Phacidiaceae endophytes of Picea rubens in Eastern Canada

More than 100 fungal endophyte strains belonging to the family Phacidiaceae were isolated from surface-sterilized Picea rubens Sarg. needles collected from the Acadian Forest Region in New Brunswick, Canada. The strains were characterized morphologically by their asexual states, and phylogenetic analyses were conducted using the nuclear internal transcribed spacer rDNA (ITS) marker and the second largest subunit of ribosomal polymerase II (RPB2). Morphological and phylogenetic data revealed seven species: Darkera cf. parca; Strasseria geniculata; two novel Phacidium species: Phacidium dicosmoanum and Phacidium faciforme; and three novel monotypic genera described to accommodate distinct species: Calvophomopsis rubenticola, Cornibusella ungulata, and Gloeopycnis protuberans. Further analyses of Darkera spp. were performed with ITS and partial translation elongation factor 1-α (TEF1α), and the results suggest that D. parca is a species complex. Phacidiaceae includes hundreds of known species that are unrepresented by sequence data; therefore, ITS sequences were generated from herbarium material including type specimens of Darkera parca, Phacidium lunatum, and specimens of Allantophomopsiella, Allantophomopsis, Bulgaria, Phacidium, and Pseudophacidium species. The description of novel species combined with morphological observations and reference sequences will facilitate the identification of conifer endophytes, both from specimens or cultures and in environmental sequence data, and improve our understanding of this large and mostly neglected family.

Download Full-text

Phylogenetic relationships within Cicuta (Apiaceae tribe Oenantheae) inferred from nuclear rDNA ITS and cpDNA sequence data

Canadian Journal of Botany ◽

10.1139/b06-016 ◽

2006 ◽

Vol 84 (3) ◽

pp. 453-468 ◽

Cited By ~ 22

Author(s):

Chang-Shook Lee ◽

Stephen R. Downie

Keyword(s):

North American ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Taxonomic Status ◽

Distinct Species ◽

Sister Group ◽

Nuclear Ribosomal Dna ◽

Hybrid Origin ◽

Rdna Its ◽

The North

The genus Cicuta (Apiaceae tribe Oenantheae Dumort.) is the most virulently poisonous group of flowering plants native to the north temperate zone. A recent treatment recognized four species ( C. bulbifera L., C. douglasii (DC.) J.M. Coult. & Rose, C. maculata L., and C. virosa L.), with C. maculata divided into four varieties. We present results of phylogenetic analyses of the nuclear ribosomal DNA (rDNA) internal transcribed spacer (ITS) locus and the region bounded by the chloroplast genes psbI and trnK 5′ exon to determine taxonomic limits and relationships among these taxa, and to assess the taxonomic status of C. douglasii, a polyploid thought to be derived from C. maculata and C. virosa. Cicuta bulbifera and C. virosa are each resolved as monophyletic, the latter is a sister group to all other species. Discordance between the ITS- and plastid-derived phylogenies and lack of resolution in the ITS trees preclude unequivocal hypotheses of relationship; all trees do suggest, however, that the allotetraploid C. douglasii is polyphyletic and possibly polytopic, with all examined accessions but one nested within C. maculata. This single outstanding accession is from California and, pending further study, might warrant recognition as a distinct species. The diploid C. bulbifera may also be of hybrid origin, as revealed by significant discordance between data sets. Within C. maculata, only the western North American var. angustifolia Hook. is resolved in the ITS trees. In the cpDNA trees, C. maculata var. angustifolia comprises a strongly supported clade with C. maculata var. bolanderi (S. Watson) G.A. Mulligan and C. douglasii, both of primarily western North American distribution. The eastern North American taxa, C. maculata vars. maculata and victorinii (Fernald) B. Boivin, also comprise a clade, sister group to C. bulbifera.

Download Full-text

Taxonomic Re-Examination of Nine Rosellinia Types (Ascomycota, Xylariales) Stored in the Saccardo Mycological Collection

Microorganisms ◽

10.3390/microorganisms9030666 ◽

2021 ◽

Vol 9 (3) ◽

pp. 666

Author(s):

Niccolò Forin ◽

Alfredo Vizzini ◽

Federico Fainelli ◽

Enrico Ercole ◽

Barbara Baldan

Keyword(s):

