24 Apr Boeremia

Boeremia Aveskamp, Gruyter & Verkley, in Aveskamp, Gruyter, Woudenberg, Verkley & Crous, Stud. Mycol. 65: 36 (2010)

Background

Boeremia was established by Aveskamp et al. (2010) to accommodate phoma-like species that are morphologically similar to Phoma exigua. To date only B. lycopersici is reported to have a sexual morph (Chen et al. 2015).

Classification—Dothideomycetes,  Pleosporomycetidae, Pleosporales, Didymellaceae

Type species—Boeremia exigua (Desm.) Aveskamp, Gruyter & Verkley, in Aveskamp, Gruyter, Woudenberg, Verkley & Crous, Stud. Mycol. 65: 37 (2010)

Distribution—Worldwide

Disease Symptoms—Black node, Bulb rot, Canker, Leaf spots, Stem rot, Shoot dieback, Tan spot

All foliar parts of a plant can be affected. Dark brown sunken lesions form at the base of the plant and eventually expand to girdle the stem, resulting in yellowing and wilting of the older leaves. This will lead to the death of the plant. Fruit infection starts as a water soaked lesion that progress rapidly into a sunken brown/black/gray lesion with concentric rings. Leaf lesions begin as small spots that develop into brown/gray lesions with concentric rings (Jones et al. 2011; Zhao et al. 2016).

Hosts—Amaryllidaceae, Apocynaceae, Araliaceae, Caprifoliaceae, Chenopodiaceae, Crassulaceae, Faba– ceae, Lamiaceae, Linaceae, Oleaceae, Rubiaceae, Sali– caceae, Solanaceae, Ulmaceae and Umbelliferae (Farr and Rossman 2019).

Morphological based identification and diversity

This genus is characterized by variable conidial shape, aseptate to 2-septate conidia in the asexual morph and a sexual morph with ellipsoidal, 1-septate ascospores. Index Fungorum lists 13 species and 12 varieties of Boeremia exigua (Index Fungorum 2019). Naming of species of Boeremia and varieties of B. exigua is mainly based on host association (Aveskamp et al. 2010; Jayasiri et al. 2017). Some B. exigua varieties and Boeremia sp. are host- specific, while others seem to have a very broad host range. Original epithets of Boeremia (and Phoma) species and varieties were based on the hosts from which they were collected and later, characters from artificial culture media were used (Boerema et al. 2004). Molecular phylogenetics has only recently been employed to separate these taxa and this has often necessitated renaming (Aveskamp et al. 2010). Thus, nomenclature is still confused (Berner et al. 2015). Colony and conidial morphology are the primary characters to identify species within this genus. However, using these characters alone in identification can cause errors as these characters may overlap between species. Therefore, it is important to use DNA sequence data when identifying species of this genus (Chen et al. 2015, 2017; Marin-Felix et al. 2017).

Molecular based identification and diversity

Recent studies on the taxonomy of Boeremia have employed molecular methods to reveal the phylogenetic relationships among species (Aveskamp et al. 2010). Berner et al. (2015), Chen et al. (2015, 2017), Marin-Felix et al. (2017) and Jayasiri et al. (2017) revisited the genus and described new species. This study reconstructs the phylogeny using a combined LSU, RPB2, ITS, TUB2 and TEF1-a sequence dataset. In this study, we elevate the varieties of B. exigua and change the status of ten species based on combined phylogenetic analysis as well as synonymise three varieties under B. exigua. Until further collections are found, herein we propose to keep CBS 119730 as Boeremia sp. Based on the multigene concatenated phylogenies we accept 22 species in this genus.

Boeremia coffeae (Henn.) Jayasiri, Jayaward. & K.D. Hyde, comb. nov. IF555804

≡ Ascochyta coffeae Henn., Hedwigia 41: 307 (1902)

≡Boeremia exigua var. coffeae (Henn.) Aveskamp et al., Stud. Mycol. 65: 37 (2010)

Reference Strain: CBS 109183 (= reference specimen sensu Boerema et al. 2004; Aveskamp et al. 2010; Chen et al. 2015).

For a complete description see de Gruyter et al. (2002).

