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Acrocordiella omanensis Sp. Nov. (Requienellaceae, Xylariales) from the sultanate of Oman
Abstract and Figures
Acrocordiella omanensis sp. nov. is described and illustrated from specimens on dead stem of Juniper sp. collected in Al Jabal al-Akhdar (Green Mountain), Sultanate of Oman. It strongly resembles Acrocordiella occulta, the type of the genus, in its similar asci and ascospore anatomy. It differs from A. occulta in having bell-shaped to cap-like clypeus around the ostiole and larger asci and ascospores. The combined large subunit nuclear ribosomal DNA and internal transcribed spacer sequences support the conclusions based on the morphological data.
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... However, Jaklitsch et al. (2016) transferred Requienellaceae to Xylariales as a distinct family based on phylogenetic analysis and morphological comparison. Subsequently, Maharachchikumbura et al. (2018), and accepted four genera in Requienellaceae viz. Acrocordiella, Lacrymospora, Parapyrenis and Requienella. ...
... Wijayawardene et al. (2018) treated Acrocordiella in Pyrenulaceae. However, based on morphology and sequence data, Maharachchikumbura et al. (2018) and Hyde et al. (2020) placed Acrocordiella in Requienellaceae. They mentioned that Acrocordiella could be separated based on the solitary or aggregate immersed ascomata with white or black margins, a peridium comprising brown to hyaline, thick-walled cells of textura angularis and 3-distoseptate ascospores with rhomboid lumina , Hyde et al. 2020. ...
... Further collections and additional gene regions are essential to resolve the placement of Acrocordiella in Requienellaceae. Two other genera viz Lacrymospora and Parapyrenis were previously recognized in Requienellaceae by Wijayawardene et al. (2017) and Maharachchikumbura et al. (2018). However, Jaklitsch et al. (2016) and Voglmayr et al. (2019) only accepted Requienella and Acrocordiella for their phylogenetic analyses. ...
Acrocordiella yunnanensis sp. nov. is introduced here from dead twigs of an unidentified dicotyledonous host from Xishuangbanna Prefecture, Yunnan Province, China. Phylogenetic analyses based on LSU and ITS sequence data revealed that this new species with a distinct sexual morph belongs to Requienellaceae (Sordariomycetes, Ascomycota). Acrocordiella yunnanensis is closely related to Acrocordiella omanensis in Requienellaceae. This novel taxon is illustrated, described, and a morphology-based key is provided to facilitate the identification of species in Acrocordiella.
... Notes: Acrocordiella photiniicola is similar to A. yunnanensis in having similar sized ascomata (280-330 × 295-400 μm vs 290-325 × 325-355 μm) and peridia (10-15.5 μm vs 10-15 μm). Acrocordiella occulta (300-500 × 400-800 μm) and A. omanensis (745-810 × 645-780 μm) have comparatively large ascomata (Jaklitsch et al. 2016;Maharachchikumbura et al. 2018). However, A. yunnanensis differs from our collection in having wider asci and muriform ascospores with 3-7 distosepta with a mucilaginous sheath (Dissanayake et al. 2021b). ...
... The LSU-ITS phylogenies in Jaklitsch et al. (2016) and Maharachchikumbura et al. (2018) showed that Acrocordiella and Requienella form distinct clades. With the addition of A. yunnanensis, LSU-ITS phylogeny showed A. occulta is not monophyletic and clusters in Requienella (Dissanayake et al. 2021b). ...
inconspicuous stromatic xylarialean taxa from China, Italy, Russia, Thailand and the United Kingdom. Detailed morphological descriptions, illustrations and combined ITS-LSU-rpb2-tub2-tef1 phylogenies revealed 39 taxa from our collections belonging to Amphisphaeriales and Xylariales. A new family (Appendicosporaceae), five new genera (Magnostiolata, Melanostictus, Neoamphisphaeria, Nigropunctata and Paravamsapriya), 27 new species (Acrocordiella photiniicola, Allocryptovalsa sichuanensis, Amphisphaeria parvispora, Anthostomella lamiacearum, Apiospora guiyangensis, A. sichuanensis,
Biscogniauxia magna, Eutypa camelliae, Helicogermslita clypeata, Hypocopra zeae, Magnostiolata mucida, Melanostictus longiostiolatus, M. thailandicus, Nemania longipedicellata, N. delonicis, N. paraphysata, N. thailandensis, Neoamphisphaeria
hyalinospora, Neoanthostomella bambusicola, Nigropunctata bambusicola, N. nigrocircularis, N. thailandica, Occultitheca rosae, Paravamsapriya ostiolata, Peroneutypa leucaenae, Seiridium italicum and Vamsapriya mucosa) and seven new host/geographical records are introduced and reported. Divergence time estimates indicate that Delonicicolales diverged from Amphisphaeriales + Xylariales at 161 (123–197) MYA. Amphisphaeriales and Xylariales diverged 154 (117–190) MYA with a crown age of 127 (92–165) MYA and 147 (111–184) MYA, respectively. Appendicosporaceae (Amphisphaeriales) has a stem age of 89 (65–117) MYA. Ancestral character state reconstruction indicates that astromatic, clypeate ascomata with aseptate, hyaline ascospores that lack germ slits may probably be ancestral Xylariomycetidae having plant-fungal endophytic associations. The Amphisphaeriales remained mostly astromatic with common septate, hyaline ascospores. Stromatic variations may have developed mostly during the Cretaceous period. Brown ascospores are common in Xylariales, but they
first appeared in Amphisphaeriaceae, Melogrammataceae and Sporocadaceae during the early Cretaceous. The ascospore germ slits appeared only in Xylariales during the Cretaceous after the divergence of Lopadostomataceae. Hyaline, filiform and apiospores may have appeared as separate lineages, providing the basis for Xylariaceae, which may have diverged independently. The future classification of polyphyletic xylarialean taxa will not be based on stromatic variations, but the type of ring, the colour of the ascospores, and the presence or absence or the type of germ slit.
