Peering into the gaps: Long-read sequencing illuminates structural variants and genomic evolution in the Australasian snapper.

Even before genome sequencing, genetic resources have supported species management and breeding programs. Current technologies, such as long-read sequencing, resolve complex genomic regions, like those rich in repeats or high in GC content. Improved genome contiguity enhances accuracy in identifying structural variants (SVs) and transposable elements (TEs). We present an improved genome assembly and SV catalogue for the Australasian snapper (Chrysophrys auratus). The new assembly is more contiguous, allowing for putative identification of 14 centromeres and transfer of 26,115 gene annotations from yellowfin seabream. Compared to the previous assembly, 35,000 additional SVs, including larger and more complex rearrangements, were annotated. SVs and TEs exhibit a distribution pattern skewed towards chromosome ends, likely influenced by recombination. Some SVs overlap with growth-related genes, underscoring their significance. This upgraded genome serves as a foundation for studying natural and artificial selection, offers a reference for related species, and sheds light on genome dynamics shaped by evolution.

Acanthopagrus oconnorae, a new species of seabream (Sparidae) from the Red Sea.

A new species of sparid fish, Acanthopagrus oconnorae, is described based on 11 specimens collected in the shallow (0-1 m depth) mangrove-adjacent sandflats of Thuwal, Saudi Arabia. The new species is distinguished from its congeners by the following combination of characters: second anal-fin spine 12.8%-16.6% of standard length (SL); 3½ scale rows between the fifth dorsal-fin spine and lateral line; suborbital width 5.7%-6.7% of SL; eyes positioned at the anterior edge of the head, often forming a weakly convex break in an otherwise gently curved head profile, when viewed laterally; caudal fin light yellow with black posterior margin (approximately half of fin); anal fin dusky grey, with posterior one-fifth of the fin light yellow; black streaks on inter-radial membranes of anal fin absent. The most similar species to A. oconnorae is Acanthopagrus vagus, which differs by the presence of a w-shaped anterior edge of the scaled predorsal area, a more acute snout and black streaks on the inter-radial membranes of the anal fin. Phylogenetic placement and species delimitation of A. oconnorae are discussed based on COI, CytB and 16S sequences. It is hypothesized that ecology and behaviour explain how this species avoided detection despite its likely occurrence in coastal areas of the Red Sea with historically high fishing pressure.

Niche availability and habitat affinities of the red porgy Pagrus pagrus (Linnaeus, 1758): An important ecological player on the world's largest rhodolith beds.

The red porgy (Pagrus pagrus) is a carnivore bottom dweller sparid, inhabiting flat sandy bottoms, rhodolith and seagrass beds of the Mediterranean Sea, the Western Atlantic (from Florida to Argentina) and the Eastern Atlantic (from Britain to Gabon). Along its native range, the red porgy is highly targeted by commercial and artisanal fisheries. In the past 40 years, the population decline of the species has been widely reported. In many locations, such as the Brazilian coast, stocks have collapsed. The central portion of the Brazilian coast harbours the largest rhodolith beds in the world and the highest levels of nektonic and benthic biodiversity. Along the rhodolith megahabitat, P. pagrus density is disproportionately higher (by 480%) than that of conspicuous benthic fishes inhabiting the same environment. Despite the ecological and economic importance of such an important species along its native range, little is known regarding its habitat use, niche availability and population responses to global warming. Here we present habitat affinities based on data sampled using baited remote stereo-video systems, and modelled niche availability and global warming populational responses. Our findings reveal that the red porgy is a species highly associated with rhodolith beds along the central portion of the Brazilian coast. The presence of a disproportional density and biomass of the red porgy, compared to other marine fish species, indicates that the species plays a key ecological role as a carnivore, mesoconsumer and prey/predator tolerant species, maintaining essential ecological functions in the habitat. In a global warming scenario, the model predicted populational niche shifts poleward and a severe niche erosion at lower latitudes as expected. Conservation initiatives (implementation of Maine Protected Areas, trawling exclusion zones, mining exclusion zones, fisheries management policies) are urgent to secure future stocks of the red porgy and also preserve the fragile rhodolith beds they inhabit.

