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. 2025 Aug 15;120:295–315. doi: 10.3897/mycokeys.120.144245

 Alternariaphoenicis sp. nov. and Alternariaouedrighensis sp. nov. (Pleosporales, Pleosporaceae): Two new species associated with leaf spot and blight diseases of date palm (Phoenixdactylifera L.)

Youssef Djellid 1,2, Alla Eddine Mahamedi 1,2, Milan Spetik 3, Eliska Hakalová 3, Ales Eichmeier 3, Micael Ferreira Mota Gonçalves 4, Fouad Lamghari 5, Maryam Ali Saeed Mohamed Al Hmoudi 5, Akila Berraf-Tebbal 1,✉
PMCID: PMC12374170  PMID: 40859948

Abstract

Date palm (Phoenixdactylifera L.) is one of the oldest fruit crops grown in the semi-arid and arid regions, playing significant ecological, environmental and socio-economic roles. Recently, palm leaf spot and blight diseases have indeed emerged as significant threats to phoeniciculture. They reduce yield and quality of dates leading to economic losses. Therefore, a survey was conducted in four palm groves located in the Biskra and Ghardaia provinces of Algeria. This investigation revealed two new Alternaria species associated with leaf spot and blight symptoms on date palm. These newly identified species are designated as A.phoenicissp. nov. and A.ouedrighensissp. nov., which belong to the Ulocladioides and Embellisia sections, respectively. The isolates were phylogenetically identified using the key genetic markers of the genus including the large subunit ribosomal DNA (LSU), internal transcribed spacer region of the ribosomal RNA (ITS), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), RNA polymerase II subunit (RPB2), translation elongation factor (TEF1) and plasma membrane (ATPase) genes and illustrated based on the morphological characteristics.

Key words: Alternaria , leaf spot and blight diseases, Phoenixdactylifera L., phylogeny, taxonomy

Introduction

The date palm (Phoenixdactylifera L.) is a dioecious perennial monocot in the Arecaceae family, which comprises around 200 genera and 1500 species (Dawson 1982). It is a vital crop in desert regions, serving as a primary source of food and trade from North Africa to India and across other subtropical areas (Erskine et al. 2004). Notably, Algeria stands as the world’s third-largest date producer, generating over 1.3 million tonnes annually, where date palms underpin both traditional and modern Saharan agriculture (FAO 2023). However, despite its economic significance, date palms are vulnerable to various pathogenic fungi that can severely damage their stem, leaves, fruit, and root, leading to substantial yield reductions (Bokhary 2010; El-Juhany 2010).

Among the fungi that impact date palms, Alternaria emerges as a particularly associated group with leaf spots and blight diseases in the Middle East regions (El-Juhany 2010; Al-Sadi et al. 2012; Al-Nadabi et al. 2018). Alternaria, a genus in the family Pleosporaceae, order Pleosporales, and phylum Ascomycota, was first described by Nees in 1816 with Alternariatenuis designated as the type species. Since then, the taxonomy of Alternaria has undertaken significant revisions leading to the identification of numerous new species. Presently, the genus comprises more than 360 species encompassing 29 sections (Simmons 2007; Woudenberg et al. 2013; Wijayawardene et al. 2020; Li et al. 2023).

Species of Alternaria occupy a wide range of ecological niches, occurring as endophytes within apparently asymptomatic plant tissues, saprobes on various substrates such as dead vegetation, paper, and food, and as pathogens that impact both plants and animals, including humans, worldwide. This adaptability enables them to thrive in diverse environments and interact with a wide range of hosts (Blodgett et al. 2000; Larran et al. 2001; Feng et al. 2011; Qi et al. 2012; Li et al. 2023; He et al. 2024).

The Alternaria genus consists of several phytopathogenic species that cause diseases in a wide array of plants around the world, affecting key crops such as cabbage, cauliflower, tomato, carrot, wheat, cucurbits and date palm (Chaerani and Voorrips 2006; Logrieco et al. 2009; Rahimloo and Ghosta 2015; Al-Nadabi et al. 2018; Jayawardena et al. 2019). These pathogens primarily induce leaf spots and defoliation, characterized by necrotic lesions and yellowing on leaves (Mac Kinon et al. 1999). They can also infect various plant parts, including seedlings and fruits, leading to significant pre- and post-harvest losses (Thomma 2003; Lawrence et al. 2016). Furthermore, Alternaria species are recognized as seed-borne pathogens and are known for producing harmful secondary metabolites, including phytotoxins and mycotoxins (Thomma 2003; Simmons 2007; Gilardi et al. 2015; Lawrence et al. 2016; Chalkley 2020).

Alternaria genus includes morphologically diverse species traditionally identified by reproductive structures, sporulation patterns, and host interactions. However, taxonomic classification has been debated due to species complexes and morphological variability influenced by environmental conditions and host specificity (Elliot 1917; Fries 1832; Neergaard 1945; Joly 1964; Simmons 1967). Afterward, Simmons introduced practical criteria to standardize taxonomic concepts for Alternaria species, focusing on colony and conidial morphology (Simmons 2007). Therefore, in recent years, DNA sequencing of conserved loci has massively improved the knowledge of fungal phylogeny. Several studies have shown that phylogenetic analysis becomes a reliable approach for species-level identification. The multilocus phylogeny using genetic regions such as ITS, LSU, TEF1, RPB2, GAPDH and Alt-a1 combined with morphological data are frequently used to resolve the taxonomy and identification of Alternaria taxa. Thus, new species are increasingly described (Woudenberg et al. 2013; Al Ghafri et al. 2019; Li et al. 2023; Aung et al. 2024; He et al. 2024; Jayawardena et al. 2025).

During an investigation of Alternaria species in Algeria, two new taxa were isolated from date palm (Phoenixdactylifera L.). This study used a polyphasic approach, integrating both morphological and phylogenetic analyses, to characterize these newly introduced taxa.

