scholarly journals Identifying seaweeds species of Chlorophyta, Phaeophyta and Rhodophyta using DNA barcodes

2020 ◽  
Author(s):  
Narra Prasanthi ◽  
Chinnamani Prasannakumar ◽  
D. Annadurai ◽  
S. Mahendran
Keyword(s):  
High Throughput Sequencing ◽  
Dna Barcode ◽  
Health Assessment ◽  
Environmental Dna ◽  
Rbcl Gene ◽  
Sequencing Technologies ◽  
Assessment And Monitoring ◽  
Bio Monitoring ◽  
Resource Exploration ◽  
First Time

AbstractStrengthening the DNA barcode database is important for a species level identification, which was lacking for seaweeds. We made an effort to collect and barcode seaweeds occurring along Southeast coast of India. We barcoded 31 seaweeds species belonging to 21 genera, 14 family, 12 order of 3 phyla (viz., Chlorophyta, Phaeophyta and Rhodophyta). We found 10 species in 3 phyla and 2 genera (Anthophycus and Chnoospora) of Phaeophyta were barcoded for the first time. Uncorrected p-distance calculated using K2P, nucleotide diversity and Tajima’s test statistics reveals highest values among the species of Chlorophyta. Over all K2P distance was 0.36. The present study revealed the potentiality of rbcL gene sequences in identification of all 3 phyla of seaweeds. We also found that the present barcode reference libraries (GenBank and BOLD) were insufficient in seaweeds identification and more efforts were needed for strengthening local seaweed barcode library to benefit rapids developing field such as environmental DNA barcoding. We also show that the constructed barcode library could aid various industrial experts involved in seaweed bio-resource exploration and taxonomy/non-taxonomic researches involved in climate, agriculture and epigenetics research. Since the rise of modern high-throughput sequencing technologies is significantly altering aquatic bio-monitoring applications and surveys, reference datasets such as ours will become essential in ecosystem’s health assessment and monitoring. The DNA barcode datasets produced in his study could be exclusively accessed at http://dx.doi.org/10.5883/DS-DBISW.

Exploring the plant environmental DNA diversity in soil from two sites on Deception Island (Antarctica, South Shetland Islands) using metabarcoding

2021 ◽  
pp. 1-10
Author(s):  
Micheline Carvalho-Silva ◽  
Luiz Henrique Rosa ◽  
Otávio H.B. Pinto ◽  
Thamar Holanda Da Silva ◽  
Diego Knop Henriques ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Crater Lake ◽  
Environmental Dna ◽  
Food Sources ◽  
South Shetland Islands ◽  
Deception Island ◽  
Shetland Islands ◽  
Operational Taxonomic Units ◽  
First Time ◽  
Impacted Site

Abstract The few Antarctic studies to date to have applied metabarcoding in Antarctica have primarily focused on microorganisms. In this study, for the first time, we apply high-throughput sequencing of environmental DNA to investigate the diversity of Embryophyta (Viridiplantae) DNA present in soil samples from two contrasting locations on Deception Island. The first was a relatively undisturbed site within an Antarctic Specially Protected Area at Crater Lake, and the second was a heavily human-impacted site in Whalers Bay. In samples obtained at Crater Lake, 84% of DNA reads represented fungi, 14% represented Chlorophyta and 2% represented Streptophyta, while at Whalers Bay, 79% of reads represented fungi, 20% represented Chlorophyta and < 1% represented Streptophyta, with ~1% of reads being unassigned. Among the Embryophyta we found 16 plant operational taxonomic units from three Divisions, including one Marchantiophyta, eight Bryophyta and seven Magnoliophyta. Sequences of six taxa were detected at both sampling sites, eight only at Whalers Bay and two only at Crater Lake. All of the Magnoliophyta sequences (flowering plants) represent species that are exotic to Antarctica, with most being plausibly linked to human food sources originating from local national research operator and tourism facilities.

scholarly journals Transcriptomic Analysis of Marine Gastropod Hemifusus tuba Provides Novel Insights into Conotoxin Genes

