A haplotype-resolved draft genome of the European sardine (Sardina pilchardus)

Santamaría MT, Faria R, Machado AM, Fonseca MM, Froufe E, C. Castro LF. Population Genomics Reveals the Underlying Structure of the Small Pelagic European Sardine and Suggests Low Connectivity within Macaronesia

The European sardine (Sardina pilchardus, Walbaum 1792) is indisputably a commercially important species. Previous studies using uneven sampling or a limited number of makers have presented sometimes conflicting evidence of the genetic structure of S. pilchardus populations. Here, we show that whole genome data from 108 individuals from 16 sampling areas across 5000 km of the species' distribution range (from the Eastern Mediterranean to the archipelago of Azores) support at least three genetic clusters. One includes individuals from Azores and Madeira, with evidence of substructure separating these two archipelagos in the Atlantic. Another cluster broadly corresponds to the center of the distribution, including the sampling sites around Iberia, separated by the Almeria-Oran front from the third cluster that includes all of the Mediterranean samples, except those from the Alboran Sea. Individuals from the Canary Islands appear to belong to the Mediterranean cluster. This suggests at least two important geographical barriers to gene flow, even though these do not seem complete, with many individuals from around Iberia and the Mediterranean showing some patterns compatible with admixture with other genetic clusters. Genomic regions corresponding to the top outliers of genetic differentiation are located in areas of low recombination indicative that genetic architecture also has a role in shaping population structure. These regions include genes related to otolith formation, a calcium carbonate structure in the inner ear previously used to distinguish S. pilchardus populations. Our results provide a baseline for further characterization of physical and genetic barriers that divide European sardine populations, and information for transnational stock management of this highly exploited species towards sustainable fisheries.

The sequence and de novo assembly of the genome of the Indian oil sardine, Sardinella longiceps

The Indian oil sardine, Sardinella longiceps, is a widely distributed and commercially important small pelagic fish of the Northern Indian Ocean. The genome of the Indian oil sardine has been characterized using Illumina and Nanopore platforms. The assembly is 1.077 Gb (31.86 Mb Scaffold N50) in size with a repeat content of 23.24%. The BUSCO (Benchmarking Universal Single Copy Orthologues) completeness of the assembly is 93.5% when compared with Actinopterygii (ray finned fishes) data set. A total of 46316 protein coding genes were predicted. Sardinella longiceps is nutritionally rich with high levels of omega-3 polyunsaturated fatty acids (PUFA). The core genes for omega-3 PUFA biosynthesis, such as Elovl 1a and 1b,Elovl 2, Elovl 4a and 4b,Elovl 8a and 8b,and Fads 2, were observed in Sardinella longiceps. The presence of these genes may indicate the PUFA biosynthetic capability of Indian oil sardine, which needs to be confirmed functionally.

Sardines at a junction: Seascape genomics reveals ecological and oceanographic drivers of variation in the NW Mediterranean Sea

By evaluating genetic variation across the entire genome, one can address existing questions in a novel way while raising new ones. The latter includes how different local environments influence adaptive and neutral genomic variation within and among populations, providing insights into local adaptation of natural populations and their responses to global change. Here, under a seascape genomic approach, ddRAD data of 4609 single nucleotide polymorphisms (SNPs) from 398 sardines (Sardina pilchardus) collected in 11 Mediterranean and one Atlantic site were generated. These were used along with oceanographic and ecological information to detect signals of adaptive divergence with gene flow across environmental gradients. The studied sardines constitute two clusters (F_ST  = 0.07), a pattern attributed to outlier loci, highlighting putative local adaptation. The trend in the number of days with sea surface temperature above 19°C, a critical threshold for successful sardine spawning, was crucial at all levels of population structuring with implications on the species' key biological processes. Outliers link candidate SNPs to the region's environmental heterogeneity. Our findings provide evidence for a dynamic equilibrium in which population structure is maintained by physical and ecological factors under the opposing influences of migration and selection. This dynamic in a natural system warrants continuous monitoring under a seascape genomic approach that might benefit from a temporal and more detailed spatial dimension. Our results may contribute to complementary studies aimed at providing deeper insights into the mechanistic processes underlying population structuring. Those are key to understanding and predicting future changes and responses of this highly exploited species in the face of climate change.