Strengths and weaknesses in the long-term sustainability of two sympatric seabreams (Argyrops spinifer and Rhabdosargus haffara, Sparidae).

Argyrops spinifer and Rhabdosargus haffara are two sympatric seabream species making important contributions to fisheries landings in the western Arabian/Persian Gulf. We identified the strengths and weaknesses in the long-term sustainability of A. spinifer and R. haffara stocks by integrating multiple sources of data, including fisheries catch and effort statistics, life history traits, scientific trawl surveys and historical length frequency distribution. Four strengths were identified in A. spinifer: wide distribution of juveniles, positive association to the network of de facto fishing exclusion areas created by hundreds of oil-gas facilities, early maturation and the existence of large and old individuals. A. spinifer suffers from two potential weaknesses: slow growth rate and higher exploitation pressure on the small-sized individuals. R. haffara, on the other hand, has a strength of having a short life span and a fast growth rate, characteristics that make it robust to unfavourable conditions. R. haffara suffers from two weaknesses: the lack of association to the oil and gas facilities, and the preference for nearshore shallow waters with stronger negative anthropogenic impacts. Identified strengths and weaknesses of these two sparids provided a preliminary assessment about their long-term sustainability, as well as a roadmap about how to develop different management strategies to meet specific objectives.

Reproductive biology of black seabream Acanthopagrus schlegelii, threadfin porgy Evynnis cardinalis and red pargo Pagrus major in the northern South China Sea with consideration of fishery status and management needs.

The reproductive biology of three commercially significant seabream species (family: Sparidae) Acanthopagrus schlegelii, Evynnis cardinalis and Pagrus major, taken from Hong Kong and adjacent northern South China Sea (SCS) waters, were investigated for their sexual patterns, spawning seasons, length at maturity and exploitation in relation to their conservation and management status. Histological analysis showed E. cardinalis and P. major to be functionally gonochoristic, the latter having a bisexual juvenile stage and being a rudimentary hermaphrodite. Acanthopagrus schlegelii is a protandric hermaphrodite. Standard length (LS ) at 50% sex change for A. schlegelii is 291 mm. LS at 50% female maturity for E. cardinalis and P. major are 117 and 332 mm, respectively. For all three species, the spawning period falls between November and March. The study highlights geographical differences in reproductive biology among the species and a paucity of fishery or other population-related data. While heavy fishing pressure, life-history characteristics and absence of effective management throughout the geographic ranges of these species make them susceptible to overfishing, they nonetheless appear to be generally more resilient than many other taxa that comprise the multi-species fisheries of the region, possibly due to their relatively rapid sexual maturation and spatial movement patterns. Overall, however, little is known of the biology, fishing history and current fishery status of sparids in general in the northern SCS and the current study is one of the first to examine such aspects of this family in the region and to consider appropriate management options.

Comparison of otolith and scale readings for age and growth estimation of common dentex Dentex dentex.

Three methods of age estimation were compared for Dentex dentex. Based on sectioned otoliths, scales appeared to be relevant only up to 5 years and whole otoliths up to 12 years. The maximum estimated age was 36 years, which constitutes to date the oldest age reported.

Link between bacterial communities and contrasted loads in ectoparasitic monogeneans from the external mucus of two wild sparid species (Teleostei).