Xylariomycetidae ( Ascomycota ) is a highly diversified group with variable stromatic characters. Our research focused on inconspicuous stromatic xylarialean taxa from China, Italy, Russia, Thailand and the United Kingdom. Detailed morphological descriptions, illustrations and combined ITS-LSU- rpb 2- tub 2- tef 1 phylogenies revealed 38 taxa from our collections belonging to Amphisphaeriales and Xylariales . A new family ( Appendicosporaceae ), five new genera ( Magnostiolata , Melanostictus , Neoamphisphaeria , Nigropunctata and Paravamsapriya ), 27 new species ( Acrocordiella photiniicola , Allocryptovalsa sichuanensis , Amphisphaeria parvispora , Anthostomella lamiacearum , Apiospora guiyangensis , Ap. sichuanensis , Biscogniauxia magna , Eutypa camelliae , Helicogermslita clypeata , Hypocopra zeae , Magnostiolata mucida , Melanostictus longiostiolatus , Me. thailandicus , Nemania longipedicellata , Ne. delonicis , Ne. paraphysata , Ne. thailandensis , Neoamphisphaeria hyalinospora , Neoanthostomella bambusicola , Nigropunctata bambusicola , Ni. nigrocircularis , Ni. thailandica , Occultitheca rosae , Paravamsapriya ostiolata , Peroneutypa leucaenae , Seiridium italicum and Vamsapriya mucosa ) and seven new host/geographical records are introduced and reported. Divergence time estimates indicate that Delonicicolales diverged from Amphisphaeriales + Xylariales at 161 (123–197) MYA. Amphisphaeriales and Xylariales diverged 154 (117–190) MYA with a crown age of 127 (92–165) MYA and 147 (111–184) MYA, respectively. Appendicosporaceae ( Amphisphaeriales ) has a stem age of 89 (65–117) MYA. Ancestral character state reconstruction indicates that astromatic, clypeate ascomata with aseptate, hyaline ascospores that lack germ slits may probably be ancestral Xylariomycetidae having plant-fungal endophytic associations. The Amphisphaeriales remained mostly astromatic with common septate, hyaline ascospores. Stromatic variations may have developed mostly during the Cretaceous period. Brown ascospores are common in Xylariales , but they first appeared in Amphisphaeriaceae , Melogrammataceae and Sporocadaceae during the early Cretaceous. The ascospore germ slits appeared only in Xylariales during the Cretaceous after the divergence of Lopadostomataceae . Hyaline, filiform and apiospores may have appeared as separate lineages providing the basis to Xylariaceae , which may have diverged independently. The future classification of polyphyletic xylarialean taxa will not be based on stromatic variations, but the type of ring, the colour of the ascospores, and the presence or absence of the type of germ slit.
During our investigation of palm fungi in Thailand, two interesting taxa from Elaeis guineensis and Metroxylon sagu (Arecaceae) were collected. Based on phylogenetic analyses of a combined dataset of ITS, LSU, rpb2, and tub2 nucleotide sequences as well as unique morphological characteristics, we introduce the new genus Haploanthostomella within Xylariales, and a new species Endocalyx metroxyli. Additionally, in our study, the genus Endocalyx is transferred to the family Cainiaceae based on its brown conidia and molecular phylogenetic evidence.
A fungus within the genus Phaeosphaeriaceae was isolated from brown leaf spot samples of Dracaena serrulata Baker (Yemen dragon tree) collected from Oman Botanic Garden, Muscat, Oman. Detailed morphological studies showed that this strain fits well within the species concept of the genus Phaeosphaeriopsis. Multilocus phylogeny based on LSU, ITS and TEF confirmed its uniqueness and supports its recognition as a new species, Phaeosphaeriopsis omaniana. Geography, pathogenic life mode and subglobose, smooth and brown conidia of the newly described species clearly differ from those of phylogenetically related species. A comprehensive description and illustrations of the new species, P. omaniana is provided and discussed with comparable taxa.
