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Research Article
Three novel species of Alternaria (Pleosporales, Pleosporaceae) from cereal crops (Poaceae) in China
expand article infoHai-Feng Liu‡§, Feng-Yin Liu‡, Hai-Yan Ke‡, Qing-Xiao Shi‡, Jian-Xin Deng‡, Hyunkyu Sang§
‡ Yangtze University, Jingzhou, China
§ Chonnam National University, Gwangju, Republic of Korea

Corresponding author: Jian-Xin Deng ( djxin555@yangtzeu.edu.cn )

Corresponding author: Hyunkyu Sang ( hksang@jnu.ac.kr )

Academic editor: Rungtiwa Phookamsak
© 2025 Hai-Feng Liu, Feng-Yin Liu, Hai-Yan Ke, Qing-Xiao Shi, Jian-Xin Deng, Hyunkyu Sang.
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: Liu H-F, Liu F-Y, Ke H-Y, Shi Q-X, Deng J-X, Sang H (2025) Three novel species of Alternaria (Pleosporales, Pleosporaceae) from cereal crops (Poaceae) in China. MycoKeys 116: 167-183. https://doi.org/10.3897/mycokeys.116.145681
Open Access

Abstract

The genus Alternaria (Pleosporales, Pleosporaceae) comprises saprophytes and pathogens that are widespread around the world. Currently, more than 400 species are recognized within this genus and are classified into 29 sections. In this study, Alternaria strains were isolated from diseased leaves of two cereal crops, rice (Oryza sativa) and maize (Zea mays) in China. These Alternaria spp. were characterized by morphological characterization and phylogenetic analysis using maximum likelihood and Bayesian inference with multiple loci (ITS, GAPDH, RPB2, TEF1, Alt a 1, EndoPG, and OPA10-2). Based on the above analyses, three novel species of Alternaria section Alternaria were introduced, namely A. oryzicola sp. nov., A. poae sp. nov., and A. zeae sp. nov. This study expands the species diversity of Alternaria associated with Poaceae plants in China.

Key words:

Dematiaceous hyphomycetes, maize and rice diseases, morphology, new taxa, multigene phylogeny, taxonomy

Introduction

The genus Alternaria consists of more than 400 species of dematiaceous hyphomycetes (Li et al. 2022, Gou et al. 2023, Liao et al. 2023, Hyde et al. 2024). Species in this genus have been mainly described as saprophytes, endophytes, or phytopathogens and currently accommodated in the family Pleosporaceae (Hyde et al. 2024). Historically, taxonomy of Alternaria has gone through different stages since it was first established by Nees in 1816 (Lawrence et al. 2016). In brief, Alternaria and related genera, especially Macrosporum and Stemphylium, were confused in earlier stages. Although attempts were made by researchers to determine their taxonomic status, issues in nomenclature and generic boundaries persisted for a long time. Afterwards, a complete revision of taxa related to Alternaria based on sporulation patterns and conidial morphology was undertaken by Simmons (Simmons 2007), which accelerated the establishment of order in the nomenclature of alternarioid hyphomycetes.

Nowadays, a DNA-based molecular approach has been used to better understand taxonomy of Alternaria (Lawrence et al. 2016). A variety of loci have been used in the classification of this genus, such as the internal transcribed spacer (ITS) of the rDNA region, small subunit ribosomal RNA gene (SSU), large subunit ribosomal RNA gene (LSU), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), second largest subunit of the RNA polymerase (RPB2), translation elongation factor 1-α (TEF1), Alternaria major allergen (Alt a 1), endopolygalacturonase gene (EndoPG), an anonymous genomic region (OPA10-2), calmodulin (CAM), and the plasma membrane ATPase gene (ATP). Based on multi-locus phylogenetic analysis, this genus consists of 29 sections (Gannibal et al. 2022, Li et al. 2023). Currently, both morphology and multi-locus phylogeny are crucial for the taxonomy of Alternaria spp. and have been widely employed in charactering novel species (Aung et al. 2024; He et al. 2024; Nwe et al. 2024; Bessadat et al. 2025).

