scholarly journals Assessment of species gaps in DNA barcode libraries of non-indigenous species (NIS) occurring in European coastal regions

2020 ◽  
Vol 4 ◽  
Author(s):  
Sofia Duarte ◽  
Pedro E. Vieira ◽  
Filipe O. Costa
Keyword(s):  
Sequence Data ◽  
Dna Barcode ◽  
Indigenous Species ◽  
Coastal Environments ◽  
Taxonomic Assignment ◽  
Dna Sequence Data ◽  
Marker Data ◽  
Dna Metabarcoding ◽  
Assessment Techniques ◽  
Non Indigenous Species

DNA metabarcoding has the capacity to bolster current biodiversity assessment techniques, including the early detection and monitoring of non-indigenous species (NIS). However, the success of this approach is greatly dependent on the availability, taxonomic coverage and reliability of reference sequences in genetic databases, whose deficiencies can potentially compromise species identifications at the taxonomic assignment step. In this study we assessed lacunae in availability of DNA sequence data from four barcodes (COI, 18S, rbcL and matK) for NIS occurring in European marine and coastal environments. NIS checklists were based on EASIN and AquaNIS databases. The highest coverage was found for COI for Animalia and rbcL for Plantae (up to 63%, for both) and 18S for Chromista (up to 51%), that greatly increased when only high impact species were taken into account (up to 82 to 89%). Results show that different markers have unbalanced representations in genetic databases, implying that the parallel use of more than one marker can act complimentarily and may greatly increase NIS identification rates through DNA-based tools. Furthermore, based on the COI marker, data for approximately 30% of the species had maximum intra-specific distances higher than 3%, suggesting that many NIS may have undescribed or cryptic diversity. Although completing the gaps in reference libraries is essential to make the most of the potential of the DNA-based tools, a careful compilation, verification and annotation of available sequences is fundamental to assemble large curated and reliable reference libraries that provide support for rigorous species identifications.

scholarly journals Current limitations and future prospects of detection and biomonitoring of NIS in the Mediterranean Sea through environmental DNA

NeoBiota ◽  
2021 ◽  
Vol 70 ◽  
pp. 151-165
Author(s):  
Francesco Zangaro ◽  
Benedetta Saccomanno ◽  
Eftychia Tzafesta ◽  
Fabio Bozzeda ◽  
Valeria Specchia ◽  
...  
Keyword(s):  
Mediterranean Sea ◽  
Dna Barcode ◽  
Environmental Dna ◽  
Special Focus ◽  
Indigenous Species ◽  
Dna Barcodes ◽  
Identification Of Species ◽  
The Mediterranean ◽  
Taxonomic Groups ◽  
Non Indigenous Species

The biodiversity of the Mediterranean Sea is currently threatened by the introduction of Non-Indigenous Species (NIS). Therefore, monitoring the distribution of NIS is of utmost importance to preserve the ecosystems. A promising approach for the identification of species and the assessment of biodiversity is the use of DNA barcoding, as well as DNA and eDNA metabarcoding. Currently, the main limitation in the use of genomic data for species identification is the incompleteness of the DNA barcode databases. In this research, we assessed the availability of DNA barcodes in the main reference libraries for the most updated inventory of 665 confirmed NIS in the Mediterranean Sea, with a special focus on the cytochrome oxidase I (COI) barcode and primers. The results of this study show that there are no barcodes for 33.18% of the species in question, and that 45.30% of the 382 species with COI barcode, have no primers publicly available. This highlights the importance of directing scientific efforts to fill the barcode gap of specific taxonomic groups in order to help in the effective application of the eDNA technique for investigating the occurrence and the distribution of NIS in the Mediterranean Sea.

A review of the fern genus Pellaea (Pteridaceae) in Australasia

2020 ◽  
Author(s):  
Patrick J. Brownsey ◽  
Daniel J. Ohlsen ◽  
Lara D. Shepherd ◽  
Whitney L. M. Bouma ◽  
Erin L. May ◽  
...  
Keyword(s):  
New Zealand ◽  
Chloroplast Dna ◽  
Dna Sequences ◽  
Sequence Data ◽  
Indigenous Species ◽  
Ploidy Levels ◽  
Dna Sequence Data ◽  
Australian Species ◽  
The Status ◽  
Chloroplast Dna Sequences

