Historical biogeography of the widespread macroalga Sargassum (Fucales, Phaeophyceae)

Organellar Genomes of Sargassum hemiphyllum var. chinense Provide Insight into the Characteristics of Phaeophyceae

Sargassum hemiphyllum var. chinense, a prevalent seaweed along the Chinese coast, has economic and ecological significance. However, systematic positions within Sargassum and among the three orders of Phaeophyceae, Fucales, Ectocarpales, and Laminariales are in debate. Here, we reported the organellar genomes of S. hemiphyllum var. chinense (34,686-bp mitogenome with 65 genes and 124,323 bp plastome with 173 genes) and the investigation of comparative genomics and systematics of 37 mitogenomes and 22 plastomes of Fucales (including S. hemiphyllum var. chinense), Ectocarpales, and Laminariales in Phaeophyceae. Whole genome collinearity analysis showed gene number, type, and arrangement were consistent in organellar genomes of Sargassum with 360 SNP loci identified as S. hemiphyllum var. chinense and two genes (rps7 and cox2) identified as intrageneric classifications of Sargassum. Comparative genomics of the three orders of Phaeophyceae exhibited the same content and different types (petL was only found in plastomes of the order Fucales and Ectocarpales) and arrangements (most plastomes were rearranged, but trnA and trnD in the mitogenome represented different orders) in genes. We quantified the frequency of RNA-editing (canonical C-to-U) in both organellar genomes; the proportion of edited sites corresponded to 0.02% of the plastome and 0.23% of the mitogenome (in reference to the total genome) of S. hemiphyllum var. chinense. The repetition ratio of Fucales was relatively low, with scattered and tandem repeats (nine tandem repeats of 14-24 bp) dominating, while most protein-coding genes underwent negative selection (Ka/Ks < 1). Collectively, these findings provide valuable insights to guide future species identification and evolutionary status of three important Phaeophyceae order species.

Macroalgal deep genomics illuminate multiple paths to aquatic, photosynthetic multicellularity

Macroalgae are multicellular, aquatic autotrophs that play vital roles in global climate maintenance and have diverse applications in biotechnology and eco-engineering, which are directly linked to their multicellularity phenotypes. However, their genomic diversity and the evolutionary mechanisms underlying multicellularity in these organisms remain uncharacterized. In this study, we sequenced 110 macroalgal genomes from diverse climates and phyla, and identified key genomic features that distinguish them from their microalgal relatives. Genes for cell adhesion, extracellular matrix formation, cell polarity, transport, and cell differentiation distinguish macroalgae from microalgae across all three major phyla, constituting conserved and unique gene sets supporting multicellular processes. Adhesome genes show phylum- and climate-specific expansions that may facilitate niche adaptation. Collectively, our study reveals genetic determinants of convergent and divergent evolutionary trajectories that have shaped morphological diversity in macroalgae and provides genome-wide frameworks to understand photosynthetic multicellular evolution in aquatic environments.

Distinct bacterial succession and functional response to alginate in the South, Equatorial, and North Pacific Ocean

The availability of alginate, an abundant macroalgal polysaccharide, induces compositional and functional responses among marine microbes, but these dynamics have not been characterized across the Pacific Ocean. We investigated alginate-induced compositional and functional shifts (e.g., heterotrophic production, glucose turnover, hydrolytic enzyme activities) of microbial communities in the South Subtropical, Equatorial, and Polar Frontal North Pacific in mesocosms. We observed that shifts in response to alginate were site-specific. In the South Subtropical Pacific, prokaryotic cell counts, glucose turnover, and peptidase activities changed the most with alginate addition, along with the enrichment of the widest range of particle-associated taxa (161 amplicon sequence variants; ASVs) belonging to Alteromonadaceae, Rhodobacteraceae, Phormidiaceae, and Pseudoalteromonadaceae. Some of these taxa were detected at other sites but only enriched in the South Pacific. In the Equatorial Pacific, glucose turnover and heterotrophic prokaryotic production increased most rapidly; a single Alteromonas taxon dominated (60% of the community) but remained low (<2%) elsewhere. In the North Pacific, the particle-associated community response to alginate was gradual, with a more limited range of alginate-enriched taxa (82 ASVs). Thus, alginate-related ecological and biogeochemical shifts depend on a combination of factors that include the ability to utilize alginate, environmental conditions, and microbial interactions.

