Another plea for ‘best practice’ in molecular approaches to trematode systematics: Diplostomum sp. clade Q identified as Diplostomum baeri Dubois, 1937 in Europe

Parasitology ◽  
2022 ◽  
pp. 1-16
Author(s):  
Anna Faltýnková ◽  
Olena Kudlai ◽  
Camila Pantoja ◽  
Galina Yakovleva ◽  
Daria Lebedeva
Keyword(s):  
Dna Sequence ◽  
Dna Sequences ◽  
Best Practice ◽  
Sequence Data ◽  
Integrative Taxonomy ◽  
Systematic Parasitology ◽  
Intermediate Hosts ◽  
Accurate Identification ◽  
Molecular Approaches ◽  
Radix Auricularia

Abstract DNA sequence data became an integral part of species characterization and identification. Still, specimens associated with a particular DNA sequence must be identified by the use of traditional morphology-based analysis and correct linking of sequence and identification must be ensured. Only a small part of DNA sequences of the genus Diplostomum (Diplostomidae) is based on adult isolates which are essential for accurate identification. In this study, we provide species identification with an aid of morphological and molecular (cox1, ITS-5.8S-ITS2 and 28S) characterization of adults of Diplostomum baeri Dubois, 1937 from naturally infected Larus canus Linnaeus in Karelia, Russia. Furthermore, we reveal that the DNA sequences of our isolates of D. baeri are identical with those of the lineage Diplostomum sp. clade Q , while other sequences labelled as the ‘D. baeri’ complex do not represent lineages of D. baeri. Our new material of cercariae from Radix balthica (Linnaeus) in Ireland is also linked to Diplostomum sp. clade Q. We reveal that D. baeri is widely distributed in Europe; as first intermediate hosts lymnaeid snails (Radix auricularia (Linnaeus), R. balthica) are used; metacercariae occur in eye lens of cyprinid fishes. In light of the convoluted taxonomy of D. baeri and other Diplostomum spp., we extend the recommendations of Blasco-Costa et al. (2016, Systematic Parasitology 93, 295–306) for the ‘best practice’ in molecular approaches to trematode systematics. The current study is another step in elucidating the species spectrum of Diplostomum based on integrative taxonomy with well-described morphology of adults linked to sequences.

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.

Association of larvae and adults of Mexican species of Macrelmis (Coleoptera: Elmidae): a preliminary analysis using DNA sequences

Zootaxa ◽  
2012 ◽  
Vol 3361 (1) ◽  
pp. 56-62 ◽  
Author(s):  
JOSEFINA CURIEL ◽  
JUAN J. MORRONE
Keyword(s):  
Dna Sequence ◽  
Dna Sequences ◽  
Preliminary Analysis ◽  
Sequence Data ◽  
Strong Association ◽  
Life Stages ◽  
Adult Morphology ◽  
Dna Sequence Data ◽  
Mexican Species ◽  
Major Impediment

Insect life stages are known imperfectly in many cases, and classifications are usually based on adult morphology. This isunfortunate as information on other life stages may be useful for biomonitoring. The major impediment to using elmid(Coleoptera) larvae for freshwater biomonitoring is the lack of larval descriptions and illustrations. Reliable molecular proto-cols may be used to associate larvae and adults. After adults of seven species of Mexican Macrelmis were identified morpho-logically, seven larval specimens were associated to them based on two gene fragments: Cox1 and Cob. The phylogeneticanalysis allowed identifying the larval specimens as Macrelmis leonilae, M. scutellaris, M. species 7, M. species 10, and M.species 11. Two species based on adults associated uncertainly with one larva, and one larva did not match with any adult. Adult/larval association in elmids using DNA sequence data seems to be promising in terms of speed and reliability.

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.

scholarly journals AN INTEGRATIVE TAXONOMY OF MOLECULAR AND TRADITIONAL APPROACHES FOR IDENTIFICATION OF A STORAGE MITE, ALEUROGLYPHUS OVATUS (ACARI: ASTIGMATA: ACARIDAE) IN MALAYSIA

2016 ◽  
Vol 6 (2) ◽  
pp. 882-889
Author(s):  
Ernieenor Faraliana Che Lah
Keyword(s):  
Molecular Identification ◽  
Dna Sequences ◽  
Correct Diagnosis ◽  
Morphological Characters ◽  
Integrative Taxonomy ◽  
Its2 Region ◽  
Morphological Identification ◽  
Taxonomic Identification ◽  
Internal Transcribed Spacer Region ◽  
Accurate Identification