The endophytic Talaromyces omanensis sp. nov., a new microfungus isolated from the desert plant Rhazya stricta in Oman, is described and illustrated. The new species forms a distinct sister clade to the section Subinflati in the phylogeny of internal transcribed spacer (ITS), β-tubulin (benA) and Calmodulin (CaM). Talaromyces omanensis remains distinct and unique from the other species in the section Subinflati in having monoverticillate conidiophores.
Specimens of a new pleosporalean taxon were obtained on the bark of Juniperus excels from the northern mountains of Oman; from the Jebel Akhdar (‘Green Hills’). Sequence analyses based on the regions of large subunit rRNA (LSU), small subunit rRNA (SSU), translation elongation factor 1-α (TEF) and internal transcribed spacers (ITS) were performed to resolve the phylogenetic relationships of the new taxon in Phaeosphaeriaceae. The data concluded that the taxon represents a novel genus of the family Phaeosphaeriaceae and the generic name Hydeomyces and the species name H. desertipleosporoides are introduced for the new taxon. An outline of the characters which differentiate the new genus from phylogenetically closely related genera Dematiopleospora and Dlhawksworthia is given and its morphology of asexual and sexual morphs is described.
The genus Cladosporium is cosmopolitan in distribution and can be isolated from various sources including plants as endophytes. A strain of Cladosporium was isolated from living leaves of Zygophyllum coccineum in a desert habitat in Oman. Phylogenetic analysis based on the combined internal transcribed spacer (ITS), partial translation elongation factor 1-alpha (TEF) and partial actin (ACT) sequence data shows that this is a novel species, which groups with Cladosporium sphaerospermum complex. The new species is introduced as Cladosporium omanense and is described, illustrated and compared with other known species in the genus. Cladosporium omanense differs from its phylogenetically related species C. endophyticum by its fast growing colonies, longer macronematous and micronematous conidiophores, thickened-walled conidia with conspicuously protuberant shrivelling surface ornamentations.
Bipolaris species are responsible for important cereal diseases, worldwide and are often isolated as endophytes as well as saprobes. We are investigating the fungi in Oman. In this paper, we report a novel taxon of Bipolaris, collected from the leaves of Hibiscus rosa-sinensis, during the survey. The taxon is shown to be novel based on morphological and sequence data and introduced here as Bipolaris omanensis sp. nov. Bipolaris omanensis forms a sister clade to B. cookei based on the combined sequence analysis of internal transcribed spacers (ITS) and partial glyceraldehyde-3-phosphate dehydrogenase (GAPD) region, being distinct from the latter species in having shorter conidiophores, narrower conidia and having a higher number of septa.
The pyrenomycetous ascomycete Requienella seminuda (Eurotiomycetes, Pyrenulales, Requienellaceae) is presented. The species is known from Europe and North America but was not previously reported from Norway and Sweden. The first find in Norway was made in Grinde, Leikanger, Sogn og Fjordane in 2011 and during 2012-2013 we found 15 additional localities in different parts of southern Norway from Akershus to Sogn og Fjordane. It was growing on bark of old living Fraxinus trees, often in association with rare or red-listed lichenized fungi.
Knowledge of the relationships and thus the classification of fungi, has developed rapidly with increasingly widespread use of molecular techniques, over the past 10–15 years, and continues to accelerate. Several genera have been found to be polyphyletic, and their generic concepts have subsequently been emended. New names have thus been introduced for species which are phylogenetically distinct from the type species of particular genera. The ending of the separate naming of morphs of the same species in 2011, has also caused changes in fungal generic names. In order to facilitate access to all important changes, it was desirable to compile these in a single document. The present article provides a list of generic names of Ascomycota (approximately 6500 accepted names published to the end of 2016), including those which are lichen-forming. Notes and summaries of the changes since the last edition of ‘Ainsworth & Bisby’s Dictionary of the Fungi’ in 2008 are provided. The notes include the number of accepted species, classification, type species (with location of the type material), culture availability, life-styles, distribution, and selected publications that have appeared since 2008. This work is intended to provide the foundation for updating the ascomycete component of the “Without prejudice list of generic names of Fungi” published in 2013, which will be developed into a list of protected generic names. This will be subjected to the XIXth International Botanical Congress in Shenzhen in July 2017 agreeing to a modification in the rules relating to protected lists, and scrutiny by procedures determined by the Nomenclature Committee for Fungi (NCF). The previously invalidly published generic names Barriopsis, Collophora (as Collophorina), Cryomyces, Dematiopleospora, Heterospora (as Heterosporicola), Lithophila, Palmomyces (as Palmaria) and Saxomyces are validated, as are two previously invalid family names, Bartaliniaceae and Wiesneriomycetaceae. Four species of Lalaria, which were invalidly published are transferred to Taphrina and validated as new combinations. Catenomycopsis Tibell & Constant. is reduced under Chaenothecopsis Vain., while Dichomera Cooke is reduced under Botryosphaeria Ces. & De Not. (Art. 59).
