Sarcoma in the thymus of juvenile meagre Argyrosomus regius reared in an intensive system

Chromosome genome assembly for the meagre, Argyrosomus regius, reveals species adaptations and sciaenid sex-related locus evolution

The meagre, Argyrosomus regius, has recently become a species of increasing economic interest for the Mediterranean aquaculture and there is ongoing work to boost production efficiency through selective breeding. Access to the complete genomic sequence will provide an essential resource for studying quantitative trait-associated loci and exploring the genetic diversity of different wild populations and aquaculture stocks in more detail. Here, we present the first complete genome for A. regius, produced through a combination of long and short read technologies and an efficient in-house developed pipeline for assembly and polishing. Scaffolding using previous linkage map data allowed us to reconstruct a chromosome level assembly with high completeness, complemented with gene annotation and repeat masking. The 696 Mb long assembly has an N50 = 27.87 Mb and an L50 = 12, with 92.85% of its length placed in 24 chromosomes. We use this new resource to study the evolution of the meagre genome and other Sciaenids, via a comparative analysis of 25 high-quality teleost genomes. Combining a rigorous investigation of gene duplications with base-wise conservation analysis, we identify candidate loci related to immune, fat metabolism and growth adaptations in the meagre. Following phylogenomic reconstruction, we show highly conserved synteny within Sciaenidae. In contrast, we report rapidly evolving syntenic rearrangements and gene copy changes in the sex-related dmrt1 neighbourhood in meagre and other members of the family. These novel genomic datasets and findings will add important new tools for aquaculture studies and greatly facilitate husbandry and breeding work in the species.

Influence of Age on Stress Responses of White Seabream to Amyloodiniosis

Amyloodiniosis is a disease that represents a major bottleneck for semi-intensive aquaculture, especially in Southern Europe. The inefficacy of many of the treatments for this disease on marine fish produced in semi-intensive aquaculture has led to a new welfare approach to amyloodiniosis. There is already some knowledge of several welfare issues that lead to amyloodiniosis as well as the stress, physiological, and immunological responses to the parasite by the host, but no work is available about the influence of fish age on the progression of amyloodiniosis. The objective of this work was to determine if stress, hematological, and histopathological responses are age dependent. For that purpose, we determined the mortality rate, histopathological lesions, hematological indexes, and stress responses (cortisol, glucose, lactate, and total protein) in “Small” (total weight: 50 ± 5.1 g, age: 273 days after eclosion (DAE)) and “Big” (total weight: 101.3 ± 10.4 g, age: 571 DAE) white seabream (Diplodus sargus) subjected to an Amyloodinium ocellatum infestation (8000 dinospores mL−1) during a 24-h period. The results demonstrated a strong stress response to A. ocellatum, with marked differences in histopathological alterations, glucose levels, and some hematological indexes between the fish of the two treatments. This work elucidates the need to take in account the size and age of the fish in the development and establishment of adequate mitigating measures and treatment protocols for amyloodiniosis.

The ages of the cancer-associated genes

In the accompanying manuscript (Litman and Stein, 2018) we list the ages of all the protein-coding genes and of many of the noncoding genes of the human genome. The present manuscript uses those results to derive the ages of the genes on the COSMIC list of somatic mutations in cancer. The lymphoma-associated genes in the COSMIC list are younger than the sarcoma-associated or the carcinoma-associated genes, or the genes shared by lymphomas and carcinomas. Genes that accreted to the evolving genome with the appearance of the fish are major contributors to the sarcoma-, lymphoma-, or carcinoma-associated gene sets, but it is genes accreted during the development of multicellularity that contribute most to the genes common to the classes. Genes arising with the evolution of the fish are also dominant in a list of noncoding genes associated with cancer. A list is provided of the COSMIC genes which have not yet been reported as drug targets.

Physiological responses of reared sea bream (Sparus aurata Linnaeus, 1758) to an Amyloodinium ocellatum outbreak

Amyloodiniosis represents a major bottleneck for semi-intensive aquaculture production in Southern Europe, causing extremely high mortalities. Amyloodinium ocellatum is a parasitic dinoflagellate that can infest almost all fish, crustacean and bivalves that live within its ecological range. Fish mortalities are usually attributed to anoxia, associated with serious gill hyperplasia, inflammation, haemorrhage and necrosis in heavy infestations; or with osmoregulatory impairment and secondary microbial infections due to severe epithelial damage in mild infestation. However, physiological information about the host responses to A. ocellatum infestation is scarce. In this work, we analysed the proteome of gilthead sea bream (Sparus aurata) plasma and relate it with haematological and immunological indicators, in order to enlighten the different physiological responses when exposed to an A. ocellatum outbreak. Using 2D-DIGE, immunological and haematological analysis and in response to the A. ocellatum contamination we have identified several proteins associated with acute-phase response, inflammation, lipid transport, homoeostasis, and osmoregulation, wound healing, neoplasia and iron transport. Overall, this preliminary study revealed that amyloodiniosis affects some fish functional pathways as revealed by the changes in the plasma proteome of S. aurata, and that the innate immunological system is not activated in the presence of the parasite.