Marine Drugs ◽  
2019 ◽  
Vol 17 (8) ◽  
pp. 466 ◽  
Author(s):  
Ronghua Li ◽  
Michaël Bekaert ◽  
Luning Wu ◽  
Changkao Mu ◽  
Weiwei Song ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
De Novo ◽  
Average Length ◽  
Bioactive Molecules ◽  
Asian Countries ◽  
Marine Gastropod ◽  
Sequencing Technologies ◽  
First Time ◽  
Aquaculture Development ◽  
Simple Sequence

The marine gastropod Hemifusus tuba is served as a luxury food in Asian countries and used in traditional Chinese medicine to treat lumbago and deafness. The lack of genomic data on H. tuba is a barrier to aquaculture development and functional characteristics of potential bioactive molecules are poorly understood. In the present study, we used high-throughput sequencing technologies to generate the first transcriptomic database of H. tuba. A total of 41 unique conopeptides were retrieved from 44 unigenes, containing 6-cysteine frameworks belonging to four superfamilies. Duplication of mature regions and alternative splicing were also found in some of the conopeptides, and the de novo assembly identified a total of 76,306 transcripts with an average length of 824.6 nt, of which including 75,620 (99.1%) were annotated. In addition, simple sequence repeats (SSRs) detection identified 14,000 unigenes containing 20,735 SSRs, among which, 23 polymorphic SSRs were screened. Thirteen of these markers could be amplified in Hemifusus ternatanus and seven in Rapana venosa. This study provides reports of conopeptide genes in Buccinidae for the first time as well as genomic resources for further drug development, gene discovery and population resource studies of this species.

scholarly journals Chondrophycus anabeliae and Laurencia digitata (Ceramiales, Rhodophyta) are recorded for the first time for Venezuela expanding their geographic distributions beyond the type localities

2020 ◽  
Vol 98 (4) ◽  
pp. 624-643
Author(s):  
Valéria Cassano ◽  
Luanda P. Soares ◽  
Beatriz Esther Vera-Vegas ◽  
Sonia Ardito ◽  
Santiago Gómez ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Species Diversity ◽  
Atlantic Ocean ◽  
Geographic Distribution ◽  
Dna Barcode ◽  
Rbcl Gene ◽  
Molecular Studies ◽  
Anatomical Characters ◽  
First Time ◽  
High Diversity

Background: Over the course of approximately 12 years, the species of the Laurencia complex have been systematically studied in the tropical and subtropical Atlantic Ocean, showing high diversity (48 species), which has been underestimated for the coast of Venezuela. Questions: What is the species diversity of the Laurencia complex in Venezuela? Studied species: Chondrophycus anabeliae, Laurencia digitata. Study site and dates: Cayo Muerto, Parque Nacional Morrocoy, Estado Falcón, Venezuela, 2015. Methods: For molecular studies, the plastid rbcL gene and the mitochondrial DNA barcode marker COI-5P were used, combined with the study of current morpho-anatomical characters used for the identification of the species of the complex. Results: The occurrence of Chondrophycus, as currently circumscribed, was confirmed for the first time for Venezuela. Chondrophycus anabeliae and Laurencia digitata are reported for the first time beyond the type localities. Tetrasporophytes are described for the first time for L. digitata. Conclusions: Our findings expand the geographic distribution of Ch. anabeliae and L. digitata for the Venezuelan Caribbean and the Atlantic Ocean, respectively.

scholarly journals Perspectives and benefits of high-throughput long-read sequencing in microbial ecology

2021 ◽  
Author(s):  
Leho Tedersoo ◽  
Mads Albertsen ◽  
Sten Anslan ◽  
Benjamin Callahan
Keyword(s):  
Microbial Ecology ◽  
High Throughput ◽  
Single Molecule ◽  
High Throughput Sequencing ◽  
Environmental Dna ◽  
Nanopore Sequencing ◽  
High Quality ◽  
Short Read ◽  
Sequencing Technologies ◽  
Long Read

