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School of Biological Sciences and Biotechnology, Murdoch University, Perth 6150, Australia
Sari Mohali
Universidad de Los Andes, Facultad de Ciencias, Forestales y Ambientales, Laboratorio de Patologia Forestal, Merida, Venezuela
Geoff Pegg
Department of Primary Industries and Fisheries, Horticulture and Forestry Science, Indooroopilly, Brisbane 4068, Australia
Wilhelm de Beer
Michael J. Wingfield
Forestry and Agriculture Biotechnology Institute, University of Pretoria, Pretoria, 0002, Republic of South Africa
| ABSTRACT |
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Botryosphaeria rhodina (anamorph Lasiodiplodia theobromae) is a common endophyte and opportunistic pathogen on more than 500 tree species in the tropics and subtropics. During routine disease surveys of plantations in Australia and Venezuela several isolates differing from L. theobromae were identified and subsequently characterized based upon morphology and ITS and EF1-
nucleotide sequences. These isolates grouped into three strongly supported clades related to but different from the known taxa, B. rhodina and L. gonubiensis, These have been described here as three new species L. venezuelensis sp. nov., L. crassispora sp. nov. and L. rubropurpurea sp. nov. The three could be distinguished easily from each other and the two described species of Lasiodiplodia, thus confirming phylogenetic separations. Furthermore all five Lasiodiplodia spp. now recognized separated from Diplodia spp. and Dothiorella spp. with 100% bootstrap support.
Key words: Botryosphaeria, Diplodia, Dothiorella, Fusicoccum, ITS, molecular phylogenetics, translation elongation factor EF1-
| INTRODUCTION |
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Numerous anamorphs have been assigned to Botryosphaeria spp., but recent studies based on DNA sequence comparisons have indicated there is a clear phylogenetic boundary between species with thin-walled, hyaline conidia and those with thick-walled, pigmented spores (Denman et al 2000
, Zhou and Stanosz 2001
). Those with hyaline conidia have been assigned a Fusicoccum anamorph and those with pigmented conidia a Diplodia anamorph (Denman et al 2000
). However, among the species with pigmented conidia, B. rhodina always groups separately from the other species (Denman et al 2000
, Zhou and Stanosz 2001
, Pavlic et al 2004
, Slippers et al 2004
). The anamorph of B. rhodina, Lasiodiplodia theobromae, has conidia much larger than other Diplodia species and currently retains the name Lasiodiplodia (Punithalingam 1976
, Pavlic et al 2004
, Phillips et al 2005
).
The taxonomic history of B. rhodina/L. theobromae is confused. During the past 150 y this fungus has had many names and has been treated as many different species. This trend ended with the monograph of Punithalingam (1976)
which reduced most species to synonymy with L. theobromae. Recently Pavlic et al (2004)
conducted an extensive review of Lasiodiplodia literature and searched for herbarium specimens associated with original descriptions of the genus (Clendinin 1896
) and its species (Patouillard and de Lagerheim 1892
). These could not be found and cultures from the original host and location, Theobroma cacao in Ecuador, also were not located. It thus was necessary to rely on descriptions from the literature and Pavlic et al (2004)
found that isolates from USA, South America, South Africa and Asia typically have conidia that are 1830 x 1015 µm. This led to the description of the new species L. gonubiensis, which could be distinguished by both DNA-based phylogenies and morphological characteristics.
In a study using SSR markers to examine host relationships and geographic isolation among isolates of L. theobromae, Mohali et al (2005)
identified several isolates that shared no common alleles with 177 other isolates at any of the eight SSR loci. This is considered to be indicative of the presence of related but different species. In addition disease surveys in tropical Australia have led to the discovery of several Lasiodiplodia isolates with conidia morphologically different from those of L. theobromae. These observations prompted the current study aimed at characterizing isolates of Lasiodiplodia based on morphology and multiple gene genealogies.
