scholarly journals Impact of DNA data on fungal and yeast taxonomy

2011 ◽  
Vol 32 (2) ◽  
pp. 100
Author(s):  
Johannes Z Groenewald ◽  
Marizeth Groenewald ◽  
Pedro W Crous
Keyword(s):  
Dna Sequencing ◽  
Sequence Data ◽  
Species Recognition ◽  
Morphological Characters ◽  
Molecular Techniques ◽  
Specific Reference ◽  
Pleomorphic Fungi ◽  
Detection And Identification ◽  
Genealogical Concordance ◽  
Phylogenetic Lineages

The species richness and diversity existing in microorganisms are unparalleled on our planet. In recent years, the use of molecular techniques for the detection and identification of microorganisms, especially through DNA sequencing, has revolutionised the way taxonomists look at the systematics of a species, especially when applying multilocus sequence data and concepts such as the genealogical concordance phylogenetic species recognition (GCPSR) concept1. Particularly problematic topics arising in the fungi are, for example, naming pleomorphic fungi (that is, fungi for which a teleomorph, meaning sexual form, and one or more anamorphs, meaning asexual forms, are formed), polyphyletic genera (that is, the same genus being presented in several distinct phylogenetic lineages or clades), morphospecies (a species which is differentiated from other species based on its distinctive morphological characters) that in fact represent distinct phylogenetic lineages and how to deal with species that are only known by their DNA sequence(s). Here we provide a brief overview of the effects and implications that the applications of molecular techniques such as DNA sequencing are having on the taxonomy of fungi (part 1) and yeasts (part 2), with specific reference to those which can be cultured. Although fungi and yeasts both belong to the kingdom Fungi, sometimes different approaches to the taxonomy of these two ?groups? were followed in the past and, therefore, they are treated individually below. For the purpose of this overview, genera of Oomycetes are excluded.

Combined multi-gene backbone tree for the genus Coniochaeta with two new species from Uzbekistan

Phytotaxa ◽  
2018 ◽  
Vol 336 (1) ◽  
pp. 43 ◽  
Author(s):  
MILAN C. SAMARAKOON ◽  
YUSUFJON GAFFOROV ◽  
NINGGUO LIU ◽  
SAJEEWA S. N. MAHARACHCHIKUMBURA ◽  
JAYARAMA D. BHAT ◽  
...  
Keyword(s):  
New Species ◽  
Sequence Data ◽  
Species Recognition ◽  
Phylogenetic Species ◽  
Phylogenetic Studies ◽  
Genealogical Concordance ◽  
Two New Species ◽  
Backbone Tree

The genus Coniochaeta is an important ascomycete because its members live in diversified habitats and nutritional modes. In this study, two new species, C. acaciae and C. coluteae, are introduced from dead branches of Acacia sp. and Colutea paulsenii Freyn (both Fabaceae) respectively from Uzbekistan, based on morphological and phylogenetic studies. Analyses of combined ITS and LSU sequence data with Genealogical Concordance Phylogenetic Species Recognition (GCPSR) and comparison of similar taxa, provide evidences for placement of these new species in Coniochaeta, as distinct lineages.

scholarly journals Confusion surrounding Didymosphaeria—phylogenetic and morphological evidence suggest Didymosphaeriaceae is not a distinct family

Phytotaxa ◽  
2014 ◽  
Vol 176 (1) ◽  
pp. 102 ◽  
Author(s):  
HIRAN A. ARIYAWANSA ◽  
ERIO CAMPORESI ◽  
KASUN M. THAMBUGALA ◽  
AUSANA MAPOOK ◽  
JI-CHUAN KANG ◽  
...  
Keyword(s):  
New Species ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Morphological Evidence ◽  
Nucleotide Sequence Data ◽  
The Family ◽  
Family Based ◽  
Phylogenetic Lineages ◽  
A New Species

Didymosphaeriaceae is a ubiquitous fungal family that is reported to include saprobic, endophytic and pathogenic species associated with a wide variety of substrates. The family is characterized by 1-septate ascospores and trabeculate pseudoparaphyses, mainly anastomosing above the asci. In recent treatments Appendispora, Didymosphaeria, Roussoella, Phaeodothis and Verruculina were placed in the family. The aim of the present study is to delineate phylogenetic lineages within Didymosphaeriaceae and allied genera. A new species, Didymosphaeria rubi-ulmifolii, was isolated and identified based on morphological characters and phylogenetic analyses of partial 18S nrDNA and 28S nrDNA nucleotide sequence data. Didymosphaeria rubi-ulmifolii clustered with Montagnulaceae as a separate genus, while two putative strains (HKUCC 5834 and CMW 22186) of D. futilis from GenBank clustered with Cucurbitariaceae and Didymellaceae, respectively. The new species is characterized by immersed to slightly erumpent ascomata immersed under a clypeus, a peridium with compressed cells of textura intricata, long trabeculate pseudoparaphyses, anastomosing mostly above the asci and brown, 1-septate ascospores with granulate ornamentation. Phylogenetic analysis in combination with morphology and a review of literature show that Appendispora, Phaeodothis, Roussoella and Verruculina should be excluded from the family. Phaeodothis belongs in Montagnulaceae, Verruculina in Testudinaceae, while Appendispora and Roussoella belong in Roussoellaceae. The position of Didymosphaeriaceae as a distinct family, based on 1-septate ascospores and trabeculate pseudoparaphyses, mainly anastomosing above the asci is doubtful. Fresh collections of more Didymosphaeria strains are needed for epitypification and to obtain sequence data to establish if this family can be maintained.

