into the virulence of the snow mold causal fungus Microdochium nivale. IMA Fungus 14(1): 2. https://doi.org/10.1186/s43008-022-00107-0
  • Von Arx JA (1987) Plant pathogenic fungi. Nova Hedwigia 87: 1–288.
  • Vu D, Groenewald M, De VM, Gehrmann T, Stielow B, Eberhardt U, Al-Hatmi A, Groenewald JZ, Cardinali G, Houbraken J, Boekhout T, Crous PW, Robert V, Verkley GJM (2019) Large-scale generation and analysis of filamentous fungal DNA barcodes boosts coverage for kingdom fungi and reveals thresholds for fungal species and higher taxon delimitation. Studies in Mycology 2019(92): 135–154. https://doi.org/10.1016/j.simyco.2018.05.001
  • Wang X, Zhang X, Liu L, Xiang M, Wang W, Sun X, Che Y, Guo L, Liu G, Guo L, Wang C, Yin WB, Stadler M, Zhang X, Liu X (2015) Genomic and transcriptomic analysis of the endophytic fungus Pestalotiopsis fici reveals its lifestyle and high potential for synthesis of natural products. BMC Genomics 16(1): 28. https://doi.org/10.1186/s12864-014-1190-9
  • White T, Burns T, Lee S, Taylor J (1990) Amplification and direct sequencing of ribosomal RNA genes for phylogenetics. In: Innis MA (Ed.) PCR Protocols: A Guide to Methods and Applications. Academic Press, New York, 315–322. https://doi.org/10.1016/B978-0-12-372180-8.50042-1
  • Zhang Z, Xiao JF, Wu JY, Zhang HY, Liu GM, Wang XM, Dai L (2012) ParaAT: A parallel tool for constructing multiple protein-coding DNA alignments. Biochemical and Biophysical Research Communications 419(4): 779–781. https://doi.org/10.1016/j.bbrc.2012.02.101
  • Zhang W, Nan ZB, Tian P, Hu MJ, Gao ZY, Li M, Liu GD (2015) Microdochium paspali, a new species causing seashore paspalum disease in southern China. Mycologia 107(1): 80–89. https://doi.org/10.3852/14-119
  • Zhang J, Zhang ZX, Li DH, Xia JW, Li Z (2023a) Three New Species of Microdochium (Microdochiaceae, Xylariales) on Bambusaceae sp. and Saprophytic Leaves from Hainan and Yunnan, China. Journal of Fungi 9(12): 1176. https://doi.org/10.3390/jof9121176
  • Zhang ZY, Li X, Chen WH, Liang JD, Han YF (2023b) Culturable fungi from urban soils in China II, with the description of 18 novel species in Ascomycota (Dothideomycetes, Eurotiomycetes, Leotiomycetes and Sordariomycetes). MycoKeys 98: 167–220. https://doi.org/10.3897/mycokeys.98.102816

Supplementary materials

Supplementary material 1 

The PCR primers, sequence and cycles used in this study

Zhao-Xue Zhang, Yu-Xin Shang, Meng-Yuan Zhang, Yun Geng, Ji-Wen Xia, Xiu-Guo Zhang

Data type: docx

This dataset is made available under the Open Database License (http://opendatacommons.org/licenses/odbl/1.0/). The Open Database License (ODbL) is a license agreement intended to allow users to freely share, modify, and use this Dataset while maintaining this same freedom for others, provided that the original source and author(s) are credited.
Download file (15.78 kb)
Supplementary material 2 

GenBank accession number of the taxa used in phylogenetic reconstruction

Zhao-Xue Zhang, Yu-Xin Shang, Meng-Yuan Zhang, Yun Geng, Ji-Wen Xia, Xiu-Guo Zhang

Data type: docx

This dataset is made available under the Open Database License (http://opendatacommons.org/licenses/odbl/1.0/). The Open Database License (ODbL) is a license agreement intended to allow users to freely share, modify, and use this Dataset while maintaining this same freedom for others, provided that the original source and author(s) are credited.
Download file (15.84 kb)
Supplementary material 3 

The sequence of phylogenetic analysis

Zhao-Xue Zhang, Yu-Xin Shang, Meng-Yuan Zhang, Yun Geng, Ji-Wen Xia, Xiu-Guo Zhang

Data type: txt

This dataset is made available under the Open Database License (http://opendatacommons.org/licenses/odbl/1.0/). The Open Database License (ODbL) is a license agreement intended to allow users to freely share, modify, and use this Dataset while maintaining this same freedom for others, provided that the original source and author(s) are credited.
Download file (23.69 MB)
Supplementary material 4 

The sequence of phylogenomic analysis

Zhao-Xue Zhang, Yu-Xin Shang, Meng-Yuan Zhang, Yun Geng, Ji-Wen Xia, Xiu-Guo Zhang

Data type: txt

This dataset is made available under the Open Database License (http://opendatacommons.org/licenses/odbl/1.0/). The Open Database License (ODbL) is a license agreement intended to allow users to freely share, modify, and use this Dataset while maintaining this same freedom for others, provided that the original source and author(s) are credited.
Download file (267.68 kb)
Supplementary material 5 

The complete ML phylogenetic tree

Zhao-Xue Zhang, Yu-Xin Shang, Meng-Yuan Zhang, Yun Geng, Ji-Wen Xia, Xiu-Guo Zhang

Data type: pdf

This dataset is made available under the Open Database License (http://opendatacommons.org/licenses/odbl/1.0/). The Open Database License (ODbL) is a license agreement intended to allow users to freely share, modify, and use this Dataset while maintaining this same freedom for others, provided that the original source and author(s) are credited.
Download file (141.13 kb)
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