Acquiring DNA sequence data from dried archival red algae (Florideophyceae) for the purpose of applying available names to contemporary genetic species: a critical assessment

Botany ◽  
2012 ◽  
Vol 90 (3) ◽  
pp. 191-203 ◽  
Author(s):  
Gary W. Saunders ◽  
Daniel C. McDevit
Keyword(s):  
Red Algae ◽  
Sequence Data ◽  
Algal Species ◽  
Extraction Procedure ◽  
Dna Barcode ◽  
Resolving Power ◽  
Universal Primers ◽  
Success Rates ◽  
Mitochondrial Coi ◽  
Red Algal

Two DNA extraction protocols and nine variations of advocated DNA barcode markers (nuclear LSU D2/D3, ITS1, ITS2, mitochondrial COI-5P, plastid rbcL, UPA) were assessed for their abilities to yield species-level resolution from archival collections of red algae. With the exception of LSU D2/D3, all markers trialed displayed the potential to resolve red algal species. However, shortened COI-5P (COIms) and ITS (ITS2r) markers displayed four to five times the intrageneric divergence of shortened plastid markers and are preferred for their resolving power. For recent archival samples (4–11 years), COIms, ITS2r, and UPA displayed >90% amplification success. However, success rates declined rapidly as samples ranging in age from ca. 45–180 years old were tested. Further, contamination was a serious concern in reamplifications (partially nested PCR), especially for markers using universal primers (e.g., UPA) and for trials that employed the best extraction procedure, i.e., the better an extraction protocol is at isolating small DNA fragments from archival material, the better it is at acquiring small contaminating fragments from the laboratory — an intuitive and unfortunate reality. The ramifications of our results for ongoing attempts to extract DNA from archival red algal collections using PCR-based protocols is discussed along with recommendations to improve the likelihood of authentic outcomes.

Genetic barcoding resolves the historically known red alga Champia parvula from southern New England, USA, as C. farlowii sp. nov.  (Champiaceae, Rhodymeniales)

Phytotaxa ◽  
2017 ◽  
Vol 302 (1) ◽  
pp. 77 ◽  
Author(s):  
MAURA K. GRIFFITH ◽  
CRAIG W. SCHNEIDER ◽  
DANIEL I. WOLF ◽  
GARY W. SAUNDERS ◽  
CHRISTOPHER E. LANE
Keyword(s):  
New York ◽  
New Species ◽  
New England ◽  
Rhode Island ◽  
Algal Species ◽  
Mitochondrial Coi ◽  
Southern New England ◽  
Red Algal ◽  
Genetic Barcoding ◽  
A New Species

Using mitochondrial COI-5P and plastid rbcL genetic markers, the red algal species historically known in southern New England, USA, as Champia parvula is found to be genetically distinct from the species to which it has historically been aligned. This necessitates the description of a new species, C. farlowii, for plants from Rhode Island, Massachusetts, Connecticut and New York, USA. The new species is morphologically compared with true European C. parvula and congeners, especially those with similar features previously aligned under the same species name. Champia farlowii is a morphologically cryptic species, the sixth in the expanding C. parvula complex, with overlapping characteristic measurements despite differences at the range extremes, when compared to C. parvula.

Eucheumatopsis sanibelensis sp. nov. from the Gulf coast of Florida, USA

Phytotaxa ◽  
2020 ◽  
Vol 440 (3) ◽  
pp. 215-224 ◽  
Author(s):  
ELIAS S. PETERSON ◽  
CRAIG W. SCHNEIDER ◽  
GARY W. SAUNDERS
Keyword(s):  
Gulf Coast ◽  
Sequence Data ◽  
Algal Species ◽  
Morphological Characteristics ◽  
Caribbean Sea ◽  
Lsu Rdna ◽  
Eastern Gulf Of Mexico ◽  
Single Location ◽  
Red Algal ◽  
Morphological Differences

Based upon COI-5P, LSU rDNA and rbcL sequence data, as well as its morphological characteristics, a new red algal species, Eucheumatopsis sanibelensis E.S.Peterson, C.W.Schneider et G.W.Saunders sp. nov., was discovered on the Gulf coast of Florida, USA and shown to be distinct from the generitype E. isiformis with a type locality in the eastern Caribbean Sea. The new more attenuate taxon from Sanibel Island represents only the second species in this newly described genus, a genus recently segregated from Eucheuma based upon significant molecular and morphological differences. The two species have overlapping geographic distributions in the eastern Gulf of Mexico, but thus far E. sanibelensis is only known from a single location.

scholarly journals Species detections in environmental DNA using metabarcoding: a useful tool in estuaries monitoring