scholarly journals Pragmatic Assignment of Species Groups Based on Primary Species Hypotheses: The Case of a Dominant Component of the Southern Ocean Benthic Fauna

2021 ◽  
Vol 8 ◽  
Author(s):  
Chester J. Sands ◽  
Timothy D. O’Hara ◽  
Rafael Martín-Ledo
Keyword(s):  
Southern Ocean ◽  
Sequence Data ◽  
Species Recognition ◽  
Benthic Fauna ◽  
Integrated Approach ◽  
Morphological Characters ◽  
Natural World ◽  
Biological Knowledge ◽  
Molecular Sequence Data ◽  
Species Groups

Ecological studies that enhance our understanding of the structure and function of the natural world rely heavily on accurate species identification. With rapid sample accumulation and declining taxonomic expertise, cladistics, phylogenetics and coalescent-based analyses have become key tools for identification or discrimination of species. These tools differ in effectiveness and interpretation depending on researcher perspective and the unique evolutionary histories of the taxa. Given the cost and time required for taxonomic assessment of ambiguous species groups, we advocate a pragmatic approach to clarify species assignment. We carried out a case-study on species from the diverse ophiuroid genus Ophiacantha common in shelf habitats around the Southern Ocean. Although several of the species are formally described with clear and distinctive morphological characters and reproductive strategies (O. vivipara, O. pentactis, O. densispina, O. antarctica, and O. wolfarntzi), recent molecular data has highlighted issues with these morphospecies, the characters that formally define them and their evolutionary histories. Here we provide evidence that key morphological features of species can be deceptive and show that six-armed O. vivipara, for example, is not a widely distributed Southern Ocean species as currently accepted, rather, three disparate clades. Ophiacantha pentactis, described as having five arms, frequently has six arms and the six-armed form is mistakenly classified as O. vivipara. All six-armed specimens collected from the Antarctic continental shelf fall into the O. pentactis species clade. Molecular tools designed for species delimitation appear to fail to reflect the “true” species composition. Rather than rely on a single tool for species recognition, we advocate an integrated approach using traditional detailed taxonomic morphology, summary statistics of molecular sequence data from populations, robust phylogenies, sufficient geographical sampling and local biological knowledge to ensure that species hypotheses can be built on mutually supporting lines of evidence.

A review of species recognition in the Phenacoccus aceris species-group (Hemiptera: Coccomorpha: Pseudococcidae) using molecular and morphological data

Zootaxa ◽  
2017 ◽  
Vol 4319 (3) ◽  
pp. 483
Author(s):  
XU-BO WANG ◽  
SAN-AN WU
Keyword(s):  
Sequence Data ◽  
Species Recognition ◽  
Morphological Characters ◽  
Species Group ◽  
Morphological Data ◽  
Character State ◽  
Relative Width ◽  
Nucleotide Sequence Data ◽  
Putative Species ◽  
Species Separation

The maple mealybug, Phenacoccus aceris (Signoret) (Hemiptera: Pseudococcidae), is a widespread polyphagous pest. The taxonomy of P. aceris and some congeners is controversial. This study utilized molecular analysis of one mitochondrial (cytochrome oxidase I) and two nuclear (EF-1α and 28S D2D3) genes, and morphological data, to investigate the P. aceris species-group based on 120 individuals collected from 16 localities in China. Analyses of the nucleotide sequence data recovered four well-supported clades that enabled us to reassess the taxonomic utility of some morphological characters used for species recognition in the P. aceris species-group, such as the number, location and width of circuli, and the distribution pattern of oral-collar tubular ducts on the dorsum. Polymorphism in the number of circuli indicated that this character-state alone is unreliable for species separation, but a combination of the number, location and relative width of the circuli provides a significant taxonomic character. The distribution of oral-collar tubular ducts on dorsal segments of the cephalothorax can be used also for species separation. In addition, specimens that keyed morphologically to P. aceris contained three putative species that are not separated by host-plant preferences. These putative species are genetically and morphologically different from P. aceris in France (the type locality of P. aceris) and are thus probably new to science. A network analysis of the COI haplotypes showed that the hosts Fraxinus spp. (Oleaceae) and Zanthoxylum bungeanum (Rutaceae) in North China are attacked by both P. aceris and P. azaleae, so previous identifications of this group based on the identity of these host plants is misleading. The taxonomic confusion in the P. aceris species-group may be due to the co-occurrence of multiple putative species. 