The Preservation of PPARγ Genome Duplicates in Some Teleost Lineages: Insights into Lipid Metabolism and Xenobiotic Exploitation

Three peroxisome proliferator-activated receptor paralogues (PPARα, -β and -γ) are currently recognized in vertebrate genomes. PPARγ is known to modulate nutrition, adipogenesis and immunity in vertebrates. Natural ligands of PPARγ have been proposed; however, the receptor also binds synthetic ligands such as endocrine disruptors. Two paralogues of PPARα and PPARβ have been documented in teleost species, a consequence of the 3R WGD. Recently, two PPARγ paralogue genes were also identified in Astyanax mexicanus. We aimed to determine whether the presence of two PPARγ paralogues is prevalent in other teleost genomes, through genomic and phylogenetic analysis. Our results showed that besides Characiformes, two PPARγ paralogous genes were also identified in other teleost taxa, coinciding with the teleost-specific, whole-genome duplication and with the retention of both genes prior to the separation of the Clupeocephala. To functionally characterize these genes, we used the European sardine (Sardina pilchardus) as a model. PPARγA and PPARγB display a different tissue distribution, despite the similarity of their functional profiles: they are unresponsive to tested fatty acids and other human PPARγ ligands yet yield a transcriptional response in the presence of tributyltin (TBT). This observation puts forward the relevance of comparative analysis to decipher alternative binding architectures and broadens the disruptive potential of man-made chemicals for aquatic species.

Effect of fish paste products, fish balls 'tsumire', intake in Sprague-Dawley rats

The fish paste product, fish balls ‘tsumire’, is a traditional type of Japanese food made from minced fish as well as imitation crab, kamaboko and hanpen. Although tsumire is known as a high-protein and low-fat food, there is a lack of scientific evidence on its health benefits. Hence, we aimed to investigate the effects of tsumire intake on organ weight and biomarker levels in Sprague–Dawley rats for 84 d as a preliminary study. Six-week-old male Sprague–Dawley rats were divided into two groups: group I, fed normal diets, and group II, fed normal diets with 5 % dried tsumire. Throughout the administration period, we monitored their body weight and food intake; at the end of this period, we measured their organ weight and analysed their blood biochemistry. No significant differences were observed with respect to body weight, food intake, organ weight and many biochemical parameters between the two groups. It was found that inorganic phosphorus and glucose levels were higher in group II rats than in group I rats. On the other hand, sodium, calcium, amylase and cholinesterase levels were significantly lower in group II than in group I. Interestingly, we found that the levels of aspartate aminotransferase, alanine transaminase, lactate dehydrogenase and leucine aminopeptidase in group II were significantly lower than in group I, and that other liver function parameters of group II tended to be lower than in group I. In conclusion, we consider that the Japanese traditional food, ‘tsumire,’ may be effective as a functional food for human health management worldwide.

Twelve quick steps for genome assembly and annotation in the classroom

Eukaryotic genome sequencing and de novo assembly, once the exclusive domain of well-funded international consortia, have become increasingly affordable, thus fitting the budgets of individual research groups. Third-generation long-read DNA sequencing technologies are increasingly used, providing extensive genomic toolkits that were once reserved for a few select model organisms. Generating high-quality genome assemblies and annotations for many aquatic species still presents significant challenges due to their large genome sizes, complexity, and high chromosome numbers. Indeed, selecting the most appropriate sequencing and software platforms and annotation pipelines for a new genome project can be daunting because tools often only work in limited contexts. In genomics, generating a high-quality genome assembly/annotation has become an indispensable tool for better understanding the biology of any species. Herein, we state 12 steps to help researchers get started in genome projects by presenting guidelines that are broadly applicable (to any species), sustainable over time, and cover all aspects of genome assembly and annotation projects from start to finish. We review some commonly used approaches, including practical methods to extract high-quality DNA and choices for the best sequencing platforms and library preparations. In addition, we discuss the range of potential bioinformatics pipelines, including structural and functional annotations (e.g., transposable elements and repetitive sequences). This paper also includes information on how to build a wide community for a genome project, the importance of data management, and how to make the data and results Findable, Accessible, Interoperable, and Reusable (FAIR) by submitting them to a public repository and sharing them with the research community.