A survey of epibiont hydrozoans on Sargassum

The brown alga Sargassum provides a natural substrate occupied by hydrozoans in shallow marine waters. A global count in 2007 listed 39 epibiotic species of Hydrozoa growing on Sargassum, but more studies have been published since, therefore, an update is timely, particularly due to the increased abundance of Sargassum in the Caribbean. This review, based on a recent literature survey and new records from Mexico, includes 133 publications of epibiotic hydrozoans on Sargassum spanning 220 years, from 1802 to 2022. A total of 131 hydrozoan species were recorded on 26 species of Sargassum, most belonging to the subclass Hydroidolina (130), with only one record of a trachyline medusa (Gonionemus vertens, subclass Trachylinae). Most publications centered on the Tropical Atlantic, where the greatest number of hydrozoan species (67 species) were recorded. All hydrozoan species possess a hydrorhiza, except one hydromedusae species that attach to Sargassum via adhesive tentacles. Most of the hydrozoan species associated with Sargassum exhibited a benthic life cycle (93 species) and are comprised of erect, branched colonies (67 species) and large hydrothecae (69 species). Although the number of studies of epibiotic hydrozoans on Sargassum has increased since the mid-20th century, nevertheless hydrozoan richness has not reached an asymptote. Therefore, more sampling of Sargassum species would likely identify more hydrozoan species associated with Sargassum, especially among benthic Sargassum, and might help reveal potential biogeographical and ecological patterns between Sargassum and hydrozoan epibionts.

Roles of Marine Macroalgae or Seaweeds and Their Bioactive Compounds in Combating Overweight, Obesity and Diabetes: A Comprehensive Review

Obesity and diabetes are matters of serious concern in the health sector due to their rapid increase in prevalence over the last three decades. Obesity is a severe metabolic problem that results in energy imbalance that is persistent over a long period of time, and it is characterized by insulin resistance, suggesting a strong association with type 2 diabetes (T2D). The available therapies for these diseases have side effects and some still need to be approved by the Food and Drug Administration (FDA), and they are expensive for underdeveloped countries. Hence, the need for natural anti-obesity and anti-diabetic drugs has increased in recent years due to their lower costs and having virtually no or negligible side effects. This review thoroughly examined the anti-obesity and anti-diabetic effects of various marine macroalgae or seaweeds and their bioactive compounds in different experimental settings. According to the findings of this review, seaweeds and their bioactive compounds have been shown to have strong potential to alleviate obesity and diabetes in both in vitro and in vivo or animal-model studies. However, the number of clinical trials in this regard is limited. Hence, further studies investigating the effects of marine algal extracts and their bioactive compounds in clinical settings are required for developing anti-obesity and anti-diabetic medicines with better efficacy but lower or no side effects.

Chemical Constituents and Anti-Angiogenic Principles from a Marine Algicolous Penicillium sumatraense SC29

In this study, a marine brown alga Sargassum cristaefolium-derived fungal strain, Penicillium sumatraense SC29, was isolated and identified. Column chromatography of the extracts from liquid fermented products of the fungal strain was carried out and led to the isolation of six compounds. Their structures were elucidated by spectroscopic analysis and supported by single-crystal X-ray diffraction as four previously undescribed (R)-3-hydroxybutyric acid and glycolic acid derivatives, namely penisterines A (1) and C-E (3-5) and penisterine A methyl ether (2), isolated for the first time from natural resources, along with (R)-3-hydroxybutyric acid (6). Of these compounds identified, penisterine E (5) was a unique 6/6/6-tricyclic ether with an acetal and two hemiketal functionalities. All the isolates were subjected to in vitro anti-angiogenic assays using a human endothelial progenitor cell (EPCs) platform. Among these, penisterine D (4) inhibited EPC growth, migration, and tube formation without any cytotoxic effect. Further, in in vivo bioassays, the percentages of angiogenesis of compound 3 on Tg (fli1:EGFP) transgenic zebrafish were 54% and 37% as the treated concentration increased from 10.2 to 20.4 µg/mL, respectively, and the percentages of angiogenesis of compound 4 were 52% and 41% as the treated concentration increased from 8.6 to 17.2 µg/mL, respectively. The anti-angiogenic activity of penisterine D (4) makes it an attractive candidate for further preclinical investigation.