Phylogenetic analyses of a combined DNA data matrix containing ITS, LSU, rpb2 and tub2 sequences of representative Xylariales revealed that the genus Barrmaelia is a well-defined monophylum, as based on four of its described species (B. macrospora, B. moravica, B. oxyacanthae, B. rhamnicola) and the new species B. rappazii. The generic type of Entosordaria, E. perfidiosa, is revealed as the closest relative of Barrmaelia, being phylogenetically distant from the generic type of Clypeosphaeria, C. mamillana, which belongs to Xylariaceae sensu stricto. Entosordaria and Barrmaelia are highly supported and form a distinct lineage, which is recognised as the new family Barrmaeliaceae. The new species E. quercina is described. Barrmaelia macrospora, B. moravica and B. rhamnicola are epitypified and E. perfidiosa is lecto- and epitypified. Published sequences of Anthostomella and several Anthostomella-like species from the genera Alloanthostomella, Anthostomelloides, Neoanthostomella, Pseudoanthostomella and Pyriformiascoma are evaluated, demonstrating the necessity of critical inspection of published sequence data before inclusion in phylogenies. Verified isolates of several species from these genera should be re-sequenced to affirm their phylogenetic affinities. In addition, the generic type of Anthostomella should be sequenced before additional generic re-arrangements are proposed.
Electronic supplementary material
The online version of this article (doi:10.1007/s11557-017-1329-6) contains supplementary material, which is available to authorized users.
A multigene phylogeny was constructed including a significant number of representative species of the main lineages in the Xylariaceae and four DNA loci – the internal transcribed spacer region (ITS), the large subunit (LSU) of the nuclear rDNA; the second largest subunit of the RNA polymerase II (RPB2) and beta-tubulin (TUB2). Specimens were selected based on more than a decade of intensive morphological and chemotaxonomic work and cautious taxon sampling was performed to cover the major lineages of the Xylariaceae, however with emphasis on hypoxyloid species. The comprehensive phylogenetic analysis revealed a clear-cut segregation of the Xylariaceae into several major clades, which was well in accordance with previously established morphological and chemotaxonomic concepts. One of these clades contained Annulohypoxylon, Hypoxylon, Daldinia and other related genera that have stromatal pigments and a nodulisporium-like anamorph. They are
accommodated in the family Hypoxylaceae, which is resurrected and emended. Representatives of genera with a nodulisporium-like anamorph and bipartite stromata, lacking stromatal pigments (i.e.
Biscogniauxia, Camillea and Obolarina) appeared in a clade basal to the xylarioid taxa. As they clustered with Graphostroma platystomum, they are accommodated in the Graphostromataceae. The new genus Jackrogersella with J. multiformis as type species is segregated from Annulohypoxylon. The genus Pyrenopolyporus is resurrected for Hypoxylon polyporus and allied species. The genus Daldinia and its allies Entonaema, Rhopalostroma, Ruwenzoria and Thamnomyces appeared in two separate subclades, which may warrant further splitting of Daldinia in the future, and even Hypoxylon was divided in several clades. However, more species of these genera need to be studied before a conclusive taxonomic rearrangement can be envisaged. Epitypes were designated for several important species in which living cultures and molecular data are available, in order to stabilise the taxonomy of the Xylariales.
Fresh material, type studies and molecular phylogeny were used to clarify phylogenetic relationships of the nine genera Acrocordiella, Blogiascospora, Clypeosphaeria, Hymenopleella, Lepteutypa, Pseudapiospora, Requienella, Seiridium and Strickeria. At first sight, some of these genera do not seem to have much in common, but all were found to belong to the Xylariales, based on their generic types. Thus, the most peculiar finding is the phylogenetic affinity of the genera Acrocordiella, Requienella and Strickeria, which had been classified in the Dothideomycetes or Eurotiomycetes, to the Xylariales. Acrocordiella and Requienella are closely related but distinct genera of the Requienellaceae. Although their ascospores are similar to those of Lepteutypa, phylogenetic analyses do not reveal a particularly close relationship. The generic type of Lepteutypa, L. fuckelii, belongs to the Amphisphaeriaceae. Lepteutypa sambuci is newly described. Hymenopleella is recognised as phylogenetically distinct from Lepteutypa, and Hymenopleella hippopha?icola is proposed as new name for its generic type, Sphaeria (= Lepteutypa) hippopha?s. Clypeosphaeria uniseptata is combined in Lepteutypa. No asexual morphs have been detected in species of Lepteutypa. Pseudomassaria fallax, unrelated to the generic type, P. chondrospora, is transferred to the new genus Basiseptospora, the genus Pseudapiospora is revived for P. corni, and Pseudomassaria carolinensis is combined in Beltraniella (Beltraniaceae). The family Clypeosphaeriaceae is discontinued, because the generic type of Clypeosphaeria, C. mamillana, is a member of the Xylariaceae. The genus Seiridium, of which the sexual morph Blogiascospora is confirmed, is unrelated to Lepteutypa, as is Lepteutypa cupressi. The taxonomy of the cypress canker agents is discussed. The family Sporocadaceae is revived for a large clade of the Xylariales that contains Hymenopleella, Seiridium and Strickeria among a number of other genera. Neotypes are proposed for Massaria fuckelii and Sphaeriahippopha?s. Didymella vexata, Seiridium marginatum, Sphaeria corni, Sphaeria hippopha?s, Sphaeria seminuda are epitypified, Apiosporina fallax, Massaria occulta, Sphaeria mamillana and Strickeriakochii are lecto- and epitypified. We also provide DNA data for Broomella vitalbae, Cainia desmazieri and Creosphaeriasassafras.
