Identification of endophytic fungi from leaves of Pandanaceae based on their morphotypes and DNA sequence data from southern Thailand

The authors established the taxonomic status of endophytic fungi associated with leaves of Pandanaceae collected from southern Thailand. Morphotypes were initially identified based on their characteristics in culture and species level identification was done based on both morphological characteristics and phylogenetic analyses of DNA sequence data. Twenty-two isolates from healthy leaves were categorised into eight morphotypes. Appropriate universal primers were used to amplify specific gene regions and phylogenetic analyses were performed to identify these endophytes and established relationships with extant fungi. The authors identified both ascomycete and basidiomycete species, including one new genus, seven new species and nine known species. Morphological descriptions, colour plates and phylogenies are given for each taxon.

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Identification of endophytic fungi from leaves of Pandanaceae based on their morphotypes and DNA sequence data from southern Thailand

MycoKeys ◽

10.3897/mycokeys.32.23670 ◽

2018 ◽

Vol 33 ◽

pp. 25-67 ◽

Cited By ~ 2

Author(s):

Saowaluck Tibpromma ◽

Kevin D. Hyde ◽

Jayarama D. Bhat ◽

Peter E. Mortimer ◽

Jianchu Xu ◽

...

Keyword(s):

Dna Sequence ◽

Endophytic Fungi ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Morphological Characteristics ◽

Taxonomic Status ◽

Universal Primers ◽

Specific Gene ◽

Dna Sequence Data ◽

Southern Thailand

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Toward a Natural Classification of Botryosphaeriaceae: A Study of the Type Specimens of Botryosphaeria sensu lato

Frontiers in Microbiology ◽

10.3389/fmicb.2021.737541 ◽

2021 ◽

Vol 12 ◽

Author(s):

Ying Zhang ◽

Yupei Zhou ◽

Wei Sun ◽

Lili Zhao ◽

D. Pavlic-Zupanc ◽

...

Keyword(s):

Dna Sequence ◽

Dna Sequences ◽

Sequence Data ◽

Morphological Characteristics ◽

Taxonomic Status ◽

Morphological Characters ◽

Phylogenetic Position ◽

Type Specimens ◽

Natural Classification ◽

Dna Sequence Data

The genus Botryosphaeria includes more than 200 epithets, but only the type species, Botryosphaeria dothidea and a dozen or more other species have been identified based on DNA sequence data. The taxonomic status of the other species remains unconfirmed because they lack either morphological information or DNA sequence data. In this study, types or authentic specimens of 16 “Botryosphaeria” species are reassessed to clarify their identity and phylogenetic position. nuDNA sequences of four regions, ITS, LSU, tef1-α and tub2, are analyzed and considered in combination with morphological characteristics. Based on the multigene phylogeny and morphological characters, Botryosphaeria cruenta and Botryosphaeria hamamelidis are transferred to Neofusicoccum. The generic status of Botryosphaeria aterrima and Botryosphaeria mirabile is confirmed in Botryosphaeria. Botryosphaeria berengeriana var. weigeliae and B. berengeriana var. acerina are treated synonyms of B. dothidea. Botryosphaeria mucosa is transferred to Neodeightonia as Neodeightonia mucosa, and Botryosphaeria ferruginea to Nothophoma as Nothophoma ferruginea. Botryosphaeria foliicola is reduced to synonymy with Phyllachorella micheliae. Botryosphaeria abuensis, Botryosphaeria aesculi, Botryosphaeria dasylirii, and Botryosphaeria wisteriae are tentatively kept in Botryosphaeria sensu stricto until further phylogenetic analysis is carried out on verified specimens. The ordinal status of Botryosphaeria apocyni, Botryosphaeria gaubae, and Botryosphaeria smilacinina cannot be determined, and tentatively accommodate these species in Dothideomycetes incertae sedis. The study demonstrates the significance of a polyphasic approach in characterizing type specimens, including the importance of using of DNA sequence data.

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Reappraisal of Immotthia in Dictyosporiaceae, Pleosporales: Introducing Immotthia bambusae sp. nov. and Pseudocyclothyriella clematidis comb. et gen. nov. Based on Morphology and Phylogeny

Frontiers in Microbiology ◽

10.3389/fmicb.2021.656235 ◽

2021 ◽

Vol 12 ◽

Author(s):

Hong-Bo Jiang ◽

Rajesh Jeewon ◽

Samantha C. Karunarathna ◽

Chayanard Phukhamsakda ◽

Mingkwan Doilom ◽

...