Alternaria spp. have been associated with more than 4,000 host plants, ranking the genus 10th among the 100 most cited fungal genera (Lawrence et al. 2013; Woudenberg et al. 2013, 2015; Pinto and Patriarca 2017; Li et al. 2022; Bhunjun et al. 2024). Collectively, certain Alternaria spp. cause diseases that lead to economic losses in agricultural crops, including cereals, oil crops, fruits, and vegetables (Li et al. 2022; Haituk et al. 2023; Alasadi 2024). Cereal crops (Poaceae), such as wheat (Triticum aestivum), maize (Zea mays), and rice (Oryza sativa), have been widely cultivated and consumed since they are popular staple foods with most of the world’s population. Infections on cereal crops caused by Alternaria spp. occur constantly and have attracted increasing attention worldwide (Tralamazza et al. 2018; Orina et al. 2021; Zhong et al. 2022). For instance, wheat black point is an important disease mainly caused by different Alternaria species (A. alternata, A. infectoria, and A. tenuissima), with A. alternata being isolated more frequently (Pinto and Patriarca 2017; Tralamazza et al. 2018). In addition, A. tricitina has been considered as another important pathogen causing leaf blight on wheat (Mercado Vergnes et al. 2006; Amatulli et al. 2013). Recently, A. alternata, A. tenuissima, A. burnsii, and an unclassified species Alternaria sp. were identified as causal agents of leaf blight on maize in China (Xu et al. 2022). In rice, A. padwickii (Syn Trichoconis padwickii) has been frequently detected as a seed pathogen (Gutiérrez et al. 2010). Moreover, A. arborescens and A. gaisen were also reported as leaf spot pathogens of rice in Pakistan (Akhtar et al. 2014a, 2014b).

In this study, Alternaria spp. were isolated from symptomatic leaves of rice and maize in Guangxi Province and in Hainan Province in China, respectively. The aim of this study was to characterize these species taxonomically using morphological traits and multi-locus phylogenetic analysis.

Materials and methods

Isolation

In 2023, diseased maize (Zea mays) and rice (Oryza sativa) leaves exhibiting leaf spot and blight symptoms were collected in Guangxi and Hainan provinces, respectively. Leaf tissues were cut into small pieces with sterile blades and placed in petri dishes containing wet filter papers. After incubation at 25 °C for 1–2 days, fungal development on tissue samples were observed with a stereo microscope. Spores of Alternaria spp. developed from the edge of the leave tissues were singly picked using sterile glass needles and inoculated onto PDA (potato dextrose agar, Difco, Montreal, Canada). Pure cultures were deposited in the Fungi Herbarium of Yangtze University in Jingzhou, China. Dried cultures of the strains were also preserved in the herbarium for long-term storage.

Morphology

Colony characteristics of strains of Alternaria spp. were observed and recorded following 7 days of incubation at 25 °C on 90-mm PDA plates under dark conditions. To determine their conidial morphology, the strains were grown on potato carrot agar (PCA) and V8 juice agar (V8A) at 25 °C for 7 days under a photoperiod of 8 hours of light per day. Conidia of the strains were observed and imaged with an ECLIPSE Ni-U optical microscope (Nikon, Tokyo, Japan). The dimensions of the conidia were measured (n = 50). Conidial morphology was determined based on sporulation pattern and conidial characteristics.

PCR amplification

Fresh mycelia of the fungal strains grown on PDA were harvested and used for genomic DNA extraction following the procedures described by Watanabe et al. (2010). DNA solutions were then used to amplify fragments from several gene regions, including ITS, GAPDH, RPB2, TEF1, Alt a 1, EndoPG, and OPA10-2. Polymerase chain reaction (PCR) amplification of the above-mentioned regions was performed by a Bio-Rad T100TM Thermal Cycler with primer pairs ITS5/ITS4 (White et al. 1990), gpd1/gpd2 (Berbee et al. 1999), EF1-728F/EF1-986R (Carbone and Kohn 1999), RPB2-5F/RPB2-7cR (Liu et al. 1999), Alt-for/Alt-rev (Hong et al. 2005), PG3/PG2b (Andrew et al. 2009), and OPA10-2L/OPA10-2R (Andrew et al. 2009), respectively. Reaction conditions for the PCR amplification were referred to previous studies (Woudenberg et al. 2015, Nwe et al. 2024). Successful amplification products were sent to TSINGKE (Beijing, China) for purification and Sanger sequencing in both directions. Sequences obtained from the company were manually examined with BioEdit v7.0.9 (Hall 1999) and then trimmed using MEGA X (Kumar et al. 2018). Consensus sequences were deposited in GenBank (https://www.ncbi.nlm.nih.gov/) with accession numbers shown in Table 1. New species are established based on the recommendations outlined by Jeewon and Hyde (2016).

Table 1.
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GenBank accession numbers of Alternaria spp. used for phylogenetic analysis.

