DNA barcoding reveals that the common cupped oyster in Taiwan is the Portuguese oyster Crassostrea angulata (Ostreoida; Ostreidae), not C. gigas

Microplastics in coastal farmed oyster (Crassostrea angulata) shells: Abundance, characteristics, and diversity

One of the most concerning emerging pollutants is microplastics (MPs), which can infiltrate soft tissues of organisms by ingestion, adhesion, and fusing and may even become embedded in biominerals. However, very little evidence is available about MPs in biominerals found in the wild. This study detected the abundance and characteristics of MPs in the shells of farmed oysters (Crassostrea angulata) off the coast of Taiwan and discussed the distribution, accumulation, and diversity in the oyster shells. The results showed that MPs were ubiquitous in oyster shells, with an average abundance of 0.70 ± 0.40 MPs/g. MPs abundance was significantly (p < 0.01) higher in small oyster shells (shell length < 6.5 cm, weight 5-10 g) and inorganic (CaCO3) fraction (HCl digestion) than in large oyster shells (>6.5 cm, 10-25 g) and an organic fraction (H2O2 digestion), respectively. However, there was no significant difference in MPs abundance between the top and bottom shells (p > 0.05). MPs with a size <2 mm accounted for 78.5 %, fibrous MPs for 93.7 %, and rayon for 89.5 %. The MPs diversity integrated index (MPDII) in oyster shells was low (0.27), and the small and fibrous MPs seemed more easily embedded in biominerals. The findings confirm the presence of MPs in oyster shells in coastal environments. In addition, oyster shells may contain higher amounts of MPs than soft tissues 4-5 times, which needs to be confirmed. Further revealing the distribution and accumulation of MPs in water/terrestrial biominerals will help to understand the fate of MPs in the environment.

Cryptic Marine Diversity in the Northern Arabian Gulf: An Integrative Approach Uncovers a New Species of Oyster (Bivalvia: Ostreidae), Ostrea oleomargarita

Animal biodiversity is greatly underestimated in nontemperate marine regions, especially for intertidal benthic organisms such as oysters. Recent surveys in the northern Arabian Gulf suggest the presence of numerous unidentified species, some of which form shallow reef ecosystems while others are cryptic and found under rocks. In this study, we focused on small oysters from Kuwait, which show typical characteristics in common with the genus Ostrea except for the presence of lophine chomata that would link it to the genera Lopha, Dendostrea, and Alectryonella. Phylogenetic analyses based on mitochondrial and nuclear markers unambiguously placed the Kuwait oyster within the Ostreinae as a sister to the Japanese species Ostrea futamiensis. The hypothesis that the Kuwait oyster represents a new species was assessed with phylogenetic and species delimitation methods combined with a morphological assessment. Results corroborated the Kuwait oysters as a new species herein described as Ostrea oleomargarita Oliver, Salvi, and Al-Kandari, sp. nov. The phylogeny of the Ostreinae shows extensive disagreement between morphology-based genera and phylogenetic clades. The genus Ostrea is polyphyletic, and the form and distribution of taxonomic characters such as chomata are not as definitive as suggested in previous studies. This study, along with other recent investigations, confirmed the Arabian Gulf as a key region for discovering marine animal diversity and suggested a possible biogeographic divide between the Eastern and Western Indo-Pacific. A pattern that has been documented in a growing number of taxa and that warrants further research attention.

The complete chloroplast genome and characteristics analysis of Musa basjoo Siebold

BACKGROUND

An ornamental plant often seen in gardens and farmhouses, Musa basjoo Siebold can also be used as Chinese herbal medicine. Its pseudostem and leaves are diuretic; its root can be decocted together with ginger and licorice to cure gonorrhea and diabetes; the decoct soup of its pseudostem can help relieve heat, and the decoct soup of its dried flower can treat cerebral hemorrhage. There have not been many chloroplast genome studies on M. basjoo Siebold.

METHODS AND RESULTS

We characterized its complete chloroplast genome using Novaseq 6000 sequencing. This paper shows that the length of the chloroplast genome M. basjoo Siebold is 172,322 bp, with 36.45% GC content. M. basjoo Siebold includes a large single-copy region of 90,160 bp, a small single-copy region of 11,668 bp, and a pair of inverted repeats of 35,247 bp. Comparing the genomic structure and sequence data of closely related species, we have revealed the conserved gene order of the IR and LSC/SSC regions, which has provided a very inspiring discovery for future phylogenetic research.

CONCLUSIONS

Overall, this study has constructed an evolutionary tree of the genus Musa species with the complete chloroplast genome sequence for the first time. As can be seen, there is no obvious multi-branching in the genus, and M. basjoo Siebold and Musa itinerans are the closest relatives.