BACKGROUND: While teleost fishes represent two thirds of marine vertebrates, the role of their external microbiota in relationship with their environment remains poorly studied, especially in wild populations. Hence, the interaction of their microbiota with ectoparasites is largely unknown. Microbiota can act as a protective barrier against pathogens, and/or be involved in host recognition by parasites. Thus, host-parasite associations should now be considered as a tripartite interplay where the microbiota shapes the host phenotype and its relation to parasites. Monogeneans (Platyhelminthes) are direct life cycle ectoparasites commonly found on teleost skin and gills. The role of bacterial communities within skin and gill mucus which either pre-exist monogeneans infestation or follow it remain unclear. This is investigated in this study using the association between Sparidae (Teleostei) and their specific monogenean ectoparasites of the Lamellodiscus genus. We are exploring specificity mechanisms through the characterization of the external mucus microbiota of two wild sparid species using 16s rRNA amplicon sequencing. We investigated how these bacterial communities are related to constrated Lamellodiscus monogeneans parasitic load. RESULTS: Our results revealed that the increase in Lamellodiscus load is linked to an increase in bacterial diversity in the skin mucus of D. annularis specimens. The date of capture of D. annularis individuals appears to influence the Lamellodiscus load. Correlations between the abundance of bacterial taxa and Lamellodiscus load were found in gill mucus of both species. Abundance of Flavobacteriaceae family was strongly correlated with the Lamellodiscus load in gill mucus of both species, as well as the potentially pathogenic bacterial genus Tenacibaculum in D. annularis gill mucus. Negative correlations were observed between Lamellodiscus load and the abundance in Vibrionaceae in gill mucus of D. annularis, and the abundance in Fusobacteria in gill mucus of P. acarne specimens, suggesting potential applications of these bacteria in mitigating parasitic infections in fish. CONCLUSIONS: Our findings highlight the dynamic nature of fish microbiota, in particular in relation with monogeneans infestations in two wild sparid species. More generally, this study emphasizes the links between hosts, bacterial communities and parasites, spanning from the dynamics of co-infection to the potential protective role of the host's microbiota.

Do fish gut microbiotas vary across spatial scales? A case study of Diplodus vulgaris in the Mediterranean Sea.

BACKGROUND: Biogeography has been linked to differences in gut microbiota in several animals. However, the existence of such a relationship in fish is not clear yet. So far, it seems to depend on the fish species studied. However, most studies of fish gut microbiotas are based on single populations. In this study, we investigated the gut microbiota of fish from three wild populations of the two-banded sea bream Diplodus vulgaris (Geoffroy Saint-Hilaire, 1817) to determine whether its diversity, structure and potential functionality reflect the geographic origin of the fish, at large and small geographical scale. Additionally, we explored the host- and environmental-related factors explaining this relationship. RESULTS: We showed that the taxonomy and potential functionality of the mucosa-associated gut microbiota of Diplodus vulgaris differ to varying degrees depending on the spatial scale considered. At large scale, we observed that both the taxonomical structure and the potential functionality of the fish microbiota differed significantly between populations. In contrast, the taxonomical diversity of the microbial community displayed a significant relationship with factors other than the geographic origin of the fish (i.e. sampling date). On the other hand, at small scale, the different composition and diversity of the microbiota differ according to the characteristics of the habitat occupied by the fish. Specifically, we identified the presence of Posidonia oceanica in the benthic habitat as predictor of both the microbiota composition and diversity. Lastly, we reported the enrichment of functions related to the metabolism of xenobiotics (i.e. drugs and 4-aminobenzoate) in a population and we indicated it as a potential target of future monitoring. CONCLUSIONS: With this study, we confirmed the importance of investigating the gut microbiota of wild fish species using multiple populations, taking into account the different habitats occupied by the individuals. Furthermore, we underscored the use of the biodegradation potential of the gut microbiota as an alternative means of monitoring emerging contaminants in Mediterranean fish.

Quantitative trait loci affecting morphology traits in gilthead seabream (Sparus aurata L.).

We report a quantitative trait loci (QTL) mapping study on 18 morphometric characters in gilthead seabream based on a total of 74 informative microsatellite markers genotyped in 409 offspring coming from 10 paternal half-sib families. Statistical analysis was carried out using a linear regression approach, and various suggestive and significant morphology QTL were detected in three (9, 21 and 25) of nine linkage groups examined. Fitting body weight as a covariate reduced the significance of some QTL but revealed three new QTL in other linkage groups (LG6 and LG10). Current results combined with those obtained from previous studies underline highly significant loci affecting overall growth and morphology in S. aurata.

Mitochondrial Analysis of Sparidae Species to Detect a New DNA Barcoding Marker for Dentex gibbosus to Utilize against Fraud.