This species was described from leaves of coffee plants as Ascochyta coffeae. Based on phylogenetic analyses, Aveskamp et al. (2010) placed this species in the Boeremia exigua species complex. In our phylogenetic analyses based on LSU, RPB2, ITS, TUB2 and TEF1-a, the reference strain of this species is closely related with the type strain of B. rhapontica (Fig. 2). However, B. coffeae can be differentiated from B. rhapontica by smaller pycnidia (70–80 lm vs 4–6 lm) (de Gruyter et al. 2002; Berner et al. 2015). Aveskamp et al. (2010) listed two strains under this species, CBS 119730 and CBS 109183 even though they do not cluster together in the combined multigene analysis of LSU, ITS and TUB2. CBS 119730 strain was introduced by Stewart (1957) as Ascochyta tarda, the causal agent of coffee leaf blight and stem die- back. In the combined multigene analyses of Jayasiri et al. (2017) and this study the above mentioned two strains do not cluster together. When we compared the base pair differences among these two strains, we found that CBS 119730 has 1 bp, 9 bp and 5 bp differences in ITS, RPB2 and TUB2 regions respectively. CBS 119730 differs from B. coffeae in having larger pycnidia (70–110 lm vs 70–80 lm) and conidia (9–14 lm vs 50–199 lm). According to the original description, CBS 119730 has been observed to occur together with a Mycosphaerella sp., however, the connection between these species have not yet been proven. Therefore, here we assign CBS 109183 as the reference strain (= reference specimen sensu Ariyawansa et al. 2014) for this species and keep CBS 119730 as Boeremia sp. until further collection is found.

Boeremia exigua (Desm.) Aveskamp, Gruyter & Verkley, Aveskamp et al., Stud. Mycol. 65: 37 (2010) IF515624

≡ Phoma exigua Desm. Annls Sci Nat Bot se´r 3 11(2): 282(1849)

= Boeremia exigua var. forsythia (Sacc.) Aveskamp, Gruyter & Verkley, Aveskamp et al., Stud. Mycol. 65: 37 (2010)

= Boeremia exigua var. viburni (Roum. ex. Sacc.) Aveskamp, Gruyter & Verkley, Aveskamp et al., Stud. Mycol. 65: 37 (2010)

Reference Strain: CBS 431.74 (= reference specimen sensu Boerema et al. 2004; Aveskamp et al. 2010; Chen et al. 2015).

For a complete description see Aveskamp et al. (2010).

This is the type species of the genus Boeremia. Boerema et al. (2004) assigned a reference strain (= reference specimen sensu Ariyawansa et al. 2014) for this species as CBS 431.74 and this was followed in the studies of Aveskamp et al. (2010), Chen et al. (2017) and Jayasiri et al. (2017). In the multigene phylogenetic analyses of this study, B. exigua var. forsythia and B. exigua var. vibruni clustered together with the reference strain of B. exigua (CBS 431.74). Sequences of B. exigua (CBS 431.74) and B. exigua var. forsythia (CBS 101213) are almost identical, with only 1 bp difference in each ITS and RPB2 gene regions. Between B. exigua and B. exigua var. vibruni (CBS 100354) we found only 1 bp difference in the RPB2 region. Therefore, in this study we synonymise B. exigua var. forsythia and B. exigua var. vibruni under B. exigua.

Boeremia gilvescens (Aveskamp et al.) Jayaward., Jayasiri & K.D. Hyde, comb. nov. stat. nov. IF555805

≡Boeremia exigua var. gilvescens Aveskamp, Gruyter & Verkley, Aveskamp et al., Stud. Mycol. 65: 37 (2010)

Holotype: The Netherlands, Baarn, from leaves of Dactylis purpurea, 1970, H.A. van der Aa, CBS H-16281, ex-type culture CBS 761.70.

For a complete description see Aveskamp et al. (2010).

This species differs from B. exigua by having yellowish conidial matrix and absence of positive reaction to NaOH (Aveskamp et al. 2010). LSU, ITS and TUB2 sequences of B. exigua (CBS 471.34) and B. gilvescens (CBS 761.70) are almost identical. There are only 2 bp differences in RPB2. However, there are 41 bp differences in TEF1-a gene region.

Boeremia heteromorpha (Schulzer & Sacc.) Jayaward., Jayasiri & K.D. Hyde, comb. nov. IF555806

≡Phoma heteromorpha Schulzer & Sacc., Revue mycol., Toulouse 6(22): 74 (1884)

≡Phoma exigua var. heteromorpha (Schulzer & Sacc.) Noordel. & Boerema, Verslagen Meded. Plantenziektenk. Dienst Wageningen 166: 109 (1989)

≡Boeremia exigua var. heteromorpha (Schulzer & Sacc.) Aveskamp, Gruyter & Verkley, Aveskamp et al., Stud. Mycol. 65: 37 (2010)

Neotype: Italy, Perugia, from Nerium oleander (Apocy– naceae), deposited in CBS Aug. 1994, A. Zazzerini, HMAS246695; ex-neotype culture CBS 443.94.

