The chromosome-level genome assembly of the Japanese yellowtail jack Seriola aureovittata provides insights into genome evolution and efficient oxygen transport

Fishes of the genus Seriola are widely farmed and highly valued in global aquaculture production. To further understand their economically important traits and help improve aquaculture product quality and sustainability, we performed a chromosome-level genome construction for Seriola aureovittata. Combining two technologies, PacBio and BGISEQ-500, we assembled 649.86 Mb S. aureovittata genome sequences with a contig N50 of 22.21 Mb, and 98% of BUSCO genes were detected in total. The initial assembly was then further scaffolded into 24 pseudochromosomes using Hi-C data, indicating the high quality of the genome. Genome evolution analysis showed that many genes related to fatty acid metabolism and oxygen binding, or transport were expanded, which provided insights into the metabolic characteristics of fatty acids and efficient oxygen transport. Based on the genome data, we confirmed the evolutionary relationship of S. aureovittata, S. dorsalis and S. lalandi and identified chr12 as the putative sex chromosome of S. aureovittata. Our chromosome-level genome assembly provides a genetic foundation for the phylogenetic and taxonomic investigation of different Seriola species. Moreover, the genome will provide an important genomic resource for further biological and aquaculture studies of S. aureovittata.

Redescription of Zeuxapta seriolae (Meserve, 1938) and Zeuxapta australica Lebedev, 1968 (Monogenea: Heteraxinidae)

Redescription is given of heteraxinid monogeneans Zeuxapta seriolae (Meserve, 1938), type species of the genus, and Zeuxapta australica Lebedev, 1968 (formerly Z. seriolae australica). Type specimens of Z. seriolae from Seriola dorsalis from Galápagos Islands were differentiated from Z. australica specimens collected by Lebedev from Seriola glandis (now Seriola lalandi) from Tasman Sea, the type locality, by the shape of the vagina, which consisted of the transversely oval central body and horizontally extended paired tubes in the former, and the transversely oval central body and short, obliquely posteriad paired extensions in the latter. Zeuxapta japonica (Yamaguti, 1940) and Zeuxapta kahala (Yamaguti, 1968) were synonymized with Z. seriolae. Hitherto undescribed Zeuxapta specimens were also examined; those from Seriola aureovittata from Japan and China, and specimens from Seriola dumerili from Japan and Spain were identified as Z. seriolae, while those from Seriola lalandi from Chile and New Zealand were identified as Z. australica. Specimens from S. lalandi (as Seriola glandis) from Heron Island, Australia described by Rohde in 1978 as Z. seriolae consisted of Z. seriolae and Z. australica.

Now you see me: "first" records of the greater amberjack Seriola dumerili at Rapa Nui range extension or increased scientific effort?

We report new records of the fisheries-harvested subtropical greater amberjack Seriola dumerili for the south-east Pacific Ocean. Despite local fishers' asserting that three Seriola morphotypes exist in the region, only one species (the yellowtail amberjack Seriola lalandi) was previously scientifically recorded for Rapa Nui (also known as Easter Island). Whilst we present the first "scientific record", S. dumerili, traditional ecological knowledge suggests that this is likely a pre-existing (albeit transient) species of the Rapa Nui ecoregion. Establishing the existing/historic distributional limits of commercially and ecologically valuable species is key for observing climate-driven distribution shifts, and the inclusion of traditional ecological knowledge is particularly important in areas with relatively lower scientific effort.

Freshwater and brackish water fishes of Sakhalin Island (Russia) in inland and coastal waters: an annotated checklist with taxonomic comments

Based on a critical analysis of scientific publications for the last 200 years and on the collected specimens, a complete annotated list of both typical freshwater ichthyofauna of Sakhalin Island, with the inclusion of marine species that can be found in brackish coastal waters, is reported for the first time. The annotated list includes 226 species classified in three classes, 26 orders, 68 families, 29 subfamilies, and 148 genera. For 160 species, information is provided on collection samples deposited in various museums around the world, 36 of which are type specimens. For each species, conservation status (according to IUCN Red List of Threatened Species and the Red Book of the Sakhalin region), zoogeographic characteristics (distribution within Sakhalin Island and globally), abundance and commercial value are given. For a number of species, more detailed information on synonymy and nomenclature is provided. The study area is located in the western North Pacific and includes the entire coast of Sakhalin Island in the Sea of Okhotsk and the northern Sea of Japan, as well as the adjacent Sea of Okhotsk coast of northern Hokkaido, Japan.