Species Strain ITS Alt a 1 GAPDH RPB2 TEF1 OPA10-2 EndoPG
A. alstroemeriae CBS 118808 KP124296 KP123845 KP124153 KP124764 KP125071 KP124601 KP123993
A. alstroemeriae CBS 118809T KP124297 – KP124154 KP124765 KP125072 KP124602 KP123994
A. alternantherae CBS 124392 KC584179 KP123846 KC584096 KC584374 KC584633 – –
A. alternata CBS 916.96T AF347031 AY563301 AY278808 KC584375 KC584634 KP124632 JQ811978
A. alternata CBS 112249 KP124338 KP123886 KP124192 KP124806 KP125114 KP124648 KP124039
A. arborescens CBS 119544T KP124408 KP123955 JQ646321 KP124878 KP125186 KP124722 KP124112
A. arborescens CBS 102605T AF347033 AY563303 AY278810 KC584377 KC584636 KP124712 AY295028
A. arctoseptata MFLUCC 21-0139T – OK236755 OK236702 OK236655 OK236608 – –
A. baoshanensis MFLUCC 21-0124T MZ622003 OK236760 OK236706 OK236659 OK236613 – –
A. betae-kenyensis CBS 118810T KP124419 KP123966 KP124270 KP124888 KP125197 KP124733 KP124123
A. breviconidiophora MFLUCC 21-0786T MZ621997 OK236751 OK236698 OK236651 OK236604 – –
A. burnsii CBS 118816 KP124423 KP123970 KP124273 KP124892 KP125201 KP124737 KP124127
A. burnsii CBS 118817 KP124424 KP123971 KP124274 KP124893 KP125202 KP124738 KP124128
A. burnsii CBS 107.38T KP124420 KP123967 JQ646305 KP124889 KP125198 KP124734 KP124124
A. burnsii CBS 879.95 KP124422 KP123969 KP124272 KP124891 KP125200 KP124736 KP124126
A. burnsii CBS 130264 KP124425 KP123972 KP124275 KP124894 KP125203 KP124739 KP124129
A. burnsii CBS 110.50 KP124421 KP123968 KP124271 KP124890 KP125199 KP124735 KP124125
A. burnsii CBS 108.27 KC584236 KP123850 KC584162 KC584468 KC584727 KP124605 KP123997
A. eichhorniae CBS 489.92T KC146356 KP123973 KP124276 KP124895 KP125204 KP124740 KP124130
A. ellipsoidialis MFLUCC 21-0132 MZ621989 OK236743 OK236690 OK236643 OK236596 – –
A. eupatoriicola MFLUCC 21-0122 MZ621982 OK236736 OK236683 OK236636 OK236589 – –
A. falcate MFLUCC 21-0123 MZ621992 OK236746 OK236693 OK236649 OK236599 – –
A. gaisen CBS 118488R KP124427 KP123975 KP124278 KP124897 KP125206 KP124743 KP124132
A. gaisen CBS 632.93R KC584197 KP123974 KC584116 KC584399 KC584658 KP124742 AY295033
A. gossypina CBS 104.32T KP124430 JQ646395 JQ646312 KP124900 KP125209 KP124746 KP124135
A. gossypina CBS 102601 KP124433 KP123979 KP124282 KP124903 KP125212 KP124749 KP124138
A. iridiaustralis CBS 118487 KP124436 KP123982 KP124285 KP124906 KP125215 KP124752 KP124141
A. iridiaustralis CBS 118486T KP124435 KP123981 KP124284 KP124905 KP125214 KP124751 KP124140
A. jacinthicola CBS 878.95 KP124437 KP123983 KP124286 KP124907 KP125216 KP124753 KP124142
A. jacinthicola CPC 25267 KP124439 KP123985 KP124288 KP124909 KP125218 KP124755 KP124144
A. jacinthicola CBS 133751T KP124438 KP123984 KP124287 KP124908 KP125217 KP124754 KP124143
A. jingzhouensis YZU 221144T OR883772 OR887694 OR887690 OR887688 OR887686 OR887684 OR887692
A. koreana SPL2-1T LC621613 LC631831 LC621647 LC621681 LC621715 LC631857 LC631844
A. lathyri MFLUCC 21-0140T MZ621974 OK236728 OK236675 OK236628 OK236581 – –
A. lijiangensis YZU 221458T OQ679970 OQ686781 OQ686785 OQ686789 OQ686783 OQ686787 OQ686779
A. longipes CBS 540.94R AY278835 AY563304 AY278811 KC584409 KC584667 KP124758 KP124147
A. longipes CBS 121332R KP124443 KP123989 KP124292 KP124913 KP125222 KP124760 KP124149
A. longxiensis YZU 221221T OQ534546 OQ473629 OQ512732 OQ543009 OQ512726 OQ543003 OQ512720
A. lycopersici YZU 221185T OQ519795 OQ473633 OQ512736 OQ543013 OQ512730 OQ543007 OQ512724
A. macilenta MFLUCC 21-0138T MZ621972 OK236726 OK236673 OK236626 OK236579 – –
A. macroconidia MFLUCC 21-0134T MZ622001 OK236757 OK236704 OK236657 OK236610 – –
A. minimispora MFLUCC 21-0127T MZ621980 OK236734 OK236681 OK236634 OK236587 – –
A. momordicae YZU 161378T OR883774 OR887695 OR887691 OR887689 OR887687 OR887685 OR887693
A. muriformispora MFLUCC 21-0784T MZ621976 OK236730 OK236677 OK236630 OK236583 – –
A. myanmarensis YZU 231736T OR897031 OR979657 OR963612 PP508256 OR963615 PP034184 OR979663
A. oblongoellipsoidea MFLUCC 22-0074T MZ621967 OK236721 OK236668 OK236621 OK236574 – –
A. obpyriconidia MFLUCC 21-0121T MZ621978 OK236732 OK236680 OK236633 OK236585 – –
A. orobanches MFLUCC 21-0137T MZ622007 OK236763 OK236710 – – – –
A. oryzicola sp. nov. YZU 231199T PQ812549 PV155522 PV155536 PV155548 PV155528 PV155542 –
A. ovoidea MFLUCC 21-0782T MZ622005 – OK236708 OK236661 OK236614 – –
A. phragmiticola MFLUCC 21-0125T MZ621994 OK236749 OK236696 OK236649 OK236602 – –
A. poae sp. nov. YZU 231197T PQ812551 PV155524 PV155538 PV155550 PV155530 PV155544 PV155532
A. poae sp. nov. YZU 231198 PQ812550 PV155523 PV155537 PV155549 PV155529 PV155543 PV155531
A. rostroconidia MFLUCC 21-0136T MZ621969 OK236723 OK236670 OK236623 OK236576 – –
A. salicicola MFLUCC 22-0072T MZ621999 OK236753 OK236700 OK236653 OK236606 – –
A. solanicola YZU 221189T OQ534548 OQ473631 OQ512734 OQ543011 OQ512728 OQ543005 OQ512722
A. tomato CBS 103.30 KP124445 KP123991 KP124294 KP124915 KP125224 KP124762 KP124151
A. tomato CBS 114.35 KP124446 KP123992 KP124295 KP124916 KP125225 KP124763 KP124152
A. torilis MFLUCC 14-0433T MZ621988 OK236741 OK236688 OK236641 OK236594 – –
A. yamethinensis YZU 231739T OR889008 OR979655 OR963610 PP179253 OR963614 PP034182 OR979661
A. zeae sp. nov. YZU 231602T PQ812548 PV155521 PV155535 PV155547 PV155527 PV155541 –
A. zeae sp. nov. YZU 231638 PQ812547 PV155520 PV155534 PV155546 PV155526 PV155540 –
A. zeae sp. nov. YZU 231640 PQ812546 PV155519 PV155533 PV155545 PV155525 PV155539 –

