scholarly journals Marine nematode taxonomy in the age of DNA: the present and future of molecular tools to assess their biodiversity

Nematology ◽  
2010 ◽  
Vol 12 (5) ◽  
pp. 661-672 ◽  
Author(s):  
Neyvan Renato Rodrigues da Silva ◽  
Maria Cristina da Silva ◽  
Verônica Fonseca Genevois ◽  
André Morgado Esteves ◽  
Paul De Ley ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Processing Speed ◽  
Sequence Data ◽  
Molecular Taxonomy ◽  
Species Boundaries ◽  
Nominal Species ◽  
Marine Nematode ◽  
Molecular Tools ◽  
Variable Regions ◽  
Online Databases

Abstract Molecular taxonomy is one of the most promising yet challenging fields of biology. Molecular markers such as nuclear and mitochondrial genes are being used in a variety of studies surveying marine nematode taxa. Sequences from more than 600 species have been deposited to date in online databases. These barcode sequences are assigned to 150 nominal species from 104 genera. There are 41 species assigned to Enoplea and 109 species to Chromadorea. Morphology-based surveys are greatly limited by processing speed, while barcoding approaches for nematodes are hampered by difficulties in matching sequence data with morphology-based taxonomy. DNA barcoding is a promising approach because some genes contain variable regions that are useful to discriminate species boundaries, discover cryptic species, quantify biodiversity and analyse phylogeny. We advocate a combination of several approaches in studies of molecular taxonomy, DNA barcoding and conventional taxonomy as a necessary step to enhance the knowledge of biodiversity of marine nematodes.

DNA barcoding Australian macroinvertebrates for monitoring programs: benefits and current short comings

2016 ◽  
Vol 67 (3) ◽  
pp. 380 ◽  
Author(s):  
Michael Shackleton ◽  
Gavin N. Rees
Keyword(s):  
Cryptic Species ◽  
Dna Barcoding ◽  
Sequence Data ◽  
Aquatic Environments ◽  
Molecular Approaches ◽  
Monitoring Programs ◽  
Online Databases ◽  
Murray Darling Basin ◽  
Freshwater Fauna ◽  
Australian Freshwater

Identification of macroinvertebrates is a key component of monitoring programs that seek to understand the condition of aquatic environments. Classical identification approaches underpin such programs, but molecular approaches are gaining recognition as valuable ways to identify organisms for research and monitoring programs. We applied DNA barcoding data to specimens collected as part of monitoring programs in the Murray–Darling Basin, to investigate the possible informational benefits these data may provide. We also tested the performances of two online DNA databases in assigning taxon names to our sequence data. We found that relying on the online databases to determine species identifications was currently problematic for the Australian freshwater fauna because of a lack of available sequence data. However, we also found that collecting and applying barcode data to our monitoring programs gave considerable informational benefits by providing greater resolution of specimen identity, highlighting the presence of potential cryptic species, providing information on larval and adult associations, demonstrating instances where misidentification had occurred though classical approaches, and providing conformation of the performance of diagnostic characters currently used in keys to determine species identities.

scholarly journals Molecular tools for identification and classification of Myxozoan parasites (Cnidaria: Myxosporea) in India: Current status

2021 ◽  
Vol 13 (1) ◽  
pp. 51-58
Author(s):  
Abhishek Gupta ◽  
Anshu Chaudhary ◽  
Anju Tyagi ◽  
Bindu Sharma ◽  
Hridaya S. Singh
Keyword(s):  
Molecular Markers ◽  
Large Subunit ◽  
Molecular Taxonomy ◽  
Morphological Characteristics ◽  
Molecular Techniques ◽  
Classification Systems ◽  
Morphological Data ◽  
Current Status ◽  
Nominal Species ◽  
Molecular Tools