Sequence Data ◽

Phylogenetic Analyses ◽

Illumina Miseq ◽

Botanical Garden ◽

Molecular Study ◽

Its2 Sequence ◽

Type Specimens ◽

Its1 Sequence ◽

Dna Sequence Data ◽

Nomen Novum

In a recent monograph on the genus Rosellinia, type specimens worldwide were revised and re-classified using a morphological approach. Among them, some came from Pier Andrea Saccardo’s fungarium stored in the Herbarium of the Padova Botanical Garden. In this work, we taxonomically re-examine via a morphological and molecular approach nine different Roselliniasensu Saccardo types. ITS1 and/or ITS2 sequences were successfully obtained applying Illumina MiSeq technology and phylogenetic analyses were carried out in order to elucidate their current taxonomic position. Only the ITS1 sequence was recovered for Rosellinia areolata, while for R. geophila, only the ITS2 sequence was recovered. We proposed here new combinations for Rosellinia chordicola, R. geophila and R. horridula, while for R. ambigua, R. areolata, R. australis, R. romana and R. somala, we did not suggest taxonomic changes compared to the current ones. The name Rosellinia subsimilis Sacc. is invalid, as it is a later homonym of R. subsimilis P. Karst. & Starbäck. Therefore, we introduced Coniochaeta dakotensis as a nomen novum for R. subsimilis Sacc. This is the first time that these types have been subjected to a molecular study. Our results demonstrate that old types are an important source of DNA sequence data for taxonomic re-examinations.

Download Full-text

Phaeosphaeria chinensis sp. nov. (Phaeosphaeriaceae) with an asexual/sexual morph connection from GuangDong Province, China

Phytotaxa ◽

10.11646/phytotaxa.419.1.2 ◽

2019 ◽

Vol 419 (1) ◽

pp. 28-38 ◽

Cited By ~ 1

Author(s):

KE-KE ZHANG ◽

SINANG HONGSANAN ◽

DANUSHKA S. TENNAKOON ◽

SHENG-LI TIAN ◽

NING XIE

Keyword(s):

New Species ◽

Bayesian Inference ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Guangdong Province ◽

Distinct Species ◽

Bootstrap Support ◽

Comprehensive Description ◽

High Bootstrap ◽

Asexual Morphs

Phaeosphaeria chinensis sp. nov. was found on dead leaves, collected from Guangdong Province, China. Morphology of the new species was compared with other Phaeosphaeria species and related genera of Phaeosphaeriaceae. Phylogenetic analyses of combined ITS, LSU, SSU and TEF-1 sequence data based on maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference (BI) revealed that P. chinensis as a distinct species within the Phaeosphaeria with high bootstrap support. The comparison of the new species with other Phaeosphaeria species and a comprehensive description and micrographs are provided. The linkage of sexual and asexual morphs of the new species is also showed.

Download Full-text

Phylogenetic relationships of Australian Scirtidae (Coleoptera) based on mitochondrial and nuclear sequences

Invertebrate Systematics ◽

10.1071/is13046 ◽

2014 ◽

Vol 28 (6) ◽

pp. 628 ◽

Cited By ~ 3

Author(s):

Steven J. B. Cooper ◽

Christopher H. S. Watts ◽

Kathleen M. Saint ◽

Remko Leijs

Keyword(s):

Sequence Data ◽

Phylogenetic Analyses ◽

Elongation Factor ◽

Nuclear Gene ◽

Species Complexes ◽

Close Relationship ◽

Molecular Phylogenetic ◽

Coi Sequences ◽

Elongation Factor 1 ◽

Combined Data

Scirtidae is a cosmopolitan group of beetles with aquatic or saproxylic larvae. A large diversity of species has recently been described from Australia, but their systematics is uncertain. There is evidence that current genera are polyphyletic and that Australian species were wrongly placed in northern hemisphere genera. Here we investigate the systematics of Australian Scirtidae using molecular phylogenetic analyses of combined data from the mitochondrial cytochrome c oxidase subunit 1 (COI) and nuclear gene elongation factor 1-α (EF1-α) genes. We also assess the current taxonomy of Australian Scirtidae using partial COI sequences. Bayesian phylogenetic analyses of COI and EF1-α sequence data from 81 taxa show that the Australian genera Contacyphon, Pseudomicrocara and Prionocyphon are polyphyletic. There is no close relationship between Australian and Eurasian genera, with the exception of Scirtes. Phylogenetic analyses of partial COI data from Australian Scirtidae generally support the current α taxonomy, with the exception of several species that may be associated with species complexes. Geographically a high proportion of species lineages are restricted to relict patches of wet forest suggesting that they may be relict populations. The phylogeny and sequence data presented here provide a sound basis for further systematic and biogeographical studies of the Scirtidae.

Download Full-text

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.