Phylogenetic analysis

Nucleotide sequences generated in this study were subjected to BLASTn (https://blast.ncbi.nlm.nih.gov/Blast.cgi, accessed on 31 October 2024) for similarity searches against the NCBI nucleotide database. Reference sequences of Alternaria spp. used for phylogenetic analysis were obtained based on recent publications (Woudenberg et al. 2015; Li et al. 2022, 2023; Romain et al. 2022; Aung et al. 2024; Nwe et al. 2024). Phylogenetic analysis was performed using the OFPT (One-click Fungal Phylogenetic Tool) program developed by Zeng et al. (2023). In brief, sequences of each genetic region were aligned by MAFFT v7.307 online version (Katoh and Standley 2013; Katoh et al. 2019) and then trimmed using TrimAI (Capella-Gutiérrez et al. 2009). Subsequently, nucleotide substitution models of each dataset were tested by ModelFinder (Kalyaanamoorthy et al. 2017) and the best-fit model for each dataset was selected based on the Bayesian information criterion (BIC). All the datasets were concatenated with partition information and then used for maximum likelihood (ML) and Bayesian phylogenetic analyses with software IQ-TREE (Nguyen et al. 2015) and Mrbayes 3.2.7 (Ronquist et al. 2012), respectively. In the ML analysis, 1,000 replicates were performed using bootstrap approximation. In the Bayesian inference (BI) analysis, a Markov Chain Monte Carlo (MCMC) algorithm was employed, involving four MCMC chains running for 50,000,000 generations with sampling every 100 generations. Posterior probabilities (PP) were estimated after discarding the first 25% of sampled tree as burn-in. The consensus BI tree was generated once the average standard deviation of split frequencies fell below 0.01.

