Three-gene phylogeny of the genus Arthroderma: Basis for future taxonomic studies

2020 ◽  
Author(s):  
Steven Hainsworth ◽  
Ivana Kučerová ◽  
Rahul Sharma ◽  
Connie F Cañete-Gibas ◽  
Vit Hubka
Keyword(s):  
Species Identification ◽  
Elongation Factor ◽  
Biological Species ◽  
Gene Phylogeny ◽  
Animal Burrows ◽  
Geographical Regions ◽  
Eastern Australia ◽  
Reference Sequences ◽  
Trichophyton Terrestre ◽  
Taxonomic Studies

Abstract Arthroderma is the most diverse genus among dermatophytes encompassing species occurring in soil, caves, animal burrows, clinical material and other environments. In this study, we collected ex-type, reference and authentic strains of all currently accepted Arthroderma species and generated sequences of three highly variable loci (ITS rDNA, β-tubulin, and translation elongation factor 1-α). The number of accepted species was expanded to 27. One novel species, A. melbournense (ex-type strain CCF 6162T = CBS 145858T), is described. This species was isolated from toenail dust collected by a podiatrist in Melbourne, during an epidemiological study of four geographical regions of Eastern Australia. Trichophyton terrestre, Chrysosporium magnisporum, and Chrysosporium oceanitis are transferred to Arthroderma. Typification is provided for T. terrestre that is not conspecific with any of the supposed biological species from the former T. terrestre complex, that is, A. insingulare, A. lenticulare and A. quadrifidum. A multi-gene phylogeny and reference sequences provided in this study should serve as a basis for future phylogenetic studies and facilitate species identification in practice. Lay abstract The genus Arthroderma encompasses geophilic dermatophyte species that infrequently cause human and animal superficial infections. Reference sequences from three genetic loci were generated for all currently accepted Arthroderma species and phylogeny was constructed. Several taxonomic novelties are introduced. The newly provided data will facilitate species identification and future taxonomic studies.

scholarly journals Addressing widespread misidentifications of traditional medicinal mushrooms in Sanghuangporus (Basidiomycota) through ITS barcoding and designation of reference sequences

IMA Fungus ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Shan Shen ◽  
Shi-Liang Liu ◽  
Ji-Hang Jiang ◽  
Li-Wei Zhou
Keyword(s):  
Species Identification ◽  
Rolling Circle Amplification ◽  
Practical Method ◽  
Morphological Characters ◽  
Its Sequences ◽  
Commercial Development ◽  
Medicinal Mushrooms ◽  
Rolling Circle ◽  
Reference Sequences ◽  
Its Barcoding

Abstract“Sanghuang” refers to a group of important traditionally-used medicinal mushrooms belonging to the genus Sanghuangporus. In practice, species of Sanghuangporus referred to in medicinal studies and industry are now differentiated mainly by a BLAST search of GenBank with the ITS barcoding region as a query. However, inappropriately labeled ITS sequences of “Sanghuang” in GenBank restrict accurate species identification and, to some extent, the utilization of these species as medicinal resources. We examined all available 271 ITS sequences related to “Sanghuang” in GenBank including 31 newly submitted sequences from this study. Of these sequences, more than half were mislabeled so we have now corrected the corresponding species names. The mislabeled sequences mainly came from strains utilized by non-taxonomists. Based on the analyses of ITS sequences submitted by taxonomists as well as morphological characters, we separate the newly described Sanghuangporus subbaumii from S. baumii and treat S. toxicodendri as a later synonym of S. quercicola. Fourteen species of Sanghuangporus are accepted, with intraspecific distances up to 1.30% (except in S. vaninii, S. weirianus and S. zonatus) and interspecific distances above 1.30% (except between S. alpinus and S. lonicerinus, and S. baumii and S. subbaumii). To stabilize the concept of these 14 species of Sanghuangporus, their taxonomic information and reliable ITS reference sequences are provided. Moreover, ten potential diagnostic sequences are provided for Hyperbranched Rolling Circle Amplification to rapidly confirm three common commercial species, viz. S. baumii, S. sanghuang, and S. vaninii. Our results provide a practical method for ITS barcoding-based species identification of Sanghuangporus and will promote medicinal studies and commercial development from taxonomically correct material.