A substantial literature on myxosporea has been published to date using morphological characters and specificity of host tissue. Currently, there are some 2400 nominal species of myxosporea classified to 17 families and 64 genera. Approximately 300 species have been described from India and most of them have been described solely on the basis of morphological characteristics. Molecular markers like small subunit ribosomal (SSU) and large subunit ribosomal (LSU) DNA have been used worldwide for the identification and validation of fish myxosporeans. Maximum likelihood phylogenetic tree based on SSU rDNA sequences was used to study the phylogenetic relationship among myxosporeans infecting Indian fishes. Myxospore phylogenies disagree with traditional spore-based classification systems, probably due to extreme plasticity in myxospores morphologies that have resulted in extensive convergence. Morphological similarities exist among myxosporea that encounter several problems in categorizing them. That’s why present-day research has shifted to molecular techniques for identification and correct systematics of myxosporeans. Molecular studies of myxozoans in India are still scarce and in infancy. To address persisting taxonomic and phylogenetic discrepancies, validation of these species by molecular tools is needed, because earlier species were reported only on the basis of morphological data. Therefore, the present study has summarized existing molecular data and current status of molecular taxonomy of myxosporeans parasitizing fresh and marine water fishes of India along with the approaches of myxozoan phylogenetics and information about the molecular markers, their interpretation in the identification of myxozoans parasitizing fishes.

scholarly journals Identification of Lens Cultivars in Market by Molecular Tools: DNA Barcoding and SSRs

2022 ◽  
Author(s):  
Metin Burak TATLISES ◽  
Semra Hasancebi
Keyword(s):  
Dna Barcoding ◽  
Ssr Markers ◽  
Lens Culinaris ◽  
Sequence Data ◽  
Dna Barcode ◽  
Molecular Methods ◽  
Species Discrimination ◽  
Species Variation ◽  
Molecular Tools ◽  
Specific Allele

Abstract Substitution of plant cultivars of high commercial value with a cheaper, lower-quality one is a common fraud committed against consumers and producers. Since it is one of the most widely grown legumes, lentil (Lens culinaris Medik.) are a suitable for such frauds. This study aimed to identify lentil cultivars which are registered and authorized in the market in Turkey by using current molecular methods. For this purpose, 26 lentil cultivars were analyzed for 15 SSR markers and 2 DNA barcode loci (trnH-psbA and matK). A high allele diversity was observed by 12 scorable SSR markers, and the average number of alleles was determined to be 16. One of the important findings was the presence of “cultivar-specific alleles” that can be used to identify each cultivar in the lentil market in Turkey. At least one “cultivar-specific allele” was obtained for each cultivar. The lentil cultivars were analyzed in terms of 2 DNA barcode regions as trnH-psbA and matK. Sequences that could identify 14 of the 26 cultivars were obtained. While the rate of the intra-species variation for the trnH-psbA region was observed to be low, a higher rate was found for matK. Nevertheless, it was observed that intra-species discrimination can be made more effective when both loci are used together. We expect that the results of this study, especially the cultivar-specific SSR alleles and DNA barcoding sequence data may be used routinely to identify on production and packaged products that are commercially available in markets.

scholarly journals Mismatch induced speciation in Salmonella : model and data

2006 ◽  
Vol 361 (1475) ◽  
pp. 2045-2053 ◽  
Author(s):  
Daniel Falush ◽  
Mia Torpdahl ◽  
Xavier Didelot ◽  
Donald F Conrad ◽  
Daniel J Wilson ◽  
...  
Keyword(s):  
New Species ◽  
Natural Selection ◽  
Dna Sequence ◽  
Computer Simulations ◽  
De Novo ◽  
Sequence Data ◽  
Biological Species ◽  
Species Boundaries ◽  
Population Subdivision ◽  
Geographical Population

In bacteria, DNA sequence mismatches act as a barrier to recombination between distantly related organisms and can potentially promote the cohesion of species. We have performed computer simulations which show that the homology dependence of recombination can cause de novo speciation in a neutrally evolving population once a critical population size has been exceeded. Our model can explain the patterns of divergence and genetic exchange observed in the genus Salmonella , without invoking either natural selection or geographical population subdivision. If this model was validated, based on extensive sequence data, it would imply that the named subspecies of Salmonella enterica correspond to good biological species, making species boundaries objective. However, multilocus sequence typing data, analysed using several conventional tools, provide a misleading impression of relationships within S. enterica subspecies enterica and do not provide the resolution to establish whether new species are presently being formed.

