Intragenomic variations of the harmful algal bloom species Phaeocystis globosa through single-strain metabarcoding analysis.

Recent studies demonstrated that the existence of high-levels intragenomic variations (IGVs) may lead to overinterpretation of species diversity and genetic diversity in metabarcoding analysis. In this study, IGVs of the V4 region of 18S rRNA gene (18S rDNA V4) in Phaeocystis globosa were ascertained through metabarcoding analysis results of 54 P. globosa strains.

Acquisition and evolution of the neurotoxin domoic acid biosynthesis gene cluster in Pseudo-nitzschia species.

Of the hitherto over 60 taxonomically identified species in the genus of Pseudo-nitzschia, 26 have been confirmed to be toxigenic. Nevertheless, the acquisition and evolution of the toxin biosynthesis (dab) genes by this extensive group of Pseudo-nitzschia species remains unclear. Through constructing chromosome-level genomes of three Pseudo-nitzschia species and draft genomes of ten additional Pseudo-nitzschia species, putative genomic integration sites for the dab genes in Pseudo-nitzschia species were explored.

Chromosome-scale genome assembly reveals insights into the evolution and ecology of the harmful algal bloom species Scherffel.

The phytoplankton plays an important role in sulfur cycling and climate control, and can develop harmful algal blooms (HABs). Here we report a chromosome-scale reference genome assembly of , which enable in-depth analysis of molecular underpinnings of important ecological characteristics. Comparative genomic analyses detected two-rounds of genome duplications that may have fueled evolutionary innovations.

Harmonized coexistence of intragenomic variations in diatom Skeletonema strains.

Metabarcoding analysis has been demonstrated to be an effective technology for monitoring diversity and dynamics of phytoplankton including Skeletonema species. Although molecular diversity uncovered in metabarcoding projects has generally been interpreted as sum of interspecies diversity and intraspecies diversity, accumulating evidence suggests that it also harbors unprecedentedly high levels of intra-genomic variations (IGVs). As up to thousands of amplicon sequence variants (ASVs) identified in a typical metabarcoding project can be annotated to be Skeletonema species, we hypothesize that substantial portions of these ASVs are contributed by IGVs.

Positive selection in cilia-related genes may facilitate deep-sea adaptation of Thermocollonia jamsteci.

Deep-sea hydrothermal vents are characterized by high hydrostatic pressure, hypoxia, darkness and toxic substances. However, how organisms adapt to such extreme marine ecosystems remain poorly understood. We hypothesize that adaptive evolution plays an essential role in generating novelty for evolutionary adaptation to the deep-sea environment because adaptive evolution has been found to be critical for species origin and evolution.

Comparative assessment of the intragenomic variations of dinoflagellate Tripos species through single-cell sequencing.

Tripos is a large dinoflagellate genus widely distributed in the world's oceans. Morphology-based species identification is inconclusive due to high morphological intraspecific variability. Metabarcoding analysis has been demonstrated to be effective for species identification and tracking their spatiotemporal dynamics.

Chromosome-level genome assembly of marine diatom Skeletonema tropicum.

Skeletonema tropicum is a marine diatom of the genus Skeletonema that also includes many well-known species including S. marinoi. S.

Extensive intragenomic variations of the 18S rDNA V4 region in the toxigenic diatom species Pseudo-nitzschia multistriata revealed through high-throughput sequencing.

Metabarcoding analysis is an effective technique for monitoring the domoic acid-producing Pseudo-nitzschia species in marine environments, uncovering high-levels of molecular diversity. However, such efforts may result in the overinterpretation of Pseudo-nitzschia species diversity, as molecular diversity not only encompasses interspecies and intraspecies diversities but also exhibits extensive intragenomic variations (IGVs). In this study, we analyzed the V4 region of the 18S rDNA of 30 strains of Pseudo-nitzschia multistriata collected from the coasts of China.

Chromosome-level genome assembly of Oncomelania hupensis: the intermediate snail host of Schistosoma japonicum.

Background: Schistosoma japonicum is a parasitic flatworm that causes human schistosomiasis, which is a significant cause of morbidity in China, the Philippines and Indonesia. Oncomelania hupensis (Gastropoda: Pomatiopsidae) is the unique intermediate host of S. japonicum.