Results

Phylogenetic analysis

A total of 63 strains (including 6 strains from this study) of Alternaria species in section Alternaria, were used for phylogenetic analysis. The concatenated sequence matrix consisted of seven loci, with a total length of 3608 bp, including 514 bp from ITS, 566 bp from GAPDH, 753 bp from RPB2, 234 bp from TEF1, 472 bp from Alt a 1, 448 bp from EndoPG, and 621 bp from OPA10-2. The best-fit evolutionary models for each gene were as follows: JC for ITS, TNe+G4 for RPB2, TIMe+I for EndoPG, TNe+R2 for OPA10-2, and K2P+G4 for GAPDH, Alt a 1 and TEF1. In phylogenetic analyses, similar topologies were obtained from maximum likelihood and Bayesian methods. Additionally, the six strains examined in this study were placed within Alternaria section Alternaria, clustering into three distinct clades. Specifically, strains YZU 231602, YZU 231638, and YZU 231640 (isolated from Z. mays) formed one clade supported with a bootstrap (BS) value of 81% and a Bayesian posterior probability (PP) of 1.00 (Fig. 1). This clade was positioned close to another clade composed of strains YZU 231197 and YZU 231198 (isolated from O. sativa). These two clades were relatively close to A. burnsii with BS/PP support values of 69%/0.73 (Fig. 1). Strain YZU 231199 isolated from O. sativa formed a single clade sister to strains of A. tomato (CBS 103.30 and CBS 114.35), supported with BS/PP values of 72%/0.80 (Fig. 1). The phylogenetic placements of these strains indicated that they represent three novel species in the genus Alternaria section Alternaria.

Figure 1. 

Phylogenetic tree constructed using the maximum likelihood method based on concatenated sequences of ITS, GAPDH, RPB2, TEF1, Alt a 1, EndoPG, and OPA10-2 from Alternaria spp. Bootstrap support values (BS) and Bayesian posterior probability (PP) are given at the nodes (BS/PP). The strains from this study are marked in bold. Ex-type strains are indicated with ‘T’, representative strains are indicated with ‘R’. Alternaria alternantherae CBS 124392 is used as the outgroup taxon.

Taxonomy

Alternaria oryzicola H.F. Liu & J.X. Deng, sp. nov.

MycoBank No: 857595
Fig. 2

Etymology.

Name refers to its host Oryza sativa.

Type.

China • Hainan Province, Lingshui County, diseased leaves of Oryza sativa, July 2023, J.L. Yin, holotype YZU-H-2023056A (permanently preserved in a metabolically inactive state), ex-type culture YZU 231199.

Description.

Colonies on PDA sub-circular, velvety to fluffy, white to greyish-green, darker at the center, reverse side pale yellow to light brown, 61–63 mm in diameter (Fig. 2a). On PCA, conidiophores, erect or curved, unbranched, sometimes slightly expanded at the apex, 32–105 × 3–4 μm in size, with 1–6 septa (Fig. 2f). Conidiogenous cells integrated, terminal, smooth, cylindrical, apically doliiform, 5–14 × 3–4 μm, with 1 conidiogenous locus. Conidia borne in chain, 1–3 units per chain, unbranched, mostly narrow-obclavate, obclavate, or long ellipsoid, 20–48 × 9–16 μm in dimension, 1–4 transverse septa, apical beak 4–39 × 2.5–4 μm (Fig. 2b, c, g). On V8A, conidiophores unbranched, 20–67 × 3–4 μm, with 1–5 septa. Conidia solitary or in chain with 2–3 units per chain, narrow-obclavate, obclavate, or long ellipsoid, 18–56 × 9–16 μm in size, with 2–6 transverse septa, apical beak 4–39 μm in length, 3–4 μm in width (Fig. 2d, e, h).

Figure 2. 