Molecular and Morphological Characterization of Cultures from the Extreme Environmental Area of Copahue Volcano-Argentina

2009 ◽  
Vol 71-73 ◽  
pp. 93-96 ◽  
Author(s):  
Alejandra Giaveno ◽  
J. Huergo ◽  
L. Lavalle ◽  
Wolfgang Sand ◽  
Edgardo R. Donati
Keyword(s):  
Dna Sequencing ◽  
Morphological Characterization ◽  
Molecular Techniques ◽  
Close Relative ◽  
Detection And Identification ◽  
Uncultured Archaea ◽  
Microscopic Techniques

This report describes the detection and identification of archaea in several sites located in the area of Copahue volcano, Neuquén province, Argentina by mean of different molecular techniques (PCR, DGGE, DNA sequencing and FISH). In order to study the archaea morphology, cultures were examined using different microscopic techniques (SEM, TEM, EFM and AFM). The corresponding archaea were identified as close relative or members of the genus Acidianus as well as other uncultured archaea clones showing a 93% of similarity to each others.

scholarly journals Phylogeny and species delimitation of Strobilomyces (Boletaceae), with an emphasis on the Asian species

2020 ◽  
Vol 44 (1) ◽  
pp. 113-139
Author(s):  
L.H. Han ◽  
G. Wu ◽  
E. Horak ◽  
R.E. Halling ◽  
J. Xu ◽  
...  
Keyword(s):  
Rna Polymerase Ii ◽  
Molecular Phylogenetics ◽  
Species Recognition ◽  
Elongation Factor ◽  
Distribution Patterns ◽  
Distinct Species ◽  
Morphological Characters ◽  
Phylogenetic Species ◽  
Type Specimens ◽  
Genealogical Concordance

Strobilomyces is broadly distributed geographically and serves an important ecological function. However, it has been difficult to delimit species within the genus, primarily due to developmental variations and phenotypic plasticity. To elucidate phylogenetic relationships among species within the genus and to understand its species diversity, especially in Asia, materials of the genus collected from five continents (Africa, Asia, Australia, Europe, and North/Central America) were investigated. The phylogeny of Strobilomyces was reconstructed based on nucleotide sequences of four genes coding for: the largest and the second largest subunits of the RNA polymerase II (RPB1 and RPB2); the translation elongation factor subunit 1-α (TEF1); and the mitochondrial cytochrome oxidase subunit 3 (COX3). The combined results based on molecular phylogenetics, morphological characters, host tree associations, and geographical distribution patterns support a new classification consisting of two sections, sect. Strobilomyces and sect. Echinati. Using the genealogical concordance phylogenetic species recognition (GCPSR) approach, at least 33 phylogenetic species in Asia can be delimited, all of which are supported by morphological features, and five phylogenetic species remain to be described. The mountainous region of Southwest China is especially special, containing at least 21 species and likely represents a centre of diversification. We further compared our specimens with the type specimens of 25 species of Strobilomyces. Our comparisons suggest that, there are a total of 31 distinct species, while S. sanmingensis, S. verruculosus, S. subnigricans, and S. zangii/S. areolatus, are synonyms of S. mirandus, S. giganteus, S. alpinus and S. seminudus, respectively. Eight new species, namely, S. albidus, S. anthracinus, S. calidus, S. cingulatus, S. densisquamosus, S. douformis, S. microreticulatus and S. pinophilus, are described. A dichotomous key to the Asian Strobilomyces species is provided.

scholarly journals Trichuris spp. in Animals, with Specific Reference to Neo-Tropical Rodents

2021 ◽  
Vol 8 (2) ◽  
pp. 15
Author(s):  
Kegan Romelle Jones
Keyword(s):  
Guinea Pig ◽  
Guinea Pigs ◽  
Clinical Signs ◽  
Molecular Techniques ◽  
Meat Production ◽  
Specific Reference ◽  
Hydrochoerus Hydrochaeris ◽  
Present Information ◽  
Low Prevalence ◽  
A New Species