2015 ◽  
Author(s):  
Adrián Mártinez-Marqués ◽  
Carlos Enrique Carleos ◽  
Eva García-Vazquez ◽  
Yaisel J. Borrell Pichs
Keyword(s):  
Dna Analysis ◽  
Anthropogenic Activities ◽  
Dna Barcode ◽  
Environmental Dna ◽  
Coi Gene ◽  
Universal Primers ◽  
Mitochondrial Coi ◽  
Mitochondrial Coi Gene ◽  
Cantabrian Coast ◽  
Taxonomic Groups

Estuaries are amongst the most productive habitats in Earth, producing more organic materia than forests, meadows or agricultural lands. In addition, estuaries exhibit high, and precious, biodiversity levels. In this study an environmental DNA analysis of the two most important estuaries in Asturias (Cantabrian Coast, north Iberia) in terms of food production (Ría del Eo and Ría de Villaviciosa) was carried out. The objective was to monitor aquatic biodiversity and also to detect alien species that can be associated with anthropogenic activities (e.g.: aquaculture). To achieve these objectives, a metabarcoding methodology based in NGS (next generation sequencing) and the mitochondrial COI gene as a DNA Barcode was used. Results showed that this methodology was useful to detect the presence of three different non-native genera (Crepidula, Lymnaea, Macrobrachium) that are probably parasitating species cultured in these estuaries. It is true that Metabarcoding has still unsolved problems such as the lack of 100% universal primers and paucity of referenced sequences for some taxonomic groups in the databases. However, it represents already a powerful tool to manage the resources of these important ecosystems and to guarantee their long-term sustainailibity.

scholarly journals Universal Primers for Detection and Sequencing of Hepatitis B Virus Genomes across Genotypes A to G

2015 ◽  
Vol 53 (6) ◽  
pp. 1831-1835 ◽  
Author(s):  
Jack Bee Chook ◽  
Woon Li Teo ◽  
Yun Fong Ngeow ◽  
Kok Keng Tee ◽  
Kee Peng Ng ◽  
...  
Keyword(s):  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Sequence Data ◽  
Clinical Sample ◽  
High Rate ◽  
Universal Primers ◽  
Analytical Sensitivity ◽  
Success Rates ◽  
B Virus ◽  
Primer Sets

Hepatitis B virus (HBV) has been divided into 10 genotypes, A to J, based on an 8% nucleotide sequence divergence between genotypes. The conventional practice of using a single set of primers to amplify a near-complete HBV genome is hampered by its low analytical sensitivity. The current practice of using overlapping conserved primer sets to amplify a complete HBV genome in a clinical sample is limited by the lack of pan-primers to detect all HBV genotypes. In this study, we designed six highly conserved, overlapping primer sets to cover the complete HBV genome. We based our design on the sequences of 5,154 HBV genomes of genotypes A to I downloaded from the GenBank nucleotide database. These primer sets were tested on 126 plasma samples from Malaysia, containing genotypes A to D and with viral loads ranging from 20 to >79,780,000 IU/ml. The overall success rates for PCR amplification and sequencing were >96% and >94%, respectively. Similarly, there was 100% amplification and sequencing success when the primer sets were tested on an HBV reference panel of genotypes A to G. Thus, we have established primer sets that gave a high analytical sensitivity for PCR-based detection of HBV and a high rate of sequencing success for HBV genomes in most of the viral genotypes, if not all, without prior known sequence data for the particular genotype/genome.

Sheathia jinchengensis (Batrachospermales, Rhodophyta), a new freshwater red algal species described from North China

Phytotaxa ◽  
2018 ◽  
Vol 367 (1) ◽  
pp. 63 ◽  
Author(s):  
JIN-FEN HAN ◽  
FANG-RU NAN ◽  
JIA FENG ◽  
JUN-PING LV ◽  
QI LIU ◽  
...  
Keyword(s):  
New Species ◽  
North China ◽  
Cold Water ◽  
Sequence Data ◽  
Algal Species ◽  
Point Of View ◽  
Shanxi Province ◽  
Water Stream ◽  
Red Algal ◽  
Freshwater Red Algae

A new species of freshwater red algae, Sheathia jinchengensis, is described based on material collected from rocks in a clean and cold-water stream from the Jincheng region of Shanxi province in North China. Molecular sequences of rbcL and psbA genes were used to evaluate the phylogenetic relationship among samples of S. jinchengensis and other Sheathia species from several regions of the world. The results showed that S. jinchengensis formed an independent branch and separated from the previously published sequence data of other Sheathia taxa. From a morphological point of view, this new species differs also from other species of the genus by the smaller diameter of whorls (167.0–312.5 μm) and larger carpogonium diameter (17.0–29.0 μm). Comparison of sequence variation and thallus morphology with other Sheathia taxa resulted in the proposal of the new species—S. jinchengensis. Additionally, two endemic Batrachospermum species described earlier from China i.e., B. hongdongense and B. longipedicellata are now transferred to the genus Sheathia based on the present study as S. hongdongensis (S.L.Xie & J.Feng) Han, Nan, Feng, Lv, Liu, Kociolek et Xie comb. nov. and S. longipedicellata (Hua & Shi) Han, Nan, Feng, Lv, Liu, Kociolek et Xie comb. nov.