Short-read, high-throughput sequencing (HTS) methods have yielded numerous important insights into microbial ecology and function. Yet, in many instances short-read HTS techniques are suboptimal, for example by providing insufficient phylogenetic resolution or low integrity of assembled genomes. Single-molecule and synthetic long-read (SLR) HTS methods have successfully ameliorated these limitations. In addition, nanopore sequencing has generated a number of unique analysis opportunities such as rapid molecular diagnostics and direct RNA sequencing, and both PacBio and nanopore sequencing support detection of epigenetic modifications. Although initially suffering from relatively low sequence quality, recent advances have greatly improved the accuracy of long read sequencing technologies. In spite of great technological progress in recent years, the long-read HTS methods (PacBio and nanopore sequencing) are still relatively costly, require large amounts of high-quality starting material, and commonly need specific solutions in various analysis steps. Despite these challenges, long-read sequencing technologies offer high-quality, cutting-edge alternatives for testing hypotheses about microbiome structure and functioning as well as assembly of eukaryote genomes from complex environmental DNA samples.

scholarly journals Environmental DNA Barcode Sequence Capture: Targeted, PCR-free Sequence Capture for Biodiversity Analysis from Bulk Environmental Samples

2016 ◽  
Author(s):  
Shadi Shokralla ◽  
Joel F. Gibson ◽  
Ian King ◽  
Donald J. Baird ◽  
Daniel H. Janzen ◽  
...  
Keyword(s):  
Environmental Samples ◽  
High Throughput Sequencing ◽  
Dna Analysis ◽  
Dna Barcode ◽  
Environmental Dna ◽  
Amplicon Sequencing ◽  
Marker Genes ◽  
Hybridization Capture ◽  
Sequence Capture ◽  
Wide Range

ABSTRACTEnvironmental DNA analysis using PCR amplified marker genes has been a key application of high-throughput sequencing (HTS). However, PCR bias is a major drawback to gain accurate qualitative and quantitative biodiversity data. We developed a PCR-free approach using enrichment baits for species-specific mitochondrial cytochrome c oxidase 1(COI) DNA barcodes. The sequence capture was tested on species-rich bulk terrestrial and aquatic benthic samples. Hybridization capture recovered an average of 6 and 4.7 more arthropod orders than amplicon sequencing for terrestrial and benthic samples, respectively. For the terrestrial sample, the four most abundant arthropod orders comprised 94.0% of the sample biomass. These same four orders comprised 95.5% and 97.5% of the COI sequences recovered by amplification and capture, respectively. Hybridization capture recovered three arthropod orders that were detected by biomass analysis, but not by amplicon sequencing and two other insect orders that were not detected by either biomass or amplicon methods. These results indicate the advantage of using sequence capture for a more accurate analysis of biodiversity in bulk environmental samples. The protocol can be easily customized to other DNA barcode markers or gene regions of interest for a wide range of taxa or for a specific target group.

scholarly journals A new classification of Carex (Cyperaceae) subgenera supported by a HybSeq backbone phylogenetic tree

2020 ◽  
Vol 194 (2) ◽  
pp. 141-163
Author(s):  
Tamara Villaverde ◽  
Pedro Jiménez-Mejías ◽  
Modesto Luceño ◽  
Marcia J Waterway ◽  
Sangtae Kim ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
High Throughput Sequencing ◽  
Molecular Dating ◽  
Cyperus Papyrus ◽  
Sequencing Technologies ◽  
Anchored Hybrid Enrichment ◽  
Orthologous Loci ◽  
First Time ◽  
Different Sources