Materials and methods

Isolation and morphological studies

During 2017, a set of 40 samples comprising leaves, rachises, and leaflets with spot lesions was collected from date palm trees in Ghardaia and Bechar provinces, Algeria (Fig. 1). Plant material was carefully enclosed in paper bags and transported to the laboratory. Subsequently, isolations were made from the margin of symptomatic tissues. Small pieces (approx. 5 mm2) of rachis and leaflets were surface sterilized in 5% sodium hypochlorite (NaOCl) for 8 and 4 min, respectively. They were rinsed thrice with sterile distilled water, then dried with sterilized filter paper and placed onto the surface of potato dextrose agar (PDA, Difco Laboratories). Plates were incubated at 25 °C until fungal growth was perceived. The mycelium emerged from the fragments of the tissues were transferred to new PDA plates and incubated under the same conditions.

Figure 1.

Figure 1.

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Date palm tree with decline symptoms (a), rachis (b–f) and leaflets (g, h) spots.

Colony growth characteristics including surface and reverse appearance of the culture were recorded after 7 days of incubation on 90 mm diameter PDA Petri plates at 25 °C in darkness, following Li et al. (2022) and Luo et al. (2022). Growth characteristics were determined on PDA plates incubated at different temperatures from 5–40 °C at 5 °C intervals in the dark. Reference strains and specimens are maintained at the Fungal Biodiversity Centre (CBS) and MEND-F fungal collections.

Fungal colonies were subcultured onto water agar medium, supplemented with autoclaved poplar twigs to enhance sporulation (Santos and Phillips 2009). The cultures were maintained on a laboratory bench at approximately 20–25 °C, where they were exposed to diffused daylight. After two weeks, observations of micromorphological features including conidial size, shape, colour, striation, septation, conidiophores and conidiogenous cells mounted into 100% lactic acid, were made using a Nikon Eclipse 80i microscope. Photographs and measurements of fungal structures mounted in 100% lactic acid were taken with a Nikon DSRi1 camera and the software NIS-Elements D (Nikon). Thirty measurements per structure were performed and presented in the quantitative format “(min–) low – up (–max) × (min–) low – up (–max) µm (av. Length mean ± SD × Width mean ± SD µm)”, with full observed ranges (minimum–maximum), typical ranges (low–up), and mean ± standard deviation.

DNA extraction and sequencing

Genomic DNA of our isolates was extracted from 7-day-old mycelium grown on PDA at 25 °C. The NucleoSpin Tissue kit (Macherey-Nagel, Düren, Germany) was used according to the manufacturer’s instructions (https://www.mn-net.com).

Polymerase chain reaction amplifications of the large subunit ribosomal DNA (LSU), internal transcribed spacer of ribosomal DNA (ITS), parts of glyceraldehyde-3-phosphate dehydrogenase (GAPDH), RNA polymerase II subunit (RPB2), translation elongation factor (TEF1) and plasma membrane adenosine triphosphatase (ATPase) genes were performed using primer pairs (Table 1). Polymerase chain reaction (PCR) mixtures and amplification conditions were conducted following the protocols described by Berbee et al. (1999) and Woudenberg et al. (2013). PCR mixture contained 10 μM of primer, 200 μMdNTP, 1×Taq reaction buffer, 2 Units of AmpliTaq-DNA polymerase, 2.5 mMMgCl2 and 10 ng of template DNA for a final reaction volume of 25 μl. After amplification, the obtained PCR amplicons were purified and sequenced by the company Eurofins (Germany).

Table 1.

Primers used for PCR amplification and sequencing of Alternaria genes.

Genes Primers References
ITS ITS1 White et al. 1990
ITS4
TEF1 EF1-728F Carbone and Kohn 1999
EF1-986R
RPB2 RPB2–5F2 Sung et al. 2007
RPB2–7cR Liu et al. 1999
GAPDH gpd 1 Berbee et al.1999
gpd 2
ATPase ATPDF1 Lawrence et al. 2013
ATPDR1
LSU LROR Rehner and Samuels 1994
LR7 Vilgalys and Hester 1990
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Phylogenetic analysis

The obtained sequences of ITS, LSU, GAPDH, RPB2, TEF1 and ATPase regions were checked and manually adjusted, when necessary, using BioEdit Sequence Alignment Editor v.7.0.4.1 (Hall 1999). Sequence alignments were conducted through the online version of the multiple sequence alignment program (MAFFT) v.7 (Katoh et al. 2019) using the default settings. Newly generated sequences were deposited in GenBank (Table 2).

Table 2.

Alternaria species used for phylogenetic analysis. Newly generated sequences are indicated in bold face.

