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

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.

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

Phytotaxa ◽  
2019 ◽  
Vol 395 (2) ◽  
pp. 51 ◽  
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.

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

MycoKeys ◽  
2018 ◽  
Vol 33 ◽  
pp. 25-67 ◽  
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

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.

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

MycoKeys ◽  
2018 ◽  
Vol 33 ◽  
pp. 25-67 ◽  
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

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.

Molecular phylogeny confirms the placement of enigmatic Stachys persepolitana in Lamium (Lamiaceae; subfam. Lamioideae)

Phytotaxa ◽  
2015 ◽  
Vol 192 (4) ◽  
pp. 254
Author(s):  
Yasaman Salmaki ◽  
MIKA BENDIKSBY ◽  
GÜNTHER HEUBL
Keyword(s):  
Molecular Phylogeny ◽  
Dna Sequence ◽  
Sequence Data ◽  
Nuclear Data ◽  
Morphological Characters ◽  
Morphological Features ◽  
Phylogenetic Position ◽  
Rps16 Intron ◽  
Dna Sequence Data ◽  
Anterior Pair

The main purpose of this study was to test the hypothesis that Stachys persepolitana is extraneous in Stachys (tribe Stachydeae, subfam. Lamioideae, Lamiaceae) and instead belongs to the genus Lamium (Lamieae, Lamioideae). We investigated the phylogenetic position of S. persepolitana using plastid (rps16 intron, trnL-F and matK regions) and nuclear (nrITS) DNA sequence data with both parsimony and Bayesian phylogenetic approaches. Plastid and nuclear data strongly support that S. persepolitana is extraneous in Stachys and belongs in fact to the genus Lamium. Morphological characters also corroborate its placement in Lamium. Most of the morphological features used to distinguish S. persepolitana from the rest of Stachys fit with Lamium. Anterior pair of stamens bending outward after pollination, anthers hairy and mericarps triquetrous are the most important characters correlating S. persepolitana to Lamium.

scholarly journals Multigene evidence reveals the systematic position of Pleurocladopsis simulans (C. Massal.) R. M. Schust. within Schistochila Dumort., Schistochilaceae

2013 ◽  
Vol 58 (2) ◽  
pp. 467-474 ◽  
Author(s):  
Xiaolan He ◽  
Yu Sun
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Sequence ◽  
Sequence Data ◽  
Taxonomic Status ◽  
Systematic Position ◽  
New Combination ◽  
Phylogenetic Position ◽  
Dna Sequence Data ◽  
Starting Point ◽  
The Family

Abstract The monotypic Pleurocladopsis, endemic to Chile, was established by Schuster in 1964 based on an earlier poorly known species Cephalozia (?) simulans C. Massal. The phylogenetic position of Pleurocladopsis simulans had been considered uncertain until it was placed in the family Schistochilaceae on account of the gynoecial and sporophytic characters. It has been assumed that Pleurocladopsis represents the starting point of evolution in Schistochilaceae. In the present study, the phylogenetic position and taxonomic status of Pleurocladopsis simulans are inferred from phylogenetic analysis of three chloroplast DNA sequence data. The result suggests that the genus was established solely based on the autapomorphic characters, thus obscuring its actual phylogenetic relationship with Schistochila and that these characters are later derived rather than ancestral. The result also confirms that the gynoecial and sporophytic characters are important in taxonomy, but they may be not sufficient at the infrafamilial level and at other lower taxonomic levels. In accordance with the results of the present study, Pleurocladopsis is synonymised with Schistochila, and the new combination Schistochila simulans (C. Massal.) Xiao L. He & Yu Sun is made.

A Reexamination of the Phylogenetic Position of Callimico (Primates) Incorporating New Mitochondrial DNA Sequence Data

1998 ◽  
Vol 47 (1) ◽  
pp. 32-41 ◽  
Author(s):  
Jennifer Pastorini ◽  
Michael R.J. Forstner ◽  
Robert D. Martin ◽  
Don J. Melnick
Keyword(s):  
Mitochondrial Dna ◽  
Dna Sequence ◽  
Sequence Data ◽  
Phylogenetic Position ◽  
Dna Sequence Data ◽  
Mitochondrial Dna Sequence

Molecular phylogeny and systematics of the centipede genus Ethmostigmus Pocock (Chilopoda : Scolopendromorpha) from peninsular India

2018 ◽  
Vol 32 (6) ◽  
pp. 1316 ◽  
Author(s):  
Jahnavi Joshi ◽  
Gregory D. Edgecombe
Keyword(s):  
Dna Sequence ◽  
Molecular Phylogenetics ◽  
Sequence Data ◽  
Indian Plate ◽  
Eastern Ghats ◽  
Integrative Approach ◽  
Phylogenetic Position ◽  
Ecological Data ◽  
Peninsular India ◽  
Dna Sequence Data