Download Full-text

Phomopsis Stem Canker: A Reemerging Threat to Sunflower (Helianthus annuus) in the United States

Phytopathology ◽

10.1094/phyto-11-14-0336-fi ◽

2015 ◽

Vol 105 (7) ◽

pp. 990-997 ◽

Cited By ~ 28

Author(s):

Febina M. Mathew ◽

Kholoud M. Alananbeh ◽

James G. Jordahl ◽

Scott M. Meyer ◽

Lisa A. Castlebury ◽

...

Keyword(s):

United States ◽

Helianthus Annuus ◽

Great Plains ◽

Phylogenetic Analyses ◽

Elongation Factor ◽

Stem Canker ◽

The United States ◽

Northern Great Plains ◽

Type Specimens ◽

Internal Transcribed Spacer Region

Phomopsis stem canker causes yield reductions on sunflower (Helianthus annuus L.) on several continents, including Australia, Europe, and North America. In the United States, Phomopsis stem canker incidence has increased 16-fold in the Northern Great Plains between 2001 and 2012. Although Diaporthe helianthi was assumed to be the sole causal agent in the United States, a newly described species, D. gulyae, was found to be the primary cause of Phomopsis stem canker in Australia. To determine the identity of Diaporthe spp. causing Phomopsis stem canker in the Northern Great Plains, 275 infected stems were collected between 2010 and 2012. Phylogenetic analyses of sequences of the ribosomal DNA internal transcribed spacer region, elongation factor subunit 1-α, and actin gene regions of representative isolates, in comparison with those of type specimens, confirmed two species (D. helianthi and D. gulyae) in the United States. Differences in aggressiveness between the two species were determined using the stem-wound method in the greenhouse; overall, D. helianthi and D. gulyae did not vary significantly (P ≤ 0.05) in their aggressiveness at 10 and 14 days after inoculation. These findings indicate that both Diaporthe spp. have emerged as sunflower pathogens in the United States, and have implications on the management of this disease.

Download Full-text

Two new species of Leptographium associated with Tomicus spp. infesting Pinus spp. in Southwestern China

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijsem.0.004349 ◽

2020 ◽

Vol 70 (8) ◽

pp. 4798-4807

Author(s):

Yue Pan ◽

Jun Lu ◽

Xu-Dong Zhou ◽

Ze-fen Yu ◽

Peng Chen ◽

...

Keyword(s):

Sequence Data ◽

Phylogenetic Analyses ◽

Elongation Factor ◽

Optimal Growth ◽

Morphological Characters ◽

Lsu Rdna ◽

Optimal Growth Temperature ◽

Two New Species ◽

Pinus Spp ◽

Elongation Factor 1

Leptographium panxianense and L. puerense are proposed as new taxa based on sequence data and morphological characters. The phylogenetic analyses based on ITS2-partial LSU rDNA region, β-tubulin and elongation factor 1-α genes showed that L. panxianense and L. puerense formed well-supported clades and were closely related to L. yunnanense, L. wushanense and L. conjunctum, and then nested within the L. lundbergii complex. The two species differ in their conidial size and shape. The conidia of L. panxianense are larger than those of L. puerense while the conidial shape of L. puerense is more ovovoid. The optimal growth temperature of both L. panxianense and L. puerense is at 20 °C, which is different from those of L. yunnanense, L. wushanense and L. conjunctum. Comparison of sequence data and morphological characters confirmed the placement of the two undescribed taxa in the genus of Leptographium.

Download Full-text

Three, two, one! Revision of the long-bodied sphaerodorids (Sphaerodoridae, Annelida) and synonymization ofEphesiella,EphesiopsisandSphaerodorum

PeerJ ◽

10.7717/peerj.5783 ◽

2018 ◽

Vol 6 ◽

pp. e5783 ◽

Cited By ~ 1

Author(s):

María Capa ◽

Torkild Bakken ◽

Karin Meißner ◽

Arne Nygren

Keyword(s):

Dna Sequences ◽

Nuclear Dna ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Intraspecific Variability ◽