Species Strain No Section Host Country GenBank accession numbers
GAPDH RPB2 TEF1 ITS LSU ATPase
A.abundans CBS 534.83 Chalastospora Fragaria sp. New Zealand KC584154 KC584448 KC584707 JN383485 KC584323 JQ671802
A.allii-tuberosi CBS 124112 Ulocladioides - China KF533907 - - - - -
A.alstroemeriae MAFF 241374 Alternaria Alstroemeria sp. Japan AB744034 LC275231 LC275050 AB678214 - -
A.alternantherae CBS 124392 Alternantherae Solanummelongena China KC584096 KC584374 KC584633 KC584179 -
A.alternariae CBS126989 Ulocladium Daucuscarota USA AY376329 KC584470 KC584730 AY376642 KC584346 -
A.alternata CBS 102598 Alternaria - - KP124184 KP124797 KP125105 MH862798 MH874394 JQ671884
CBS 916.96 Alternaria Arachishypogaea India AY278808 KC584375 KC584634 AF347031 - -
CBS 918.96 Alternaria Dianthus sp. UK AY278809 KC584435 KC584693 AF347032 KC584311 -
A.anthropophila FMR 16235 Infectoriae Human Spain LR537034 LR537040 LR537046 LR537444 - LR537052
A.arborescens CBS 102605 Alternaria Lycopersicon sp. USA AY278810 KC584377 KC584636 AF347033 NG_069124 -
A.argyranthemi CBS 116530 - Argyranthemum sp. New Zealand KC584098 KC584378 KC584637 KC584181 KC584254 -
A.armoraciae CBS 118702 Chalastospora Armoraciarusticana New Zealand KC584099 KC584379 KC584638 KC584182 KC584255 LR134098
A.aspera CBS 115269 Pseudoulocladium Pistaciavera Japan KC584166 KC584474 KC584734 KC584242 KC584349 -
A.atra CBS 195.67 Ulocladioides Soil USA KC584167 KC584475 KC584735 AF229486 KC584350 JQ671833
CBS 102060 Ulocladioides Soil Canada KC584174 KC584484 KC584744 FJ266486 MH874371 JQ671837
A.atrobrunnea FMR 16868 Infectoriae Human skin lesion Spain LR537039 LR537044 LR537051 LR537033 - LR537057
A.betae-kenyensis CBS 118810 Alternaria Betavulgaris Kenya KP124270 KP124888 KP125197 KP124419 NG_069256 MH10180
A.bornmuelleri DAOM 231361 Undifilum Securigeravaria Austria FJ357305 KC584491 KC584751 FJ357317 KC584366 JQ671791
A.botryospora CBS 478.90 Embellisioides Leptinelladioica New Zealand AY278831 KC584461 KC584720 AY278844 KC584336 JQ671779
A.brassicicola CBS 118699 Brassicicola Brassicaoleracea USA KC584103 KC584383 KC584642 JX499031 KC584259 -
A.brassicifolii CNU 111118 - Brassicapekinensis South Korea KM821537 - - JQ317188 - KY412558
A.breviconidio-phora MFLUCC 21-0786 Alternaria Digitalis sp. Italy OK236604 OK236651 OK236698 MZ621997 MZ621944 -
A.breviramosa CBS 121331 Chalastospora Triticum sp. Australia KC584148 KC584442 KC584700 FJ839608 KC584318 LR134099
A.brevirostra MFLUCC 21-0129 Radicina Plantago sp. Italy OK236619 OK236666 OK236717 MZ622015 - -
A.burnsii CBS 107.38 Alternaria Cuminumcyminum India JQ646305 KP124889 KP125198 KP124420 NG_069257 JQ671860
A.cantlous CBS 123007 Ulocladioides Cucumismelo China KC584171 KC584479 KC584739 KC584245 MH874786 -
A.alternarina CBS 119396 Infectoriae Avenasativa USA JQ646289 JQ905199 LR134367 JQ693648 JQ671817
A.celosiicola MAFF 243058 Alternantherae Celosiaargentea Japan AB744033 LC476781 LC480205 AB678217 - -
A.oblongo-obovoidea CBS 126317 Ulocladioides - China FJ266494 - - - - -
CBS 201.67 Ulocladioides - China FJ266495 JQ905212 JQ672439 - - JQ671839
A.caespitosa CBS 177.80 Infectoriae - Spain KC584178 KC584492 KC584752 MH861255 KC584367 -
A.cantlous MF-P 262011 Ulocladioides Carrot seed Russia MW658286 OQ262917 OQ262897 - - -
A.capsici-annui CBS 504.74 Ulocladium Capsicumannuum - KC584105 KC584385 KC584644 KC584187 KC584261 KC584385
A.caricis CBS 480.90 Nimbya Carexhoodia USA AY278826 KC584467 KC584726 AY278839 KC584342 JQ671780
A.castaneae CBS 124390 Ulocladioides - - KF533902 - - - - -
A.cetera EGS 41.072 Chalastospora Elymusscabrus Australia AY562398 KC584441 KC584699 JN383482 KC584317 JQ671801
A.chartarum MAFF 246888 Pseudoulocladium Capsicumannuum Japan LC482041 LC476826 LC480245 LC440618 KC584356 -
CBS 115269 Pseudoulocladium Pistaciavera Japan KC584166 KC584474 KC584734 NR_145169 NG_069147
A.cheiranthi CBS 109384 Cheiranthus Cheiranthuscheiri Italy KC584107 KC584387 KC584646 AF229457 KC584263 -
A.chlamydospora CBS 491.72 Phragmosporae Soil Egypt KC584108 KC584388 KC584647 KC584189 KC584264 JQ671786
A.chlamydosporigena CBS 341.71 Embellisia Air USA KC584156 KC584451 KC584710 KC584231 KC584326 -
A.conjuncta CBS 196.86 Infectoriae Pastinacasativa Switzerland AY562401 KC584390 KC584649 FJ266475 KC584266 JQ671824
A.consortialis CBS 104.31 Ulocladioides Cucumber leaf Russia KC584173 KC584482 KC584742 MH855147 MH866597 -
CBS 121493 Ulocladioides Brassicarapasubsp.Pekinensis China KC584170 KC584478 KC584738 NG_067641 KC584353 -
CBS 101229 Ulocladioides Cucumissativus New Zealand FJ266498 KC584485 KC584745 KC584618 KC584360 JQ671838
CBS 483.81 Ulocladioides Cucumissativus New Zealand AY562418 KC584483 KC584743 KC584616 KC584358 -
CBS 202.67 Ulocladioides - USA KC584177 KC584490 KC584750 NR_103600 NG_069728 JQ671835
CBS 198.67 Ulocladioides Soil USA KC584169 KC584477 KC584737 KC584610 KC584352 -