A contaminant DNA barcode sequence reveals a new red algal order, Corynodactylales (Nemaliophycidae, Florideophyceae)

Botany ◽  
2017 ◽  
Vol 95 (6) ◽  
pp. 561-566 ◽  
Author(s):  
Gary W. Saunders ◽  
Katelyn L. Wadland ◽  
Eric D. Salomaki ◽  
Christopher E. Lane
Keyword(s):  
Phylogenetic Analysis ◽  
Red Algae ◽  
Dna Barcode ◽  
Genomic Data ◽  
Red Alga ◽  
Vegetative Development ◽  
Red Algal ◽  
Multigene Phylogenetic Analysis

Routine DNA barcode surveys of red algae can occasionally yield contaminant sequences owing to the diverse epi/endo flora and fauna that can inhabit these species. Often discarded as nuisance data, further exploration in this study led to the discovery of an unusual red alga with a highly characteristic vegetative development in which the diminutive primary vegetative filaments are terminated by distinctive monosporangia. This entity is described here as Corynodactylus rejiciendus G.W. Saunders gen. et sp. nov. Generating genomic data from the host and associated epiphytic flora, and subsequently subtracting out genes of the former, facilitated a multigene phylogenetic analysis supporting recognition of Corynodactylaceae fam. nov. and Corynodactylales ord. nov. as a distant sister to the order Balliales in the subclass Nemaliophycidae.

scholarly journals Species detections in environmental DNA using metabarcoding: a useful tool in estuaries monitoring

2015 ◽  
Author(s):  
Adrián Mártinez-Marqués ◽  
Carlos Enrique Carleos ◽  
Eva García-Vazquez ◽  
Yaisel J. Borrell Pichs
Keyword(s):  
Dna Analysis ◽  
Anthropogenic Activities ◽  
Dna Barcode ◽  
Environmental Dna ◽  
Coi Gene ◽  
Universal Primers ◽  
Mitochondrial Coi ◽  
Mitochondrial Coi Gene ◽  
Cantabrian Coast ◽  
Taxonomic Groups

Estuaries are amongst the most productive habitats in Earth, producing more organic materia than forests, meadows or agricultural lands. In addition, estuaries exhibit high, and precious, biodiversity levels. In this study an environmental DNA analysis of the two most important estuaries in Asturias (Cantabrian Coast, north Iberia) in terms of food production (Ría del Eo and Ría de Villaviciosa) was carried out. The objective was to monitor aquatic biodiversity and also to detect alien species that can be associated with anthropogenic activities (e.g.: aquaculture). To achieve these objectives, a metabarcoding methodology based in NGS (next generation sequencing) and the mitochondrial COI gene as a DNA Barcode was used. Results showed that this methodology was useful to detect the presence of three different non-native genera (Crepidula, Lymnaea, Macrobrachium) that are probably parasitating species cultured in these estuaries. It is true that Metabarcoding has still unsolved problems such as the lack of 100% universal primers and paucity of referenced sequences for some taxonomic groups in the databases. However, it represents already a powerful tool to manage the resources of these important ecosystems and to guarantee their long-term sustainailibity.

Phylogenesis of pit-plug-associated features in the Rhodophyta: inferences from molecular systematic data

1997 ◽  
Vol 75 (9) ◽  
pp. 1436-1447 ◽  
Author(s):  
Gary W. Saunders ◽  
J. Craig Bailey
Keyword(s):  
Ribosomal Rna ◽  
Sequence Data ◽  
Algal Species ◽  
Small Subunit ◽  
Future Research ◽  
Molecular Systematic ◽  
Rna Sequences ◽  
Small Subunit Ribosomal Rna ◽  
Cap Layer ◽  
Red Algal