Abstract Taxonomic names are key links between various
databases that store information on different organisms. Several
global fungal nomenclural and taxonomic databases (notably
Index Fungorum, Species Fungorum and MycoBank)
can be sourced to find taxonomic details about fungi, while
DNA sequence data can be sourced from NCBI, EBI and UNITE databases. Although the sequence data may be linked
to a name, the quality of the metadata is variable and generally
there is no corresponding link to images, descriptions or herbarium
material. There is generally no way to establish the
accuracy of the names in these genomic databases, other than
whether the submission is from a reputable source. To tackle
this problem, a new database (FacesofFungi), accessible at
www.facesoffungi.org (FoF) has been established. This fungal
database allows deposition of taxonomic data, phenotypic details
and other useful data, which will enhance our current
taxonomic understanding and ultimately enable mycologists
to gain better and updated insights into the current fungal
classification system. In addition, the database will also allow
access to comprehensive metadata including descriptions of
voucher and type specimens. This database is user-friendly,
providing links and easy access between taxonomic
ranks, with the classification system based primarily
on molecular data (from the literature and via updated
web-based phylogenetic trees), and to a lesser extent on
morphological data when molecular data are unavailable.
In FoF species are not only linked to the closest
phylogenetic representatives, but also relevant data is
provided, wherever available, on various applied aspects,
such as ecological, industrial, quarantine and
chemical uses. The data include the three main fungal
groups (Ascomycota, Basidiomycota, Basal fungi) and
fungus-like organisms. The FoF webpage is an output
funded by the Mushroom Research Foundation which is
an NGO with seven directors with mycological expertise.
The webpage has 76 curators, and with the help of
these specialists, FoF will provide an updated natural
classification of the fungi, with illustrated accounts of
species linked to molecular data. The present paper introduces
the FoF database to the scientific community
and briefly reviews some of the problems associated
with classification and identification of the main fungal
groups. The structure and use of the database is then
explained. We would like to invite all mycologists to
contribute to these web pages.
Keywords Classification . Database . FacesofFungi . Fungi .
Phylogeny . Taxonomy
A study was conducted to characterize fungal and oomycete pathogens associated with root diseases of acid lime and sweet lime in Oman. A survey which covered 17 administrative districts and 166 farms showed prevalence of dieback symptoms in 8.8% of acid limes and in 15.9% of sweet limes. Some of the acid limes (3.0%) and sweet limes (3.5%) were also found to suffer from gummosis at the trunk base. Isolations from bark and root samples obtained from diseased acid lime and sweet lime trees showed association of 19 fungal species with these plants, with Lasiodiplodia hormozganensis, L. theobromae and Fusarium solani being the most common. When the most common fungi were inoculated on acid lime and sweet lime seedlings, L. hormozganensis, L. theobromae, Neoscytalidium dimidiatum and F. solani reproduced wilt, decline or gummosis symptoms on the inoculated plants. Isolations from 14 nursery seedlings of acid lime and sweet lime showed association of 12 fungal species, which implies that nurseries act as a main source for some citrus pathogens in Oman. The study reports for the first time sweet lime as a host for L. hormozganensis and N. dimidiatum. It also reports for the first time the presence of six new fungi to Oman.
Recent estimates of the global species numbers of fungi suggest that the much-used figure of 1.5 million is low, and figures up to 5.1 million have been proposed in the last few years. Data emerging from tropical studies, and from large-scale sequencing of environmental samples, have the potential to contribute towards a more robust figure. Additional evidence of species richness is coming from long-term studies of particular non-tropical sites, and also from molecular phylogenetic studies revealing extensive cryptic speciation. However, uncertainties remain over fungus:plant species ratios and how they should be extrapolated to the global scale, and also as to the geographical distribution of fungi known only as sequences. Also unclear is the extent to which figures should be modified to allow for insect-associated fungi. The need for comprehensive studies, especially in the tropics, to address the uncertainties used in past extrapolations, is stressed. For the present, it is recommended that the phrase “at least 1.5, but probably as many as 3 million” be adopted for general use until some of the current uncertainties are resolved.