scholarly journals Nothing in (sponge) biology makes sense – except when based on holotypes

2015 ◽  
Vol 96 (2) ◽  
pp. 305-311 ◽  
Author(s):  
Dirk Erpenbeck ◽  
Merrick Ekins ◽  
Nicole Enghuber ◽  
John N.A. Hooper ◽  
Helmut Lehnert ◽  
...  
Keyword(s):  
New Species ◽  
Reference Material ◽  
Species Identification ◽  
Dna Sequences ◽  
Morphological Plasticity ◽  
Morphological Characters ◽  
Molecular Techniques ◽  
Reference Sequences ◽  
Species Descriptions ◽  
Preservation History

Sponge species are infamously difficult to identify for non-experts due to their high morphological plasticity and the paucity of informative morphological characters. The use of molecular techniques certainly helps with species identification, but unfortunately it requires prior reference sequences. Holotypes constitute the best reference material for species identification, however their usage in molecular systematics and taxonomy is scarce and frequently not even attempted, mostly due to their antiquity and preservation history. Here we provide case studies in which we demonstrate the importance of using holotype material to answer phylogenetic and taxonomic questions. We also demonstrate the possibility of sequencing DNA fragments out of century-old holotypes. Furthermore we propose the deposition of DNA sequences in conjunction with new species descriptions.

scholarly journals Ophyiulus in Victoria: results of millipede surveys from south-eastern Australia

2015 ◽  
Vol 127 (2) ◽  
pp. 69
Author(s):  
Briony A. Norton ◽  
Linda J. Thomson ◽  
Michael A. Nash
Keyword(s):  
Species Identification ◽  
Preliminary Data ◽  
Native Species ◽  
South Eastern ◽  
Eastern Australia ◽  
The Future ◽  
South Eastern Australia

The composition and ecology of the millipede fauna of Victoria remain poorly understood. We collected millipedes as part of a series of ecological arthropod surveys across south-eastern Australia, focusing mainly on Victoria. These samples almost exclusively contained millipedes from the introduced order Julida. We pursued species identification of the julids when it became apparent there were species other than the well-recorded Ommatoiulus moreleti (Lucas, 1860) (Portuguese millipede) in the samples. The majority of specimens were O. moreleti, but we also detected at least one species of Cylindroiulus Verhoeff, 1894, as well as an Ophyiulus Berlese, 1884, species, specimens of which have been identified as Ophyiulus cf. targionii. These are the first Ophyiulus records for Victoria to our knowledge. We present preliminary data on the abundance through the year of Ophyiulus. This is the first study to examine this species in Victoria and little is currently known about its likely impact on agriculture or on native species. Monitoring and research of the species in the future is therefore warranted.

scholarly journals Harnessing mtDNA variation to resolve ambiguity in ‘Redfish’ sold in Europe

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3746 ◽  
Author(s):  
Peter Shum ◽  
Lauren Moore ◽  
Christophe Pampoulie ◽  
Cristina Di Muri ◽  
Sara Vandamme ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Species Identification ◽  
Fisheries Management ◽  
North Atlantic ◽  
Molecular Approach ◽  
Mtdna Variation ◽  
Control Region Sequences ◽  
Market Product ◽  
Reference Sequences ◽  
Pacific Rockfish