For a complete description see Chen et al. (2015).

Chen et al. (2015) designate a neotype for Phoma heteromorpha. In the phylogenetic analyses of Chen et al. (2015) and in this paper (Fig.), this species clusters with B. populi and we were unable to identify any base pair differences among these two species. However, Chen et al. (2015) maintained these as two separate species as B. heteromorpha occurred on Nerium oleander and B. populi on Populus and Salix sp. respectively. Therefore, in this study we follow Chen et al. (2015) and maintain B. heteromorpha and B. populi as two distinct species.

Boeremia inoxydabilis (Boerema & Vegh) Jayaward., Jaysiri & K.D. Hyde, comb. nov. IF555812

= Phoma exigua var. inoxydabilis Boerema & Vegh, in Vegh et al., Bull. Trimest. Soc. Mycol. Fr. 90(2): 130(1974)

Reference Strain: CBS 372.75/ATCC 32161.

Phoma exigua var. inoxydabilis was introduced to accommodate a taxon found on Vinca minor and V. major in Europe and North America (Vegh et al. 1974). Van der Aa (1973) mentioned that the French type culture PC 2198 has been lost. Aveskamp et al. (2010) mentioned that this variety may be identical to B. gilvescens. However, CBS 372.75 is closely related to B. pseudolilacis in the phylogenetic analyses (Fig). The LSU sequence of strain CBS 372.75 is short and is identical with B. gilvescens and B. pseudolilacis. The same can be seen in the ITS gene region. There is one base pair difference in the TUB2 locus among these three strains. The TEF1-α sequence of CBS 372.75 is almost identical with B. pseudolilacis. There are 25 bp differences with B. gilvescens which makes it a different species from B. gilvescens. Here we elevate this taxon to B. inoxydabilis.

Boeremia lilacis (Sacc.) Qian Chen & L. Cai, in Chen et al. Stud. Mycol. 82:170 (2015) IF515629

≡Phoma herbarum f. lilacis Sacc., Michelia 2(1):93 (1880)

≡Phoma exigua var. lilacis (Sacc.) Boerema, Phy- topath. Mediterr. 18:106 (1979)

≡Boeremia exigua var. lilacis (Schulzer & Sacc.) Aveskamp, Gruyter & Verkley, in Aveskamp et al., Stud. Mycol. 65: 38 (2010)

Reference Strain: CBS 569.79 (= reference specimen sensu Berner et al. 2015; Chen et al. 2015).

For a complete description see Chen et al. (2015).

Chen et al. (2015) elevated this taxon to species level based on the multigene phylogeny in Berner et al. (2015). In our multigene phylogenetic analysis we identified CBS 588.67, CBS 569.79, LC 8116 and LC 5178 as B. lilacis. However, CBS 588.67, LC 8116 and LC 5178 lack TEF1- α sequence data and the LSU sequences are shorter (964 bp) than the type strain CBS 569.79. This may be the reason for these four strains do not cluster together. However, further collection and sequence data are needed for clarification. Until then, we treat CBS 588.67, LC 8116 and LC 5178 as B. lilacis.

Boeremia linicola (Naumov & Vassilijevsky) Jayaward., Jayasiri & K.D. Hyde comb. nov. IF555807

≡Ascochyta linicola Namov & Vassilijecsky, Mater.

Mycol. Phytopath. Leningrad 5: 3 (1926)

≡Boeremia exigua var. linicola (Naumov & Vassili- jevsky) Aveskamp, Gruyter & Verkley, in Aveskamp et al., Stud. Mycol. 65: 39 (2010)

Reference Strain: CBS 116.76 (= reference specimen sensu Van der Aa et al. 1973; Boerema et al. 2004; Aveskamp   et al. 2010; Chen et al. 2015).

The strains CBS 109.49, CBS 114.28 and CBS 248.38 clustered together with the representative strain CBS 116.76 of B. exigua var. linicola assigned by Van der Aa et al. (1973) in our phylogenetic analyses (Fig). The multigene loci sequence data for these four strains are almost identical. Here we elevate B. exigua var. linicola to B. linicola and assign CBS 116.76 as the reference specimen for this species.

Boeremia opuli (Qian Chen, Crous & L. Cai) Jayaward., Jayasiri & K.D. Hyde, comb. nov. stat. nov. IF555809

≡Boeremia exigua var. opuli Qian Chen, Crous & L. Cai, in Chen et al., Stud. Mycol. 87: 128 (2017)

Holotype: USA, from seedlings of Viburmum opulus (Caprifoliaceae), 2014, W.J Duan, HMAS 247147, ex-type culture CGMCC 3.18354.