A reliable and rapid taxonomic identification of a mite is the basis for a correct diagnosis of important mite associated allergies as they produce species-specific allergens. A double approach (molecular and morphological) to the taxonomic identification of Aleuroglyphus ovatus was presented. Molecular identification was performed with amplification of the internal transcribed spacer region (ITS2), whilst morphological characters were examined under light microscope. The BLAST results obtained from molecular analysis of A. ovatus was shown to be in concordance with the morphological identification with 97% genetic similarity. Thus, the molecular identification based on the ITS2 region can be applied as a reliable and efficient tool for species identification of Aleuroglyphus and probably any other astigmatid mites. Our findings suggest the need for a broad taxonomic sampling especially from closely related species for an accurate identification of local mites using both DNA sequences and morphology.

scholarly journals Evaluating methodologies for species delimitation: the mismatch between phenotypes and genotypes in lichenized fungi (Bryoria sect. Implexae, Parmeliaceae)

2019 ◽  
Vol 42 (1) ◽  
pp. 75-100 ◽  
Author(s):  
C.G. Boluda ◽  
V.J. Rico ◽  
P.K. Divakar ◽  
O. Nadyeina ◽  
L. Myllys ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Species Delimitation ◽  
Sequence Data ◽  
Species Recognition ◽  
Phylogenetic Analyses ◽  
Phylogenetic Reconstruction ◽  
Haplotype Network ◽  
Molecular Data ◽  
Integrative Taxonomy ◽  
Molecular Sequence Data

In many lichen-forming fungi, molecular phylogenetic analyses lead to the discovery of cryptic species within traditional morphospecies. However, in some cases, molecular sequence data also questions the separation of phenotypically characterised species. Here we apply an integrative taxonomy approach – including morphological, chemical, molecular, and distributional characters – to re-assess species boundaries in a traditionally speciose group of hair lichens, Bryoria sect. Implexae. We sampled multilocus sequence and microsatellite data from 142 specimens from a broad intercontinental distribution. Molecular data included DNA sequences of the standard fungal markers ITS, IGS, GAPDH, two newly tested loci (FRBi15 and FRBi16), and SSR frequencies from 18 microsatellite markers. Datasets were analysed with Bayesian and maximum likelihood phylogenetic reconstruction, phenogram reconstruction, STRUCTURE Bayesian clustering, principal coordinate analysis, haplotype network, and several different species delimitation analyses (ABGD, PTP, GMYC, and DISSECT). Additionally, past population demography and divergence times are estimated. The different approaches to species recognition do not support the monophyly of the 11 currently accepted morphospecies, and rather suggest the reduction of these to four phylogenetic species. Moreover, three of these are relatively recent in origin and cryptic, including phenotypically and chemically variable specimens. Issues regarding the integration of an evolutionary perspective into taxonomic conclusions in species complexes, which have undergone recent diversification, are discussed. The four accepted species, all epitypified by sequenced material, are Bryoria fuscescens, B. glabra, B. kockiana, and B. pseudofuscescens. Ten species rank names are reduced to synonymy. In the absence of molecular data, they can be recorded as the B. fuscescens complex. Intraspecific phenotype plasticity and factors affecting the speciation of different morphospecies in this group of Bryoria are outlined.

scholarly journals The challenge of integrative taxonomy of rare, deep-water gastropods: the genus Exilia (Neogastropoda: Turbinelloidea: Ptychatractidae)

2020 ◽  
Vol 86 (2) ◽  
pp. 120-138
Author(s):  
Yuri I Kantor ◽  
Nicolas Puillandre ◽  
Philippe Bouchet
Keyword(s):  
Dna Sequence ◽  
Sequence Data ◽  
Taxonomic Revision ◽  
Distinct Species ◽  
First Record ◽  
Integrative Taxonomy ◽  
Molecular Systematic ◽  
Dna Sequence Data ◽  
In The Wild ◽  
Anatomical Characters