Morphology-based identification of North AtlanticSebasteshas long been controversial and misidentification may produce misleading data, with cascading consequences that negatively affect fisheries management and seafood labelling. North AtlanticSebastescomprises of four species, commonly known as ‘redfish’, but little is known about the number, identity and labelling accuracy of redfish species sold across Europe. We used a molecular approach to identify redfish species from ‘blind’ specimens to evaluate the performance of the Barcode of Life (BOLD) and Genbank databases, as well as carrying out a market product accuracy survey from retailers across Europe. The conventional BOLD approach proved ambiguous, and phylogenetic analysis based on mtDNA control region sequences provided a higher resolution for species identification. By sampling market products from four countries, we found the presence of two species of redfish (S. norvegicusandS. mentella) and one unidentified Pacific rockfish marketed in Europe. Furthermore, public databases revealed the existence of inaccurate reference sequences, likely stemming from species misidentification from previous studies, which currently hinders the efficacy of DNA methods for the identification ofSebastesmarket samples.

Identification and Classification of Prokaryotes using whole-genome sequences.

2021 ◽  
pp. 217-230
Author(s):  
Luis M. Rodriguez-R ◽  
Ramon Rosselló-Móra ◽  
Konstantinos T. Konstantinidis
Keyword(s):  
Species Identification ◽  
Special Focus ◽  
Whole Genome ◽  
Genome Sequences ◽  
Future Directions ◽  
The Past ◽  
Major Genome ◽  
Taxonomic Studies

Abstract This book chapter attempts to summarize the major findings from genome-based taxonomic studies in the past two decades, and briefly describe the major genome-based approaches currently available for species identification and classification with special focus on the 'uncultivated majority' and associated limitations, as well as outlines future directions towards a truly genome-based taxonomy for prokaryotes that will equally encompass cultured and uncultivated taxa. Importantly, the need for a system to catalogue uncultivated taxa is very urgent, because the genomes and ecological/functional data that are becoming available are already overwhelming, and alphanumeric identifiers and synonyms are creating confusion of Babylonian dimensions.

scholarly journals Podostemaceae in Southern Brazil

Rodriguésia ◽  
2011 ◽  
Vol 62 (4) ◽  
pp. 867-885 ◽  
Author(s):  
Anderson Santos de Mello ◽  
Aldaléa Sprada Tavares ◽  
Rafael Trevisan
Keyword(s):  
South America ◽  
Species Identification ◽  
Equatorial Region ◽  
Southern Brazil ◽  
Taxonomic Treatment ◽  
Dichotomous Key ◽  
Taxonomic Studies ◽  
Aquatic Angiosperms

Abstract This study provides a taxonomic treatment of the Podostemaceae family in southern Brazil. Podostemaceae is the largest family of strictly aquatic angiosperms. The center of family richness is the equatorial region of South America. Taxonomic studies are still scarce in Brazil. For southern Brazil there are six genera and 10 species recognized. Dichotomous key and illustrations are presented for species identification.

scholarly journals Development of a reference data set for assigning Streptococcus and Enterococcus species based on next generation sequencing of the 16S–23S rRNA region

2019 ◽  
Vol 8 (1) ◽  
Author(s):  
Maja Kosecka-Strojek ◽  
Artur J. Sabat ◽  
Viktoria Akkerboom ◽  
Anna M. D. Kooistra-Smid ◽  
Jacek Miedzobrodzki ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Sequence Analysis ◽  
16S Rrna ◽  
Species Identification ◽  
23S Rrna ◽  
Clinical Samples ◽  
Next Generation ◽  
Enterococcal Species ◽  
Reference Sequences ◽  
Generation Sequencing