Keyword(s):

Dna Sequence ◽

Phylogenetic Trees ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Morphological Characteristics ◽

Single Species ◽

Type Specimen ◽

Morphological Identification ◽

Ongoing Research ◽

Dna Sequence Data

Immotthia is a poorly known genus, and currently, no DNA sequence data are available to ascertain its proper phylogenetic placement and evolutionary relationships with other bitunicate fungi. To date, there are only two species accepted in the genus. During our ongoing research study of bambusicolous fungi in southwest China and Thailand, a fungus associated with stromata of Hypoxylon sp. was found on dead bamboo culms in Loei Province, Thailand. Preliminary morphological identification revealed that the fungal collection belongs to Immotthia. A novel species, Immotthia bambusae, is introduced herein based on a comparison of morphological characteristics with the type specimen of I. hypoxylon (≡ Amphisphaeria hypoxylon Ellis and Everh.), a synonym of I. atrograna (Cooke and Ellis) M. E. Barr. Phylogenetic analyses of a concatenated ITS, LSU, SSU, and TEF1-α DNA sequence matrix showed that Immotthia belongs to Dictyosporiaceae, Pleosporales. Despite I. bambusae strains constituting a supported subclade, they are nested with the genus Pseudocoleophoma. Pseudocoleophoma clematidis is morphologically different from all other Pseudocoleophoma species, while its conidial characteristics are similar to Cyclothyriella. Multigene phylogenetic analyses showed that P. clematidis formed a clade basal to Immotthia, separated from Pseudocoleophoma with strong statistical support. Therefore, we introduce a monotypic genus, Pseudocyclothyriella Phukhams. and Phookamsak, gen. nov. to accommodate the single species, Pseudocyclothyriella clematidis (Phukhams. and K. D. Hyde) Phukhams. and Phookamsak, comb. nov. Detailed descriptions, color micrographs, and phylogenetic trees to show the placement of the new taxa are provided. In addition, an updated taxonomic treatment of the genera Immotthia and Pseudocyclothyriella is also provided based on the study of the type materials and phylogeny generated from DNA sequence data.

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Two novel Acervus species extend their distribution within Yunnan, China

Phytotaxa ◽

10.11646/phytotaxa.283.1.5 ◽

2016 ◽

Vol 283 (1) ◽

pp. 74 ◽

Cited By ~ 4

Author(s):

ANUSHA H. EKANAYAKA ◽

QI ZHAO ◽

GARETH E.B. JONES ◽

EN-DA PU ◽

KEVIN D. HYDE

Keyword(s):

New Species ◽

Dna Sequence ◽

Yunnan Province ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Morphological Characteristics ◽

Morphological Features ◽

Dna Sequence Data ◽

Two New Species ◽

Small Genus

Acervus is a small genus in Pyronemataceae. Most of the species in this genus have been recorded from China. In the present study, two species of Acervus from Yunnan Province, in southwestern China, were investigated by using morphology and DNA sequence data. This paper introduces two new species A. stipitatus and A. globulosus, with morphological descriptions, and compares them with morphologically similar taxa. Multi-gene phylogenetic analyses inferred from 28S, TEF1 and RPB2 sequence data strongly support the lineages for taxa of Acervus, corresponding to morphological features. We also provide a summarized comparison of the important morphological characteristics of Acervus species.

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Revision of Batrachospermum sections Acarposporophytum and Aristata (Batrachospermales, Rhodophyta) with the establishment of the new genera Acarposporophycos and Visia

Phytotaxa ◽

10.11646/phytotaxa.395.2.1 ◽

2019 ◽

Vol 395 (2) ◽

pp. 51 ◽

Cited By ~ 6

Author(s):

ORLANDO NECCHI JR ◽

AURO GARCIA FILHO ◽

MONICA O. PAIANO

Keyword(s):