A.cumini CBS 121329 Eureka Cuminumcyminum India KC584110 KC584391 KC584650 KC584191 KC584267 -
A.cylindrica MAFF 246770 Alternaria Petuniaatkinsiana USA LC482006 LC476791 LC480211 LC440584 - -
A.dactylidicola MFLUCC 15-0466 Infectoriae Loliummultiflorum China MK051155 MK051157 - NG_063635 NG_069434 -
A.daucifolii CBS 118812 Alternaria Daucuscarota USA KC584112 KC584393 KC584652 KC584193 NG_069131 MH101801
A.dennisii CBS 476.90 - Seneciojacobaea Isle of Man JN383469 KC584454 KC584713 JN383488 KC584329 -
A.dianthicola CBS 116491 Dianthicola Dianthus sp. New Zealand KC584113 KC584394 KC584653 KC584194 KC584270 -
A.dongshanqi-aoensis DSQ2.2 Alternaria Chinese fir leaf China OR252415 OR252511 OR233901 OR229433 OR229638 -
A.eichhorniae CBS 489.92 Alternaria Eichhorniasp. India KP124276 KP124895 KP125204 KC146356 KP124579 MH101806
A.elegans CBS 109159 Dianthicola Lycopersiconesculentum Burkina Faso KC584114 C584395 KC584654 KC584195 KC584271 -
A.embellisia CBS 339.71 Embellisia Alliumsativum USA KC584155 KC584449 KC584708 KC584230 KC584324 -
A.ershadii IRAN 3275C Pseudoalternaria Wheat Iran MK829645 - - MK829647 - MK829643
A.ethzedia CBS 197.86 Infectoriae Brassicanapus Switzerland AY278795 KC584398 KC584657 NG_062882 NG_069134 JQ671805
A.eupatoriicola MFLUCC 21-0122 Alternaria Eupatorium sp. Italy OK236589 OK236636 OK236683 MZ621982 MZ621929 -
A.euphorbiacola CBS 119410 Radicina Euphorbia sp. USA KJ718018 - KJ718521 KJ718173 - KJ718346
A.eureka CBS 193.86 Eureka Medicagorugosa Australia JN383471 KC584456 KC584715 JN383490 KC584331 JQ671771
A.gaisen CBS 632.93 Alternaria Pyruspyrifolia UK KC584116 KC584399 KC584658 KC584197 KC584275 -
A.geniostomatis CBS 118701 Eureka Geniostoma sp. N. Zealand KC584117 KC584400 KC584659 KC584198 KC584276 -
A.geophila CBS 101.13 Alternaria Peat soil Switzrland KP124244 KP124862 KP125170 KP124392 - KP124862
A.gomphrenae MAFF 246769 Alternantherae Gomphrenaglobosa Japan LC481999 LC476782 LC480206 LC440579 - -
A.graminicola CBS 119400 Infectoriae Solanaceae Algeria MK904514 LR134180 LR134249 NR_136024 MK913529
A.guarroi FMR 16556 Infectoriae Human skin lesion Spain LR537037 LR537045 LR537050 LR537031 - LR537056
A.halotolerans CBS 146348 Infectoriae Qatar KY387604 - KY387608 KY387606 - -
A.helianthiinfi-ciens CBS 117370 Helianthiinficientes Helianthusannuus UK KC584119 KC584402 KC584661 KC584200 KC584279 -
A.hyacinthi CBS 416.71 Embellisioides Hyacinthussp. Netherlands KC584158 KC584457 KC584716 KC584233 KC584332 JQ671778
A.indefessa CBS 536.83 Cheiranthus Soil USA KC584159 KC584458 KC584717 KC584234 KC584333 JQ671831
A.infectoria CBS 210.86 Infectoriae Triticumaestivum UK DQ323697 KC584404 KC584662 DQ323697 KC584280 -
A.hordeiaus-tralica CBS 119402 Infectoriae Hordeumvulgare Australia JQ646283 LR134179 LR134243 NR_136018 - JQ671811
A.inflata FMR 16477 Pseudoalternaria - - MT108483 - - MT109376 MT108479
A.intercepta CBS 119406 Infectoriae Viburnum sp. Netherlands FJ214831 LR134170 FJ214927 NR_135957 JQ671826
A.juxtiseptata CBS 119673 Gypsophilae Gypsophila sp. Australia KC584122 KC584406 KC584664 KC584202 KC584282 -
A.lathyri MFLUCC 21-0140 Alternaria Lathyrus sp. Italy OK236581 OK236628 OK236675 MZ621974 MZ621921 -
A.leucanthemi CBS 421.65 Teretispora Chrysanthemummaximum Netherlands KC584164 KC584472 KC584732 KC584240 KC584347 -
A.limaciformis CBS 481.81 Phragmosporae Soil UK KC584123 KC584407 KC584665 KC584203 KC584283 JQ671798
A.limoniasperae CBS 102595 Alternaria Citrusjambhiri USA AY562411 KC584408 KC584666 FJ266476 KC584284 JQ671879
A.lolii CBS 115266 Embellisioides Loliumperenne N. Zealand JN383473 KC584460 KC584719 JN383492 KC584335 JQ671774
A.longipes CBS 540.94 Alternaria Nicotianatabacum USA AY278811 KC584409 KC584667 AY278835 KC584285 -
A.malicola CGMCC3.18704 Ulocladioides - China MF426953 MF426957 MF426959 - - -
A.malorum CBS 135.31 Chalastospora - - JQ646278 JQ646481 JQ672413 JQ693638 - JQ693638
A.merytae CBS 119403 Infectoriae - USA JQ646292 LR134119 LR134198 NR_136025 JQ671820
A.metachroma-tica EGS 38.132 Infectoriae - China AY762956 JQ905189 JQ672437 JQ693660 - JQ671809
A.microspora CBS 124391 Ulocladioides - - KF533901 JQ905206 - - - -
A.momordicae YZU 161378 Alternaria Momordicacharantia China OR887691 OR887689 OR887687 OR883774 - -
A.mouchaccae CBS 119671 Phragmosporae Soil Egypt AY562399 KC584413 KC584671 KC584206 LC776460 JQ671799
A.myanmarensis YZU 231736 Alternaria Helianthusannuus Myanmar OR963612 PP508256 OR963615 OR897031 - -
A.nepalensis CBS 118700 Japonicae Brassica sp. Nepal KC584126 KC584414 KC584672 KC584207 KC584290 -
A.obclavata CBS 124120 Chalastospora Air USA KC584149 KC584443 KC584701 KC584225 FJ839651 LR134100
A.oblongoellip-soidea MFLUCC 22-0074 Alternaria Cichorium sp. Italy OK236574 OK236621 OK236668 MZ621967 MZ621914 -
A.obovoidea CBS 101229 Ulocladioides Cucumissativus New Zealand FJ266498 KC584485 KC584745 FJ266487 KC584360 -