Checklist of marine and estuarine fishes from the AlaskaYukon Border, Beaufort Sea, to Cabo San Lucas, Mexico

This paper is a checklist of the fishes that have been documented, through both published and unpublished sources, in marine and estuarine waters, and out 200 miles, from the United States-Canadian border on the Beaufort Sea to Cabo San Lucas, Mexico. A minimum of 241 families and 1,644 species are known within this range, including both native and nonnative species. For each of these species, we include maximum size, geographic and depth ranges, whether it is native or nonnative, as well as a brief mention of any taxonomic issues.

First Report of Blood Fluke Pathogens with Potential Risk for Emerging Yellowtail Kingfish (Seriola lalandi) Aquaculture on the Chilean Coast, with Descriptions of Two New Species of Paradeontacylix (Aporocotylidae)

Blood flukes are digeneans that infect wild and farmed fish that can cause a severe and potentially lethal disease in farmed fish. These parasites are undetectable in the larval stage based on macroscopic observations in the definitive host with the infection becoming evident when eggs accumulate in the branchial vessels. There are nine known species of the genus Paradeontacylix and seven exclusively parasitize Seriola spp. from several geographical areas. Seriola lalandi aquaculture farms are emerging at various localities in northern Chile. Here, we report, for the first time, two blood fluke species parasitizing S. lalandi in the Southeastern Pacific (Chile). In the laboratory, the gills and heart of fish were removed. The retained blood flukes were separated according to the infection site, fixed in 70% or 95% ethanol for taxonomic and molecular analysis, respectively. Morphometrical differences among the fluke species were evaluated with a principal component analysis (PCA) using proportional body measurements. Phylogenetic trees were constructed based on 28S rDNA, cox1 mDNA using Bayesian inference (BI), and maximum likelihood (ML). Based on morphology, morphometry, and molecular analyses, two new species are proposed: P. humboldti n. sp. from the gills and P. olivai n. sp. from the heart of S. lalandi. Both were clearly distinguished from other species of Paradeontacylix by a combination of morphologic features (posterior tegumental spines, testes arrangement, body size). The genetic distance (based on cox1) among species was >10%. P. humboldti n. sp. and P. olivai n. sp. are sister species (with a common ancestor) independent of P. godfreyi from S. lalandi in Australia. The newly identified parasites may pose a risk to farmed S. lalandi as aporocotylids have been the cause of diseases in farmed fish from other geographical areas. In addition, some cages of S. lalandi are currently maintained in an open circulating system, which could favor the transmission of these parasites (if involved hosts are present in the environment).

Complete, closed and curated genome sequences of Photobacterium damselae subsp. piscicida isolates from Australia indicate mobilome-driven localized evolution and novel pathogenicity determinants

Despite the recent advances in sequencing technologies, the complete assembly of multi-chromosome genomes of the Vibrionaceae, often containing several plasmids, remains challenging. Using a combination of Oxford Nanopore MinION long reads and short Illumina reads, we fully sequenced, closed and curated the genomes of two strains of a primary aquatic pathogen Photobacterium damselae subsp. piscicida isolated in Australia. These are also the first genome sequences of P. damselae subsp. piscicida isolated in Oceania and, to our knowledge, in the Southern hemisphere. We also investigated the phylogenetic relationships between Australian and overseas isolates, revealing that Australian P. damselae subsp. piscicida are more closely related to the Asian and American strains rather than to the European ones. We investigated the mobilome and present new evidence showing that a host specialization process and progressive adaptive evolution to fish are ongoing in P. damselae subsp. piscicida, and are largely mediated by transposable elements, predominantly in chromosome 2, and by plasmids. Finally, we identified two novel potential virulence determinants in P. damselae subsp. piscicida - a chorismate mutase gene, which is ubiquitously retained and co-localized with the AIP56 apoptogenic toxin-encoding gene on the pPHDP10 plasmid, and transfer-messenger RNA gene ssrA located on the main chromosome, homologous to a critical-to-virulence determinant in Yersinia pseudotuberculosis. Our study describes, to our knowledge, the only fully closed and manually curated genomes of P. damselae subsp. piscicida available to date, offering new insights into this important fish pathogen and its evolution.