| MATERIALS AND METHODS |
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Two gene regions were used for phylogenetic comparisons. A part of the internal transcribed spacer (ITS) region of the ribosomal DNA operon was amplified with the primers ITS-1F (5' CTT GGT CAT TTA GAG GAA GTA A) (Gardes and Bruns 1993
) and ITS4 (5' TCC TCC GCT TAT TGA TAT GC) (White et al 1990
). In addition a part of the elongation factor 1-
was amplified with primers EF1-728F (5' CAT CGA GAA GTT CGA GAA GG) and EF1-986R (5' TAC TTG AAG GAA CCC TTA CC) (Carbone and Kohn 1999
). The PCR reaction mixture (25 µL), PCR conditions and visualization of products were as described by Pavlic et al (2004)
except that 0.5 U of Taq polymerase (Biotech International, Needville, Texas) were used in each reaction. PCR products were cleaned with Ultrabind® DNA purification kit (MO BIO Laboratories). Products were sequenced with the BigDye terminator cycle sequencing kit (PE Applied Biosystems) with the same primers used in the initial amplification. The products were separated with an ABI 3730 48 capillary sequencer (Applied Biosystems, Foster City, California) and a BioRad Biofocus 2000 capillary gel electrophoresis system. Data were collected with ABI data collection software.
To compare the Botryosphaeria isolates used in this study with other Botryosphaeria spp., 30 ITS rDNA and 15 EF-1
sequences obtained from GenBank were included in the phylogenetic analysis (TABLE I
). Sequence data were analyzed with Sequence Navigator version 1.0.1TM (Perkin Elmer Corp., Foster City, California) and manually aligned by inserting gaps. PCR products of approximately 500 bp and 300 bp were amplified for the ITS and EF-1
regions respectively. Ambiguous sequences at the 5' and 3' ends were deleted in the aligned dataset. Lasiodiplodia spp. have a large deletion (3538 bp), compared with other Botryosphaeria spp. in this study, in the ITS1 region, which was excluded and coded. Two regions in EF-1
sequences were also excluded and liberally coded. The first region was a 9 bp insertion found only in B. rhodina and the second a 13 bp insertion found only in B. ribis. Gaps were treated as a fifth character, all ambiguous characters and parsimony uninformative characters were excluded before analysis. The initial analysis was performed on an ITS dataset that included 33 isolates of B. rhodina (TABLE I
). Subsequent analyses, including 11 isolates of B. rhodina, were performed on individual datasets as well as combined datasets after partition homogeneity tests (PHT) were performed in PAUP version 4.0b10 (Swofford 2000
) to determine statistical congruence (Farris et al 1995
, Huelsenbeck et al 1996
).
The most parsimonious trees were obtained by using heuristic searches with random stepwise addition in 100 replicates, with the tree bisection-reconnection branch-swapping option on and the steepest-descent option off. MAXTREES were unlimited, branches of zero length were collapsed and all multiple equally parsimonious trees were saved. Estimated levels of homoplasy and phylogenetic signal (retention and consistency indices) also were determined with PAUP (Hillis and Huelsenbeck 1992
). In the initial analysis all characters were unweighted and unordered; for the ITS analysis, characters were reweighted according to the consistency index. Branch and branch node supports were determined with 1000 bootstrap replicates (Felsenstein 1985
) and characters were sampled with equal probability but weights were applied. ITS trees were rooted with Saccharata protea (Wakefield) Denman & Crous. This study focussed on Botryosphaeria spp. with Lasiodiplodia anamorphs, and to avoid long-branch attraction associated with phylogenetically distant outgroups trees from the combined dataset were rooted with B. ribis, a species with hyaline conidia and a Fusicoccum anamorph.
Morphological characteristics.
A total of 32 single conidium isolates representing the different cultural morphologies were used in this study (TABLE I
). Sporulation was induced by transferring isolates to tap water agar overlaid with pine needles and/or eucalypt twigs as a substrate and exposing these to near UV light on a 24 h light cycle at 22 C for 24 wk. Cultures were maintained on one-half strength potato-dextrose agar (one-half PDA; Becton, Dickinson & Co., Sparks, Maryland) at 25 C and stored on this medium at 4 C. Cultures also were stored at room temperature in sterile water.