Integrative taxonomy assesses the congruence between different lines of evidence for delimiting species, such as morphological, molecular or ecological data. Herein molecular phylogenetics is used to test monophyly and determine the phylogenetic position of the Old World tropical centipede genus Ethmostigmus Pocock, 1898, and to define species boundaries for Ethmostigmus in peninsular India. A phylogeny of the family Scolopendridae based on DNA sequence data for three markers from 427 specimens sampling in all major lineages (144 individuals generated in this study) recovers Ethmostigmus as a monophyletic group, but relationships among the genera in its subfamily Otostigminae are poorly supported. Two species delimitation methods for DNA sequence data and phylogeny are integrated with morphology and geographic data to propose a well-supported species hypothesis for Ethmostigmus on the peninsular Indian plate. Five species of Ethmostigmus are recognised in peninsular India, of which E. coonooranus Chamberlin, 1920 and three new species, namely, E. agasthyamalaiensis, sp. nov., E. sahyadrensis, sp. nov. and E. praveeni, sp. nov., occur in the Western Ghats, a biodiversity hotspot. The lesser-known Eastern Ghats harbour one species, E. tristis (Meinert, 1886), which has been nearly unreported for 130 years. This study highlights the value of an integrative approach to systematics, especially in underexplored, high biodiversity regions and where morphological variation is limited among closely related species.

scholarly journals Characterization of an unusually conserved AluI highly reiterated DNA sequence family from the honeybee, Apis mellifera.

Genetics ◽  
1993 ◽  
Vol 134 (4) ◽  
pp. 1195-1204
Author(s):  
S Tarès ◽  
J M Cornuet ◽  
P Abad
Keyword(s):  
Apis Mellifera ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Sequence Data ◽  
Sequence Divergence ◽  
Repeated Sequence ◽  
Consensus Sequences ◽  
Dna Sequence Data ◽  
Repeat Class ◽  
Honeybee Subspecies

Abstract An AluI family of highly reiterated nontranscribed sequences has been found in the genome of the honeybee Apis mellifera. This repeated sequence is shown to be present at approximately 23,000 copies per haploid genome constituting about 2% of the total genomic DNA. The nucleotide sequence of 10 monomers was determined. The consensus sequences is 176 nucleotides long and has an A + T content of 58%. There are clusters of both direct and inverted repeats. Internal subrepeating units ranging from 11 to 17 nucleotides are observed, suggesting that it could have evolved from a shorter sequence. DNA sequence data reveal that this repeat class is unusually homogeneous compared to the other class of invertebrate highly reiterated DNA sequences. The average pairwise sequence divergence between the repeats is 2.5%. In spite of this unusual homogeneity, divergence has been found in the repeated sequence hybridization ladder between four different honeybee subspecies. Therefore, the AluI highly reiterated sequences provide a new probe for fingerprinting in A. m. mellifera.

Molecular phylogeny of the Fusarium solani species complex (FSSC) isolated from soils in Iran

Botany ◽  
2014 ◽  
Vol 92 (11) ◽  
pp. 815-820 ◽  
Author(s):  
Khosrow Chehri
Keyword(s):  
Dna Sequences ◽  
Fusarium Solani ◽  
Species Complex ◽  
Agricultural Soils ◽  
Sequence Data ◽  
Morphological Characteristics ◽  
Taxonomic Status ◽  
Its Region ◽  
Phylogenetic Study ◽  
Fusarium Solani Species Complex

Members of Fusarium solani species complex (FSSC) are frequently isolated from soils, food, feeds, trees, and to some extent from humans and other animals. The taxonomic status of these fungi is being revised but no attempt has been made to identify those isolated in Iran, a mountainous country with a high biodiversity. The objective of the present research was to study the phylogenetic diversity of FSSC strains recovered from soils in Iran by analyzing morphological characteristics and DNA sequences. A total of 65 strains belonging to the FSSC were recovered from agricultural soils in western Iran. Based on differences in their morphological characters, 25 strains were selected for phylogenetic analysis employing translation elongation factor-1α (tef1) and internal transcribed spacer (ITS) region sequences. Comparisons of DNA sequence data revealed that all isolates belonged to Fusarium falciforme, Fusarium keratoplasticum, Fusarium petroliphilum, the unnamed species FSSC 5, and unknown species of Fusarium, which represents a new lineage within members of Clade 3. Based on morphological features and phylogenetic study, F. keratoplasticum and F. petroliphilum were reported for the first time in Iran.

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