For a complete description see Chen et al. (2017).

Chen et al. (2017) introduced this variety based on multigene analyses and morphological characters. Herein we elevate this taxon to species level as B. opuli. Morphologically this species can be distinguished based on larger pycnidia (Chen et al. 2017). It is phylogenetically closely related to B. exigua and B. gilvescens (Fig ) and differs in nine positions and eight positions in the RPB2 locus respectively.

Boeremia populi (Gruyter & P. Scheer) Jayaward., Jayasiri & K.D. Hyde, comb. nov. stat. nov. IF555810

≡Phoma exigua var. populi Gruyter & P. Scheer, J. Phytopath. 146(8–9): 413 (1998)

≡Boeremia exigua var. populi (Gruyter & P. Scheer) Aveskamp, Gruyter & Verkley, in Aveskamp et al., Stud. Mycol. 65: 39 (2010)

Holotype: The Netherlands, Deil, from a twig of Populus (×) euramericana cv. Robusta (Salicaceae), Feb 1993, A.J.P. Oort, L 995.263.325, ex-type culture CBS 100167.

For a complete description see de Gruyter et al. (2002).

Boeremia exigua var. populi is known from Populus and Salix sp. (Aveskamp et al. 2010). Herein we elevate this variety to species level and introduce B. populi. In the phylogenetic analyses of Chen et al. (2015) (based on four gene regions) and in this paper (based on five gene regions), the type strain clusters with B. heteromorpha and we were unable to identify any base pair differences among these two species. Following Chen et al. (2015) and based on the host association of these two species and until further collections are done, herein we maintain B. populi as a distinct species from B. heteromorpha.

Boeremia pseudolilacis (Aveskamp, Gruyter & Verkley), Jayaward., Jayasiri & K.D. Hyde, comb. nov. stat. nov. IF555811

≡Boeremia exigua var. pseudolilacis Aveskamp, Gruyter & Verkley, in Aveskamp et al., Stud. Mycol. 65: 39 (2010)

Holotype: The Netherlands, near Boskoop, from Syringa vulgaris (Oleaceae), 1994, J. de Gruyter, CBS H-20371, ex-type culture CBS 101207.

For a complete description see Aveskamp et al. (2010).

Boeremia exigua var. pseudolilacis was introduced by Aveskamp et al. (2010), based on morphological and phylogenetic support. Herein we raise the status to B. pseudolilacis to accommodate this taxon. This species can be identified from other Boeremia species on the basis of DAF and AFLP analyses (Aveskamp et al. 2009, 2010).

Boeremia rhapontica (Berner, Woudenb. & Tunali) Jayaward., Jayasiri & K.D. Hyde, comb. nov. stat. nov. IF555808

≡Boeremia exigua var. rhapontica Berner, Woudenb. & Tunali, in Berner et al., Biological Control 81: 70 (2014) Holotype: Turkey, from Rhaponticum repens (Asteraceae), 2002, D. Berner, BPI 843350; ex-type culture CBS 113651. For a complete description see Berner et al. (2015).

Boeremia exigua var. rhapontica was introduced by Berner et al. (2015) to accommodate the pathogen on Rhaponticum repens. Herein we elevate this to the species level and introduce B. rhapontica (for phylogenetic differences please see notes under B. coffeae).

Recommended genetic markers (Genus level) –LSU and ITS

Recommended genetic markers (Species level)—RPB2, TUB2, TEF1-a

Accepted number of species: Twenty two species

References: Boerema et al. (2004) (morphology and pathogenicity), Aveskamp et al. (2010), Chen et al. (2015, 2017), Jayasiri et al. (2017) (morphology and phylogeny), Berner et al. (2015) (morphology, pathogenicity and phylogeny).

Fig. Phylogenetic tree inferred from a maximum likelihood analysis based on analyses of a concatenated alignment of LSU, ITS, RPB2, TUB and TEF1-a sequence data of 41 strains representing the genus Boeremia, which comprise 2746 characters including gaps. Tree is rooted with Phoma herbarum (CBS 615.75). Tree topology of the ML analysis was similar to the MP and BI (not shown). The best scoring RAxML tree with a final likelihood value of -8078.423038 is presented. The matrix had 393 distinct alignment patterns, with19.32% of undetermined characters or gaps. Estimated base frequencies were as follows; A = 0.238158, C = 0.240395,  G = 0.268922,  T = 0.252525; substitution rates AC = 1.084080,  AG = 2.823706, AT = 1.555532, CG = 0.936952, CT = 8.695282, GT = 1.000000;gamma distribution shape parameter a = 0.1000000000. The RAxML and MP bootstrap support values above 50% and Bayesian posterior probabilities above 0.90 are given near to each branch. The scale bar indicates 0.1 changes per site. The ex-type strains are in bold.