Abstract According to a recent taxonomic revision by Kantor et al. (2001), the neogastropod genus Exilia Conrad, 1860, comprises ten mostly rare species that live at depths between 200 and 2000 m. Adult Exilia measure between 30 and 90 mm in shell length, and the genus is mostly represented in museum collections by empty shells. The abundance of this genus is low in the wild, but recent expeditions organized by the Muséum national d’Histoire naturelle have yielded several dozen specimens. These new collections include samples preserved for molecular studies. Here, we present the results of the first molecular systematic study of Exilia. Our aim was to investigate the species limits proposed by Kantor et al. (2001) on the basis of shell and anatomical characters. Analysis of DNA sequence data for the cytochrome c oxidase I gene suggests that Exilia hilgendorfi, previously considered to be a single, polymorphic and broadly distributed species, is a complex of at least six species (four of which we sequenced). Two of these species, Exilia cognata n. sp. and E. fedosovi n. sp., are described as new to science. Exilia gracilior, E. claydoni and E. prellei are resurrected from the synonymy of Exilia hilgendorfi; of these three, only the last was sequenced. Exilia vagrans is a well-defined taxon, but our molecular systematic data shows that it consists of two distinct species, which occur sympatrically off Taiwan and are strikingly similar in shell and radular morphology; due to the absence of DNA sequence data from the type locality of E. vagrans (Vanuatu), it is unclear to which of these two species the name would apply. Exilia karukera n. sp., which is conchologically very similar to E. vagrans, was discovered off Guadeloupe, represents the first record of the genus from the Atlantic. For E. elegans, which was previously known only from a single shell, we provide new data including new distributional records (South Africa and the Mozambique Channel), details of the radula and DNA sequence data.

Accurate deep learning off-target prediction with novel sgRNA-DNA sequence encoding in CRISPR-Cas9 gene editing

2021 ◽  
Author(s):  
Jeremy Charlier ◽  
Robert Nadon ◽  
Vladimir Makarenkov
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Gene Editing ◽  
Sequence Data ◽  
Target Prediction ◽  
Feedforward Neural Networks ◽  
Strong Impact ◽  
Sequence Encoding

Abstract Motivation Off-target predictions are crucial in gene editing research. Recently, significant progress has been made in the field of prediction of off-target mutations, particularly with CRISPR-Cas9 data, thanks to the use of deep learning. CRISPR-Cas9 is a gene editing technique which allows manipulation of DNA fragments. The sgRNA-DNA (single guide RNA-DNA) sequence encoding for deep neural networks, however, has a strong impact on the prediction accuracy. We propose a novel encoding of sgRNA-DNA sequences that aggregates sequence data with no loss of information. Results In our experiments, we compare the proposed sgRNA-DNA sequence encoding applied in a deep learning prediction framework with state-of-the-art encoding and prediction methods. We demonstrate the superior accuracy of our approach in a simulation study involving Feedforward Neural Networks (FNNs), Convolutional Neural Networks (CNNs) and Recurrent Neural Networks (RNNs) as well as the traditional Random Forest (RF), Naive Bayes (NB) and Logistic Regression (LR) classifiers.We highlight the quality of our results by building several FNNs, CNNs and RNNs with various layer depths and performing predictions on two popular CRISPOR and GUIDE-seq gene editing data sets. In all our experiments, the new encoding led to more accurate off-target prediction results, providing an improvement of the area under the Receiver Operating Characteristic (ROC) curve up to 35%. Availability The code and data used in this study are available at: https://github.com/dagrate/dl-offtarget

scholarly journals Hierarchical Models for Mitochondrial DNA Sequence Data

2016 ◽  
Vol 36 (1) ◽  
Author(s):  
Paola Berchialla
Keyword(s):  
Mitochondrial Dna ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Sequence Data ◽  
Population History ◽  
Parametric Models ◽  
Italian Population ◽  
Bayesian Hierarchical ◽  
Dna Sequence Data ◽  
Mitochondrial Dna Sequence

We introduce a Bayesian hierarchical model for mitochondrial DNA sequence data, which is fitted via acceptance-rejection algorithms. The model incorporates parametric models of population history explicitly as well as a mutational process allowing for a simultaneous parameter estimation whose importance has become increasingly clear in many recent studies. The model is applied to a sample of DNA sequences from the Italian population.

scholarly journals Ecology and seasonality of Pseudo-nitzschia species (Bacillariophyceae) in the northwestern Adriatic Sea over a 30-years period (1988–2020)

2021 ◽  
Vol 22 (3) ◽  
pp. 505
Author(s):  
SONIA GIULIETTI ◽  
TIZIANA ROMAGNOLI ◽  
ALESSANDRA CAMPANELLI ◽  
CECILIA TOTTI ◽  
STEFANO ACCORONI
Keyword(s):  
Dna Sequence ◽  
Dna Sequences ◽  
Species Complex ◽  
Adriatic Sea ◽  
Sequence Data ◽  
Coastal Station ◽  
Dna Sequence Data ◽  
The Mean ◽  
First Time ◽  
North Western