Comparative analysis of proximate compositions, mineral and functional chemical groups of 15 different seaweed species

Seaweed is a popular edible source and is associated with many foods and pharmaceutical industries around the world. The current research aims to provide information on the chemical composition of 15 seaweed species, consisted of Chlorophyta, Ochrophyta/Phaeophyceae, and Rhodophyta macroalgae, collected from coastal areas of Sri Lanka. Seaweed samples were subjected to the analysis of lipids, proteins, ash and macro, micro, trace and ultra-trace elements. The highest protein content was recorded in the brown algae. Maximum dietary fiber and ash contents were recorded from green algae. The highest predominant fatty acids were observed from green seaweeds (Caulerpa racemosa); however, linoleic acid (C18:2n6) is the dominant fatty acid of all macroalgae. Mineral contents were highest in the red macroalga; however, copper, zinc and magnesium were also comparatively higher in green alga Ulva lactuca. In conclusion, 15 seaweed species belonging to the three different classes of seaweeds are investigated in details to obtain their biochemical, mineral and fatty acid compositions for the synthesis of novel therapeutic agents. In order to explore biorefinery processes for these seaweeds, as well as how they can potentially be cultivated, more extensive studies are required. Studying and determining the nutritional values of seaweeds will be beneficial with the potentials for future industrial uses and research.

Organellar genome comparisons of Sargassum polycystum and S. plagiophyllum (Fucales, Phaeophyceae) with other Sargassum species

BACKGROUND

Sargassum polycystum C. Agardh and Sargassum plagiophyllum C. Agardh are inhabitants of tropical coastal areas, their populations are negatively influenced by global warming and marine environment changes. The mitochondrial and chloroplast genomes of these species have not been sequenced.

RESULTS

The mitochondrial genomes of S. polycystum and S. plagiophyllum were 34,825 bp and 34,862 bp, respectively, and their corresponding chloroplast genomes were 124,493 bp and 124,536 bp, respectively. The mitochondrial and chloroplast genomes of these species share conserved synteny, sequence regions and gene number when compared with the organellar genomes of other Sargassum species. Based on sequence analysis of 35 protein-coding genes, we deduced that S. polycystum and S. plagiophyllum were closely related with S. ilicifolium; these species diverged approximately 0.3 million years ago (Ma; 0.1-0.53 Ma) during the Pleistocene period (0.01-2.59 Ma). Rates of synonymous and non-synonymous substitutions in the mitochondrial genome of the Sargassum genus were 3 times higher than those in the chloroplast genome. In the mitochondrial genome, rpl5, rpl31 and rps11 had the highest synonymous substitution rates. In the chloroplast genome, psaE, rpl14 and rpl27 had the highest synonymous substitution rates.

CONCLUSIONS

Phylogenetic analysis confirms the close relationship between the two sequenced species and S. ilicifolium. Both synonymous and non-synonymous substitution rates show significant divergence between the group of mitochondrial genomes versus the group of chloroplast genomes. The deciphering of complete mitochondrial and chloroplast genomes is significant as it advances our understanding of the evolutionary and phylogenetic relationships between species of brown seaweeds.