Quality assessment of cryopreserved Portuguese oyster (Crassostrea angulata) sperm through ultrastructural and flow cytometry analysis

We investigated the effects of cryopreservation on the quality of Portuguese oyster (Crassostrea angulata) sperm, which were examined before and after freezing; sperm motility, fertilizing capacity, and ultrastructural morphology were analyzed. The motility percentage and fertilizing capacity of the cryopreserved sperm (mean ± standard error) were 16% ± 1% and 17% ± 8%, respectively. In the pre-freezing sperm, these were 58% ± 2% and 76% ± 4%, respectively. The sperm sustained substantial morphological and ultrastructural damage during cryopreservation. The morphological changes varied considerably in nature and extent, ranging from no apparent damage to virtual disintegration. Sperm were stained with fluorescent dyes to assess viability, plasma membrane integrity, mitochondrial activity, acrosomal membrane integrity, oxidation level, and DNA compaction and examined through flow cytometry. The methods used for the flow cytometry assays were slightly modified from those used for evaluating the semen quality of livestock. Relative to the pre-freezing sperm, the frozen-thawed sperm exhibited lower acrosomal membrane integrity (acrosomal damage, 59.86 ± 5.29; P < 0.05) and substantially higher oxidation levels (free radicals, 60.06 ± 0.82; P < 0.003). Oxidation level was found to be the most sensitive indicator of cryodamage. Along with ultrastructural analysis, we used flow cytometry to measure the qualitative and quantitative characteristics of Portuguese oyster sperm before and after cryopreservation rapidly, objectively, and accurately. This is the first study to assess the quality of Portuguese oyster sperm through these methods.

Revision shock in Pacific oysters taxonomy: the genus Magallana (formerly Crassostrea in part) is well-founded and necessary

The description of the genus Magallana provoked taxonomic ‘revision shock’ among Bayne and colleagues, who criticised: (1) the supporting evidence for this taxonomic change, (2) the procedure used and (3) its impact on the nomenclatural stability of oysters. Here, we demonstrate that the description of the genus Magallana fulfils the norms of taxonomic and indexing revisions, and is well-founded on a scientific basis. The clade named Magallana is supported by a robust phylogeny based on comprehensive taxon sampling, independent datasets and varied analytical methods. A new maximum likelihood phylogenetic analysis of oysters, based on mitochondrial gene order data (representing molecular phenotypes above the sequence level), has provided additional support for this classification. These results are fully consistent with all previously published phylogenetic studies, thus providing an unambiguous indication of the stability of the clade that meets all the currently accepted criteria for naming clades as taxa. We show that, while the criterion of ‘morphological diagnosability’ is not applicable at any level of oyster classification, several striking molecular phenotypes are diagnostic of Magallana, both at the nuclear and the mitochondrial genome level. The classification with three genera Magallana, Crassostrea and Talonostrea reflects the evolutionary diversity of Crassostreinae and is consistent with taxonomic ranking criteria adopted for other oyster subfamilies.

Genetic Characterization of Cupped Oyster Resources in Europe Using Informative Single Nucleotide Polymorphism (SNP) Panels

The Pacific oyster, Crassostrea gigas, was voluntarily introduced from Japan and British Columbia into Europe in the early 1970s, mainly to replace the Portuguese oyster, Crassostrea angulata, in the French shellfish industry, following a severe disease outbreak. Since then, the two species have been in contact in southern Europe and, therefore, have the potential to exchange genes. Recent evolutionary genomic works have provided empirical evidence that C. gigas and C. angulata exhibit partial reproductive isolation. Although hybridization occurs in nature, the rate of interspecific gene flow varies across the genome, resulting in highly heterogeneous genome divergence. Taking this biological property into account is important to characterize genetic ancestry and population structure in oysters. Here, we identified a subset of ancestry-informative makers from the most differentiated regions of the genome using existing genomic resources. We developed two different panels in order to (i) easily differentiate C. gigas and C. angulata, and (ii) describe the genetic diversity and structure of the cupped oyster with a particular focus on French Atlantic populations. Our results confirm high genetic homogeneity among Pacific cupped oyster populations in France and reveal several cases of introgressions between Portuguese and Japanese oysters in France and Portugal.

Impacts of the combined exposure to seawater acidification and arsenic on the proteome of Crassostrea angulata and Crassostrea gigas