Five indigenous species of Pellaea in Australasia belong to section Platyloma. Their taxonomic history is outlined, morphological, cytological and genetic evidence for their recognition reviewed, and new morphological and chloroplast DNA-sequence data provided. Australian plants of P. falcata (R.Br.) Fée are diploid and have longer, narrower pinnae than do New Zealand plants previously referred to P. falcata, which are tetraploid. Evidence indicates that P. falcata does not occur in New Zealand, and that collections so-named are P. rotundifolia (G.Forst.) Hook. Chloroplast DNA sequences are uninformative in distinguishing Australian P. falcata from New Zealand P. rotundifolia, but show that Australian P. nana is distinct from both. Sequence data also show that Australian and New Zealand populations of P. calidirupium Brownsey & Lovis are closely related, and that Australian P. paradoxa (R.Br.) Hook. is distinct from other Australian species. Although P. falcata is diploid and P. rotundifolia tetraploid, P. calidirupium, P. nana (Hook.) Bostock and P. paradoxa each contain multiple ploidy levels. Diploid populations of Pellaea species are confined to Australia, and only tetraploids are known in New Zealand. Evolution of the group probably involved hybridisation, autoploidy, alloploidy, and possibly apomixis. Further investigation is required to resolve the status of populations from Mount Maroon, Queensland and the Kermadec Islands.

scholarly journals All non-indigenous species were introduced recently? The case study of Cassiopea (Cnidaria: Scyphozoa) in Brazilian waters

2016 ◽  
Vol 97 (2) ◽  
pp. 321-328 ◽  
Author(s):  
André C. Morandini ◽  
Sergio N. Stampar ◽  
Maximiliano M. Maronna ◽  
Fábio L. Da Silveira
Keyword(s):  
Coastal Waters ◽  
Sequence Data ◽  
Divergence Time ◽  
Indigenous Species ◽  
Styela Plicata ◽  
Morphological Criteria ◽  
Non Indigenous Species ◽  
Janeiro State ◽  
Cabo Frio

Upside-down jellyfish (genus Cassiopea) can be found in tropical coastal waters worldwide. Until now reports of the genus from Brazilian waters have been scant. We report here medusae and scyphistomae collected from Cabo Frio, Rio de Janeiro state. Although we could not unambiguously identify the material using morphological criteria, genetic sequence data (COI) indicate that the Brazilian jellyfishes are genetically similar to those from Bermuda, Hawaii and Florida, which are related to specimens from the Red Sea (Cassiopea andromeda). We hypothesize that the presence of C. andromeda in Brazil is due to an invasion event, as the scyphistomae were found growing over the known invasive ascidian Styela plicata. Estimation of divergence time between Brazil (Cabo Frio) and Florida/Bermuda populations is that it occurred at the beginning of ship movement to South America.

scholarly journals PrimerMiner: an R package for development and in silico validation of DNA metabarcoding primers

2016 ◽  
Author(s):  
Vasco Elbrecht ◽  
Florian Leese
Keyword(s):  
In Silico ◽  
Sequence Data ◽  
Dna Barcode ◽  
R Package ◽  
Primer Design ◽  
Reference Sequence ◽  
Gene Marker ◽  
Sequence Alignments ◽  
Variable Binding ◽  
Dna Metabarcoding

1) DNA metabarcoding is a powerful tool to assess biodiversity by amplifying and sequencing a standardized gene marker region. Its success is often limited due to variable binding sites that introduce amplification biases. Thus the development of optimized primers for communities or taxa under study in a certain geographic region and/or ecosystems is of critical importance. However, no tool for obtaining and processing of reference sequence data in bulk that serve as a backbone for primer design is currently available. 2) We developed the R package PrimerMiner, which batch downloads DNA barcode gene sequences from BOLD and NCBI databases for specified target taxonomic groups and then applies sequence clustering into operational taxonomic units (OTUs) to reduce biases introduced by the different number of available sequences per species. Additionally, PrimerMiner offers functionalities to evaluate primers in silico, which are in our opinion more realistic then the strategy employed in another available software for that purpose, ecoPCR. 3) We used PrimerMiner to download cytochrome c oxidase subunit I (COI) sequences for 15 important freshwater invertebrate groups, relevant for ecosystem assessment. By processing COI markers from both databases, we were able to increase the amount of reference data 249-fold on average, compared to using complete mitochondrial genomes alone. Furthermore, we visualized the generated OTU sequence alignments and describe how to evaluate primers in silico using PrimerMiner. 4) With PrimerMiner we provide a useful tool to obtain relevant sequence data for targeted primer development and evaluation. The OTU based reference alignments generated with PrimerMiner can be used for manual primer design, or processed with bioinformatic tools for primer development.

scholarly journals New morphological and DNA evidence supports the existence of Calligonum jeminaicum Z. M. Mao (Calligoneae, Polygonaceae) in China