The ecology and seasonality of Pseudo-nitzschia species and their contribution to phytoplankton community were analysed for the first time at the coastal station of the LTER-Senigallia-Susak transect (north-western Adriatic Sea) from 1988 to 2020. Species composition was addressed using DNA sequence data obtained from 106 monoclonal strains isolated from January 2018 to January 2020. The mean annual cycle of total phytoplankton in the study period (Feb 1988–Jan 2020) showed maximum abundances in winter followed by other peaks in spring and autumn. Diatoms were the main contributors in terms of abundance during the winter and the spring blooms. The autumn peak was due to phytoflagellates and diatoms. In summer phytoflagellates dominated the community, followed by diatoms and dinoflagellates, which in this season reached their annual maximum. Pseudo-nitzschia spp. represented on average 0.4–17.6% of diatom community, but during their blooms they could reach up to up to 90% of the total diatom abundances with 106 cells l-1. By LM, six different taxa were recognized: Pseudo-nitzschia cf. delicatissima and P. cf. pseudodelicatissima were the most abundant, followed by P. cf. fraudulenta, P. pungens, P. multistriata and P. cf. galaxiae. P. cf. fraudulenta and P. pungens were indicator taxa of winter. P. cf. delicatissima and P. cf. pseudodelicatissima were spring and summer taxa, respectively. P. galaxiae showed maximum abundances in autumn. DNA sequences revealed the presence of two species belonging to the ’P. seriata group’ (i.e. P. fraudulenta and P. pungens) and four species belonging to the ‘P. delicatissima group’ (P. calliantha and P. mannii within the P. pseudodelicatissima species complex, and P. delicatissima and P. cf. arenysensis within the P. delicatissima species complex). The presence of several cryptic and pseudo-cryptic species highlights the need to combine LM observations with DNA sequence data when the ecology of Pseudo-nitzschia is investigated. 

scholarly journals DNA Sequence Analysis of dtxR Gene (Partial) of Corynebacterium diphtheriae Causing Diphtheria in Jawa and Kalimantan Islands, Indonesia

2017 ◽  
Vol 9 (2) ◽  
pp. 91
Author(s):  
Sunarno Sunarno ◽  
Yuanita Mulyastuti ◽  
Nelly Puspandari ◽  
Kambang Sariadji
Keyword(s):  
Sequence Analysis ◽  
Multiplex Pcr ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Sequence Data ◽  
Clinical Specimen ◽  
Corynebacterium Diphtheriae ◽  
Dna Sequence Analysis ◽  
Local Alignment ◽  
Pcr Products

BACKGROUND: dtxR gene is a global regulator that can be used as a marker for detection of Corynebacterium diphtheriae (C. diphtheriae) and it is also a representative tool for mapping purpose (molecular typing) of this bacteria. The aim of this study was to analyze the DNA sequences of partial dtxR gene of C. diphtheriae causing diphtheria in some region of Indonesia. DNA sequence analysis was used to verify the accuracy of the in-house multiplex polymerase chain reaction (PCR) method that used for detection of C. diphtheriae in the clinical specimen as well as a preliminary study to determine the strain diversity of C. diphtheriae circulating in Indonesia.METHODS:Ten PCR products targeting the dtxR gene that have been detected as positive C. diphtheriae previously by in-house multiplex PCR used as samples in this study. The DNA sequencing carried out by Sanger method and the sequence data was analyzed by Bioedit software offline and basic local alignment sequence typing (BLAST) online.RESULTS: All of DNA sequence analyzed in this study were similar or identical to the dtxR gene sequence data of C. diphtheriae registered in GenBank. Within the 162 nucleotides (base 150-311) of dtxR gene that analyzed, at least 2 clonals were found among 10 samples. Substitutions of 2 nucleotides (base 225 and 273) was detected, both were silent mutation.CONCLUSION:Ten partial DNA sequences of dtxR genes in this study verify the accuracy of in-house multiplex PCR which used to identify the bacteria causing diphtheria in the clinical specimen. The DNA sequences also represent the existing diversity of the bacteria causing diphtheria circulating in Indonesia.KEYWORDS: dtxR, C. diphtheriae, diphtheria, Indonesia

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