Abstract The field of systematics is experiencing a new molecular revolution driven by the increased availability of high-throughput sequencing technologies. As these techniques become more affordable, the increased genomic resources have increasingly far-reaching implications for our understanding of the Tree of Life. With c. 2000 species, Carex (Cyperaceae) is one of the five largest genera of angiosperms and one of the two largest among monocots, but the phylogenetic relationships between the main lineages are still poorly understood. We designed a Cyperaceae-specific HybSeq bait kit using transcriptomic data of Carex siderosticta and Cyperus papyrus. We identified 554 low-copy nuclear orthologous loci, targeting a total length of c. 1 Mbp. Our Cyperaceae-specific kit shared loci with a recently published angiosperm-specific Anchored Hybrid Enrichment kit, which enabled us to include and compile data from different sources. We used our Cyperaceae kit to sequence 88 Carex spp., including samples of all the five major clades in the genus. For the first time, we present a phylogenetic tree of Carex based on hundreds of loci (308 nuclear exon matrices, 543 nuclear intron matrices and 66 plastid exon matrices), demonstrating that there are six strongly supported main lineages in Carex: the Siderostictae, Schoenoxiphium, Unispicate, Uncinia, Vignea and Core Carex clades. Based on our results, we suggest a revised subgeneric treatment and provide lists of the species belonging to each of the subgenera. Our results will inform future biogeographic, taxonomic, molecular dating and evolutionary studies in Carex and provide the step towards a revised classification that seems likely to stand the test of time.

scholarly journals Strengthening marine amphipod DNA barcode libraries for environmental monitoring

2020 ◽  
Author(s):  
Chinnamani Prasannakumar ◽  
Ganesh Manikantan ◽  
J. Vijaylaxmi ◽  
Balakrishnan Gunalan ◽  
Seerangan Manokaran ◽  
...  
Keyword(s):  
Environmental Monitoring ◽  
Nucleotide Diversity ◽  
Dna Barcode ◽  
Environmental Dna ◽  
Reference Database ◽  
Amphipod Species ◽  
Marine Amphipod ◽  
Specific Pair ◽  
Specific Species ◽  
First Time

AbstractEnvironmental DNA barcoding technology is gaining innovative applications. The effectiveness of current DNA barcode reference libraries in identifying amphipod barcodes and/or strengthening the existing library was tested. From 2500 amphipod individuals we barcoded 22 amphipod species belonging to 17 genera, 13 families among which 13 species were first time barcoded. More than 80 percent of the species were new distributional records. The minimum and maximum inter-specific pair-wise distance values was respectively 0.16 and 5.51 percent. Defining family specific species threshold values would be imperative, rather than expecting a universal barcode gap for amphipod species. The overall mean pair-wise distance, nucleotide diversity and Tajima’s statistics were 3.59 percent, 0.27 and 2.62, respectively. There is a strong need to increase the number of amphipod species barcodes in the reference database. For better facilitation of environmental monitoring, the datasets could be exclusively accessed at BOLD through http://dx.doi.org/10.5883/DS-MAOI.

scholarly journals Ecosystems Monitoring Powered by Environmental Genomics: A Review of Current Strategies with An Implementation Roadmap

2020 ◽  
Author(s):  
Tristan Cordier ◽  
Laura Alonso Sáez ◽  
Laure Apotheloz-Perret-Gentil ◽  
Eva Aylagas ◽  
David A. Bohan ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
De Novo ◽  
Anthropogenic Impacts ◽  
Implementation Strategies ◽  
Environmental Dna ◽  
Environmental Genomics ◽  
Sequencing Technologies ◽  
Dna And Rna ◽  
Regulatory Frameworks ◽  
Legal Frameworks

A decade after environmental scientists integrated high-throughput sequencing technologies in their toolbox, the genomics-based monitoring of anthropogenic impacts on biodiversity and ecosystems is yet to be implemented by regulatory frameworks. Despite the broadly acknowledged potential of environmental DNA and RNA to cost-efficiently and accurately monitor biodiversity, technical limitations and conceptual issues still stand in the way of its routine application by end-users. In addition, the multiplicity of potential implementation strategies may contribute to a perception of the methodology as being premature or &ldquo;in development&rdquo;, hence restraining regulators from binding these tools into legal frameworks. This review focuses on the strengths and limitations of genomics-based strategies that have emerged over the past ten years and have been classified for this purpose into three broad strategies: (A) Taxonomy-based approaches that focus on known bio-indicators or the diversity of taxonomically described taxa, (B) De novo approaches that do not require well-established taxonomy, and (C) Function-based approaches that rely on community-wide metrics, where taxa are interchangeable, or on functional profiles instead of compositional turnovers. We finally propose a roadmap for the implementation of environmental genomics into routine monitoring programs that leverage recent analytical advancements, upon which some critical limitations are alleviated.