Characterization of miRNAs from sardine (Sardina pilchardus Walbaum, 1792) and their tissue-specific expression analysis in brain and liver

MicroRNAs are endogenous highly conserved short (~ 21 nucleotides) non-coding RNA molecules that play key roles in post-transcriptional gene regulation by translational inhibition or by target mRNA cleavage. In this report, using high stringent computational-based methods, a total of 101 putative miRNAs were identified from European sardine fish (Sardina pilchardus Walbaum, 1792). All the precursors of identified sardine miRNAs formed stable stem-loop structures and displayed high minimum free energy index (MFEI) values. For the experimental validation of the computationally predicted miRNAs, a tissue-specific quantitative study of eight randomly selected putative sardine miRNAs (spi-miR9, spi-miR26, spi-miR128, spi-miR129, spi-miR132, spi-miR212, spi-miR219, and spi-miR338) was performed in brain and liver and all the selected miRNAs were found to be overexpressed in brain tissue. Moreover, using RNAhybrid, a total of 83 potential target proteins of the characterized sardine miRNAs were identified those are involved in transcription, cellular development, defense mechanism, and various signaling pathways. To the best of our knowledge, this is the first report of sardine microRNAs and their targets.

The fatty acid elongation genes elovl4a and elovl4b are present and functional in the genome of tambaqui (Colossoma macropomum)

Long-chain (C_20-24) polyunsaturated fatty acids (LC-PUFA) are physiologically important nutrients for vertebrates including fish. Previous studies have addressed the metabolism of LC-PUFA in the Amazonian teleost tambaqui (Colossoma macropomum), an emerging species in Brazilian aquaculture, showing that all the desaturase and elongase activities required to convert C₁₈ polyunsaturated fatty acids (PUFA) into LC-PUFA are present in tambaqui. Yet, elongation of very long-chain fatty acid 4 (Elovl4) proteins, which participate in the biosynthesis of very long-chain (>C₂₄) saturated fatty acids (VLC-SFA) and very long-chain polyunsaturated fatty acids (VLC-PUFA), had not been characterized in this species. Here, we investigate the repertoire and function of two Elovl4 in tambaqui. Furthermore, we present the first draft genome assembly from tambaqui, and demonstrated the usefulness of this resource in nutritional physiology studies by isolating one of the tambaqui elovl4 genes. Our results showed that, similarly to other teleost species, two elovl4 gene paralogs termed as elovl4a and elovl4b, are present in tambaqui. Tambaqui elovl4a and elovl4b have open reading frames (ORF) of 948 and 912 base pairs, encoding putative proteins of 315 and 303 amino acids, respectively. Functional characterization in yeast showed that both Elovl4 enzymes have activity toward all the PUFA substrates assayed (18:3n-3, 18:2n-6, 18:4n-3, 18:3n-6, 20:5n-3, 20:4n-6, 22:5n-3, 22:4n-6 and 22:6n-3), producing elongated products of up to C₃₆. Moreover, both Elovl4 were able to elongate 22:5n-3 to 24:5n-3, a key elongation step required for the synthesis of docosahexaenoic acid via the Sprecher pathway.

Characterization of a Y-specific duplication/insertion of the anti-Mullerian hormone type II receptor gene based on a chromosome-scale genome assembly of yellow perch, Perca flavescens