A low-latitude species pump: Peripheral isolation, parapatric speciation and mating-system evolution converge in a marine radiation

Geologically recent radiations can shed light on speciation processes, but incomplete lineage sorting and introgressive gene flow render accurate evolutionary reconstruction and interpretation challenging. Independently evolving metapopulations of low dispersal taxa may provide an additional level of phylogeographic information, given sufficiently broad sampling and genome-wide sequencing. Evolution in the marine brown algal genus Fucus in the south-eastern North Atlantic was shaped by Quaternary climate-driven range shifts. Over this timescale, divergence and speciation occurred against a background of expansion-contraction cycles from multiple refugia, together with mating-system shifts from outcrossing (dioecy) to selfing hermaphroditism. We tested the hypothesis that peripheral isolation of range edge (dioecious) F. vesiculosus led to parapatric speciation and radiation of hermaphrodite lineages. Species tree methods using 876 single-copy nuclear genes and extensive geographic coverage produced conflicting topologies with respect to geographic clades of F. vesiculosus. All methods, however, revealed a new and early diverging hermaphrodite species, Fucus macroguiryi sp. nov. Both the multispecies coalescent and polymorphism-aware models (in contrast to concatenation) support sequential paraphyly in F. vesiculosus resulting from distinct evolutionary processes. Our results support (1) peripheral isolation of the southern F. vesiculosus clade prior to parapatric speciation and radiation of hermaphrodite lineages-a "low-latitude species pump". (2) Directional introgressive gene flow into F. vesiculosus around the present-day secondary contact zone (sympatric-allopatric boundary) between dioecious/hermaphrodite lineages as hermaphrodites expanded northwards, supported by concordance analysis and statistical tests of introgression. (3) Species boundaries in the extensive sympatric range are probably maintained by reproductive system (selfing in hermaphrodites) and reinforcement.

Antioxidant potential of low molecular weight fucoidans from Sargassum autumnale against H2O2-induced oxidative stress in vitro and in zebrafish models based on molecular weight changes

In this study, we investigated the potential antioxidant abilities of low-molecular weight fucoidans from enzyme-assisted hydrolysates of Sargassum autumnale, based on molecular weight changes, in vitro and in vivo. The yield and free radical-scavenging activities of enzyme-assisted hydrolysates of S. autumnale were screened. The protamex-assisted hydrolysate of S. autumnale (SAP) presented the highest yield and 2,2-diphenyl-1-picrylhydrazyl (DPPH)-scavenging activity; therefore, it was chosen for fucoidan purification. Three fucoidan fractions were observed in SAP, and their antioxidant activity was assessed. Fucoidan fraction 3 of protamex-assisted hydrolysate of S. autumnale (SAPF3) offered significant protection against H2O2-induced oxidative stress, and was structurally and physically similar to commercial fucoidan. Fucose and low-molecular weight fucoidans were highly concentrated in SAPF3. The results of our study show that SAPF3, a low-molecular weight fucoidan from S. autumnale, possesses strong antioxidant properties and may be an effective alternative to antioxidant agents in the functional food industry.

The organellar genomes of Silvetia siliquosa (Fucales, Phaeophyceae) and comparative analyses of the brown algae

The brown alga Silvetia siliquosa (Tseng et Chang) Serrão, Cho, Boo & Brawly is endemic to the Yellow-Bohai Sea and southwestern Korea. It is increasingly endangered due to habitat loss and excessive collection. Here, we sequenced the mitochondrial (mt) and chloroplast (cp) genomes of S. siliquosa. De novo assembly showed that the mt-genome was 36,036 bp in length, including 38 protein-coding genes (PCGs), 26 tRNAs, and 3 rRNAs, and the cp-genome was 124,991 bp in length, containing 139 PCGs, 28 tRNAs, and 6 rRNAs. Gene composition, gene number, and gene order of the mt-genome and cp-genome were very similar to those of other species in Fucales. Phylogenetic analysis revealed a close genetic relationship between S. siliquosa and F. vesiculosus, which diverged approximately 8 Mya (5.7-11.0 Mya), corresponding to the Late Miocene (5.3-11.6 Ma). The synonymous substitution rate of mitochondrial genes of phaeophycean species was 1.4 times higher than that of chloroplast genes, but the cp-genomes were more structurally variable than the mt-genomes, with numerous gene losses and rearrangements among the different orders in Phaeophyceae. This study reports the mt- and cp-genomes of the endangered S. siliquosa and improves our understanding of its phylogenetic position in Phaeophyceae and of organellar genomic evolution in brown algae.