Dentex gibbosus (Pink dentex) is a fish species of increasing economic interest in the Mediterranean Sea that is consumed both whole and processed. The growing value of this sparid in European markets is responsible for its substitution with fraudulent species. The distinctive morphologic feature of D. gibbosus is the conspicuous hump on the forehead in the older and larger specimens. However, the head is regularly convex in young individuals, requiring high skills and competencies for correct identification. Authentication becomes even more challenging in the case of prepared and processed products. Therefore, the molecular characterization of Pink dentex plays a crucial role in preventing commercial fraud with species substitution. This paper proposes a comparative mitogenome analysis between 19 sparid species of commercial interest as a tool to accurately design species-specific primers targeting a fragment of the NAD2 gene for the identification of D. gibbosus. We successfully detected Pink dentex DNA both using endpoint and real-time PCR. The findings showed the high specificity of the designed primers, demonstrating this a suitable, fast, and cost-effective method that could be used for the unambiguous identification of Pink dentex. This innovative approach for sparid authentication is expected to contribute to seafood traceability, public health assurance, integrity, and the credibility of the seafood industry.

Impact of Hermodice carunculata (Pallas, 1766) (Polychaeta: Amphinomidae) on artisanal fishery: A case study from the Mediterranean sea.

Invasive species can cause severe economic damages, ecosystem alterations, and can even threat human health. In the global warming scenario, which can act as a driving force for the expansion of thermophilic species, we investigated for the first time the economic damage caused by the invasive bearded fireworm, Hermodice carunculata, to artisanal longline fishery in the Mediterranean Sea. We focused on bottom longline fishery targeting the highly prized white seabream Diplodus sargus, investigating catch composition of the fishing gear and Catch Per Unit Effort (CPUE) of species caught, with particular emphasis on the economic damage caused by the bearded fireworm, H. carunculata, in relation to water temperature. Our results clearly indicated direct and indirect economic damage to fishing activities practiced in the southeastern coast of Sicily (Ionian Sea). Type and extent of the damage caused by the invasive worm (H. carunculata) were discussed in relation to temporal scale and overall yields obtained by this traditional artisanal fishery, and some solutions are proposed. However, the actual situation requires special attention because it is expected to worsen in the context of the global warming future scenarios, such that further studies are urgently needed.

Maintenance of Genetic Diversity of Black Sea Bream despite Unmonitored and Large-Scale Hatchery Releases.

Stock enhancement, used for replenishing depleted wild finfish populations, is an aggressive approach. Stock enhancement projects in Taiwan involve black sea bream (Acanthopagrus schlegelii), a major commercial species. During 2004-2015, even management agencies conducted stock enhancement projects, leading to numerous private releases that have not been recorded. Stock enhancement by a private hatchery without accurate genetic records may lead to a genetic structure change in wild populations. Using allele frequencies at nine microsatellite loci, we studied the genetic effects of stock enhancement in 19 samples collected from populations in the hatcheries and the wild. In 458 individuals from nine hatchery samples, most populations showed weak but significant genetic differences and complex clusters in structure analysis, indicating dramatic stock change within and among hatcheries. The 10 wild populations (n = 773) also had a complex genetic composition and were genetically different among sampling sites and times. However, a simple and clear cluster in structure analysis was found for only one sampling site, which had no release history. Thus, stock enhancement with complex genetic sources helps maintain genetic diversity but dramatically changes the genetic structure within and among wild populations, especially when stock enhancement is successful.

An Evaluation of the Genera Longicollum and Paralongicollum (Pomphorhynchidae: Acanthocephala) in Australia.

PURPOSE: To confirm the identity of Longicollum edmondsi Golvan, 1969, Pomphorhynchidae Yamaguti, 1939, from Australia. METHODS: All the relevant specimens registered in Australian museums were examined. Those held as permanent slide preparations were examined directly and those stored in 70% ethanol were examined as temporary wet mounts, after clearing in lactophenol, using an Olympus BH-2 microscope with differential interference optics. Measurements were made with an eyepiece micrometer and figures drawn using a drawing tube. RESULTS: All the material registered as either Longicollum edmondsi or Paralongicollum sp. was determined to be Paralongicollum edmondsi (Golvan, 1969) comb. nov. based, amongst other characters, on the morphology of the neck. DISCUSSION: The significance of known host species of P. edmondsi and their geographical distribution around the Australian coast was analysed. The geographical distribution of the genus Paralongicollum, Amin, Bauer & Siderov, 1991, across the Indo Pacific was compared to that of the acanthocephalan genus Sclerocollum Schmidt & Paperna, 1978.