Trichuriasis is the clinical disease of animals infected with the parasite of the genus Trichuris. This review attempts to present information on Trichuris spp. infestation in neo-tropical rodents that are utilized for meat consumption by humans. Neo-tropical rodents utilized for meat production can be divided into two categories: those that have been domesticated, which include the guinea pig (Cavia porcellus), and those that are on the verge of domestication, such as the capybara (Hydrochoerus hydrochaeris), lappe (Cuniculus paca/Agouti paca), and agouti (Dasyprocta leporina). This document reviews the literature on the species of Trichuris that affects the rodents mentioned above, as well as the clinical signs observed. The literature obtained spans over sixty years, from 1951 to 2020. Trichuris spp. was found in these neo-tropical rodents mentioned. However, there is a dearth of information on the species of Trichuris that parasitize these animals. The capybara was the only rodent where some molecular techniques were used to identify a new species named T. cutillasae. In most cases, Trichuris spp. was found in combination with other endoparasites, and was found at a low prevalence in the lappe and guinea pig. The presence of Trichuris spp. ranged from 4.62–53.85% in the agouti, 4.21–10.00% in the lappe, 50% in the capybaras, and 1–31% in guinea pigs. Further work must be done towards molecular identification of various Trichuris spp. present in these rodents, as well as the clinical effect of infection on the performance of agouti, lappe, capybara, and guinea pigs.

Revised circumscription of Nothofagus and recognition of the segregate genera Fuscospora, Lophozonia, and Trisyngyne (Nothofagaceae)

Phytotaxa ◽  
2013 ◽  
Vol 146 (1) ◽  
pp. 1 ◽  
Author(s):  
PETER B. HEENAN ◽  
ROB D. SMISSEN
Keyword(s):  
Phylogenetic Analysis ◽  
South America ◽  
Papua New Guinea ◽  
New Genus ◽  
New Caledonia ◽  
Sequence Data ◽  
Morphological Characters ◽  
New Combinations ◽  
Southern South America ◽  
Dna Sequence Data

The generic taxonomy of the Nothofagaceae is revised. We present a new phylogenetic analysis of morphological characters and map these characters onto a recently published phylogenetic tree obtained from DNA sequence data. Results of these and previous analyses strongly support the monophyly of four clades of Nothofagaceae that are currently treated as subgenera of Nothofagus. The four clades of Nothofagaceae are robust and well-supported, with deep stem divergences, have evolutionary equivalence with other genera of Fagales, and can be circumscribed with morphological characters. We argue that these morphological and molecular differences are sufficient for the four clades of Nothofagaceae to be recognised at the primary rank of genus, and that this classification will be more informative and efficient than the currently circumscribed Nothofagus with four subgenera.        Nothofagus is recircumscribed to include five species from southern South America, Lophozonia and Trisyngyne are reinstated, and the new genus Fuscospora is described. Fuscospora and Lophozonia, with six and seven species respectively, occur in New Zealand, southern South America and Australia. Trisyngyne comprises 25 species from New Caledonia, Papua New Guinea and Indonesia. New combinations are provided where necessary in each of these genera.

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 BAQALC: Blockchain Applied Lossless Efficient Transmission of DNA Sequencing Data for Next Generation Medical Informatics

2018 ◽  
Vol 8 (9) ◽  
pp. 1471 ◽  
Author(s):  
Seo-Joon Lee ◽  
Gyoun-Yon Cho ◽  
Fumiaki Ikeno ◽  
Tae-Ro Lee
Keyword(s):  
Dna Sequencing ◽  
Medical Informatics ◽  
Compression Ratio ◽  
Sequence Data ◽  
Lossless Compression ◽  
World Health ◽  
Smart Devices ◽  
Next Generation ◽  
And Storage ◽  
Efficient Transmission

Due to the development of high-throughput DNA sequencing technology, genome-sequencing costs have been significantly reduced, which has led to a number of revolutionary advances in the genetics industry. However, the problem is that compared to the decrease in time and cost needed for DNA sequencing, the management of such large volumes of data is still an issue. Therefore, this research proposes Blockchain Applied FASTQ and FASTA Lossless Compression (BAQALC), a lossless compression algorithm that allows for the efficient transmission and storage of the immense amounts of DNA sequence data that are being generated by Next Generation Sequencing (NGS). Also, security and reliability issues exist in public sequence databases. For methods, compression ratio comparisons were determined for genetic biomarkers corresponding to the five diseases with the highest mortality rates according to the World Health Organization. The results showed an average compression ratio of approximately 12 for all the genetic datasets used. BAQALC performed especially well for lung cancer genetic markers, with a compression ratio of 17.02. BAQALC performed not only comparatively higher than widely used compression algorithms, but also higher than algorithms described in previously published research. The proposed solution is envisioned to contribute to providing an efficient and secure transmission and storage platform for next-generation medical informatics based on smart devices for both researchers and healthcare users.

Sign in / Sign up

Export Citation Format

Share Document