Lasiodiplodia is a common pathogen causing dieback, gummosis, or root necrosis on the three most important fruit crops in Oman and the United Arab Emirates (UAE): date palm (Phoenix dactylifera), Citrus spp., and mango (Mangifera indica). A study was conducted to examine diversity in 64 Lasiodiplodia isolates infecting date palm (24), Citrus (11), and mango (29) in Oman and the UAE. Identification based on sequences of the internal transcribed spacer (ITS) rDNA and EF1 alpha gene showed that date palm isolates belonged to L. hormozganensis (75% of isolates) and L. theobromae (25%); Citrus isolates belonged to L. hormozganensis (45%), L. theobromae (45%), and L. iraniensis (10%); and mango isolates belonged to L. theobromae (59%), L. iraniensis (34%), and L. hormozganensis (7%). Amplified fragment length polymorphism (AFLP) fingerprinting of the 64 isolates using four primer pair combinations produced 64 genotypes and 972 polymorphic alleles. Cluster analysis separated the isolates into four clusters representing the three species. A higher level of genetic diversity was observed in L. iraniensis (0.3105) compared to L hormozganensis (0.2503) and L. theobromae (0.2331) in Oman. Analysis of molecular variance (AMOVA) indicated the existence of low levels of genetic differentiation among date palm populations of L. hormozganensis obtained from Oman and the UAE (F-ST = 0.025) and among populations of L. hormozganensis (0.0485) and L. theobromae (0.0703) from date palm, Citrus, and mango. These findings imply a high rate of movement of L. hormozganensis and L. theobromae isolates among date palm, Citrus, and mango and between the two countries. Findings from the pathogenicity test supported the AMOVA analysis and suggested a lack of host specialization in L. honnozganensis, L. iraniensis, and L. theobromae on date palm, acid lime, and mango. Although this is the first record of L hormozganensis and L iraniensis in Oman, the relatively moderate level of genetic diversity in the two species compared to L. theobromae suggests that the two species have been in Oman for a long time but misidentified by morphology and ITS rDNA sequences as L theobromae. This study is also the first record of date palm and acid lime as natural hosts for L honnozganensis and the first record of L hormozganensis in the UAE. The diversity in Lasiodiplodia species affecting date palm, Citrus, and mango in Oman and the UAE should be taken into consideration when planning future management programs for diseases caused by these pathogens.
Al-Sadi, A. M., Al-Ghaithi, A. G., Al-Balushi, Z. M., and Al-Jabri, A. H. 2012. Analysis of diversity in Pythium aphanidermatum populations from a single greenhouse reveals phenotypic and genotypic changes over 2006 to 2011. Plant Dis. 96:852-858. A study was conducted to investigate phenotypic and genotypic changes within Pythium aphanidermatum populations during the period 2006 to 2011. In total, 92 isolates of P. aphanidermatum (59 in 2006 and 33 in 2011) were obtained from different planting sites (soil) of cucumber from a single greenhouse. Generated sequences of the internal transcribed spacer (ITS) ribosomal DNA showed that all, except one isolate, share an identical sequence of the ITS region. Most (89%) P. aphanidermatum isolates were found to be aggressive on cucumber seedlings, with no significant differences in the aggressiveness level between populations obtained from different planting rows or different years. Sensitivity to metalaxyl among populations of P aphanidermatum increased significantly from concentration resulting in 50% growth inhibition levels of 0.070 to 1.823 (average 0.824 mu g ml(-1)) in 2006 to 0.002 to 0.564 (average 0.160 mu g ml(-1)) in 2011. Amplified fragment length polymorphism analysis of the 92 isolates produced 92 different genotypes and 985 polymorphic loci. P. apha-nidermatum populations from 2006 and 2011 were found to have low levels of genetic diversity (H = 0.1425), which implies introduction of the isolates into the greenhouse via common sources. Results from analysis of molecular variance (F-ST = 0.0307 in 2006 and 0.0222 in 2011) provided evidence for frequent exchange of Pythium inoculum between different planting locations within the same year. However, the analysis showed moderate levels (F-ST = 0.1731) of genetic differentiation among populations from the 2 years. This was supported by unweighted pair group method with arithmetic means analysis, which showed clustering of many of the 2006 isolates in separate clusters. The change in the metalaxyl sensitivity of the populations from 2006 to 2011 accompanied by the genetic differences among these two populations may suggest that many of the isolates from 2006 were lost and were replaced by new and highly sensitive P. aphanidermatum isolates by 2011.