Morphology of Alternaria oryzicola sp. nov. (YZU 231199) a colony on PDA for 7 days at 25 °C b, c sporulation on PCA d, e sporulation on V8A f conidiophore and conidiogenous cell g conidia on PCA h conidia on V8A. Scale bars: 50 µm (b, c, d, e); 15 µm (f); 25 µm (g, h).

Notes.

Based on phylogenetic analysis using combined dataset of multiple regions, strain YZU 231199 was relatively close to strains of Alternaria tomato (CBS 103.30 and CBS 114.35). Comparative analysis of nucleotide sequences revealed that strain YZU 231199 differed from representative strain of A. tomato (CBS 103.30) at four regions: 3 bp differences in GAPDH with 1 gap; 4 bp differences in RPB2, 1 bp difference in TEF1, and 1 bp difference in OPA10-2. Morphologically, the present fungus (YZU 231199) was also different with A. tomato in having smaller body size, less septa, and shorter beak (Table 2). Therefore, strain YZU 231199 was introduced as a novel species A. oryzicola sp. nov. in this study.

Table 2.
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Conidial morphology of Alternaria spp. from this study and previous publication.

Species Conidia Conidia per chain Substrate Reference
Shape Body size (μm) Septa Beak size (μm)
Alternaria burnsii ovoid or ellipsoid 30–50 × 9–13 5–8 – Short chain Host Simmons (2007)
narrow-ovoid or narrow-ellipsoid 30–40 × 8–14 3–7 – – PCA,V8A Simmons (2007)
A. oryzicola sp. nov. narrow-obclavate, obclavate, or long ellipsoid 20–48 × 9–16 1–4 4–39 × 2.5–4 1–3 PCA This study
18–56 × 9–16 2–6 4–39 × 3–4 1–3 V8A This study
A. poae sp. nov. subellipsoid, obclavate, or narrow-ovoid 20–42 × 10–19 1–4 6–26 × 3–4 1–4 PCA This study
20–45 × 10–17 2–7 5–17 × 3–4 1–4 V8A This study
A. tomato ellipsoid to long-ovoid 39–65 × 13–22 6–9 60–105 × 2 Solitary Host Simmons (2007)
A. zeae sp. nov. ovate, ellipsoid or obclavate 26–46 × 10–18 3–6 9–93 × 2.5–4 1–4 PCA This study
26–45 × 10–17 3–6 4.5–65 × 2.5–4 1–4 V8A This study

Alternaria poae H.F. Liu & J.X. Deng, sp. nov.

MycoBank No: 857596
Fig. 3

Etymology.

Name refers to its host family Poaceae.

Type.

China • Hainan Province, Lingshui County, diseased leaves of Oryza sativa, July 2023, J.L. Yin, holotype YZU-H-2023056B (permanently preserved in a metabolically inactive state), ex-type culture YZU 231197.

Description.

On PDA, colonies sub-rounded, fluffy, cottony, white to pale green or yellow-green, reverse side pale yellow to light yellow, 55–56 mm in diameter (Fig. 3a). On PCA, conidiophores unbranched, curved or straight, 15–77 × 3–4 μm in size, with 1–5 septa (Fig. 3f). Conidiogenous cells 5–9 × 3–4 μm, integrated, terminal, cylindrical, thin-walled, smooth, apically doliiform, with 1 conidiogenous locus. Conidia borne single or in chain with at least 2–4 conidia per chain, unbranched, narrow-ovoid, subellipsoid, or obclavate, smooth, 20–42 × 10–19 μm, with 1–4 transverse septa. basal rounded, apical beak 6–26 × 3–4 μm (Fig. 3b, c, g). On V8A, conidiophores unbranched, smooth, 30–96 × 3–4 μm, with 2–7 septa. Conidia produced in chain with at least 2–4 conidia per chain, subellipsoid, obclavate, or narrow-ovoid, 20–45 × 10–17 μm, 1–4 transverse septa, beak 5–17 × 3–4 μm (Fig. 3d, e, h).

Figure 3. 

Morphology of Alternaria poae sp. nov. (YZU 231197) a colony on PDA for 7 days at 25 °C b, c sporulation on PCA d, e sporulation on V8A f conidiophore and conidiogenous cell g conidia on PCA h conidia on V8A. Scale bars: 50 µm (b, c, d, e); 15 µm (f); 25 µm (g, h).

Additional isolated examined.

China • Hainan Province, Lingshui County, diseased leaves of Oryza sativa, July 2023, J.L. Yin, living culture YZU 231198.