scholarly journals NGSpeciesID: DNA barcode and amplicon consensus generation from long-read sequencing data

2020 ◽  
Author(s):  
Kristoffer Sahlin ◽  
Marisa Lim ◽  
Stefan Prost
Keyword(s):  
High Throughput Sequencing ◽  
Dna Barcode ◽  
Amplicon Sequencing ◽  
Error Rates ◽  
Sequencing Data ◽  
Sequencing Platform ◽  
Consensus Sequences ◽  
Sequencing Technologies ◽  
Oxford Nanopore ◽  
Long Read

Third generation sequencing technologies, such as Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio), have gained popularity over the last years. These platforms can generate millions of long read sequences. This is not only advantageous for genome sequencing projects, but also for amplicon-based high-throughput sequencing experiments, such as DNA barcoding. However, the relatively high error rates associated with these technologies still pose challenges for generating high quality consensus sequences. Here we present NGSpeciesID, a program which can generate highly accurate consensus sequences from long-read amplicon sequencing technologies, including ONT and PacBio. The tool includes clustering of the reads to help filter out contaminants or reads with high error rates and employs polishing strategies specific to the appropriate sequencing platform. We show that NGSpeciesID produces consensus sequences with improved usability by minimizing preprocessing and software installation and scalability by enabling rapid processing of hundreds to thousands of samples, while maintaining similar consensus accuracy as current pipelines

scholarly journals Reassortment of Genome Segments Creates Stable Lineages Among Strains of Orchid Fleck Virus Infecting Citrus in Mexico

2020 ◽  
Vol 110 (1) ◽  
pp. 106-120 ◽  
Author(s):  
Avijit Roy ◽  
Andrew L. Stone ◽  
Gabriel Otero-Colina ◽  
Gang Wei ◽  
Ronald H. Brlansky ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Sensu Stricto ◽  
Genome Segment ◽  
Rt Pcr ◽  
Sequence Comparisons ◽  
Orchid Fleck Virus ◽  
Reverse Transcription Pcr ◽  
Sequencing Technologies ◽  
Negative Sense

The genus Dichorhavirus contains viruses with bipartite, negative-sense, single-stranded RNA genomes that are transmitted by flat mites to hosts that include orchids, coffee, the genus Clerodendrum, and citrus. A dichorhavirus infecting citrus in Mexico is classified as a citrus strain of orchid fleck virus (OFV-Cit). We previously used RNA sequencing technologies on OFV-Cit samples from Mexico to develop an OFV-Cit–specific reverse transcription PCR (RT-PCR) assay. During assay validation, OFV-Cit–specific RT-PCR failed to produce an amplicon from some samples with clear symptoms of OFV-Cit. Characterization of this virus revealed that dichorhavirus-like particles were found in the nucleus. High-throughput sequencing of small RNAs from these citrus plants revealed a novel citrus strain of OFV, OFV-Cit2. Sequence comparisons with known orchid and citrus strains of OFV showed variation in the protein products encoded by genome segment 1 (RNA1). Strains of OFV clustered together based on host of origin, whether orchid or citrus, and were clearly separated from other dichorhaviruses described from infected citrus in Brazil. The variation in RNA1 between the original (now OFV-Cit1) and the new (OFV-Cit2) strain was not observed with genome segment 2 (RNA2), but instead, a common RNA2 molecule was shared among strains of OFV-Cit1 and -Cit2, a situation strikingly similar to OFV infecting orchids. We also collected mites at the affected groves, identified them as Brevipalpus californicus sensu stricto, and confirmed that they were infected by OFV-Cit1 or with both OFV-Cit1 and -Cit2. OFV-Cit1 and -Cit2 have coexisted at the same site in Toliman, Queretaro, Mexico since 2012. OFV strain-specific diagnostic tests were developed.

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