A.omanensis SQUCC 15560 Omanenses Dead wood Oman MK880900 MK880894 MK880897 MK878563 MK878557 -
SQUCC 13580 Omanenses Dead wood Oman MK880899 MK880893 MK880896 NG_074901 MK878556 -
A.ouedrighensis G92 = CBS 152587 = MEND-F-1168 Embellisia Phoenixdactylifera L. Algeria OP985422 OP985434 OP985443 OP295213 PQ349940 -
A.panax CBS 482.81 Panax Araliaracemosa USA KC584128 KC584417 KC584675 KC584209 KC584293 -
A.papavericola CBS 116608 Crivellia Papaverrhoeas Austria FJ357299 KC584440 KC584698 FJ357311 KC584321 -
A.paragomph-renae MAFF 246768 Alternantherae Gomphrena sp. Japan LC482000 LC476783 LC480207 – - -
A.parvicaespi-tosa LEP 014858 Pseudoalternaria Diseased wheat heads Iran MF033842 - - MF033859 - KJ908217
A.penicillata CBS 116608 Crivellia Papaversomniferum USA FJ357299 KC584440 KC584698 FJ357311 KC584316 -
A.perpunctulata CBS 115267 Alternantherae Alternantheraphiloxeroides USA KC584129 KC584418 KC584676 KC584210 KC584294 JQ671893
A.phoenicis G11 = CBS 152585 = MEND-F-1166 Ulocladioides Phoenixdactylifera L. Algeria OP985418 OP985431 OP985440 OP295203 PQ349938 OP985453
A26 Ulocladioides Phoenixdactylifera L. Algeria OP985416 OP985432 OP985441 OP295200 PQ349937 OP985444
A28 Ulocladioides Phoenixdactylifera L. Algeria OP985417 OP985433 OP985442 OP295201 PQ349939 OP985445
A.photistica CBS 212.86 Panax Digitalispurpurea UK KC584131 KC584420 KC584678 KC584212 KC584296 JQ671807
A.phragmos-pora CBS 274.70 Phragmosporae Soil Netherlands JN383474 KC584462 KC584721 JN383493 KC584337 JQ671797
A.preussii CBS 102062 Ulocladioides - USA FJ266495 JQ905212 - - - -
A.phytolaccae MFLUCC 21-0135 Radicina Phytolaccaamericana Italy OK236616 OK236663 OK236719 MZ622013 MZ621961 -
A.qatarensis CBS 146387 Chalastospora Sea water Qatar KY387603 - KY387607 KY387605 KY781811 -
A.radicicola NB830 Embellisia Daucuscarota Algeria OP297090 OP320887 OP320893 OR085521 - -
A.radicina CBS 245.67 Radicina Daucuscarota USA KC584133 KC584423 KC584681 NG067633 NG_069139 JQ671851
A.rostroconidia MFLUCC 21-0136 Alternaria Arabis sp. Italy OK236576 OK236623 OK236670 MZ621969 MZ621916 -
A.salicicola MFLUCC 22.0072 Alternaria Aster sp. Russia OK236606 OK236653 OK236700 MZ621999 MZ621946 -
A.scirpicola CBS 481.90 Nimbya Scirpus sp. UK KC584163 KC584469 KC584728 KC584237 KC584344 -
A.selini CBS 109382 Radicina Petroselinum sp. Saudi Arabia AY278800 KC584426 KC584684 AF229455 NG_069140 JQ671853
A.slovaca CBS 567.66 Infectoriae Homosapiens Slovakia KC584150 KC584444 KC584702 KC584226 KC584319 LR134368
A.smyrnii CBS 109380 Radicina Smyrnium sp. UK KC584138 KC584429 KC584687 AF229456 KC584305 -
A.soliaridae CBS 118387 - Soil USA KC584140 KC584431 KC584689 KC584218 KC584307 -
A.subcucurbitae CBS 123376 Ulocladioides - China KC584176 KC584488 KC584748 MH863292 MH874816 -
CBS 121491 Ulocladioides Oxybasisglauca China EU855803 KC584489 KC584749 NR_136053 NG_069148 -
A.tellustris CBS 538.83 Embellisia Soil USA AY562419 KC584465 KC584724 FJ357316 KC584340 JQ671794
A.thalictrigena CBS 121712 - Thalictrum sp. Germany KC584144 KC584436 KC584694 EU040211 KC584312 -
A.tomato CBS 114.35 Alternaria Solanum sp. Unknown KP124295 KP124916 KP125225 KP124446 KP124600 -
A.torilis MFLUCC 14-0433 Alternaria Torilis sp. Italy OK236593 OK236640 OK236687 MZ621986 MZ621933 -
A.triangularis MAFF 246776 - Bupleurumrotundifolium Japan LC482050 LC476837 LC480255 LC440629 - -
A.triticimacul-ans CBS 578.94 Infectoriae Triticumaestivum Argentina FJ214834 LR134183 FJ214930 NR_136030 - -
A.vaccariicola CBS 118714 Gypsophilae Vaccariahispanica USA KC584147 KC584439 KC584697 KC584224 KC584315 -
A.vignae YZU 171714 Helianthiinficientes Vignaunguiculata China OK094678 OL763423 OL763421 OL739889 - -
A.yamethinen-sis YZU 231739 Alternaria Helianthusannuus Myanmar OR963610 PP179253 OR963614 OR889008 - -
A.zantedesch-iae CBS 124113 Ulocladioides - - KF533900 - - - - -
Cicatriceasalina CBS 302.84 - Cancerpagurus North Sea JN383467 KC584450 KC584709 JN383486 - JQ671766
Stemphyliumbotryosum CBS 714.68 - Medicagosativa Canada OR269991 - KC584729 NR_163547 NG_069738 -
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The phylogenetic analysis was conducted through Maximum Likelihood (ML) and Maximum Parsimony (MP) methods using MEGA11 v.11.0.13 (Tamura et al. 2021). The best-fit evolutionary model was determined automatically by MEGA11 software. The ML analysis was conducted using heuristic searches consisted of 1000 step utilizing the Nearest-Neighbour-Interchange (NNI) algorithm with a Neighbour-Joining starting tree automatically generated. Whereas for the MP analysis, the Tree-Bisection-Regrafting (TBR) algorithm was applied. One thousand (1000) bootstrap replications were conducted to evaluate the generated MP trees robustness. CicatriceasalinaCBS 302.84 and StemphyliumherbarumCBS 191.86 were used as outgroup taxa.