Notes.

In phylogenetic analysis using concatenated sequences of ITS, GAPDH, RPB2, TEF1, Alt a 1, EndoPG, and OPA10-2, strains of Alternaria poae (YZU 231197 and YZU 231198) fell into a separate clade close to clades of A. zeae and A. burnsii. Based on nucleotide sequences, A. poae differs from A. zeae in five loci (3 bp in GAPDH with 1 gap, 5 bp in RPB2, 3 bp in TEF1, 3 bp in Alt a 1, and 7 bp in OPA10-2), and differs from A. burnsii in six loci (2 bp in GAPDH, 2 bp in RPB2, 3 bp in TEF1, 2 bp in Alt a 1, 2 bp in EndoPG, and 4 bp in OPA10-2). In morphology, A. poae can be distinguished from A. zeae by its shorter beak length, and from A. burnsii by its wider conidia bodies (Table 2).

Alternaria zeae H.F. Liu & J.X. Deng, sp. nov.

MycoBank No: 857597
Fig. 4

Etymology.

Name refers to its host Zea mays.

Type.

China • Guangxi Province, Liuzhou City, diseased leaves of Zea mays, September 2023, F.Y Liu, holotype YZU-H-2023150A (permanently preserved in a metabolically inactive state), ex-type culture YZU 231602.

Description.

Colonies on PDA round, fluffy, cottony, greenish-gray, white at the margin, reverse side pale yellow, 58–59 mm in diameter (Fig. 4a). The conidial morphology on PDA and PCA was similar, with only slight differences. On PCA, conidiophores straight or curved, unbranched, 25–123 × 2.5–4.5 μm, with 1–8 septa (Fig. 4d). Conidia borne singly or in chain with 2–4 conidia per chain, ovate, ellipsoid or obclavate, with 3–6 transverse septa, 26–46 × 10–18 μm in size, mostly with septate apical beak, 9–93 × 2.5–4 μm in size (Fig. 4b, e). On V8A, conidiophores straight or curved, unbranched, 38–118 × 2.5–4 μm, with 1–7 septa. Conidiogenous cells 5–14 × 3–5 μm, integrated, apical, cylindrical, light brown, smooth, apically doliiform, with 1 conidiogenous locus. Conidia solitary or produced in chain with 2–4 conidia, ovate, ellipsoid or obclavate, with 3–6 transverse septa, 26–45 × 10–17 μm, apical beak 4.5–65 × 2.5–4 μm, with 0–4 septa (Fig. 4c, f).

Figure 4. 

Morphology of Alternaria zeae sp. nov. (YZU 231602) a colony on PDA for 7 days at 25 °C b, c sporulation on PCA d conidiophore and conidiogenous cell e conidia on PCA f conidia on V8A. Scale bars: 50 µm (b, c); 15 µm (d); 25 µm (e, f).

Additional isolates examined.

China • Guangxi Province, Liuzhou City, diseased leaves of Zea mays, September 2023, F.Y. Liu, living culture YZU 231638 and YZU 231640.

Notes.

Strains of Alternaria zeae (YZU 231602, YZU 231638 and YZU 231640) formed a distinct clade in the multi-locus phylogenetic analysis. Alternaria poae and A. burnsii were genetically close to A. zeae. In nucleotide sequences, A. zeae differs from A. poae at five loci: 3 bp in GAPDH with 1 gap, 5 bp differences in RPB2, 3 bp in TEF1, 3 bp in Alt a 1, and 7 bp in OPA10-2. Nucleotide sequence differences were also observed between A. zeae and A. burnsii (3 bp in GAPDH with 1 gap, 2 bp in RPB2, 1 bp in Alt a 1, and 1 bp in OPA10-2). Morphologically, A. zeae has obviously longer beak than A. poae and A. burnsii (Table 2). In addition, conidia bodies of A. zeae are also wider than those of A. burnsii (Simmons 2007).

Discussion

Based on integrated analyses of morphological characterization and multi-locus phylogenetic study, three novel species of Alternaria (A. oryzicola sp. nov., A. poae sp. nov., and A. zeae sp. nov.) from two different cereal crops (O. sativa and Z. mays) were described in this study. These findings contribute to the understanding of the diversity of Alternaria spp. on cereal crops in China.