Chromosome-level Genome Assembly of Acanthopagrus latus Provides Insights into Salinity Stress Adaptation of Sparidae.

The yellowfin seabream, Acanthopagrus latus, is widely distributed throughout the Indo-West Pacific. This species, as a euryhaline Sparidae fish, inhabits in coastal environments with large and frequent salinity fluctuation. So the A. latus can be considered as an ideal species for elucidating the evolutionary mechanism of salinity stress adaption on teleost fish species. Here, a chromosome-scale assembly of A. latus was obtained with PacBio and Hi-C hybrid sequencing strategy. The final assembly genome of A. latus is 685.14 Mbp. The values of contig N50 and scaffold N50 are 14.88 Mbp and 30.72 Mbp, respectively. 29,227 genes were successfully predicted for A. latus in total. Then, the comparative genomics and phylogenetic analysis were employed for investigating the different osmoregulation strategies of salinity stress adaption on multiple whole genome scale of Sparidae species. The highly accurate chromosomal information provides the important genome resources for understanding the osmoregulation evolutionary pattern of the euryhaline Sparidae species.

Diversity and structure of sparids external microbiota (Teleostei) and its link with monogenean ectoparasites.

BACKGROUND: Animal-associated microbial communities appear to be key factors in host physiology, ecology, evolution and its interactions with the surrounding environment. Teleost fish have received relatively little attention in the study of surface-associated microbiota. Besides the important role of microbiota in homeostasis and infection prevention, a few recent studies have shown that fish mucus microbiota may interact with and attract some specific parasitic species. However, our understanding of external microbial assemblages, in particular regarding the factors that determine their composition and potential interactions with parasites, is still limited. This is the objective of the present study that focuses on a well-known fish-parasite interaction, involving the Sparidae (Teleostei), and their specific monogenean ectoparasites of the Lamellodiscus genus. We characterized the skin and gill mucus bacterial communities using a 16S rRNA amplicon sequencing, tested how fish ecological traits and host evolutionary history are related to external microbiota, and assessed if some microbial taxa are related to some Lamellodiscus species. RESULTS: Our results revealed significant differences between skin and gill microbiota in terms of diversity and structure, and that sparids establish and maintain tissue and species-specific bacterial communities despite continuous exposure to water. No phylosymbiosis pattern was detected for either gill or skin microbiota, suggesting that other host-related and environmental factors are a better regulator of host-microbiota interactions. Diversity and structure of external microbiota were explained by host traits: host species, diet and body part. Numerous correlations between the abundance of given bacterial genera and the abundance of given Lamellodiscus species have been found in gill mucus, including species-specific associations. We also found that the external microbiota of the only unparasitized sparid species in this study, Boops boops, harbored significantly more Fusobacteria and three genera, Shewenella, Cetobacterium and Vibrio, compared to the other sparid species, suggesting their potential involvement in preventing monogenean infection. CONCLUSIONS: This study is the first to explore the diversity and structure of skin and gill microbiota from a wild fish family and present novel evidence on the links between gill microbiota and monogenean species in diversity and abundance, paving the way for further studies on understanding host-microbiota-parasite interactions.

Genetic population structure of the Blackspot seabream (Pagellus bogaraveo): contribution of mtDNA control region to fisheries management.

Marine fisheries management models have traditionally considered biological parameters and geopolitical boundaries. The result is the existence of fisheries management units that do not match genetic populations. However, this panorama is changing with the contribution of genetic and genomic data. Pagellus bogaraveo is a commercially important sparid in the northeast Atlantic, with three stock components being considered by ICES: the Celtic Sea and Bay of Biscay, Atlantic Iberian waters and the Azores. The northern stock collapsed (1975-1985) and is essential to characterize the genetic makeup of the species, particularly in the Iberian Peninsula, where it is managed as a single stock. The mitochondrial control region was used to screen the intraspecific diversity and population structure of individuals from six locations across the species range. The genetic diversity found is similar among sites, and there is differentiation between the Azores and the remaining locations.