The high molecular diversity in Noctiluca scintillans is dominated by intra-genomic variations revealed by single cell high-throughput sequencing of 18S rDNA V4.

The application of high-throughput sequencing (HTS) technologies has revolutionized research on phytoplankton biodiversity by generating an unprecedented amount of molecular data in marine ecosystem surveys. However, high-level of molecular diversity uncovered in HTS-based metabarcoding analyses may lead to overinterpretation of phytoplankton diversity due to excessive intra-genomic variations (IGVs). The aims in this study are to explore the nature of phytoplankton molecular diversity and to test the hypothesis.

Rich diversity and active spatial-temporal dynamics of species revealed by time-series metabarcoding analysis.

is a species-rich genus in that not only contributes positively as primary producer, but also poses negative impacts on ecosystems by causing harmful algal blooms. Although taxonomical studies have identified a large number of species, however, the composition of species and their geographical distribution in marine ecosystems were not well understood due primarily to the lack of resolution of morphology-based approaches used previously in ecological expeditions. In this study, we systematically analyzed the composition and spatial-temporal dynamic distributions of in the model marine ecosystem Jiaozhou Bay by applying metabarcoding analysis.

Chromosome-level genome assembly of the Pacific geoduck Panopea generosa reveals major inter- and intrachromosomal rearrangements and substantial expansion of the copine gene family.

The Pacific geoduck Panopea generosa (class Bivalvia, order Adapedonta, family Hiatellidae, genus Panopea) is the largest known burrowing bivalve with considerable commercial value. Pacific geoduck and other geoduck clams play important roles in maintaining ecosystem health for their filter feeding habit and coupling pelagic and benthic processes. Here, we report a high-quality chromosome-level genome assembly of P.

Expansion of photoreception-related gene families may drive ecological adaptation of the dominant diatom species Skeletonema marinoi.

Diatom species of the genus Skeletonema are dominant in global coastal waters with important roles in marine primary production and global biogeochemical cycling. Many Skeletonema species have been extensively studied also because they can cause harmful algae blooms (HABs) with negative impacts on marine ecosystems and aquaculture. In this study, the first chromosome-level assembly of the genome of Skeletonema marinoi was constructed.

Evolutionary dynamics of plastomes in coscinodiscophycean diatoms revealed by comparative genomics.

To understand the evolution of coscinodiscophycean diatoms, plastome sequences of six coscinodiscophycean diatom species were constructed and analyzed in this study, doubling the number of constructed plastome sequences in Coscinodiscophyceae (radial centrics). The platome sizes varied substantially in Coscinodiscophyceae, ranging from 119.1 kb of to 135.

Mechanisms of Phaeocystis globosa blooms in the Beibu Gulf revealed by metatranscriptome analysis.

The haptophyceae Phaeocystis globosa is a species responsible for harmful algal blooms in the global ocean, forming blooms in the Beibu Gulf annually since 2011. This species can alternate between solitary free-living cells and colonies. Colonies are the dominant morphotype during blooms.

Novel insights into chloroplast genome evolution in the green macroalgal genus (Ulvophyceae, Chlorophyta).

To understand the evolutionary driving forces of chloroplast (or plastid) genomes (plastomes) in the green macroalgal genus (Ulvophyceae, Chlorophyta), in this study, we sequenced and constructed seven complete chloroplast genomes from five species, and conducted comparative genomic analysis of plastomes in Ulvophyceae. plastome evolution reflects the strong selection pressure driving the compactness of genome organization and the decrease of overall GC composition. The overall plastome sequences including canonical genes, introns, derived foreign sequences and non-coding regions show a synergetic decrease in GC content at varying degrees.

Genetic Diversity and Geographical Distribution of the Red Tide Species Revealed Using a High-Resolution Molecular Marker.

Diatoms are responsible for approximately 40% of the global primary photosynthetic production and account for up to 20% of global carbon fixation. is a red tide forming species of the phylum Bacillariophyta that has been detected in a wide range of coastal regions, suggesting the possibility of the existence of high genetic diversity with differential adaptation. Common molecular markers including 18S rDNA, 16S rDNA, ITS, , and do not provide sufficient resolution for distinguishing intra-species genetic diversity, hindering in-depth research on intra-species genetic diversity and their spatial and temporal dynamics.