Dna Sequence ◽

Sequence Data ◽

Morphological Characteristics ◽

Sequence Divergence ◽

Morphological Evidence ◽

Similar Species ◽

Type Specimens ◽

Generic Level ◽

Dna Sequence Data ◽

Cell Layers

Sections of the paraphyletic genus Batrachospermum have been recently investigated using molecular (DNA sequence data) and morphological evidence. Some sections have been recognized as distinct genera in order to resolve paraphyly. Batrachospermum species of sections Acarposporophytum and Aristata are showed to form well-supported clades and, in this study, we propose to raise them to the generic level, Acarposporophycos gen. nov. and Visia gen. nov., respectively. In addition, we re-evaluated the characters used to circumscribe species by reexamining type specimens as well as new collections. Acarposporophycos, with the sole species A. brasiliensis, is characterized by the lack of carposporophytic stage, with the fertilized carpogonia germinating to form directly the filaments of the ‘Chantransia’ stage on the gametophyte. Of the five previously accepted species in the genus Visia, we recognize four species: V. cayennensis—type species (synonym Batrachospermum beraense), V. cylindrocellularis, V. longiarticulata and V. turgida. The species are circumscribed on the basis of morphological characteristics (shape and cell layers of primary fascicles, occurrence of secondary fascicles, post-fertilization development of carpogonia) and DNA sequence data (rbcL and COI-5P). Specimens described as Visia cayennensis from Australia and Brazil had a high sequence divergence in comparison to those from or near the type locality (French Guiana), and are here referred to as Visia spp. Further studies are recommended to better discriminate these morphologically similar species on a broad geographical scale and define their status at the species level. Descriptions, identification key and photomicrographs are presented for each recognized species.

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Molecular phylogenetics of the Onobrychis genus (Fabaceae: Papilionoideae) using ITS and trnL–trnF DNA sequence data

Australian Journal of Botany ◽

10.1071/bt13279 ◽

2014 ◽

Vol 62 (3) ◽

pp. 235 ◽

Cited By ~ 2

Author(s):

S. Safaei Chaei Kar ◽

F. Ghanavati ◽

M. R. Naghavi ◽

H. Amirabadi-zade ◽

R. Rabiee

Keyword(s):

Dna Sequence ◽

Molecular Phylogenetics ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Dna Sequence Data ◽

Group I ◽

Molecular Phylogenetic ◽

Nuclear Its ◽

Cultivated Species ◽

Relationship Of

Onobrychis, comprising more than 130 species, is a genus of the family Fabaceae. At this time, the interspecies relationship of this biologically important genus is still a subject of great discussion and debate. To help resolve this disagreement, we used molecular phylogeny to analyse internal transcribed spacer (ITS) and trnL–trnF sequences of 76 species of Onobrychis. Bayesian interference, maximum parsimony and maximum likelihood analyses of nuclear ITS and plastid trnL–trnF DNA sequence data generated trees with strong posterior probability for two groups: Onobrychis subgen. Sisyrosema (including: Heliobrychis, Hymenobrychis, Afghanicae and Anthyllium sections) along with Laxiflorae section in Group I and Onobrychis subgen. Onobrychis (except Laxiflorae section) in the other (Group II). The Laxiflorae section roots back to the ancestral node for Sisyrosema subgen. O. viciifolia (cultivated species), which is closely associated with O. cyri var. cyri, suggesting that the latter may be a wild progenitor of O. viciifolia. The present study supported the paraphyly of subgenera Onobrychis and Sisyrosema. The study proposed the paraphyletic nature of the sections Onobrychis, Dendrobrychis, Heliobrychis and Hymenobrychis. Together with our molecular phylogenetic analyses we present a review of Onobrychis morphology and discuss and compare our results with those of earlier morphological and molecular phylogenetic analyses.

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Veterinary Fusarioses within the United States

Journal of Clinical Microbiology ◽

10.1128/jcm.01607-16 ◽

2016 ◽

Vol 54 (11) ◽

pp. 2813-2819 ◽

Cited By ~ 21

Author(s):

Kerry O'Donnell ◽

Deanna A. Sutton ◽

Nathan Wiederhold ◽

Vincent A. R. G. Robert ◽

Pedro W. Crous ◽

...