Morphological Data ◽

Nominal Species ◽

Type Specimens ◽

Diagnostic Features ◽

28S Rdna Sequence

BackgroundLong-bodied sphaerodorids (Annelida, Sphaerodoridae) is the common name for members of the three closely and morphologically homogenous currently accepted genera of benthic marine bristle worms:Ephesiella,EphesiopsisandSphaerodorum. Members of this group share the presence of two dorsal and longitudinal rows of macrotubercles with terminal papillae, and two longitudinal rows of microtubercles, features that are unique among sphaerodorids. Genera are distinguished by the chaetae morphology. Members ofEphesiellaare characterised by having compound chaetae (except, sometimes, simple chaetae in the first chaetigers),Sphaerodorumbear only simple chaetae, andEphesiopsishave both compound and simple chaetae in all parapodia.MethodsMitochondrial (partial COI and 16S rDNA) and nuclear (partial 18S rDNA and 28S rDNA) sequence data of long-bodied sphaerodorids with compound and simple chaetae, and an outgroup of additional seven sphaerodorid species were analysed separately and in combination using Bayesian inference (BA), and Maximum Likelihood (ML) methods. Long-bodied sphaerodorids from around the world (including type specimens) were examined under a range of optical equipment in order to evaluate putative generic and specific diagnostic features, in addition to intraspecific variability.ResultsPhylogenetic analyses of mitochondrial and nuclear DNA sequences of specimens identified asEphesiellaandSphaerodorum,based on chaeta morphology, were performed.SphaerodorumandEphesiellawere recovered as paraphyletic and nested within each other. Revision of current nominal species diagnostic features are performed and discussed.DiscussionResults contradict current generic definitions. Recovery of paraphyletic compound and simple chaetae clades urge the synonymization of these two genera of long-bodied sphaerodorids. Morphological data also suggest the synonymization ofEphesiopsis.

Download Full-text

Taxonomy and Phylogeny of the Fomitopsis pinicola Complex With Descriptions of Six New Species From East Asia

Frontiers in Microbiology ◽

10.3389/fmicb.2021.644979 ◽

2021 ◽

Vol 12 ◽

Author(s):

Shun Liu ◽

Mei-Ling Han ◽

Tai-Min Xu ◽

Yan Wang ◽

Dong-Mei Wu ◽

...

Keyword(s):

New Species ◽

East Asia ◽

Rna Polymerase Ii ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Elongation Factor ◽

Brown Rot ◽

Morphological Characters ◽

Host Specialization ◽

Fomitopsis Pinicola

Fomitopsis pinicola is a common brown-rot fungal species found in northern hemisphere. It grows on many different gymnosperm and angiosperm trees. Recent studies show that it is a species complex; three species from North America and one species from Europe have been recognized in this complex. In the current study, six new species in the Fomitopsis pinicola complex were discovered from East Asia, based on morphological characters and phylogenetic analyses inferred from the sequence data of the internal transcribed spacer (ITS) regions, the second subunit of RNA polymerase II (RPB2), and the translation elongation factor 1-α gene (TEF). Detailed descriptions of the six new species are provided. Our results also indicates that species of the F. pinicola complex from East Asia usually have limited distribution areas and host specialization.

Download Full-text

Occurrence and Morpho-Molecular Identification of Botryosphaeriales Species from Guizhou Province, China

Journal of Fungi ◽

10.3390/jof7110893 ◽

2021 ◽

Vol 7 (11) ◽

pp. 893

Author(s):

Asha J. Dissanayake ◽

Ya-Ya Chen ◽

Ratchadawan Cheewangkoon ◽

Jian-Kui Liu

Keyword(s):

Fungal Pathogens ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Large Subunit ◽

Elongation Factor ◽

Morphological Characteristics ◽

Guizhou Province ◽

Southwestern China ◽

Rrna Gene ◽

Large Subunit Rrna

Botryosphaeriales is an important order of diverse fungal pathogens, saprobes, and endophytes distributed worldwide. Recent studies of Botryosphaeriales in China have discovered a broad range of species, some of which have not been formerly described. In this study, 60 saprobic isolates were obtained from decaying woody hosts in southwestern China. The isolates were compared with other species using morphological characteristics, and available DNA sequence data was used to infer phylogenetic analyses based on the internal transcribed spacer (ITS), large subunit rRNA gene (LSU), and translation elongation factor 1-α (tef) loci. Three novel species were illustrated and described as Botryobambusa guizhouensis, Sardiniella elliptica, and Sphaeropsis guizhouensis, which belong to rarely identified genera within Botryosphaeriaceae. Botryobambusa guizhouensis is the second species identified from the respective monotypic genus. The previously known species were identified as Aplosporella hesperidica, Barriopsis tectonae, Botryosphaeria dothidea, Diplodia mutila, Di. neojuniperi, Di. pseudoseriata, Di. sapinea, Di. seriata, Dothiorella sarmentorum, Do. yunnana, Lasiodiplodia pseudotheobromae, Neofusicoccum parvum, Sardiniella celtidis, Sa. guizhouensis, and Sphaeropsis citrigena. The results of this study indicate that numerous species of Botryosphaeriales are yet to be revealed in southwestern China.

Download Full-text