Despite discovery more than 100years ago and documented global occurrence from shallow waters to the deep sea, the life cycle of the enigmatic crustacean y-larvae isincompletely understood and adult forms remain unknown. To date, only 2 of the 17 formally described species, all based on larval stages, have been investigated using an integrative taxonomic approach. This approach provided descriptions of the morphology of the naupliar and cyprid stages, and made use of exuvial voucher material and DNA barcodes.
View Article and Find Full Text PDFPCR-based high-throughput sequencing has permitted comprehensive resolution analyses of zooplankton diversity dynamics. However, significant methodological issues still surround analyses of complex bulk community samples, not least as in prevailing PCR-based approaches. Marine drifting animals-zooplankton-play essential ecological roles in the pelagic ecosystem, transferring energy and elements to higher trophic levels, such as fishes, cetaceans and others.
View Article and Find Full Text PDFMetatranscriptomics allows profiling of community mRNA and rRNA transcript abundance under certain environmental conditions. However, variations in the proportion of RNA transcripts across different community size structures remain less explained, thus limiting the possible applications of metatranscriptomics in community studies. Here, we extended the assumptions of the growth-rate hypothesis (GRH) and the metabolic theory of ecology (MTE) to validate the allometric scaling of interspecific RNA transcript (mRNA and rRNA) abundance through metatranscriptomic analysis of mock communities consisting of model organisms.
View Article and Find Full Text PDFHigh-throughput sequencing has enabled genome skimming approaches to produce complete mitochondrial genomes (mitogenomes) for species identification and phylogenomics purposes. In particular, the portable sequencing device from Oxford Nanopore Technologies (ONT) has the potential to facilitate hands-on training from sampling to sequencing and interpretation of mitogenomes. In this study, we present the results from sampling and sequencing of six gastropod mitogenomes (Aplysia argus, Cellana orientalis, Cellana toreuma, Conus ebraeus, Conus miles and Tylothais aculeata) from a graduate level biodiversity course.
View Article and Find Full Text PDFGrowth rate estimation is important to understand the flow of energy and nutrient elements in an ecosystem, but it has remained challenging, especially on microscopic organisms. In this study, we propose four growth rate indices that use mRNA abundance ratios between nuclear and mitochondrial genes: (1) total nuclear and mitochondrial mRNA ratio (Nuc:Mito-TmRNA); (2) nuclear and mitochondrial ribosomal protein mRNA ratio (Nuc:Mito-RPmRNA); (3) gene ontology (GO) terms and total mitochondrial mRNA ratios; and (4) nuclear and mitochondrial specific gene mRNA ratio. We examine these proposed ratios using RNA-Seq datasets of Daphnia magna, and Saccharomyces cerevisiae retrieved from the NCBI Short Read Archive.
View Article and Find Full Text PDFDNA metabarcoding is a rapid, high-resolution tool used for biomonitoring complex zooplankton communities. However, diversity estimates derived with this approach can be biased by the co-detection of sequences from environmental DNA (eDNA), nuclear-encoded mitochondrial (NUMT) pseudogene contamination, and taxon-specific PCR primer affinity differences. To avoid these methodological uncertainties, we tested the use of metatranscriptomics as an alternative approach for characterizing zooplankton communities.
View Article and Find Full Text PDFThe deep seafloor is teeming with life, most of which remains poorly known to science. It also constitutes an important reserve of natural resources, particularly minerals, that mining companies will start harvesting in the next few years (Nat Rev Earth Environ, 1, 2020, 158). In this context, broad biodiversity assessments of deep-sea ecosystems are urgently needed to establish a baseline prior to mining.
View Article and Find Full Text PDFProc Natl Acad Sci U S A
November 2019
Traditional methods of characterizing biodiversity are increasingly being supplemented and replaced by approaches based on DNA sequencing alone. These approaches commonly involve extraction and high-throughput sequencing of bulk samples from biologically complex communities or samples of environmental DNA (eDNA). In such cases, vouchers for individual organisms are rarely obtained, often unidentifiable, or unavailable.
View Article and Find Full Text PDFExamination of leucothoid amphipods from Penghu, Green Island, and Dongsha Atoll revealed 16 species not previously reported from Taiwan. sp. nov.
View Article and Find Full Text PDFSummary: We present MIDORI server, a user-friendly web platform that uses a curated reference dataset, MIDORI, for high throughput taxonomic classification of unknown metazoan mitochondrial-encoded gene sequences. Currently three methods of taxonomic assignments: RDP Classifier, SPINGO and SINTAX, are implemented.
Availability And Implementation: The web server is freely available at {http://reference-midori.
Mitochondrial-encoded genes are increasingly targeted in studies using high-throughput sequencing approaches for characterizing metazoan communities from environmental samples (e.g., plankton, meiofauna, filtered water).
View Article and Find Full Text PDFA portion of the mitochondrial cytochrome c oxidase I gene was sequenced using both genomic DNA and complement DNA from three planktonic copepod Neocalanus species (N. cristatus, N. plumchrus, and N.
View Article and Find Full Text PDFBackground: The 5' untranslated regions of mRNA play an important role in their translation.