Results

Phylogenetic analyses

The PCR amplification of the LSU, ITS, GAPDH, RPB2, TEF1 and ATPase regions yielded DNA fragments of about 1200, 600, 580, 950, 300 and 1200 bp, respectively. Given the lack of the ATPase sequences for several species of the Alternaria genus and the majority of the species in the Ulocladioides sections, this marker has been discarded from the phylogenetic analysis. Those, the concatenated LSU, ITS, GAPDH, RPB2, and TEF1 datasets consisted of 90 strains corresponding to 78 species and two outgroup taxa. The alignment contained 2915 characters of which 2031 were constant, 23 were excluded, 161 were variable and parsimony-uninformative and 700 were parsimony-informative. Maximum parsimony (MP) analyses of combined dataset produced a single most parsimonious tree (score = 3577, CI = 0.327, RI = 0.684 and HI = 0.673), which resulted in the identification of the strains. Furthermore, maximum likelihood analyses on concatenated dataset yielded a phylogenetic tree (Fig. 2), which was similar with maximum parsimony tree in terms of either major topology or results. So, it was chosen for the phylogeny demonstration. Alignment and phylogenetic trees were deposited at TreeBASE (ID: 31850).

Figure 2.

Figure 2.

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Phylogenetic tree based on the maximum likelihood analysis of Alternaria species inferred from combined LSU, ITS, GAPDH, RPB2 and TEF1. Maximum likelihood (ML) and maximum parcimony (MP) bootstrap values (≥ 50%) given at the nodes (ML/MP) are computed at from 1000 replicates. The tree is rooted to Cicatriceasalina (CBS 302.84) and Stemphyliumherbarum (CBS 191.86). The novel species are highlighted in bold. The monotypic lineages are indicated by black dots.

In the phylogenetic analysis, all the clades corresponding to the Alternaria sections were well resolved. Of these, 2 clades corresponding to the sections Ulocladioides and Embellisia encompassed the strains of this study. The isolates G11, A26 and A28 formed independent well-supported subclade with high bootstrap support (100% ML and 94% MP; Fig. 2) within the section Ulocladioides and were considered to represent a distinct species, which was described here as Alternariaphoenicis sp. nov. The strain G92 clustered within the section Embellisia with a high boostrap support (100% ML and 94% MP; Fig. 1), but was phylogenetically different from the closest species within the section. It represented a further distinct species, which was described here as Alternariaouedrighensis sp. nov. (Fig. 2).

Taxonomy

. Alternaria phoenicis

Y. Djellid, A. E. Mahamedi, F. Lamghari & A. Berraf-Tebbal sp. nov.

81F77603-8411-5874-9CC8-D9BF375059FD

856854

Fig. 3

Figure 3.

Figure 3.

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Morphology of Alternariaphoenicis. Colony on PDA after 7 days at 25 °C (A); Conidiophores and conidiogenouse cells (B, C); Conidia (D–M). Scale bars: 10 μm.

Type.

Algeria • Ghardaia Province (32°10'18.174"N, 3°34'56.6976"E), on symptomatic leaflet and rachis of Phoenixdactylifera L., 2017, Y Djellid, (MEND-F-1166, holotype), ex-type culture CBS 152585.

Etymology.

Named after the host genus (Phoenix) from which the fungus was isolated.

Description.

Colonies on PDA reaching 75 mm diam. after 7 d at 25 °C, circular, cottony with dense hyphae, off-white to light grey in the center, reverse buff to dark brown in the center. Minimum temperature for growth 5 °C, optimum 25 °C, maximum 37 °C. On Potato dextrose agar (PDA; Fig. 3), conidiophores arising directly from lateral of aerial hyphae, straight or curved, geniculate, smooth-walled, with up to 5–septate, unbranched or with up to two branches, pale brown; Conidia solitary, subcylindrical to obclavate, (18.1–) 21.4 – 29.1 (–38.8) × (7.4–) 9.7 – 12.8 (–14.8) μm, (av. 25.3 ± 3.9 × 11.2 ± 1.6), non-beaked with a narrow base, light brown, with some darkened middle transverse septa, 3–6 transverse septa, and 0–1 longitudinal or oblique septa per transverse segment; these primary conidia produce secondary conidiophores that consist in a subapical extension from the conidial body. Sexual morph not observed.

Notes.

Phylogenetically, this species grouped within Ulocladioides section but was different from the closest species (A.malicola, A.preussii and A.cantlous) in a distinct lineage with 100% ML / 94% MP statistical support. Alternariaphoenicis sp. nov. is different from its sister species A.malicola, A.preussii and A.cantlous, based on sequences derived from five loci (Fig. 2). After conducting a nucleotide pairwise comparison as recommended by Jeewon and Hyde (2016), the present species can be distinguished from the closet species A.malicola, A.preussii and A.cantlous. Based on GAPDH, RPB2 and TEF1 genes, A.phoenicis sp. nov. has 7 bp differences (2%, no gap) in GAPDH, 1 bp (1%, no gap) in RPB2 and 29 bp (7%, 6 gaps) in TEF1 when compared to A.malicola. Alternariapreussii presents 5 bp differences (2%, no gap) in GAPDH and 11 bp (2%, no gap) in RPB2. However, A.cantlous shows 1 bp difference (1%, no gap) in RPB2 and 29 bp (11%, 6 gaps) in TEF1. Morphologically, A.phoenicis (Fig. 3) can be distinguished by having narrower conidia (7.4–14.8 µm) compared to the three closely related species: A.cantlous (7.4–14.8 µm), A.preussii (13.0–13.7 µm), and A.malicola (8–16 µm). In terms of length, its conidia are shorter than those of A.cantlous (24–36 µm) but longer when compared to A.preussii (18.3–20.4 µm). However, the conidial length of A.malicola (16–35 µm) is comparable to that of A.phoenicis (18.1–38.8 µm). Regarding the conidial septation, A.phoenicis is characterized by multiple transverse septa (up to 6). In contrast, its closely related species exhibit fewer transverse septa, up to four in A.canlous and up to three in both A.preussii and A.malicola. Additionally, A.phoenicis has the fewest longitudinal septa (0–1), compared to A.preussii (1–2), A.malicola (1–5), and A.canlous (0–2) (Runa et al. 2009; Wang et al. 2010; Dang et al. 2018).