Colony morphology, color (Rayner 1970
) and growth rates at 535 C of representative isolates were determined on one-half strength PDA. Fruiting structures were mounted in lactoglycerol. Observations and measurements of conidial characteristics (3040 per isolate) were made with a light microscope and an Axiocam digital camera (Carl Zeiss, Germany) and drawings prepared with a drawing tube. Approximately 30 conidia were measured for each isolate. All isolates in this study are maintained in the culture collection (CMW) of the Forestry and Agriculture Biotechnology Institute, University of Pretoria, South Africa, and the Department of Agriculture, Perth, Western Australia (WAC). Herbarium material is held at the Murdoch University Herbarium (MURU).
| RESULTS |
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sequences consisted of 877 characters of which three indels of 57 bp were coded and excluded leaving 276 parsimony informative characters that were included in the analysis. A partition homogeneity test showed no significant difference (P = 0.77) between the data from the different gene regions (sum of lengths of original partition was 549, range for 1000 randomizations was 543552) and these therefore could be combined. The combined dataset contained significant phylogenetic signal compared to 1000 random trees (P < 0.01, g1 = 0.75). Initial heuristic searches of unweighted characters in PAUP resulted in eight most parsimonious trees of 552 steps (CI = 0.75, RI = 0.93). Sequence alignments are available from Tree-BASE (SN2399-9016). The resulting tree (FIG. 2
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| TAXONOMY |
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Lasiodiplodia crassispora MB500235 Burgess, Barber, sp. nov. FIGS. 3AC
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Pycnidia superficial, mostly solitary, conical, smooth, iron gray (2123""k), 0.51 mm diam. Paraphyses cylindrical, septate, hyaline (21)3062(66) x 23.5(4) µm (average of 50 paraphyses 45.7 x 2.7 µm). Conidiogenous cells holoblastic, hyaline, subcylindrical to cylindrical to ampulliform, (6)816(19) x 37 µm (average of 50 conidiogenous cells 11.8 x 5.0 µm), proliferating percurrently. Conidia produced in culture initially hyaline, unicellular, ellipsoid to obovoid, thick-walled (23 µm, average of 50 conidia 2.6 µm) with granular content, round at apex, occasionally truncate at base, becoming pigmented with one septa when mature or before germination, vertical striations observed at maturation, 2730(33) x 1417 µm (average of 75 conidia, 28.8 x 16.0, l/w 1.8). Cultural characteristics. Moderately dense, appressed mycelial mat. Aerial mycelia/ colonies initially white to buff turning pale olivaceous gray (21""d) within 7 d and becoming olivaceous gray (21""i) with age. At 7 d the submerged mycelia are olivaceous gray (21""i), becoming iron gray (2123""k) to black with age. Optimum temperature for growth 30 C, reaching 74 mm diam on PDA after 3 d at 30 C in the dark.
Teleomorph. Botryosphaeria sp. (based on phylogenetic inferences, but unknown)
Etymology. Having thick-walled spores
Specimens examined. AUSTRALIA, Western Australia: Kununurra from canker of Santalum album, Dec 2003, T.I. Burgess (HOLOTYPE MURU 407) (culture WAC12533); Kununurra, S. album, T.I. Burgess (MURU 408) (culture WAC12534): VENEZUELA, Portuguesa State: Acarigua from wood of living Eucalyptus urophylla, Oct 2003, S. Mohali (culture CMW13448)
Lasiodiplodia rubropurpurea MB500236 Burgess, Barber, Pegg, sp.nov. FIGS. 3DF
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Pycnidia superficial, globose, livid red (69"i) to dark vinaceous (69"m), mostly solitary, 0.51.5 mm diam and covered with mycelium. Paraphyses cylindrical, aseptate, hyaline (30)3252(58) x 1.53.5 µm (average of 50 paraphyses 42.4 x 2.6 µm). Conidiogenous cells holoblastic, hyaline, subcylindrical to ampulliform, 713(15) x 35 µm (average of 50 conidiogenous cells 10.2 x 4.0 µm), proliferating percurrently with up to 1 annellation. Conidia initially hyaline, unicellular, ellipsoid to obovoid, thick-walled (1 µm, average of 50 conidia = 1 µm) with granular content, round at apex, occasionally truncate at base, initially hyaline and unicellular, becoming pigmented with one septa when mature or before germination, vertical striations observed at maturation, 2433 x 1317 µm (average of 100 conidia 28.2 x 14.6, l/w 1.9). Cultural characteristics. Moderately dense, appressed mycelial mat. Aerial mycelia/colonies initially white to buff turning smoke gray (21""d) to pale olivaceous gray (21""d) within 7 d and becoming gray olivaceous (21""b) to olivaceous gray (21""i) with age. At 7 d the submerged mycelia are gray olivaceous (21""b) to olivaceous gray (21""i), becoming iron gray (23""k) to black with age. Optimum temperature for growth 2530 C, reaches 76 mm diam on PDA after 3 d at both 25 C and 30 C in the dark.