PhytoKeys ◽  
2019 ◽  
Vol 132 ◽  
pp. 53-73
Author(s):  
Wei Shi ◽  
Pei-Liang Liu ◽  
Jun Wen ◽  
Ying Feng ◽  
Borong Pan
Keyword(s):  
Morphological Traits ◽  
Sequence Data ◽  
Dna Barcode ◽  
Taxonomic Status ◽  
Current Evidence ◽  
Molecular Analyses ◽  
Dna Evidence ◽  
Dna Sequence Data ◽  
Naturally Occurring ◽  
Iucn Criteria

Calligonum jeminaicum Z. M. Mao, a species regarded as endemic to China, was thought to be nonexistent owing to a lack of scientific records. The similarity of C. jeminaicum to C. mongolicum Turcz. warranted an investigation into the taxonomical relationship between these species. In this study, a naturally occurring population of C. jeminaicum was discovered and the taxonomical relationships of this species with C. mongolicum were resolved. Morphological traits, including fruit and flower characteristics, as well as nuclear (ETS, ITS) and chloroplast (psbA-trnH, ycf6-psbM, rpl32-trnL, rbcL, and trnL-F) DNA sequence data were studied to confirm the taxonomic status of C. jeminaicum. The nrDNA data (ITS1-2 and ETS) from C. jeminaicum reflected variability from the whole C. mongolicum complex, showing distinctive haplotypes in the Calligonum sect. Medusa Sosk. & Alexandr. The cpDNA data supplied similar evidence, showing unique branching in Bayesian and ML tree analyses. The specific status of C. jeminaicum is confirmed based on both morphological and molecular analyses. Here we present a revised description of C. jeminaicum along with its DNA barcode and discuss suggestions for the conservation of this species. Based on current evidence, this species was evaluated as Critically Endangered (CR) according to the IUCN criteria.

scholarly journals PrimerMiner: an R package for development and in silico validation of DNA metabarcoding primers

2016 ◽  
Author(s):  
Vasco Elbrecht ◽  
Florian Leese
Keyword(s):  
In Silico ◽  
Sequence Data ◽  
Dna Barcode ◽  
R Package ◽  
Primer Design ◽  
Reference Sequence ◽  
Gene Marker ◽  
Sequence Alignments ◽  
Variable Binding ◽  
Dna Metabarcoding

1) DNA metabarcoding is a powerful tool to assess biodiversity by amplifying and sequencing a standardized gene marker region. Its success is often limited due to variable binding sites that introduce amplification biases. Thus the development of optimized primers for communities or taxa under study in a certain geographic region and/or ecosystems is of critical importance. However, no tool for obtaining and processing of reference sequence data in bulk that serve as a backbone for primer design is currently available. 2) We developed the R package PrimerMiner, which batch downloads DNA barcode gene sequences from BOLD and NCBI databases for specified target taxonomic groups and then applies sequence clustering into operational taxonomic units (OTUs) to reduce biases introduced by the different number of available sequences per species. Additionally, PrimerMiner offers functionalities to evaluate primers in silico, which are in our opinion more realistic then the strategy employed in another available software for that purpose, ecoPCR. 3) We used PrimerMiner to download cytochrome c oxidase subunit I (COI) sequences for 15 important freshwater invertebrate groups, relevant for ecosystem assessment. By processing COI markers from both databases, we were able to increase the amount of reference data 249-fold on average, compared to using complete mitochondrial genomes alone. Furthermore, we visualized the generated OTU sequence alignments and describe how to evaluate primers in silico using PrimerMiner. 4) With PrimerMiner we provide a useful tool to obtain relevant sequence data for targeted primer development and evaluation. The OTU based reference alignments generated with PrimerMiner can be used for manual primer design, or processed with bioinformatic tools for primer development.

scholarly journals Development and validation of DNA metabarcoding COI primers for aquatic invertebrates using the R package "PrimerMiner"

2016 ◽  
Author(s):  
Vasco Elbrecht ◽  
Florian Leese
Keyword(s):  
In Silico ◽  
Sequence Data ◽  
Dna Barcode ◽  
R Package ◽  
Gene Marker ◽  
Amplification Efficiency ◽  
Mock Community ◽  
Dna Metabarcoding ◽  
Primer Sets ◽  
High Base