Ancient Tethyan Vicariance and Long-Distance Dispersal Drive Global Diversification and Cryptic Speciation in the Red Seaweed Pterocladiella

We investigated the globally distributed red algal genus Pterocladiella, comprising 24 described species, many of which are economically important sources of agar and agarose. We used DNA-based species delimitation approaches, phylogenetic, and historical biogeographical analyses to uncover cryptic diversity and infer the drivers of biogeographic patterns. We delimited 43 species in Pterocladiella, of which 19 are undescribed. Our multigene time-calibrated phylogeny and ancestral area reconstruction indicated that Pterocladiella most likely originated during the Early Cretaceous in the Tethys Sea. Ancient Tethyan vicariance and long-distance dispersal have shaped current distribution patterns. The ancestor of Eastern Pacific species likely arose before the formation of the formidable Eastern Pacific Barrier-a first confirmation using molecular data in red algae. Divergences of Northeast and Southeast Pacific species have been driven by the Central American Seaway barrier, which, paradoxically, served as a dispersal pathway for Atlantic species. Both long- and short-distance dispersal scenarios are supported by genetic relationships within cosmopolitan species based on haplotype analysis. Asymmetrical distributions and the predominance of peripatry and sympatry between sister species suggest the importance of budding speciation in Pterocladiella. Our study highlights the underestimation of global diversity in these crucial components of coastal ecosystems and provides evidence for the complex evolution of current species distributions.

Brilliantia kiribatiensis, a new genus and species of Cladophorales (Chlorophyta) from the remote coral reefs of the Southern Line Islands, Pacific Ocean

The marine green alga Brilliantia kiribatiensis gen. et sp. nov. is described from samples collected from the coral reefs of the Southern Line Islands, Republic of Kiribati, Pacific Ocean. Phylogenetic analysis of sequences of the large- and small-subunit rDNA and the rDNA internal transcribed spacer region revealed that Brilliantia is a member of the Boodleaceae (Cladophorales), containing the genera Apjohnia, Boodlea, Cladophoropsis, Chamaedoris, Phyllodictyon, and Struvea. Within this clade it formed a distinct lineage, sister to Struvea elegans, but more distantly related to the bona fide Struvea species (including the type S. plumosa). Brilliantia differs from the other genera by having a very simple architecture forming upright, unbranched, single-celled filaments attached to the substratum by a rhizoidal mat. Cell division occurs by segregative cell division only at the onset of reproduction. Based on current sample collection, B. kiribatiensis seems to be largely restricted to the Southern Line Islands, although it was also observed on neighboring islands, including Orona Atoll in the Phoenix Islands of Kiribati, and the Rangiroa and Takapoto Atolls in the Tuamotus of French Polynesia. This discovery highlights the likeliness that there is still much biodiversity yet to be discovered from these remote and pristine reefs of the central Pacific.

Brown Seaweed Sargassum siliquosum as an Intervention for Diet-Induced Obesity in Male Wistar Rats

The therapeutic potential of Sargassum siliquosum grown in Australian tropical waters was tested in a rat model of metabolic syndrome. Forty-eight male Wistar rats were divided into four groups of 12 rats and each group was fed a different diet for 16 weeks: corn starch diet (C); high-carbohydrate, high-fat diet (H) containing fructose, sucrose, saturated and trans fats; and C or H diets with 5% S. siliquosum mixed into the food from weeks 9 to 16 (CS and HS). Obesity, hypertension, dyslipidaemia, impaired glucose tolerance, fatty liver and left ventricular fibrosis developed in H rats. In HS rats, S. siliquosum decreased body weight (H, 547 ± 14; HS, 490 ± 16 g), fat mass (H, 248 ± 27; HS, 193 ± 19 g), abdominal fat deposition and liver fat vacuole size but did not reverse cardiovascular and liver effects. H rats showed marked changes in gut microbiota compared to C rats, while S. siliquosum supplementation increased gut microbiota belonging to the family Muribaculaceae. This selective increase in gut microbiota likely complements the prebiotic actions of the alginates. Thus, S. siliquosum may be a useful dietary additive to decrease abdominal and liver fat deposition.