Abstract Background Many members of Streptococcus and Enterococcus genera are clinically relevant opportunistic pathogens warranting accurate and rapid identification for targeted therapy. Currently, the developed method based on next generation sequencing (NGS) of the 16S–23S rRNA region proved to be a rapid, reliable and precise approach for species identification directly from polymicrobial and challenging clinical samples. The introduction of this new method to routine diagnostics is hindered by a lack of the reference sequences for the 16S–23S rRNA region for many bacterial species. The aim of this study was to develop a careful assignment for streptococcal and enterococcal species based on NGS of the 16S–23S rRNA region. Methods Thirty two strains recovered from clinical samples and 19 reference strains representing 42 streptococcal species and nine enterococcal species were subjected to bacterial identification by four Sanger-based sequencing methods targeting the genes encoding (i) 16S rRNA, (ii) sodA, (iii) tuf and (iv) rpoB; and NGS of the 16S–23S rRNA region. Results This study allowed obtainment and deposition of reference sequences of the 16S–23S rRNA region for 15 streptococcal and 3 enterococcal species followed by enrichment for 27 and 6 species, respectively, for which reference sequences were available in the databases. For Streptococcus, NGS of the 16S–23S rRNA region was as discriminative as Sanger sequencing of the tuf and rpoB genes allowing for an unambiguous identification of 93% of analyzed species. For Enterococcus, sodA, tuf and rpoB genes sequencing allowed for identification of all species, while the NGS-based method did not allow for identification of only one enterococcal species. For both genera, the sequence analysis of the 16S rRNA gene was endowed with a low identification potential and was inferior to that of other tested identification methods. Moreover, in case of phylogenetically related species the sequence analysis of only the intergenic spacer region was not sufficient enough to precisely identify Streptococcus strains at the species level. Conclusions Based on the developed reference dataset, clinically relevant streptococcal and enterococcal species can now be reliably identified by 16S–23S rRNA sequences in samples. This study will be useful for introduction of a novel diagnostic tool, NGS of the 16S–23S rRNA region, which undoubtedly is an improvement for reliable culture-independent species identification directly from polymicrobially constituted clinical samples.

Rhytismatales of Australasia

2001 ◽  
Vol 14 (3) ◽  
pp. 377 ◽  
Author(s):  
Peter R. Johnston
Keyword(s):  
Genetic Diversity ◽  
The Other ◽  
Tropical Species ◽  
Broad Host Range ◽  
Eastern Australia ◽  
Molecular Studies ◽  
Single Host ◽  
Close Relatives ◽  
Almost All ◽  
Taxonomic Studies

The Rhytismatales are both genetically and biologically diverse in Australasia. Although taxonomically one of the better known groups of ascomycetes from the region, almost all knowledge on the group is confined to species from south-eastern Australia and New Zealand. The indigenous Australasian species show two distinct patterns of geographic relationship—one group comprises species with a broad tropical distribution, the other comprises species that have close relatives on phylogenetically related hosts in other parts of the temperate Southern Hemisphere. While the widespread tropical species have a broad host range, the others tend to be specialised toward a single host. Further research required includes alpha-taxonomic studies from other parts of Australasia, study of the biological roles these fungi play in Australasian forests and molecular studies on the origin of the genetic diversity of the order in this region.

scholarly journals Species Identification of Rock Oysters Collected from the Dhofar Region, Sultanate of Oman

2012 ◽  
Vol 17 ◽  
pp. 61 ◽  
Author(s):  
Mikhail V. Chesalin ◽  
Salem A. Al-Ghassani ◽  
Mohammed A. Balkhair
Keyword(s):  
Phylogenetic Analysis ◽  
Species Composition ◽  
Species Identification ◽  
Dna Sequences ◽  
Dna Barcode ◽  
Rocky Shores ◽  
Data Systems ◽  
Sultanate Of Oman ◽  
Life Data ◽  
Taxonomic Studies

Oysters are commonly found on rocky shores along the Dhofar coast of Oman, but the species composition has not yet been studied. In an attempt to determine the species of these oysters, samples from four sites (Mirbat, Sadah, Hadbin, and Hasik) were collected and analyzed using DNA sequences that were compared with the database of GenBank/National Center for Biotechnology Information (NCBI) and Barcoding of Life Data Systems (BOLD). BLAST results of DNA sequences showed that there were no existing sequences available on NCBI/GenBank and BOLD. The DNA barcode sequences generated in this study can be employed as standards for this species and may be of use in taxonomic studies. Phylogenetic analysis demonstrated that the oysters from Oman exhibit homology with Saccostrea species cucullata or mordax. 

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