We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including
options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained
alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples
to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to
clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
There is a growing need in the research community to apply the molecular evolutionary genetics analysis (MEGA) software tool for batch processing a large number of datasets and to integrate it into analysis workflows. Therefore, we now make available the computing core of the MEGA software as a stand-alone executable (MEGA-CC), along with an analysis prototyper (MEGA-Proto). MEGA-CC provides users with access to all the computational analyses available through MEGA's graphical user interface version. This includes methods for multiple sequence alignment, substitution model selection, evolutionary distance estimation, phylogeny inference, substitution rate and pattern estimation, tests of natural selection and ancestral sequence inference. Additionally, we have upgraded the source code for phylogenetic analysis using the maximum likelihood methods for parallel execution on multiple processors and cores. Here, we describe MEGA-CC and outline the steps for using MEGA-CC in tandem with MEGA-Proto for iterative and automated data analysis.
http://www.megasoftware.net/
s.kumar@asu.edu.
With the increasing availability of molecular data, maximum likelihood approaches have gained a new central role in phylogenetic reconstructions. Extremely fast tree-search algorithms have been developed to handle data sets of ample size in reasonable time. In the past few years, RAxML has achieved great relevance in this field and obtained wide distribution among evolutionary biologists and taxonomists because of its high computational performance and accuracy. However, there are certain drawbacks with regard to its usability, since the program is exclusively command-line based. To overcome this problem, we developed raxmlGUI, a graphical user interface that makes the use of RAxML easier and highly intuitive, enabling the user to perform phylogenetic analyses of varying complexity. The GUI includes all main options of RAxML, and a number of functions are automated
or simplified. In addition, some features extend the standard use of RAxML, like assembling concatenated alignments with automatic partitioning. RaxmlGUI is an open source Python program, available in a cross-platform package that incorporates RAxML executables for the main operating systems. It can be downloaded from http://sourceforge.net/projects/raxmlgui/.
Keywords: Rapid bootstrap; Graphical user interface; Maximum likelihood; Phylogenetic analyses; Python; RAxML
The recently-developed statistical method known as the "bootstrap" can be used to place confidence intervals on phylogenies. It involves resampling points from one's own data, with replacement, to create a series of bootstrap samples of the same size as the original data. Each of these is analyzed, and the variation among the resulting estimates taken to indicate the size of the error involved in making estimates from the original data. In the case of phylogenies, it is argued that the proper method of resampling is to keep all of the original species while sampling characters with replacement, under the assumption that the characters have been independently drawn by the systematist and have evolved independently. Majority-rule consensus trees can be used to construct a phylogeny showing all of the inferred monophyletic groups that occurred in a majority of the bootstrap samples. If a group shows up 95% of the time or more, the evidence for it is taken to be statistically significant. Existing computer programs can be used to analyze different bootstrap samples by using weights on the characters, the weight of a character being how many times it was drawn in bootstrap sampling. When all characters are perfectly compatible, as envisioned by Hennig, bootstrap sampling becomes unnecessary; the bootstrap method would show significant evidence for a group if it is defined by three or more characters.
Mycologists and plant pathologists have long been documenting fungi in checklists or adding them to databases that list hosts and associated fungi. Most references to the fungi of Oman are scattered in journals, reports and university theses. A review of the fungal status of Oman is long overdue as soil-borne and plant pathogens have been studied to some extent. Although Waller & Bridge (1978) listed the fungal diseases on economically important crops in Oman, the present study is the first attempt to put together all hitherto recorded fungi from this part of the world. This paper presents a systematic checklist of 318 fungal species, in 173 genera, currently known to occur in Oman. A working checklist of accepted taxa in Oman is vital in progress of the systematics, agriculture, quarantine and many other applied scientific fields in the country.
Species of Pestalotiopsis occur commonly as plant pathogens, and represent a fungal group known to produce a wide range of chemically novel, diverse metabolites. In the present study, we investigated 91 Pestalotiopsis isolates from the CBS-KNAW Fungal Biodiversity Centre (CBS) culture collection. The phylogeny of the Amphisphaeriaceae was constructed based on analysis of 28S nrRNA gene (LSU) sequence data, and taxonomic changes are proposed to reflect more natural groupings. We combined morphological and DNA data, and segregated two novel genera from Pestalotiopsis, namely Neopestalotiopsis and Pseudopestalotiopsis. The three genera are easily distinguishable on the basis of their conidiogenous cells and colour of their median conidial cells. We coupled morphological and combined sequence data of internal transcribed spacer (ITS), partial β-tubulin (TUB) and partial translation elongation factor 1-alpha (TEF) gene regions, which revealed 30 clades in Neopestalotiopsis and 43 clades in Pestalotiopsis. Based on these data, 11 new species are introduced in Neopestalotiopsis, 24 in Pestalotiopsis, and two in Pseudopestalotiopsis. Several new combinations are proposed to emend monophyly of Neopestalotiopsis, Pestalotiopsis and Pseudopestalotiopsis.