. Alternaria ouedrighensis

, A. Berraf-Tebbal, A. E. Mahamedi, F. Lamghari, E. Hakalova & Y. Djellid sp. nov.

48EB7EF0-1DD2-585E-B318-2928F954C490

856855

Fig. 4

Figure 4.

Figure 4.

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Morphology of Alternariaouedrighensis. Colony on PDA after 7 days at 25 °C (A); Conidiophores and conidiogenous cells (B, C); Conidia (D–M) Scale bars: 10 μm.

Type.

Algeria • Biskra Province (34°44'16.0152"N, 5°22'10.1064"E), on symptomatic leaf of Phoenixdactylifera L. 2017, Y Djellid (MEND-F-1168, holotype), ex-type culture CBS 152587.

Etymology.

Named after the valley of Oued Righ from which the fungus was collected.

Description.

Colonies on Potato dextrose agar (PDA) reaching 51 mm diam. after 7 d at 25 °C, circular with concentric zonation of the growth, cottony with dense hyphae, dark green, reverse dark brown, with a white halo at the edge. Minimum temperature for growth 5 °C, optimum 25 °C, maximum 37 °C. On PDA media (Fig. 4), conidiophores arising directly from lateral of aerial hyphae, straight or curved, geniculate sympodial proliferation, verruculose thick-walled, with up to 12–septate, unbranched or with up to three branches, light to dark brown; Conidia solitary, ovoid to subcylindrical, (11.4–) 15.3 – 17.7 (–24.1) × (7.7–) 9.9 – 10.9 (–12.9) μm (av. 16.5 ± 3.4 × 10.4 ± 1.4), light brown to dark, rigid, and thickened transverse septa, 1–3 transverse septa, and 0–1 longitudinal or oblique septa per transverse segment; these primary conidia produce secondary conidiophores that consist of a subapical extension from the conidial body. Sexual morph not observed.

Note.

Phylogenetically A.ouedrighensis formed a sister branch with A.embellisia, A.chlamydosporigena, A.radicicola and A.tellustris in Embellisia section with 100% ML/100% MP bootstrap support. Alternariaouedrighensis sp. nov. is different from its sister species A.radicicola, A.embellisia and A.tellustris based on sequences derived from five genes (Fig. 2). After conducting a nucleotide pairwise comparison as recommended by Jeewon and Hyde (2016), the present species can be readily distinguished from the closet species A.radicicola, A.embellisia and A.tellustris constructed on any of the LSU, ITS, GAPDH, RPB2 and TEF1 genes, which has 3 bp difference (1%, no gap) in the ITS region, 6 bp (2%, no gap) in GAPDH, 16 pb (2%, no gap) in RPB2 and 15 bp (11%, 14 gap) in TEF1 when compared with A.radicicola, 1 bp (1%, no gap) in LSU, 6 bp (2%, no gap) in ITS, 24 bp (4%, 1 gap) in GAPDH, 17 bp (2%, 1 gap) in RPB2, and 17 bp (11%, 13 gaps) in TEF1 when compared with A.embellisia, and 1 bp (1%, no gap) in LSU, 3 bp (1%, no gap) in ITS, 12 bp (2%, 1 gap) in GAPDH, 17 bp (2%, no gap) in RPB2 and 13 bp (9%, 14 gaps) in TEF1 with sister species A.tellustris.

Morphologically, A.ouedrighensis (Fig. 4) is distinct from the closest species A.embellisia in conidial body size. Alternariaouedrighensis has conidia shorter and wider (11.4–24.1 × 7.7–12.9 μm; av. 16.5 ± 3.4 × 10.4 ± 1.4 µm) than those of A.radicicola (20–38 × 7–10 µm; Bessadat et al. 2025) and A.embellisia (19.18–36.2 × 2.55–5.74 µm; av. 12.64 × 4.34 µm; Delgado Ortiz et al. 2019). In addition, the conidia of A.ouedrighensis present fewer transverse septa (1–3 transverse septa) than those of A.radicicola (3–5 transverse septa) and A.embellisia (2 – 6 transverse septa). However, A.ouedrighensis presents fewer longitudinal septa (0–1 septum) compared to A.embellisia (1 – 2 septa).

Discussion

In this study, two new species of Alternaria, A.phoenicis and A.ouedrighensis, have been identified within the sections Ulocladioides and Embellisia, respectively. These species were characterized and illustrated through comprehensive morphological studies and a detailed polylocus phylogenetic analysis, which provides robust support for their classification within the genus. Both species are associated with black spot and blight diseases symptoms on date palm (Phoenixdactylifera L.). These diseases present a range of symptoms that can significantly compromise the health and productivity of this host tree. Black spot disease typically manifests as dark, circular lesions on the leaves, often surrounded by a yellow halo, which may merge to form larger necrotic areas. This condition can lead to premature fall of the leaves, thereby substantially reducing the photosynthetic capacity of the plant (Elmer and Pscheidt 2014). While the blight disease symptoms are characterized by rapid wilting and dieback of fronds. The affected leaves exhibit browning that typically initiates at the tips and progresses inward, leading to significant tissue necrosis and overall leaf decline, which can result in wilting and dieback. These conditions can impact the structural integrity and physiological function of the date palm (Namsi et al. 2019).

