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

Biophysical assessments and blood profiling reveal physiological adaptations and environmental interactions of hilsa shad (Tenualosa ilisha)

The hilsa shad (Tenualosa ilisha) is a migratory fish of great economic and cultural importance in Bangladesh. However, its physiological adaptations to diverse environmental conditions are not well understood. This study provides a comprehensive assessment of the biophysical, hematological, and biochemical characteristics of hilsa shad from riverine, estuarine, and marine environments in Bangladesh. We sampled 180 adult fish from nine sites, revealing significant habitat-specific variations in water quality, with marine sites showing the highest levels of total dissolved solids (TDS) and specific conductance. Hematological analysis showed that fish from riverine environments had higher hematocrit values, which are crucial for oxygen transport during migration. Post-spawning fish exhibited elevated hemoglobin, RBC counts, and hematocrit levels, reflecting adaptations to the metabolic demands of migration and spawning. WBC counts were higher in females, particularly in estuarine and marine environments, suggesting a stronger immune response to environmental stressors. Serum biochemical analysis showed significant variations in liver enzyme activity, albumin, and cortisol levels, with elevated cortisol in riverine fish during spawning season, indicating heightened stress. These findings enhance our understanding of hilsa shad's physiological ecology, providing critical insights for conservation and management strategies amid environmental changes.

Chromosome-Level Genome Assembly and Comparative Transcriptome Analyses Identified Energy Conservation as a Key Strategy for Anadromous Adaptation of the Hilsa Shad, Tenualosa ilisha (Clupeiformes: Dorosomatidae)

Anadromous migration toward riverine tributaries is often challenged by altered environmental cues, food scarcity, and energy demands, sometimes at the expense of life itself. Tenualosa ilisha (Clupeiformes: Dorosomatidae), the national fish of Bangladesh, an anadromous shad, offers a model for understanding the molecular mechanisms of migration. To this end, we present a chromosome-level genome of T. ilisha and compare its transcriptomic imprints from muscle and liver across environments to trace the physiological shifts driving the migration. We observed rapid expansion of gene families to facilitate efficient signaling and osmotic balance, as well as a substantial selection pressure in metabolism regulatory genes, potentially relevant to a highly anadromous fish. We detected 1298 and 252 differentially expressed transcripts between sea and freshwater in the liver and muscle of T. ilisha, respectively, reflecting habitat and organ-specific adaptations. Co-expression analysis led us to hypothesize that the strength required for breeding migration toward upstream rivers is fueled by muscle protein catabolism forming ubiquitin-proteasomal complexes. In the liver, we observed a group of genes promoting fatty acid (FA) synthesis significantly in the riverine habitat. Regulation of FADS2 and ELOVL2 in the river reasoned the natural abundance of LC-PUFAs with better energy utilization in T. ilisha. Moreover, active gluconeogenesis and reduced insulin signaling in the liver are possibly linked to glucose homeostasis, potentially induced by prolonged starvation during migration. These genomic resources will accelerate the future evolutionary and functional genomics studies of T. ilisha.

Integrated transcriptome catalog of Tenualosa ilisha as a resource for gene discovery and expression profiling

The silver pride of Bangladesh, migratory shad, Tenualosa ilisha (Hilsa), makes the highest contribution to the total fish production of Bangladesh. Despite its noteworthy contribution, a well-annotated transcriptome data is not available. Here we report a transcriptomic catalog of Hilsa, constructed by assembling RNA-Seq reads from different tissues of the fish including brain, gill, kidney, liver, and muscle. Hilsa fish were collected from different aquatic habitats (fresh, brackish, and sea water) and the sequencing was performed in the next generation sequencing (NGS) platform. De novo assembly of the sequences obtained from 46 cDNA libraries revealed 462,085 transcript isoforms that were subsequently annotated using the Universal Protein Resource Knowledgebase (UniPortKB) as a reference. Starting from the sampling to final annotation, all the steps along with the workflow are reported here. This study will provide a significant resource for ongoing and future research on Hilsa for transcriptome based expression profiling and identification of candidate genes.