In phylogenetic analysis using concatenated sequences of ITS, GAPDH, RPB2, TEF1, Alt a 1, EndoPG, and OPA10-2, all of the three novel species were assigned to distinct clades in Alternaria section Alternaria. This section contains most of the small-spored species, which include important plant, human and postharvest pathogens (Woudenberg et al. 2015). Phylogenetically, species A. zeae sp. nov. and A. poae sp. nov. were relatively close to A. burnsii and A. oryzicola sp. nov. was relatively close to A. tomato. These species were located at the top of the phylogenetic tree of section Alternaria. In terms of morphology, the three species from this study were distinguished from their related species (A. burnsii and A. tomato) based on conidial characteristics, such as conidia size, septa, and beak size, as shown in Table 2. Therefore, both morphological and phylogenetic approaches provide evidence supporting the novelty of the species identified in this study.

In addition, the host is one of the important factors in the description of Alternaria species (Zhang 2003). According to fungus-host distribution in the USDA Fungal Databases (https://fungi.ars.usda.gov, accessed on 31 October 2024) and related publications, A. burnsii and A. tomato have been associated with different sources, but most are not from Poaceae plants. For example, A. burnsii was found on Cuminum cyminum (Simmons 2007; Woudenberg et al. 2015), Tinospora cordifolia (Woudenberg et al. 2015), Rhizophora mucronata (Woudenberg et al. 2015), Gossypium sp. (Woudenberg et al. 2015; El Gobashy et al. 2018), Gomphrena globosa (Woudenberg et al. 2015), Sorghum sp. (Kim et al. 2020), human sputum (Woudenberg et al. 2015), Helianthus annuus (Nwe et al. 2024), Allium cepa (Htun et al. 2022), Apium graveolens (Zhuang 2005), Bunium persicum (Mondal et al. 2002), Cucurbita maxima (Paul et al. 2015), Pandanus sp. (Hyde et al. 2018), and Zea mays (Xu et al. 2022). Alternaria tomato was reported on several plants, including Solanum lycopersicum (Simmons 2007), Helianthus annuus (Poudel et al. 2019), Nopalea cochenillifera (Infante et al. 2021), and Phaseolus vulgaris (Allen 1995). In the present study, the three novel species were isolated from two cereal crops (Z. mays and O. sativa), suggesting an increasing association of Alternaria species with Poaceae plants. According to previous studies, Alternaria spp. have been reported as predominant mycobiota in cereal grains (Kulik et al. 2015; Puvača et al. 2020; Orina et al. 2021). Most of these Alternaria species were predominantly classified in sections Alternaria and Infectoriae (Gannibal 2018), whereas some were sporadically found in section Pseudoalternaria (Gannibal 2018, Poursafar et al. 2018). Much attention has been devoted to detecting Alternaria spp. capable of producing mycotoxins (Orina et al. 2021). On cereal grains, several mycotoxins produced by Alternaria spp., such as AOH, AME, TEN, and TeA, were detected (Orina et al. 2021), posing potential risks to food safety. The ability of the three species in this study (A. oryzicola sp. nov., A. poae sp. nov., and A. zeae sp. nov.) to produce mycotoxins warrants further investigation. Since these three species were all isolated from diseased leaves of cereal crops, they could be potential pathogens. Furthermore, they are phylogenetically closely related to A. burnsii and A. tomato, which have recently been isolated and identified as pathogens of a cereal crop, wheat (Al-Nadabi et al. 2018).

Overall, this study characterized three novel species of Alternaria from two cereal crops, rice and maize, through morphological and molecular approaches. The potential interactions between these novel species and their host plants merit further investigation to uncover their ecological and agricultural impacts.

Additional information

Conflict of interest

The authors have declared that no competing interests exist.

Ethical statement

No ethical statement was reported.

Funding

This study was funded by the National Natural Science Foundation of China (32270022).

Author contributions

Hai-Feng Liu: methodology, data curation, writing - original draft. Feng-Yin Liu: methodology, investigation, data curation. Hai-Yan Ke: methodology. Qing-Xiao Shi: methodology. Jian-Xin Deng: conceptualization, writing – review & editing, supervision, project administration. Hyunkyu Sang: writing – review & editing, supervision.

Author ORCIDs

Hai-Feng Liu https://orcid.org/0000-0002-9733-9240

Feng-Yin Liu https://orcid.org/0000-0003-3114-603X

Jian-Xin Deng https://orcid.org/0000-0001-7304-5603

Hyunkyu Sang https://orcid.org/0000-0002-7459-5217

Data availability

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

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Hai-Feng Liu and Feng-Yin Liu contributed equally to this work and share first authorship.
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