Teleomorph. Botryosphaeria sp. (based on phylogenetic inferences, but unknown)
Etymology. Refers to the reddish-purple pycnidia
Specimens examined. AUSTRALIA. Queensland: Tully, from canker of Eucalyptus grandis, May 2003, T.I. Burgess (HOLOTYPE MURU 409) (culture WAC12535); Tully, E. grandis, T.I. Burgess (MURU 410) (culture WAC12536); Tully, E. grandis, T.I. Burgess (MURU 411) (culture WAC12537); Tully, E. grandis, T.I. Burgess (MURU 412) (culture WAC12538)
Lasiodiplodia venezuelensis MB500237 Burgess, Barber, Mohali, sp. nov. FIGS. 3HJ
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Pycnidia. superficial, iron gray (2123""k), smooth, cylindrical, mostly solitary, 0.51 mm diam often oozing immature conidia. Paraphyses cylindrical, septate, hyaline (12)1641(45) x (1.5)25 (average of 50 paraphyses 28.3 x 3.5 µm). Conidiogenous cells holoblastic, hyaline, subcylindrical to cylindrical to ampulliform, (5)714 (15) x 34.5(5) µm (average of 50 conidiogenous cells 10.4 x 3.7 µm), proliferating percurrently. Conidia initially hyaline, unicellular, ellipsoid to obovoid, thick-walled (1.52.5(3) µm, average of 50 conidia = 1.96 µm) with granular content, round at apex, occasionally truncate at base, becoming pigmented with one septa when mature or before germination, vertical striations observed at maturation, 2633 x 1215 µm (average of 75 conidia 28.4 x 13.5, l/w 2.1),. Cultural characteristics. Moderately dense, appressed mycelial mat. Aerial mycelia/colonies initially white to buff turning pale olivaceous gray (21""d) within 7 d and becoming olivaceous gray (21""i) with age. At 7 d the submerged mycelia are olivaceous gray (21""i), becoming iron gray (23""k) to black with age. Optimum temperature for growth 25 C, reaching 75 mm diam on PDA after 3 d at 25 C in the dark.
Teleomorph. Botryosphaeria sp. (based on phylogenetic inferences, but unknown)
Etymology. Country of origin, Venezuela
Specimens examined. VENEZUELA, Estado Portuguesa: Acarigua from wood of living Acacia mangium, Oct 2003, S. Mohali (HOLOTYPE MURU 413) (culture WAC12539); Acarigua, A. mangium, S. Mohali (MURU 414) (culture WAC12540); Acarigua, A. mangium, S. Mohali (culture CMW13513)
| KEY TO LASIODIPLODIA SPP. |
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| DISCUSSION |
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Consideration must be given to the possibility that some of the Lasiodiplodia spp. described before the study of Punithalingam (1976)
are the same as those emerging from DNA sequence comparisons. We do not believe this to be the case because Punithalingam (1976)
was able to merge all species based on a lack of morphological differences. Pavlic et al (2004)
sought herbarium specimens for L. theobromae to compare with L. gonubiensis, but neither cultures nor herbarium specimens pertaining to the original host and location (Theobroma cacao L. in Ecuador) could be located. Thus, until original material can be located or an epitype specimen assigned, it is necessary to rely on descriptions from the literature.
The species described in this study are morphologically and phylogenetically distinct from both L. theobromae and L. gonubiensis. It is not possible to test the genetic relatedness of the new species to other previously described species due to the absence of cultures. In recent studies we have examined more than 200 isolates from pines, eucalypts, acacia, and sandalwood in Australia, South Africa, Venezuela and Mexico, and among all these isolates only 10 (less than 5%) were found to be distinct from L. theobromae. In our opinion L. theobromae is a common species in tropical parts of the world but other less common species of this genus are yet to be described.