Alternariaphoenicis, the newly described species, forms a clearly separate cluster within the section Ulocladioides, in the multi-locus phylogenetic trees derived by analyses of a concatenated DNA sequence dataset. This section encompasses a diverse group of species recognized for their significant ecological roles and potential agricultural impacts. They are mostly known as saprotrophs on a variety of host substrates as well as opportunistic human pathogens (Runa et al. 2009; Lawrence et al. 2016; Gannibal and Gomzhina 2024). The Ulocladioides section was introduced in 2013 by Woudenberg et al. to accommodate species previously classified under Ulocladium section. Thus, the Ulocladioides section included 20 species typified by Alternariacucurbitae. Recently, Gannibal and Gomzhina (2024) assessed the species boundaries within the Ulocladioidessectionby using multilocus phylogenetic analysis based on the genealogical concordance phylogenetic species recognition (GCPSR) principle. They also utilized the coalescent-based model Poisson tree processes (PTP, mPTP) and evaluated for the presence of recombination. As a result, they suggested to eradicate nine species by joining four other species. Alternariaatra and A.multiformis were united into the single species A.atra. Five species, A.brassicae-pekinensis, A.consortialis, A.cucurbitae, A.obovoidea, and A.terricola, were combined in the species A.consortialis. Alternariaheterospora and A.subcucurbitae were combined into one species, A.subcucurbitae. Alternariaaspera, A.chartarum, A.concatenata, and A.septospora were combined into a single species, A.chartarum. Morphologically, species within this section can be identified by their short, geniculate conidiophores, with sympodial proliferations and obovoid, non-beaked conidia, with a narrow base, single or in chains (Woudenberg et al. 2013; Li et al. 2023).

The second new species A.ouedrighensis is introduced and classified in section Embellisia within the genus Alternaria. This section was established to include previously described species under the genus Embellisia (Lawrence et al. 2012). It is currently limited to only four species: A.embellisia Woudenb. & Crous, the type species, along with A.chlamydosporigena Woudenb. & Crous, A.tellustris (E.G. Simmons) Woudenb. & Crous and A.radicicola Bessadat & Simoneau (Woudenberg et al. 2013; Li et al. 2023; Bessadat et al. 2025). Phylogenetic analyses revealed the close relationships among these four species and highlight their evolutionary ties to other sections of the Alternaria genus. Notably, these species exhibit consistent morphological traits, including thick, dark, and rigid conidial septa, along with a limited presence of longitudinal septa, which serve as identification keys. Additionally, members of this section have been recognized as pathogens that impact various vegetable crops, particularly tomato and garlic (Simmons 2001; Woudenberg et al. 2013). Although A.ouedrighensis is currently represented by a single isolate, its recognition as a new taxon remains valid, consistent with previous studies (Crous et al. 2015; Lücking et al. 2021), that have formally described novel species based on distinct phylogenetic placement and unique morphological characteristics. Consequently, it is necessary to set up larger surveys and isolations that include more phoenicical production areas to better understand the diversity and intraspecific variability within Alternaria species.

The identification of these new species not only enriches our understanding of the diversity within the Alternaria genus but also emphasizes the necessity for effective management strategies to minimize the impact of this genus on plant health and productivity.

Supplementary Material

XML Treatment for Alternaria phoenicis
XML Treatment for Alternaria ouedrighensis

Citation

Djellid Y, Mahamedi AE, Spetik M, Hakalová E, Eichmeier A, Gonçalves MFM, Lamghari F, Al Hmoudi MASM, Berraf-Tebbal A (2025) Alternaria phoenicis sp. nov. and Alternaria ouedrighensis sp. nov. (Pleosporales, Pleosporaceae): Two new species associated with leaf spot and blight diseases of date palm (Phoenix dactylifera L.). MycoKeys 120: 295–315. https://doi.org/10.3897/mycokeys.120.144245

Funding Statement

IGA-ZF/2021-ST2003 UIDP/50017/2020 + UIDB/50017/2020 + LA/P/0094/2020

Additional information

Conflict of interest

The authors have declared that no competing interests exist.

Ethical statement

No ethical statement was reported.

Use of AI

No use of AI was reported.

Funding

This study was supported by the Internal Grant of Mendel University in Brno with the grant number IGA-ZF/2021-ST2003. Micael F.M. Gonçalves thanks the FCT – Fundação para a Ciência e a Tecnologia I.P., under the project/grant UID/50006 + LA/P/0094/2020 (doi.org/10.54499/LA/P/0094/2020) and his contract 2022.00758.CEECIND/CP1720/CT0051 (doi.org/10.54499/2022.00758.CEECIND/CP1720/CT0051). The authors gratefully acknowledge the Fujairah Research Centre, UAE for the financial support.

Author contributions

Berraf-Tebbal A conceptualized and designed the study, Djellid Y, Mahamedi AE conducted the investigation, Djellid Y, Gonçalves MFM, Spetik M, Hakalova E, Al Hmoudi MASM conducted the experiments, Mahamedi AE analysed the data, Berraf-Tebbal A, Djellid Y, Mahamedi AE wrote and revised the original draft, Lamghari F, Eichmeier A ensured the project administration, all authors reviewed the final manuscript.

Author ORCIDs

Youssef Djellid https://orcid.org/0009-0007-6833-5439

Alla Eddine Mahamedi https://orcid.org/0000-0002-9744-8973

Milan Spetik https://orcid.org/0000-0001-7659-8852

Eliska Hakalová https://orcid.org/0000-0002-5433-8993

Ales Eichmeier https://orcid.org/0000-0001-7358-3903

Micael Ferreira Mota Gonçalves https://orcid.org/0000-0003-2295-3374

Fouad Lamghari https://orcid.org/0009-0002-2789-2240

Maryam Ali Saeed Mohamed Al Hmoudi https://orcid.org/0009-0005-9207-4924

Akila Berraf-Tebbal https://orcid.org/0000-0001-8517-8542

Data availability

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

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

XML Treatment for Alternaria phoenicis
mycokeys.120.144245-treatment1.xml (25.3KB, xml)
XML Treatment for Alternaria ouedrighensis
mycokeys.120.144245-treatment2.xml (25KB, xml)

Data Availability Statement

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

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