Potential Anticancer Lipoxygenase Inhibitors from the Red Sea-Derived Brown Algae Sargassum cinereum: An In-Silico-Supported In-Vitro Study

LC-MS-assisted metabolomic profiling of the Red Sea-derived brown algae Sargassum cinereum "Sargassaceae" dereplicated eleven compounds 1-11. Further phytochemical investigation afforded two new aryl cresol 12-13, along with eight known compounds 14-21. Both new metabolites, along with 19, showed moderate in vitro antiproliferative activity against HepG2, MCF-7, and Caco-2. Pharmacophore-based virtual screening suggested both 5-LOX and 15-LOX as the most probable target linked to their observed antiproliferative activity. The in vitro enzyme assays revealed 12 and 13 were able to inhibit 5-LOX more preferentially than 15-LOX, while 19 showed a convergent inhibitory activity toward both enzymes. Further in-depth in silico investigation revealed the molecular interactions inside both enzymes' active sites and explained the varying inhibitory activity for 12 and 13 toward 5-LOX and 15-LOX.

Global Diversity and Geographic Distributions of Padina Species (Dictyotales, Phaeophyceae): New Insights Based on Molecular and Morphological Analyses

The taxonomic status and species diversity of the brown algal genus Padina (Dictyotales, Phaeophyceae) was assessed based on DNA sequences and the morpho-anatomy of specimens collected worldwide, especially from tropical and subtropical western Pacific regions. Phylogenetic analyses using chloroplast rbcL and mitochondrial cox3 gene sequences demonstrated four distinct clades for newly collected samples with high bootstrap support. Each species clade possesses a suite of morphological features that are not shared by any known species of Padina. These are P. imbricata sp. nov., Padina lutea sp. nov., P. moffittianoides sp. nov., and P. nitida sp. nov. The occurrence of these and other species of Padina clearly points to an elevated diversity of the genus in tropical/subtropical waters of the western Pacific. Phylogenetic analyses provided new insights into biogeographic characteristics of the genus, with many species in the Pacific Ocean showing shared/overlapping distributions, whereas species from the Mediterranean/Atlantic and/or the Indian Ocean tend to be confined to particular regions. Consideration has also been given to the evolutionary time frame of the genus Padina based on molecular time trees: a time tree of the concatenated data set (rbcL + cox3) revealed the estimated divergence time in the mid-Cretaceous, whereas those of cox3 and rbcL showed older estimates pointing to the periods of mid-Jurassic and Early Cretaceous, respectively.

The Complete Plastid Genomes of Seven Sargassaceae Species and Their Phylogenetic Analysis

Sargassum is one of the most important genera of the family Sargassaceae in brown algae and is used to produce carrageenan, mannitol, iodine, and other economic substances. Here, seven complete plastid genomes of Sargassum ilicifolium var. conduplicatum, S. graminifolium, S. phyllocystum, S. muticum, S. feldmannii, S. mcclurei, and S. henslowianum were assembled using next-generation sequencing. The sizes of the seven circular genomes ranged from 124,258 to 124,563 bp, with two inverted regions and the same set of plastid genes, including 139 protein-coding genes (PCGs), 28 transfer (t)RNAs, and 6 ribosomal (r)RNAs. Compared with the other five available plastid genomes of Fucales, 136 PCGs were conserved, with two common ones shared with Coccophora langsdorfii, and one with S. fusiforme and S. horneri. The co-linear analysis identified two inversions of trnC(gca) and trnN(gtt) in ten Sargassum species, against S. horneri and C. langsdorfii. The phylogenetic analysis based on the plastid genomes of 55 brown algae (Phaeophyceae) showed four clades, whose ancient ancestor lived around 201.42 million years ago (Mya), and the internal evolutionary branches in Fucales started to be formed 92.52 Mya, while Sargassum species were divided into two subclades 14.33 Mya. Our novel plastid genomes provided evidence for the speciation of brown algae and plastid genomic evolution events.