Shallow seamounts represent speciation islands for circumglobal yellowtail Seriola lalandi

Phenotypic plasticity in life-history traits in response to heterogeneous environments has been observed in a number of fishes. Conversely, genetic structure has recently been detected in even the most wide ranging pelagic teleost fish and shark species with massive dispersal potential, putting into question previous expectations of panmixia. Shallow oceanic seamounts are known aggregation sites for pelagic species, but their role in genetic structuring of widely distributed species remains poorly understood. The yellowtail kingfish (Seriola lalandi), a commercially valuable, circumglobal, epipelagic fish species occurs in two genetically distinct Southern Hemisphere populations (South Pacific and southern Africa) with low levels of gene-flow between the regions. Two shallow oceanic seamounts exist in the ocean basins around southern Africa; Vema and Walters Shoal in the Atlantic and Indian oceans, respectively. We analysed rare samples from these remote locations and from the South African continental shelf to assess genetic structure and population connectivity in S. lalandi and investigated life-history traits by comparing diet, age, growth and maturation among the three sites. The results suggest that yellowtail from South Africa and the two seamounts are genetically and phenotypically distinct. Rather than mere feeding oases, we postulate that these seamounts represent islands of breeding populations with site-specific adaptations.

Morphology and molecular identification of the zoological origin of medicinal seahorses in Chinese herbal markets

Seahorses are a charismatic group of fish that have high economic value for their unique appearance and important medicinal values. They were heavily traded as traditional Chinese medicines. Authenticating the zoological origin of medicinal seahorses is very difficult because of their similar morphology. To study the identification characteristics of dried seahorse, and to provide a scientific basis for seahorse resource conservation and market supervision, 64 dried specimens from China's four major pharmaceutical markets were investigated based on morphology and COI sequences. Sixty-four COI sequences of 662 bp length revealed 43 unique haplotypes, which were divided into 12 main clades in both NJ and UPGMA phylogenetic trees. Eleven species including Hippocampus spinosissimus, H. barbouri, H. kuda, H. comes, H. histrix, H. trimaculatus, H. kelloggi, H. ingens, H. mohnikei, H. erectus and H. jayakari were clustered on different branches and showed respective monophyly. The results were confirmed by morphology and BLAST analysis. Hippocampus capensis and H. fuscus, which were clustered together in the phylogenetic tree, could be distinguished by different morphology. The morphological and molecular determination revealed 13 seahorse species in Chinese herbal markets. The method of DNA sequences analysis combined with morphological characteristics is conducive to accurately identify the zoological origin of commercial seahorses.

A new perspective on biogeographic barrier in the flathead grey mullet (Pisces: Mugilidae) from the northwest Pacific

BACKGROUND

The flathead grey mullet, Mugil cephalus has a global distribution in tropical, subtropical and temperate seas worldwide. Previous studies proposed that globally distributed M. cephalus comprises at least 14 different lineages, and divided into two or three groups in the northwest Pacific. Therefore, we hypothesized that there may exist at least two lineages in Korea.

OBJECTIVE

The aim of this study was to determine the number of lineages of flathead grey mullet in Korea, and detail their biogeographic boundaries, and taxonomic implications using various molecular markers.

METHODS

Two partial mitochondrial DNA (mtDNA) gene sequences (COI and 16S rRNA) and nine microsatellite loci were analyzed in 260 individuals from ten locations.