Small-subunit ribosomal RNA sequence data are presented for Rhodogorgon carriebowensis Norris et Bucher (Rhodogorgonales, Rhodophyta) and Galaxaura marginata (Ellis et Solander) Lamouroux (Nemaliales, Rhodophyta). Data for these species were included in a matrix consisting of small-subunit ribosomal RNA sequences for 70 taxonomically diverse red algal species. Distance, parsimony, and maximum-likelihood analyses of these data all strongly support (100% of bootstrap replicates for distance and parsimony) a close alliance between the Rhodogorgonales and Corallinales. Our alignment includes 19 species representing six florideophyte orders (Acrochaetiales, Batrachospermales, Corallinales, Nemaliales, Palmariales, Rhodogorgonales) in which pit plugs are characterized by two cap layers. Distance and parsimony analyses resolve a monophyletic lineage including all "two-cap-layer" species. Our parsimony-derived molecular phylogeny was used to test a published hypothesis of pit-plug evolution. Four aspects of Pueschel's hypothesis are consistent with the results of our molecular systematic study: (i) "naked" plugs represent the ancestral type, (ii) outer cap layers are homologous structures, (iii) domed outer caps are ancestral to plate-like outer caps, and (iv) cap membranes are a derived feature within the two-cap-layer lineage. Directions for future research are discussed. Key words: Acrochaetiales, Batrachospermales, Corallinales, molecular systematics, Nemaliales, Palmariales, phylogeny, pit plug, Rhodogorgonales, Rhodophyta.

Molecular characterization and phylogenetic analysis of cyclopoid copepod Mesocyclops leuckarti using mtCOI

2017 ◽  
Vol 6 (04) ◽  
pp. 5365
Author(s):  
Gomathi Jeyam ◽  
Ramanibai R*
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Barcode ◽  
Coi Gene ◽  
Universal Primers ◽  
Cyclopoid Copepod ◽  
Mitochondrial Coi ◽  
Mitochondrial Coi Gene ◽  
Mesocyclops Leuckarti ◽  
Coi Sequences ◽  
The Individual

Copepods are the most abundant metazoan zooplankton amongst multicellular animals. The present study was performed to establish the sequence variation of partial mitochondrial Cytochrome c Oxidase I gene (COI) from Mesocyclops leuckarti collected from the Retteri Lake, Chennai in order to identify and describe their genetic divergence along with the phylogenetic relatedness with other species. DNA of individual M. leuckarti was extracted and the partial mitochondrial COI gene was successfully amplified using the universal primers LCO-1490 and HCO-2198. A 576bp partial mitochondrial COI gene sequence was obtained. Analysis of partial COI sequences of M. leuckarti exposed 93% similarity amongst all the individual of copepods selected from Genbank. The obtained COI sequences of Cyclopoid copepod was confirmed with BLAST analysis. Phylogenetic analysis of M. leuckarti along with selected out groups from different taxa level further supports the clarity and maintained the authentic of taxonomy up to the subclass level: Copepoda. The results showed that, the COI barcoding of cyclopoid copepod species could be distinguished from the others very clearly. Thus, it strongly indicated that COI may be a useful construction of a comprehensive DNA barcode database for copepods inhabiting the freshwater bodies in Chennai.

A DNA barcode survey of Schizymenia (Nemastomatales, Rhodophyta) in Australia and British Columbia reveals overlooked diversity including S. tenuis sp. nov. and Predaea borealis sp. nov.

Botany ◽  
2015 ◽  
Vol 93 (12) ◽  
pp. 859-871 ◽  
Author(s):  
Gary W. Saunders ◽  
Taylor C. Birch ◽  
Kyatt R. Dixon
Keyword(s):  
British Columbia ◽  
Sequence Data ◽  
Dna Barcode ◽  
Sensu Stricto ◽  
Haida Gwaii ◽  
Closely Related Species ◽  
Genetic Groups ◽  
As Species ◽  
Red Algal ◽  
Algal Genus

This project explored species diversity for the red algal genus Schizymenia in Australia and British Columbia, Canada, for which the only recorded representatives are S. dubyi (Chauvin ex Duby) J. Agardh and S. pacifica (Kylin) Kylin, respectively. Through a combination of CO1-5P, ITS, and rbcL sequence data, we uncovered overlooked diversity in both regions. Australian populations attributed to S. dubyi were actually a mix of an entity from the S. dubyi complex (closest matches for individuals from Argentina and Italy), a second species from the S. apoda (J. Agardh) J. Agardh complex (thus far known from Australia only), and finally individuals of the same S. dubyi mito/ITS-type introgressed with a different S. apoda rbcL type (plastid; closest matches China, Korea, and New Zealand). We resolved a complex of three closely related species for Schizymenia pacifica: Schizymenia pacifica sensu stricto, which is widely distributed in the Northeast Pacific; S. tenuis sp. nov., which is distributed throughout British Columbia with a predominantly northern distribution; and Schizymenia sp._1Cal, which is distributed from California to Oregon. As part of ongoing surveys of crustose red algae, we uncovered crustose sporophytes for three of the six Schizymenia genetic groups resolved here, and the sporophytic phase of a new species of Predaea from northern British Columbia, Predaea borealis sp. nov., for a single crustose (sporophyte) specimen from Haida Gwaii. This last result is particularly surprising, as species of Predaea are typically confined to lower latitudes in both the northern and southern hemispheres.

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