Genetic Analysis of a Large-Scale Bloom Offshore Qingdao, China.

A sudden large-scale bloom event of the haptophyte that lasted over one month in the winter of 2021 was observed offshore Qingdao, China. This bloom event was unusual as it was the first bloom recorded in Qingdao offshore. Furthermore, the temperature at which this event occurred was much lower than that of previous blooms in China.

Comparative Analysis of Bacillariophyceae Chloroplast Genomes Uncovers Extensive Genome Rearrangements Associated with Speciation.

The Bacillariophyceae is a species-rich, ecologically significant class of Bacillariophyta. Despite their critical importance in marine ecosystems as primary producers and in the development of harmful algal blooms (HABs), taxonomic research on Bacillariophyceae species has been hindered because of their limited morphological features, plasticity of morphologies, and the low resolution of common molecular markers. Hence molecular markers with improved resolution are urgently needed.

Metabarcoding analysis of microbiome dynamics during a Phaeocystis globosa bloom in the Beibu Gulf, China.

Phaeocystis globosa is an ecologically important haptophyte that can form harmful algal blooms (HABs). In this study, we used 16S rDNA V3-V4 amplicon sequencing data to explore the ecological mechanisms underlying a P. globosa bloom in the Beibu Gulf, China.

Composition and spatial-temporal dynamics of phytoplankton community shaped by environmental selection and interactions in the Jiaozhou Bay.

The Jiaozhou Bay as a model marine ecosystem in China has been intensively investigated over the last 90 years. However, detailed phytoplankton community composition, spatial-temporal dynamics, and its assembly mechanism were still unclear. To address these, we systematically examined the composition and spatial-temporal dynamics of phytoplankton in the Jiaozhou Bay through high-throughput sequencing of 18S rDNA V4.

Comparative analysis of Thalassionema chloroplast genomes revealed hidden biodiversity.

The cosmopolitan Thalassionema species are often dominant components of the plankton diatom flora and sediment diatom assemblages in all but the Polar regions, making important ecological contribution to primary productivity. Historical studies concentrated on their indicative function for the marine environment based primarily on morphological features and essentially ignored their genomic information, hindering in-depth investigation on Thalassionema biodiversity. In this project, we constructed the complete chloroplast genomes (cpDNAs) of seven Thalassionema strains representing three different species, which were also the first cpDNAs constructed for any species in the order Thalassionematales that includes 35 reported species and varieties.

Diatom Biodiversity and Speciation Revealed by Comparative Analysis of Mitochondrial Genomes.

Diatoms (Bacillariophyta) constitute one of the most diverse and ecologically significant groups of phytoplankton, comprising 100,000-200,000 species in three classes Bacillariophyceae, Mediophyceae, and Coscinodiscophyceae. However, due to the limited resolution of common molecular markers including 18S rDNA, 28S rDNA, ITS, , and , diatom biodiversity has not been adequately ascertained. Organelle genomes including mitochondrial genomes (mtDNAs) have been proposed to be "super barcodes" for distinguishing diatom species because of their rich genomic content, and the rapid progress of DNA sequencing technologies that has made it possible to construct mtDNAs with increasing throughout and decreasing cost.

Genome assembly of the JD17 soybean provides a new reference genome for comparative genomics.

Cultivated soybean (Glycine max) is an important source for protein and oil. Many elite cultivars with different traits have been developed for different conditions. Each soybean strain has its own genetic diversity, and the availability of more high-quality soybean genomes can enhance comparative genomic analysis for identifying genetic underpinnings for its unique traits.

Complete mitochondrial genome of the harmful algal bloom species (Mediophyceae, Bacillariophyta) from the east China sea.

is a common harmful algal bloom (HAB) species with worldwide distribution. Although barcode sequences of this ecologically important species have been published, no genome data have been published for . In this study, we constructed the complete mitochondrial genome (mtDNA) of a strain isolated from the East China Sea.