In addition to the clear phylogenetic differences between the newly described species, these fungi differ from each other and existing species based on septation of the paraphyses, the size of the spores, thickness of spore walls and the color of pycnidia. All species described as new in this study have larger conidia than those of L. theobromae but smaller than L. gonubiensis. Lasiodiplodia venezuelensis and L. crassispora have septate paraphyses, while they are aseptate in other species. Lasiodiplodia crassispora has notably thicker cell walls in the immature spores and the striations appear to be wider and the cytoplasm wart-like in appearance, which is different from all other species. Lasiodiplodia rubropurpurea is unique in having red-purple pycnidia.
The three new species, L. crassispora, L. rubropurpurea and L. venezuelensis, have been recognized as residing in Lasiodiplodia, based on size and shape of conidia and the presence of vertical striations, which are characteristic of this genus. No teleomorph structures were found for these new species but phylogenetic inference leads us to conclude that they are species of the teleomorph genus Botryosphaeria. Botryosphaeria is a large genus with clear monophyletic groups emerging from phylogenetic studies based on DNA sequence data. Thus clear subdivisions have been recognized between those species that have Diplodia anamorphs with primarily dark-colored conidia and those that have hyaline conidia and Fusicoccum anamorphs (Denman et al 2000
, Zhou and Stanosz 2001
). These might be assigned to new genera, and if that is the case the generic placement of Lasiodiplodia will come into question.
In this study we have chosen to retain the name Lasiodiplodia and not reduce it to synonymy with Diplodia as had been considered (Denman et al 2000
, Zhou and Stanosz 2001
). This decision was made because all species of Lasiodiplodia group together in a highly supported (100% bootstrap) clade related to but distinct from the clade encompassing Diplodia and Dothiorella species. Through the addition of three new species the cohesiveness and separate nature of this clade is enhanced. Phillips et al (2005)
resurrected Dothiorella to encompass two new Botryosphaeria spp. with dark conidia. Based on a combined ITS and EF-1
phylogeny, these new species formed a clade, which like the Lasiodiplodia clade is close to but distinct from the Diplodia clade (Phillips et al 2005
).
Species in Diplodia, Dothiorella and Lasiodiplodia are clearly separated from those in Fusicoccum by thick-walled conidia with a much smaller length to width ratio (Luque et al 2005
, Phillips et al 2005
). When mature the conidia of most Diplodia, Dothiorella and Lasiodiplodia species are dark and septate, however conidia of B. stevensii and B. corticola are mostly hyaline and often aseptate and can germinate before darkening (Denman et al 2000
, Zhou and Stanosz 2001
, Alves et al 2004
). Conidia of D. pinea and B. obtusa while dark are often aseptate (de Wet et al 2003
, Alves et al 2004
). Conidia of the newly described B. iberica, B. sarmentorum and B. viticola become brown and 1-septate early in their development (Luque et al 2005
, Phillips et al 2005
). Diplodia, Dothiorella and Lasiodiplodia spp. conidia sizes overlap, although in general those of Lasiodiplodia are wider and more obovoid. The other distinguishing feature of Lasiodiplodia spp. is the obvious vertical striations in mature conidia (von Arx 1974
). We believe there is a reasonable argument to retain Lasiodiplodia as distinct from Diplodia and Dothiorella and expect that if the genus Botryosphaeria is subdivided those species with Lasiodiplodia anamorphs will be retained in a discrete teleomorph genus.
All new species described in this study were isolated from cankers on various tree species. In each case they were associated with L. theobromae and other opportunistic pathogens such as Cytospora eucalypti-cola sensu lato and B. ribis. Their distribution and host range currently is limited, especially compared with L. theobromae which has more than 500 host species and a global distribution (Punithalingam 1976
, 1980
). Pathogenicity studies were not conducted, but it would be interesting to compare the pathogenicity of the new species with that of L. theobromae. Although the new species were isolated from cankers, it is likely they are also endophytes and latent pathogens and not primary pathogens as is the case for many Botryosphaeria spp. (von Arx 1987
, Smith et al 1996
, Burgess et al 2001
, Pavlic et al 2004
).
| ACKNOWLEDGMENTS |
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| FOOTNOTES |
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1 Corresponding author. E-mail: tburgess{at}murdoch.edu.au
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