The complete mitochondrial genome of yellowfin seabream, Acanthopagrus latus (Percoiformes, Sparidae) from Beibu Bay.

The yellowfin seabream, Acanthopagrus latus Houttuyn 1782, is a commercially and ecologically important species and a good model for studies of sexual differentiation. In this study, the complete mitochondrial genome of A. latus has been determined, which is 16,635 base pairs (54.3% A + T content) in length and consists of 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and a 948 bp D-loop region. The phylogenetic analyses showed that A. latus has a close relationship with Acanthopagrus schlegelii Bleeker 1854.

Dentex dentex Frauds: Establishment of a New DNA Barcoding Marker.

The common dentex (Dentex dentex (Linnaeus, 1758)) is an iconic fish in the Mediterranean diet. Due to its commercial and organoleptic importance, this sparid is highly appreciated in European markets and is often subjected to species substitution frauds. Comparative mitogenomics is a suitable approach for identifying new and effective barcode markers. This study aimed to find a molecular tag useful for unequivocally discriminating the sparid species D. dentex. The comparison of the complete mitochondrial DNA (mtDNA) sequences of 16 sparid species allowed us to highlight the potential of the NAD2 gene for direct identification purposes. Common dentex-specific primers were created and successfully evaluated by end-point and real-rime PCR (Polymerase Chain Reaction) for several fish species, achieving amplification only in the D. dentex. The method proposed in this study appears fast, simple, and inexpensive and requires affordable instrumentation. This approach provides unambiguous results for the common dentex authentication without the sequencing step. The presence/absence assay for D. dentex can be executed in a few hours of lab work. Therefore, national authorities responsible for food safety and traceability could apply and make full use of DNA-testing methods for deterring operators from false seafood declarations.

Aflatoxicosis Dysregulates the Physiological Responses to Crowding Densities in the Marine Teleost Gilthead Seabream (Sparus aurata).

Several studies in fish have shown that aflatoxin B1 (AFB1) causes a disparity of species-dependent physiological disorders without compromising survival. We studied the effect of dietary administration of AFB1 (2 mg AFB1 kg-1 diet) in gilthead seabream (Sparus aurata) juveniles in combination with a challenge by stocking density (4 vs. 40 g L-1). The experimental period duration was ten days, and the diet with AFB1 was administered to the fish for 85 days prior to the stocking density challenge. Our results indicated an alteration in the carbohydrate and lipid metabolites mobilization in the AFB1 fed group, which was intensified at high stocking density (HSD). The CT group at HSD increased plasma cortisol levels, as expected, whereas the AFB1-HSD group did not. The star mRNA expression, an enzyme involved in cortisol synthesis in the head kidney, presented a ninefold increase in the AFB1 group at low stocking density (LSD) compared to the CT-LSD group. Adenohypophyseal gh mRNA expression increased in the AFB1-HSD but not in the CT-HSD group. Overall, these results confirmed that chronic AFB1 dietary exposure alters the adequate endocrinological physiological cascade response in S. aurata, compromising the expected stress response to an additional stressor, such as overcrowding.

Otolith mass asymmetry in three sparid fish species collected from the Iraqi waters.

Saccular otolith mass asymmetry is examined in three sparid fish species, Acanthopagrus bifasciatus, A. arabicus, and Sparidentex hasta collected from Khor Abdullah at the North Persian Gulf. This characteristic was computed as the disparity between the weight of the right and left otoliths divided by mean otolith weight in the three sparid species investigated. According to the previous cases obtained on another symmetrical fish species, the absolute value of x in these species does not determine by fish length and otolith growth ratio, while the absolute rate of otolith weight disparity is boosted with the fish length. The estimate of x was between -0.2 and +0.2. Otolith mass asymmetry can show some growth disorder of fish owing to environmental influence.