1) DNA metabarcoding is a powerful tool to assess biodiversity by amplifying and sequencing a standardized gene marker region. However, typically used barcoding genes, such as the cytochrome c oxidase subunit I (COI) region for animals, are highly variable. Thus, different taxa in communities under study are often not amplified equally well and some might even remain undetected due to primer bias. To reduce these problems, optimized region- and/or ecosystem- specific metabarcoding primers are necessary. 2) We developed the R package PrimerMiner, which batch downloads DNA barcode gene sequences from BOLD and NCBI databases for specified target taxa and then applies sequence clustering to reduce biases introduced by differed number of available sequences per species. To design primers targeted for freshwater invertebrates, we downloaded COI data for the 15 most important invertebrate groups relevant for stream ecosystem assessment. Four primer sets with high base degeneracy were developed and their performance tested by sequencing ten mock community samples consisting each of 52 freshwater invertebrate taxa. Additionally, we evaluated the developed primers against other metabarcoding primers in silico using PrimerMiner. 3) Amplification and sequencing was successful for all ten mock community samples with the four different primer combinations. The developed primers varied in amplification efficiency and amount of taxa detected, but all primer sets detected more taxa than standard Folmer barcoding primers. Additionally, the BF / BR primers amplified taxa very consistently, the BF2+BR2 and BF2+BR1 primer combination even better than a previously tested ribosomal marker (16S). Except for the BF1+BR1 primer combination, all BF / BR primers detected all 42 insect taxa present in the mock samples. In silico evaluation of the developed primers showed that they are also likely to work very well on other non aquatic invertebrate samples. 4) With PrimerMiner, we here provide a useful tool to obtain relevant sequence data for targeted primer development and evaluation. Our sequence datasets generated with the newly developed metabarcoding primers demonstrate that the design of optimized primers with high base degeneracy is superior to classical markers and enable us to detect almost 100% of animal taxa present in a sample using the standard COI barcoding gene. Therefore, the PrimerMiner package and primers developed using this tool are useful beyond assessment of biodiversity in aquatic ecosystems.

Estimating a founder’s genomic proportion for each descendant in an outbred pedigree

Genome ◽  
2007 ◽  
Vol 50 (3) ◽  
pp. 289-296 ◽  
Author(s):  
Claire G. Williams ◽  
M. Humberto Reyes-Valdés
Keyword(s):  
Pinus Taeda ◽  
Evolutionary Biology ◽  
Sequence Data ◽  
Bootstrap Method ◽  
Mean Value ◽  
Dna Sequence Data ◽  
Marker Data ◽  
Outbred Populations ◽  
Biology Research ◽  
Shortcut Method

The question of how to estimate a founder’s proportion of a single descendant’s genome has renewed relevance for outbred pedigrees, given the abundant DNA sequence data for model and nonmodel eukaryotes alike. Here we show that a donor-recurrent shortcut method can provide a robust estimation of founder proportions. In addition, we define the theoretical variance and estimate confidence intervals using a nonparameteric bootstrap method. Using actual marker data from a highly heterozygous outbred Pinus taeda pedigree, it was found that each founder’s genomic proportion varied widely for each descendant, ranging from 8.8% to 38.7%. In 1 case, skewed transmission of a founder’s genome could be statistically detected. Its founder proportions ranged from 1.54% to 48.46%, and its mean value was 17.59%, well below the expected value of 25%. Two-thirds of its 91 descendants had 1 or the other founder haplotype, despite 2 successive meioses. The donor-recurrent method was robust; variation for estimated founder’s proportions was also wide for simulated high-density datasets whether markers were dispersed or clustered. Estimating founder contributions using this computational shortcut has broad application for highly heterozygous outbred pedigrees characterized by large sibships, low population differentiation, and shallow physical mapping resources. The relevance of this computational shortcut for outbred populations used for conservation, domestication, and evolutionary biology research is discussed.

Using DNA barcodes to detect non-indigenous species: the case of the Asian copepod Mesocyclops pehpeiensis Hu, 1943 (Cyclopidae) in two regions of the world

Crustaceana ◽  
2015 ◽  
Vol 88 (12-14) ◽  
pp. 1323-1338 ◽  
Author(s):  
Lucía Montoliu ◽  
María R. Miracle ◽  
Manuel Elías-Gutiérrez
Keyword(s):  
Exotic Species ◽  
Dna Barcoding ◽  
Dna Barcode ◽  
Rice Paddy ◽  
Coi Gene ◽  
Individual Species ◽  
Indigenous Species ◽  
Worldwide Distribution ◽  
The World ◽  
Non Indigenous Species

To date, little attention has been paid to analyses of copepods as exotic species. The genusMesocyclops, a freshwater cyclopoid, has a worldwide distribution, but individual species within the genus have a quite restricted geographical range.Mesocyclops pehpeiensisHu, 1943 is a Central-East Asian species, rarely found outside of this area, and when it appears should be considered as non-native. Based on morphology and DNA barcode analyses, using the COI gene, we confirmed records ofM. pehpeiensisin two ponds in Mexico and in a rice paddy near Valencia, Spain. The morphology of this species, based on morphometric analyses, was found to be variable, but DNA barcoding confirmed the same identity for specimens from two continents. The extremely low COI genetic divergence among these disjunct populations ofM. pehpeiensisstrongly evidences anthropogenic translocations. DNA barcoding can be a fast and useful analytical tool to accurately identify exotic species across the world.

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