Systematics and Biogeography of the Red Algal Genus Yonagunia (Halymeniaceae, Rhodophyta) from the Indo-Pacific Including the Description of Two New Species from Taiwan

Carpopeltis maillardii has been regarded as a widely distributed species in the Indo-Pacific region. In this study, we analyzed the genetic diversity of C. maillardii and related species collected from Taiwan and the Indian Ocean based on rbcL sequences, in order to elucidate species boundaries, diversity, and biogeographic patterns. Our analyses show that C. maillardii specimens are only distantly related to the genus Carpopeltis (type: C. phyllophora) but instead form a clade together with species of Yonagunia. We therefore propose the new combination Yonagunia maillardii comb. nov. In addition, two new species (Yonagunia palmata sp. nov. and Yonagunia taiwani-borealis sp. nov.) are described from Taiwan. The close relationship of Yonagunia to Grateloupia is corroborated by detailed observations of the female reproductive structures, which demonstrate that the development of auxiliary cell ampullae before and after diploidization is similar to that of Grateloupia sensu stricto. Namely, the ampullae are composed of only two orders of unbranched filaments in which only a few ampullar cells are incorporated into a basal fusion cell after diploidization of the auxiliary cell and the pericarp consists almost entirely of secondary medullary filaments. Of all Yonagunia species, Y. maillardii has the widest distribution in the Indo-Pacific, and can be identified in the field by its relatively thin, feathery, and highly branched morphology. Most other species, including those that occur in Taiwan, are seemingly more range-restricted. Our phylogenetic analyses resulted in a well-resolved phylogeny of Yonagunia, with an origin estimated in the Eocene-Oligocene, and diversification of species mainly in the Miocene.

Takeaways from Mobile DNA Barcoding with BentoLab and MinION

Since the release of the MinION sequencer in 2014, it has been applied to great effect in the remotest and harshest of environments, and even in space. One of the most common applications of MinION is for nanopore-based DNA barcoding in situ for species identification and discovery, yet the existing sample capability is limited (n ≤ 10). Here, we assembled a portable sequencing setup comprising the BentoLab and MinION and developed a workflow capable of processing 32 samples simultaneously. We demonstrated this enhanced capability out at sea, where we collected samples and barcoded them onboard a dive vessel moored off Sisters' Islands Marine Park, Singapore. In under 9 h, we generated 105 MinION barcodes, of which 19 belonged to fresh metazoans processed immediately after collection. Our setup is thus viable and would greatly fortify existing portable DNA barcoding capabilities. We also tested the performance of the newly released R10.3 nanopore flow cell for DNA barcoding, and showed that the barcodes generated were ~99.9% accurate when compared to Illumina references. A total of 80% of the R10.3 nanopore barcodes also had zero base ambiguities, compared to 50-60% for R9.4.1, suggesting an improved homopolymer resolution and making the use of R10.3 highly recommended.

From marine park to future genomic observatory? Enhancing marine biodiversity assessments using a biocode approach

Few tropical marine sites have been thoroughly characterised for their animal species, even though they constitute the largest proportion of multicellular diversity. A number of focused biodiversity sampling programmes have amassed immense collections to address this shortfall, but obstacles remain due to the lack of identification tools and large proportion of undescribed species globally. These problems can be partially addressed with DNA barcodes ("biocodes"), which have the potential to facilitate the estimation of species diversity and identify animals to named species via barcode databases. Here, we present the first results of what is intended to be a sustained, systematic study of the marine fauna of Singapore's first marine park, reporting more than 365 animal species, determined based on DNA barcodes and/or morphology represented by 931 specimens (367 zooplankton, 564 macrofauna including 36 fish). Due to the lack of morphological and molecular identification tools, only a small proportion could be identified to species solely based on either morphology (24.5%) or barcodes (24.6%). Estimation of species numbers for some taxa was difficult because of the lack of sufficiently clear barcoding gaps. The specimens were imaged and added to "Biodiversity of Singapore" (http://singapore.biodiversity.online), which now contains images for > 13,000 species occurring in the country.