Table Boeremia. Details of the isolates used in the phylogenetic analyses

Species	Isolate	LSU	ITS	RPB2	TUB2	TEF1- α
Boeremia coffeae	CBS 109183; PD 2000/10506; IMI 300060	GU237943	GU237748	KT389566	GU237505	KY484678
B. crinicola	CBS 109.79	GU237927	GU237737	KT389563	GU237489	–
B. diversispora	CBS 102.80	GU237930	GU237725	KT389565	GU237492	KY484676
B. exigua	CBS 431.74; PD 74/2447	EU754183	FJ427001	KT389569	FJ427112	KY484687
	CBS 119.38	KT389707	KT389490	–	KT389784	–
	CBS 113.36	MH867235	KY484642	–	KY484742	KY484683
	CBS 534.75	MH872718	MH860950	–	KY484746	KY484689
	CBS 101197	GU237931	GU237718	KT389570	GU237493	KY484690
	CBS 101213; PD 92/959	GU237932	GU237723	KT389571	GU237494	KY484692
	CBS 100354; PD 83/448	GU237944	GU237711	KT389577	GU237506	–
B. foveata	CBS 109176; PD 94/1394	GU237946	GU237742	KT389578	GU237508	KY484714
B. galiicola	MFLUCC 15-0771*	KX698026	KX698037	–	KX698030	–
B. gilvescens	CBS 101150*; PD 79/118	EU754182	GU237715	KT389568	GU237495	KY484694
B. hedericola	CBS 367.91*; PD 87/229	GU237949	GU237842	KT389579	GU237511	KY484718
B. heteromorpha	CBS 443.94*	GU237935	GU237866	KT389573	GU237497	KY484700
	CBS 101196; PD 79/176	GU237934	GU237717	KT389572	GU237496	KY484699
B. inoxydabilis	CBS 372.75	MH872672	KY484656	–	KY484754	KY484701
B. lilacis	CBS 569.79; PD 72/741;IMI 331909	GU237936	GU237892	–	GU237498	KY484721
	CBS 588.67	KT389709	KT389492	–	KT389786	–
	LC 5178	KY742201	KY742047	–	KY742289	–
	LC 8116	KY742202	KY742048	–	KY742290	–
B. linicola	CBS 116.76*; ATCC 32332;IMI 197074; PD 75/544	GU237938	GU237754	KT389574	GU237500	KY484705
	CBS 109.49	MH867998	MH856453	–	KY484755	KY484702
	CBS 248.38	KT389703	KT389486	KT389575	KT389780	–
	CBS 114.28	GU237937	GU237752	–	GU237499	KY484704
B. lycopersici	CBS 378.67; PD 67/276	GU237950	GU237848	KT389580	GU237512	KY484726
B. noackiana	CBS 100353; PD 87/718	GU237952	GU237710	–	GU237514	KY484727
B. opuli	LC 8117*	KY742199	KY742045	KY742133	KY742287	–
	LC 8118	KY742200	KY742046	KY742134	KY742288	–
B. populi	CBS 100167*; PD 93/217	GU237939	GU237707	–	GU237501	KY484706
	CBS 101202	KY742199	KY742046	KY742133	KY742287	KY484709
B. pseudolilacis	CBS 101207*; PD 94/614	GU237941	GU237721	–	GU237503	KY484710
	CBS 462.67	KT389705	KT389488	–	KT389782	–
	CBS 423.67	KT389704	KT389487	KT389576	KT389781	–
B. rhapontica	CBS 113651*	–	KY484662	–	KY484760	KY484713
B. sambuci–nigrae	CBS 629.68*; CECT 20048;IMI 331913; PD 67/753	GU237955	GU237897	–	GU237517	KY484734
B. strasseri	CBS 126.93; PD 73/642	GU237956	GU237773	KT389584	GU237518	KY484735
B. telephii	CBS 109175; PD 79/524	GU237958	GU237741	KT389585	GU237520	KY484737
B. trachelospermi	CGMCC 3.18222*	KY064032	KY064028	KY064033	KY064051	–
Boeremia sp.	CBS 119730	GU237942	GU237759	KT389567	GU237504	–
Phoma herbarum	CBS 615.75	EU754186	FJ427022	KP330420	KF252703	KR184186

Ex-type (ex-epitype) strains are in bold and marked with an * and reference strains are in bold