A new family of Loculoascomycetes is erected for species with unbranched, sparsely septate pseudoparaphyses and pigmented, distoseptate ascospores that form in asci with broad cylinders of differentially-staining material at their apices. Requienella is reinstated and selected to typify the family. Requienella seminuda and R. lichenopsis are newly combined. Requienella seminuda, whose epithet has long been misapplied to a species of Melanomma, is selected to typify the genus.
— We studied sequence variation in 16S rDNA in 204 individuals from 37 populations of the land snail Candidula unifasciata (Poiret 1801) across the core species range in France, Switzerland, and Germany. Phylogeographic, nested clade, and coalescence analyses were used to elucidate the species evolutionary history. The study revealed the presence of two major evolutionary lineages that evolved in separate refuges in southeast France as result of previous fragmentation during the Pleistocene. Applying a recent extension of the nested clade analysis (Templeton 2001), we inferred that range expansions along river valleys in independent corridors to the north led eventually to a secondary contact zone of the major clades around the Geneva Basin. There is evidence supporting the idea that the formation of the secondary contact zone and the colonization of Germany might be postglacial events. The phylogeographic history inferred for C. unifasciata differs from general biogeographic patterns of postglacial colonization previously identified for other taxa, and it might represent a common model for species with restricted dispersal.
Corals living in the coastal waters of southern Oman experience the influence of the seasonally reversing Asian monsoon system. The objective of the research reported here is to assess the potential for using the skeletal chemistry of these corals to investigate past variability in the monsoon, climate. To this end, 20-year long, monthly resolution geochemical records are presented for cores from true massive Porites corals, located 20 km apart near Marbat on, the Arabian Sea coast of southern Oman. We consider four aspects of skeletal chemistry: oxygen and carbon isotopic com position barium content and the nature and occurrence of annual fluorescent bands within the coral skeletons. Coral skeletal delta(18)O documents variations in sea surface temperature which have regional and basin-wide significance. In particular, the delta(18)O of coral skeleton precipitated during the period of the NE monsoon is strongly correlated with annual rainfall anomalies in India, whilst that precipitated during the period of the SW monsoon appears to provide information. on variability in the strength of coastal upwelling. The stable carbon isotope composition and barium content of these particular corals display strong annual cycles, but do not appear to directly record interannual climatic/oceanographic variability. It is concluded that corals on the coast of southern. Oman have great potential to provide high-resolution, century-long records of oceanographic and climatic variability associated with the operation of the monsoon climate system.
Detailed restriction analyses of many samples often require substantial amounts of time and effort for DNA extraction, restriction digests, Southern blotting, and hybridization. We describe a novel approach that uses the polymerase chain reaction (PCR) for rapid simplified restriction typing and mapping of DNA from many different isolates. DNA fragments up to 2 kilobase pairs in length were efficiently amplified from crude DNA samples of several pathogenic Cryptococcus species, including C. neoformans, C. albidus, C. laurentii, and C. uniguttulatus. Digestion and electrophoresis of the PCR products by using frequent-cutting restriction enzymes produced complex restriction phenotypes (fingerprints) that were often unique for each strain or species. We used the PCR to amplify and analyze restriction pattern variation within three major portions of the ribosomal DNA (rDNA) repeats from these fungi. Detailed mapping of many restriction sites within the rDNA locus was determined by fingerprint analysis of progressively larger PCR fragments sharing a common primer site at one end. As judged by PCR fingerprints, the rDNA of 19 C. neoformans isolates showed no variation for four restriction enzymes that we surveyed. Other Cryptococcus spp. showed varying levels of restriction pattern variation within their rDNAs and were shown to be genetically distinct from C. neoformans. The PCR primers used in this study have also been successfully applied for amplification of rDNAs from other pathogenic and nonpathogenic fungi, including Candida spp., and ought to have wide applicability for clinical detection and other studies.
Monograph of the Pyrenulaceae (excluding Anthracothecium and Pyrenula) and the Requienellaceae
- A Aptroot
Aptroot, A. (1991) Monograph of the Pyrenulaceae (excluding Anthracothecium and Pyrenula) and the Requienellaceae. J. Cramer.
Barr, M.E. (1983) The ascomycete connection. Mycologia 75 (1): 1-13.
https://doi.org/10.2307/3792917
Notes on ascomycetes and coelomycetes from NW Europe
- O Eriksson
Eriksson, O. (1982) Notes on ascomycetes and coelomycetes from NW Europe. Mycotaxon 15 (1): 189-202.
Outline of the Ascomycetes -1983
- O Eriksson
Eriksson, O. (1984) Outline of the Ascomycetes -1983. Systema Ascomycetum 3: 1-72