Results: Here, we describe the development of four methods of profiling mRNA 5' ends using the Illumina sequencing platform; the first method utilizes SMART (Switching Mechanism At 5' end of RNA Transcript) technology, while the second involves replacing the 5' cap structure with RNA oligomers via ligation. The third and fourth methods are modifications of SMART, and involve enriching mRNA molecules with (nuclear transcripts) and without (mitochondrial transcripts) 5' end cap structures, respectively.
Introduction: The PCR-based analysis of homologous genes has become one of the most powerful approaches for species detection and identification, particularly with the recent availability of Next Generation Sequencing platforms (NGS) making it possible to identify species composition from a broad range of environmental samples. Identifying species from these samples relies on the ability to match sequences with reference barcodes for taxonomic identification. Unfortunately, most studies of environmental samples have targeted ribosomal markers, despite the fact that the mitochondrial Cytochrome c Oxidase subunit I gene (COI) is by far the most widely available sequence region in public reference libraries.
View Article and Find Full Text PDFBackground: Metagenetic analyses, which amplify and sequence target marker DNA regions from environmental samples, are increasingly employed to assess the biodiversity of communities of small organisms. Using this approach, our understanding of microbial diversity has expanded greatly. In contrast, only a few studies using this approach to characterize metazoan diversity have been reported, despite the fact that many metazoan species are small and difficult to identify or are undescribed.
View Article and Find Full Text PDFMethods Mol Biol
December 2012
Metagenetic analysis using second-generation sequencing offers a novel methodology for measuring the diversity of metazoan communities. Among commercially available second-generation sequencers, the 454 GS FLX Titanium (Roche Diagnostics) offers by far the longest read length and can produce one million sequences from a single run. Compared to the large number of sequences produced from single run, however, number of samples these machines can process is rather low.
View Article and Find Full Text PDFBackground: Assessment of the biodiversity of communities of small organisms is most readily done using PCR-based analysis of environmental samples consisting of mixtures of individuals. Known as metagenetics, this approach has transformed understanding of microbial communities and is beginning to be applied to metazoans as well. Unlike microbial studies, where analysis of the 16S ribosomal DNA sequence is standard, the best gene for metazoan metagenetics is less clear.
View Article and Find Full Text PDFBackground: A total of six Neocalanus species inhabit the oceans of the world. Of these, three species plus form variants (N. cristatus, N.
View Article and Find Full Text PDFComp Biochem Physiol Part D Genomics Proteomics
March 2010
The complete nucleotide sequences of the mitochondrial genomes were determined for the three pelagic chaetognaths, Sagitta nagae, Sagitta decipiens, and Sagitta enflata. The mitochondrial genomes of these species which were 11,459, 11,121, and 12,631bp in length, respectively, contained 14 genes (11 protein-coding genes, one transfer RNA gene, and two ribosomal RNA genes), and were found to have lost 23 genes that are present in the typical metazoan mitochondrial genome. The same mitochondrial genome contents have been reported from the benthic chaetognaths belonging to the family Spadellidae, Paraspadella gotoi and Spadella cephaloptera.
View Article and Find Full Text PDFBackground: Oceans cover more than 70% of the earth's surface and are critical for the homeostasis of the environment. Among the components of the ocean ecosystem, zooplankton play vital roles in energy and matter transfer through the system. Despite their importance, understanding of zooplankton biodiversity is limited because of their fragile nature, small body size, and the large number of species from various taxonomic phyla.
View Article and Find Full Text PDFAn approach for sequencing the entire mitochondrial genomes (mitogenomes) of decapod crustaceans using 79 newly designed and 7 published polymerase chain reaction (PCR) primers is described. The approach comprises the following steps: (1) the entire mitogenome is amplified in 2 or 3 long PCRs; (2) the 86 primers are used in different combinations to amplify contiguous, overlapping short segments of the entire mitogenome with the diluted long PCR products as templates; (3) direct cycle sequencing is conducted using the short PCR products. This strategy allows a more rapid determination of decapod mitogenomic sequences than a traditional method using cloned mitochondrial DNA and primer walking strategy.
View Article and Find Full Text PDFPartial sequences of the mitochondrial genomes were determined for two calanoid copepods, Eucalanus bungii [9530 bp (base pairs)] and Neocalanus cristatus (7965 bp), using an approach that employs a long polymerase chain reaction (PCR) technique and primer walking. In contrast to Tigriopus japonicus (Harpacticoida), in which the complete mitochondrial genome has been determined, genes are encoded on both strands of the genome. In spite of the close relationship between E.
View Article and Find Full Text PDFWe determined the nearly complete DNA sequence of the mitochondrial genome of Antarctic krill Euphausia superba (Crustacea: Malacostraca), one of the most ecologically and commercially important zooplankters in Antarctic waters. All of the genome sequences were purified by gene amplification using long polymerase chain reaction (PCR), and the products were subsequently used as templates for either direct sequencing using a primer-walking strategy or nested PCR with crustacea-versatile primers. Although we were unable to determine a portion of the genome owing to technical difficulties, the sequenced position, 14,606 bp long, contained all of the 13 protein-coding genes, 19 of the 22 transfer RNA genes, and the large subunit as well as a portion of the small subunit ribosomal RNA genes.
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