scholarly journals DNA Barcoding on Bacteria: A Review

2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
D. E. Lebonah ◽  
A. Dileep ◽  
K. Chandrasekhar ◽  
S. Sreevani ◽  
B. Sreedevi ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Agricultural Production ◽  
Sequence Data ◽  
Bacterial Pathogens ◽  
Review Article ◽  
Food Spoilage ◽  
Identification Technique

Bacteria are omnipotent and they can be found everywhere. The study of bacterial pathogens has been happening from olden days to prevent epidemics, food spoilage, losses in agricultural production, and loss of lives. Modern techniques in DNA based species identification are considered. So, there is a need to acquire simple and quick identification technique. Hence, this review article covers the efficacy of DNA barcoding of bacteria. Routine DNA barcoding involves the production of PCR amplicons from particular regions to sequence them and these sequence data are used to identify or “barcode” that organism to make a distinction from other species.

scholarly journals Comment on Falade et al. (2016) DNA-barcoding of Clarias gariepinus, Coptedon zillii and Sarotherodon melanotheron from Southwestern Nigeria

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 2654
Author(s):  
Jeremy A. Miller ◽  
Isolde van Riemsdijk ◽  
Mohd Zacaery Khalik ◽  
David J. Scager ◽  
Menno Schilthuizen
Keyword(s):  
Dna Barcoding ◽  
Sequence Data ◽  
Journal Club ◽  
Clarias Gariepinus ◽  
Southwestern Nigeria ◽  
Dna Taxonomy ◽  
Open Review ◽  
Review Model ◽  
Sarotherodon Melanotheron ◽  
Untapped Resource

A publication by Falade et al. was selected for discussion by a Naturalis Biodiversity Center-Leiden University Journal Club. The study focused on the identification of fish from Southwestern Nigeria using a DNA barcoding approach. Questions raised during the discussion led to a reanalysis and reinterpretation of the data presented. The authors characterize the process of deriving a taxonomic identification from their sequence data as straightforward, but we were concerned that their approach made it nearly impossible to fail to obtain a taxonomic name for each sequence. The value of sophisticated DNA taxonomy, as well as the pitfalls of its naïve application, are discussed. We suggest that journal discussion groups may be an untapped resource for expanding rigorous peer review, particularly for journals that have adopted an open review model.

Introduction of Neolophiotrema xiaokongense gen. et sp. nov. to the poorly represented Anteagloniaceae (Pleosporales, Dothideomycetes)

Phytotaxa ◽  
2021 ◽  
Vol 482 (1) ◽  
pp. 25-35
Author(s):  
GUANG-CONG REN ◽  
DHANUSHKA N. WANASINGHE ◽  
JUTAMART MONKAI ◽  
KEVIN D. HYDE ◽  
PETER E. MORTIMER ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Sequence Data ◽  
Species Boundaries ◽  
Identification Of Species

The monotypic Neolophiotrema (typified by N. xiaokongense) is introduced for a wood-inhabiting taxon classified in Dothideomycetes. The genus is characterized by, coriaceous, immersed to semi-immersed ascomata, hamathecium with cellular pseudoparaphyses and overlapping 1–2-seriate, hyaline ascospores. Phylogenetic analysis of combined SSU, LSU, ITS, tef1-α and rpb2 sequence data supports the placement of Neolophiotrema in Anteagloniaceae (Pleosporales). A morphology-based synopsis key is provided to facilitate the identification of species of Anteagloniaceae. The classification and nature of species boundaries in Anteagloniaceae are discussed.

scholarly journals The First Glimpse of Streptocarpus ionanthus (Gesneriaceae) Phylogenomics: Analysis of Five Subspecies’ Chloroplast Genomes