Yellow perch, Perca flavescens, is an ecologically and economically important species native to a large portion of the northern United States and southern Canada and is also a promising candidate species for aquaculture. However, no yellow perch reference genome has been available to facilitate improvements in both fisheries and aquaculture management practices. By combining Oxford Nanopore Technologies long-reads, 10X Genomics Illumina short linked reads and a chromosome contact map produced with Hi-C, we generated a high-continuity chromosome-scale yellow perch genome assembly of 877.4 Mb. It contains, in agreement with the known diploid chromosome yellow perch count, 24 chromosome-size scaffolds covering 98.8% of the complete assembly (N50 = 37.4 Mb, L50 = 11). We also provide a first characterization of the yellow perch sex determination locus that contains a male-specific duplicate of the anti-Mullerian hormone type II receptor gene (amhr2by) inserted at the proximal end of the Y chromosome (chromosome 9). Using this sex-specific information, we developed a simple PCR genotyping assay which accurately differentiates XY genetic males (amhr2by+ ) from XX genetic females (amhr2by- ). Our high-quality genome assembly is an important genomic resource for future studies on yellow perch ecology, toxicology, fisheries and aquaculture research. In addition, characterization of the amhr2by gene as a candidate sex-determining gene in yellow perch provides a new example of the recurrent implication of the transforming growth factor beta pathway in fish sex determination, and highlights gene duplication as an important genomic mechanism for the emergence of new master sex determination genes.

A haplotype-resolved draft genome of the European sardine (Sardina pilchardus)

Background

The European sardine (Sardina pilchardus Walbaum, 1792) is culturally and economically important throughout its distribution. Monitoring studies of sardine populations report an alarming decrease in stocks due to overfishing and environmental change, which has resulted in historically low captures along the Iberian Atlantic coast. Important biological and ecological features such as population diversity, structure, and migratory patterns can be addressed with the development and use of genomics resources.

Findings

The genome of a single female individual was sequenced using Illumina HiSeq X Ten 10x Genomics linked reads, generating 113.8 gigabase pairs of data. Three draft genomes were assembled: 2 haploid genomes with a total size of 935 megabase pairs (N50 103 kilobase pairs) each, and a consensus genome of total size 950 megabase pairs (N50 97 kilobase pairs). The genome completeness assessment captured 84% of Actinopterygii Benchmarking Universal Single-Copy Orthologs. To obtain a more complete analysis, the transcriptomes of 11 tissues were sequenced to aid the functional annotation of the genome, resulting in 40,777 genes predicted. Variant calling on nearly half of the haplotype genome resulted in the identification of >2.3 million phased single-nucleotide polymorphisms with heterozygous loci.

Conclusions

A draft genome was obtained, despite a high level of sequence repeats and heterozygosity, which are expected genome characteristics of a wild sardine. The reference sardine genome and respective variant data will be a cornerstone resource of ongoing population genomics studies to be integrated into future sardine stock assessment modelling to better manage this valuable resource.

First draft genome assembly and identification of SNPs from hilsa shad ( Tenualosa ilisha) of the Bay of Bengal

Background: Hilsa shad ( Tenualosa ilisha), a widely distributed migratory fish, contributes substantially to the economy of Bangladesh. The harvest of hilsa from inland waters has been fluctuating due to anthropological and climate change-induced degradation of the riverine habitats.  The whole genome sequence of this valuable fish could provide genomic tools for sustainable harvest, conservation and productivity cycle maintenance. Here, we report the first draft genome of  T. ilisha from the Bay of Bengal, the largest reservoir of the migratory fish.

Methods: A live specimen of T. ilisha was collected from the Bay of Bengal. The whole genome sequencing was performed by the Illumina HiSeqX platform (2 × 150 paired end configuration). We assembled the short reads using SOAPdenovo2 genome assembler and predicted protein coding genes by AUGUSTUS. The completeness of the T. ilisha genome assembly was evaluated by BUSCO (Benchmarking Universal Single Copy Orthologs). We identified single nucleotide polymorphisms (SNPs) by calling them directly from unassembled sequence reads using discoSnp++.

Results: We assembled the draft genome of 710.28 Mb having an N50 scaffold length of 64157 bp and GC content of 42.95%. A total of 37,450 protein coding genes were predicted of which 29,339 (78.34%) were annotated with other vertebrate genomes. We also identified 792,939 isolated SNPs with transversion:transition ratio of 1:1.8. The BUSCO evaluation showed 78.1% completeness of this genome.

Conclusions: The genomic data generated in this study could be used as a reference to identify genes associated with physiological and ecological adaptations, population connectivity, and migration behaviour of this biologically and economically important anadromous fish species of the Clupeidae family.