RESULTS

Phylogenetic trees from two partial mtDNA gene sequences revealed two distinct lineages of flathead grey mullet (P distance = 0.016-0.021). Lineage 1 (L1) consisted of mullets from all locations except for the Pacific coasts of Japan, while lineage 2 (L2) consisted of mullets from the Jeju Island, Shanghai, and the Pacific coasts of Japan. The STRUCTURE analyses of msat data also revealed two distinct groups.

CONCLUSION

This study was the first to reveal the coexistence of two lineages of flathead grey mullet in Korea. L2 was confined to the Jeju Island in Korea, implying a biogeographic boundary between the two lineages. The allopatric distribution and genetic heterogeneity between lineages may be affected by an ancient geographic isolation during the glacial period and maintained due to adaptation to oceanic characteristics. Collectively, the two lineages may be comprised of distinct species.

Annotated checklist of fishes from Monterey Bay National Marine Sanctuary with notes on extralimital species

Monterey Bay National Marine Sanctuary is a federal, marine protected area located off the central coast of California, USA. Understanding biodiversity, and how it is changing, is necessary to effectively manage the sanctuary. The large size of this sanctuary, which contains a variety of habitats and is influenced by several water masses, provides for a diverse fish fauna. The central California coast has a rich history of ichthyological research and surveys, contributing to a unique repository of information on fish diversity. Herein, we provide a checklist of fishes that occur within the sanctuary, including justification for each species. Ancillary record information including name-bearing type specimens, historic species, cold- or warm-water event species, introduced species, and occurrence at Davidson Seamount or Elkhorn Slough are also provided. This represents the first comprehensive annotated checklist of 507 fishes known to occur within the sanctuary. In addition, 18 species are considered to be extralimital. This annotated checklist of fishes can be used by those interested in zoogeography, marine protected areas, ichthyology, regional natural history, and sanctuary management.

Genomic DNA variation confirmed Seriola lalandi comprises three different populations in the Pacific, but with recent divergence

Captive breeding programs and aquaculture production have commenced worldwide for the globally distributed yellowtail kingfish (Seriola lalandi), and captive bred fingerlings are being shipped from the Southern Hemisphere to be farmed in the Northern Hemisphere. It was recently proposed that Pacific S. lalandi comprise at least three distinct species that diverged more than 2 million years ago. Here, we tested the hypothesis of different “species” in the Pacific using novel genomic data (namely single nucleotide polymorphisms and diversity array technology markers), as well as mtDNA and DNA microsatellite variation. These new data support the hypothesis of population subdivision between the Northeast Pacific, Northwest Pacific and South Pacific, and genetic divergence indicates restriction to the gene flow between hemispheres. However, our estimates of maximum mtDNA and nuclear DNA divergences of 2.43% and 0.67%, respectively, were within the ranges more commonly observed for populations within species than species within genera. Accordingly our data support the more traditional view that S. lalandi in the Pacific comprises three distinct populations rather than the subdivisions into several species.

Spatio-temporal patterns of genetic variations in populations of yellowtail kingfish Seriola lalandi from the south-eastern Pacific Ocean and potential implications for its fishery management

The genetic population structure and genetic diversity of yellowtail kingfish Seriola lalandi from the coastal south-eastern Pacific Ocean (SEP) were evaluated at spatiotemporal scale in order to understand the ecology of this species. Between 2012 and 2015, temporal and spatial population genetic structure and a low genetic diversity were detected in S. lalandi from SEP. These results suggest that S. lalandi specimens arriving annually from offshore to the SEP coast could come from at least two genetically distinct populations, revealing a particular life strategy (i.e. reproductive or habitat segregation) for this fish species. Therefore, the SEP coast might constitute a point of population mixing for this species. Additionally, the low genetic diversity of S. lalandi in the SEP could be a result of a founder effect or overfishing. Regardless of the process explaining the genetic diversity and structure of S. lalandi in this geographical area, this new information should be considered in order to implement successful fishery management of this resource in the South Pacific.