Plants ◽  
2020 ◽  
Vol 9 (4) ◽  
pp. 456 ◽  
Author(s):  
Cornelius M. Kyalo ◽  
Zhi-Zhong Li ◽  
Elijah M. Mkala ◽  
Itambo Malombe ◽  
Guang-Wan Hu ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Structural Features ◽  
Base Pairs ◽  
Protein Coding ◽  
Variable Regions ◽  
Morphological Heterogeneity ◽  
Chloroplast Genomes ◽  
Chloroplast Genome Sequence ◽  
Phylogenomic Analyses

Streptocarpus ionanthus (Gesneriaceae) comprise nine herbaceous subspecies, endemic to Kenya and Tanzania. The evolution of Str. ionanthus is perceived as complex due to morphological heterogeneity and unresolved phylogenetic relationships. Our study seeks to understand the molecular variation within Str. ionanthus using a phylogenomic approach. We sequence the chloroplast genomes of five subspecies of Str. ionanthus, compare their structural features and identify divergent regions. The five genomes are identical, with a conserved structure, a narrow size range (170 base pairs (bp)) and 115 unique genes (80 protein-coding, 31 tRNAs and 4 rRNAs). Genome alignment exhibits high synteny while the number of Simple Sequence Repeats (SSRs) are observed to be low (varying from 37 to 41), indicating high similarity. We identify ten divergent regions, including five variable regions (psbM, rps3, atpF-atpH, psbC-psbZ and psaA-ycf3) and five genes with a high number of polymorphic sites (rps16, rpoC2, rpoB, ycf1 and ndhA) which could be investigated further for phylogenetic utility in Str. ionanthus. Phylogenomic analyses here exhibit low polymorphism within Str. ionanthus and poor phylogenetic separation, which might be attributed to recent divergence. The complete chloroplast genome sequence data concerning the five subspecies provides genomic resources which can be expanded for future elucidation of Str. ionanthus phylogenetic relationships.

scholarly journals Review on the molecular study of the Diplozoidae: analyses of currently available genetic data, what it tells us, and where to go from here

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Quinton Marco Dos Santos ◽  
Annemariè Avenant-Oldewage
Keyword(s):  
Sequence Data ◽  
Molecular Study ◽  
Turn Of The Century ◽  
Phylogenetic Study ◽  
Online Databases ◽  
Crucial Component ◽  
The Family ◽  
Molecular Information ◽  
Taxonomic Approach ◽  
Species Descriptions

Abstract The use of molecular tools in the study of parasite taxonomy and systematics have become a substantial and crucial component of parasitology. Having genetic characterisation at the disposal of researchers has produced mostly useful, and arguably more objective conclusions. However, there are several groups for which limited genetic information is available and, coupled with the lack of standardised protocols, renders molecular study of these groups challenging. The Diplozoidae are fascinating and unique monogeneans parasitizing mainly freshwater cyprinid fishes in Europe, Asia and Africa. This group was studied from a molecular aspect since the turn of the century and as such, limitations and variability concerning the use of these techniques have not been clearly defined. In this review, all literature and molecular information, primarily from online databases such as GenBank, were compiled and scrupulously analysed for the Diplozoidae. This was done to review the information, detect possible pitfalls, and provide a “checkpoint” for future molecular studies of the family. Hindrances detected are the availability of sequence data for only a limited number of species, frequently limited to a single sequence per species, and the heavy reliance on one non-coding ribosomal marker (ITS2 rDNA) which is difficult to align objectively and displays massive divergences between taxa. Challenging species identification and limited understanding of diplozoid species diversity and plasticity are also likely restricting factors, all of which hamper the accurate taxonomic and phylogenetic study of this group. Thus, a more integrated taxonomic approach through the inclusion of additional markers, application of more rigorous morphological assessment, more structured barcoding techniques, alongside thorough capturing of species descriptions including genetypes, genophore vouchers and reference collections in open sources are encouraged. The pitfalls highlighted are not singular to the Diplozoidae, and the study of other groups may benefit from the points raised here as well.

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