Keyword(s):

United States ◽

Dna Sequence ◽

Species Complex ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Distinct Species ◽

The United States ◽

Content Type ◽

Dna Sequence Data ◽

Species Complexes

Multilocus DNA sequence data were used to assess the genetic diversity and evolutionary relationships of 67Fusariumstrains from veterinary sources, most of which were from the United States. Molecular phylogenetic analyses revealed that the strains comprised 23 phylogenetically distinct species, all but two of which were previously known to infect humans, distributed among eight species complexes. The majority of the veterinary isolates (47/67 = 70.1%) were nested within theFusarium solanispecies complex (FSSC), and these included 8 phylospecies and 33 unique 3-locus sequence types (STs). Three of the FSSC species (Fusarium falciforme,Fusarium keratoplasticum, andFusariumsp. FSSC 12) accounted for four-fifths of the veterinary strains (38/47) and STs (27/33) within this clade. Most of theF. falciformestrains (12/15) were recovered from equine keratitis infections; however, strains ofF. keratoplasticumandFusariumsp. FSSC 12 were mostly (25/27) isolated from marine vertebrates and invertebrates. Our sampling suggests that theFusarium incarnatum-equisetispecies complex (FIESC), with eight mycoses-associated species, may represent the second most important clade of veterinary relevance withinFusarium. Six of the multilocus STs within the FSSC (3+4-eee, 1-b, 12-a, 12-b, 12-f, and 12-h) and one each within the FIESC (1-a) and theFusarium oxysporumspecies complex (ST-33) were widespread geographically, including three STs with transoceanic disjunctions. In conclusion, fusaria associated with veterinary mycoses are phylogenetically diverse and typically can only be identified to the species level using DNA sequence data from portions of one or more informative genes.

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Senecio imbaburensis, proposed name for Lasiocephalus sodiroi in the genus Senecio (Asteraceae)

Phytotaxa ◽

10.11646/phytotaxa.152.1.8 ◽

2013 ◽

Vol 152 (1) ◽

pp. 59

Author(s):

Karol Marhold ◽

Petr Sklenář

Keyword(s):

Dna Sequence ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Plastid Dna ◽

Dna Sequence Data ◽

Number Of Species ◽

The Andes

Lasiocephalus Willd. ex Schlechtendal (1818: 308), as traditionally circumscribed (e.g., by Cuatrecasas 1978, Dušková et al. 2010), is a neotropical genus of ca 25 species confined to the Andes and distributed from Venezuela to Bolivia. Nevertheless, recent studies by Pelser et al. (2007, 2010) have shown that based on phylogenetic analyses of nrITS and plastid DNA sequence data, species of the genus Lasiocephalus are deeply embedded in Senecio Linnaeus (1753: 866), and, consequently, should be transferred into this latter genus. In fact, a number of species of Lasiocephalus were originally described as Senecio or had been, at some point, transferred into Senecio so only few transfers are necessary.

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Is Ronnbergia (Bromeliaceae, Bromelioideae) a geographically disjunct genus? Evidence from morphology and chloroplast DNA sequence data

Phytotaxa ◽

10.11646/phytotaxa.219.3.6 ◽

2015 ◽

Vol 219 (3) ◽

pp. 261 ◽

Cited By ~ 7

Author(s):

Julian Aguirre-Santoro ◽

Julio Betancur ◽

Gregory K. Brown ◽

Timothy M. Evans ◽

Fabiano Salgueiro ◽

...

Keyword(s):

Chloroplast Dna ◽

Dna Sequence ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Phylogenetic Reconstruction ◽

Morphological Data ◽

Phylogenetic Study ◽

Geographic Ranges ◽

Dna Sequence Data ◽

Disjunct Genus

A phylogenetic study testing the monophyly of the geographically disjunct genus Ronnbergia (Bromeliaceae, Bromelioideae) is presented. The phylogenetic analyses were based on taxon sampling that included all but one species of Ronnbergia, and representative lineages across the subfamily Bromelioideae. Three chloroplast DNA sequence markers (matK, psbA-trnH, and trnL-trnF) and morphological data were used for the phylogenetic reconstruction. Both the molecular and morphological datasets supported the polyphyly of Ronnbergia, either independently or in combination. These findings suggest that the geographic disjunction of this genus is most likely a product of taxonomic misinterpretation. The results also indicate that the species currently circumscribed in Ronnbergia are closely related to species in the genus Aechmea with similar geographic ranges. The datasets do not have enough resolution power to reconstruct a deep phylogenetic history that involves all the species of Ronnbergia. Nevertheless, this study provides clues for future approaches that should focus on a larger species sampling and the use of multi-locus DNA sequence data.

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