Proteomic analysis was performed to compare the effects of Arsenic (As), seawater acidification (Low pH) and the combination of both stressors (Low pH + As) on Crassostrea angulata and Crassostrea gigas juveniles in the context of global environmental change. This study aimed to elucidate if two closely related Crassostrea species respond similarly to these environmental stressors, considering both single and combined exposures, to infer if the simultaneous exposure to both stressors induced a differentiated response. Identification of the most important differentially expressed proteins between conditions revealed marked differences in the response of each species towards single and combined exposures, evidencing species-related differences towards each experimental condition. Moreover, protein alterations observed in the combined exposure (Low pH + As) were substantially different from those observed in single exposures. Identified proteins and their putative biological functions revealed an array of modes of action in each condition. Among the most important, those involved in cellular structure (Actin, Atlastin, Severin, Gelsolin, Coronin) and extracellular matrix modulation (Ependymin, Tight junction ZO-1, Neprilysin) were strongly regulated, although in different exposure conditions and species. Data also revealed differences regarding metabolic modulation capacity (ATP β, Enolase, Aconitate hydratase) and oxidative stress response (Aldehyde dehydrogenase, Lactoylglutathione, Retinal dehydrogenase) of each species, which also depended on single or combined exposures, illustrating a different response capacity of both oyster species to the presence of multiple stressors. Interestingly, alterations of piRNA abundance in C. angulata suggested genome reconfiguration in response to multiple stressors, likely an important mode of action related to adaptive evolution mechanisms previously unknown to oyster species, which requires further investigation. The present findings provide a deeper insight into the complexity of C. angulata and C. gigas responses to environmental stress at the proteome level, evidencing different capacities to endure abiotic changes, with relevance regarding the ecophysiological fitness of each species and competitive advantages in a changing environment.

Analysis of Genome-Wide Differentiation between Native and Introduced Populations of the Cupped Oysters Crassostrea gigas and Crassostrea angulata

The Pacific cupped oyster is genetically subdivided into two sister taxa, Crassostrea gigas and Crassostrea angulata, which are in contact in the north-western Pacific. The nature and origin of their genetic and taxonomic differentiation remains controversial due the lack of known reproductive barriers and the high degree of morphologic similarity. In particular, whether the presence of ecological and/or intrinsic isolating mechanisms contributes to species divergence is unknown. The recent co-introduction of both taxa into Europe offers a unique opportunity to test how genetic differentiation is maintained under new environmental and demographic conditions. We generated a pseudochromosome assembly of the Pacific oyster genome using a combination of BAC-end sequencing and scaffold anchoring to a new high-density linkage map. We characterized genome-wide differentiation between C. angulata and C. gigas in both their native and introduced ranges, and showed that gene flow between species has been facilitated by their recent co-introductions in Europe. Nevertheless, patterns of genomic divergence between species remain highly similar in Asia and Europe, suggesting that the environmental transition caused by the co-introduction of the two species did not affect the genomic architecture of their partial reproductive isolation. Increased genetic differentiation was preferentially found in regions of low recombination. Using historical demographic inference, we show that the heterogeneity of differentiation across the genome is well explained by a scenario whereby recent gene flow has eroded past differentiation at different rates across the genome after a period of geographical isolation. Our results thus support the view that low-recombining regions help in maintaining intrinsic genetic differences between the two species.

DNA Barcoding for the Identification and Authentication of Animal Species in Traditional Medicine

Animal-based traditional medicine not only plays a significant role in therapeutic practices worldwide but also provides a potential compound library for drug discovery. However, persistent hunting and illegal trade markedly threaten numerous medicinal animal species, and increasing demand further provokes the emergence of various adulterants. As the conventional methods are difficult and time-consuming to detect processed products or identify animal species with similar morphology, developing novel authentication methods for animal-based traditional medicine represents an urgent need. During the last decade, DNA barcoding offers an accurate and efficient strategy that can identify existing species and discover unknown species via analysis of sequence variation in a standardized region of DNA. Recent studies have shown that DNA barcoding as well as minibarcoding and metabarcoding is capable of identifying animal species and discriminating the authentics from the adulterants in various types of traditional medicines, including raw materials, processed products, and complex preparations. These techniques can also be used to detect the unlabelled and threatened animal species in traditional medicine. Here, we review the recent progress of DNA barcoding for the identification and authentication of animal species used in traditional medicine, which provides a reference for quality control and trade supervision of animal-based traditional medicine.

Taxonomic characterization of Tanakia species (Acheilognathidae) using DNA barcoding analyses

Tanakia is a bitterling genus with six species found in Far East Asia. Our aim was to construct the standard DNA barcode database available for the identification of six Tanakia species by comparing the range of intra- and inter-specific genetic distances, identifying the phylogenetic placement of each Tanakia species and providing the unique barcode characteristics that are specific to each species, using cytochrome oxidase I (COI) and cytochrome b (cyt b). Both loci failed to create a perfect barcoding gap between the ranges of inter- and intra-specific genetic distances, though interspecific COI distances were sufficiently greater than intraspecific values with only a few exceptions. In our phylogenetic analyses, T. koreensis and T. signifer did not form a monophyletic cluster of haplotypes in both loci. COI provided clear nucleotide characteristics that distinguish each species, whereas relatively fewer informative sites were found within the range of cyt b. Overall, COI could be regarded as appropriate species identification solution in Tanakia. Our analyses yielded some taxonomic issues that need the further investigation, and are expected to be helpful in the examination for the conservation status of Tanakia species that are on the verge of being endangered.