Chromosome-Level Assembly of the Atlantic Silverside Genome Reveals Extreme Levels of Sequence Diversity and Structural Genetic Variation

The levels and distribution of standing genetic variation in a genome can provide a wealth of insights about the adaptive potential, demographic history, and genome structure of a population or species. As structural variants are increasingly associated with traits important for adaptation and speciation, investigating both sequence and structural variation is essential for wholly tapping this potential. Using a combination of shotgun sequencing, 10x Genomics linked reads and proximity-ligation data (Chicago and Hi-C), we produced and annotated a chromosome-level genome assembly for the Atlantic silverside (Menidia menidia)-an established ecological model for studying the phenotypic effects of natural and artificial selection-and examined patterns of genomic variation across two individuals sampled from different populations with divergent local adaptations. Levels of diversity varied substantially across each chromosome, consistently being highly elevated near the ends (presumably near telomeric regions) and dipping to near zero around putative centromeres. Overall, our estimate of the genome-wide average heterozygosity in the Atlantic silverside is among the highest reported for a fish, or any vertebrate (1.32-1.76% depending on inference method and sample). Furthermore, we also found extreme levels of structural variation, affecting ∼23% of the total genome sequence, including multiple large inversions (> 1 Mb and up to 12.6 Mb) associated with previously identified haploblocks showing strong differentiation between locally adapted populations. These extreme levels of standing genetic variation are likely associated with large effective population sizes and may help explain the remarkable adaptive divergence among populations of the Atlantic silverside.

A comparative metabolomics study on anadromous clupeid Tenualosa ilisha for better understanding the influence of habitat on nutritional composition

INTRODUCTION

Fish inhabiting different aquatic habitats adapts to the environment by metabolomic readjustments. Understanding the combined activities of all the metabolic pathways (metabolome) helps in better understanding the complex interactions between gene and environment.

OBJECTIVES

The anadromous migratory Tenualosa ilisha is a high value food fish comprising the dominant fishery of the rivers Padma and Hooghly. The present study aimed at understanding the influence of the two habitats on the nutritional composition of hilsa.

METHODS

Metabolite profiling was carried out by GC/MS. De novo assembly of hilsa liver transcriptome was generated under Illumina HiSeq platform and multivariate analysis was employed for correlation and comparison.

RESULTS

GC/MS fingerprinting showed C16:0, C18:1, C20:5 and C22:6 to be the predominant fatty acids present in hilsa liver, which were also found to be significantly higher in Hooghly hilsa. Comparative transcriptome analysis revealed that the differentially expressed genes were mainly associated with 'lipid metabolism' and 'amino acid metabolism' pathways. Multivariate analysis between the metabolites amino acid, fatty acid and corresponding gene expression showed that few genes of amino acid metabolism (EZH1, ALAS2 and ALDH4A1) positively correlated with individual amino acids (lysine, glycine and glutamate) in Hooghly hilsa. Similarly, the key genes for LC-PUFA biosynthesis (ELOVL5, FADS2, CPT1) showed positive correlation with individual LC-PUFAs (C18:3, C20:4, C20:5, C22:6), indicating higher LC-PUFA biosynthesis potential in Hooghly hilsa.

CONCLUSION

Comparative metabolomic study in hilsa from the two different habitats showed that the habitats influence the nutritional composition as evidenced by high abundance of amino acids lysine, leucine and arginine and LC-PUFAs C18:3, C20:4, C20:5, C22:6 in Hooghly hilsa.

Draft genome assembly of Tenualosa ilisha, Hilsa shad, provides resource for osmoregulation studies

This study provides the first high-quality draft genome assembly (762.5 Mb) of Tenualosa ilisha that is highly contiguous and nearly complete. We observed a total of 2,864 contigs, with 96.4% completeness with N₅₀ of 2.65 Mbp and the largest contig length of 17.4 Mbp, along with a complete mitochondrial genome of 16,745 bases. A total number of 33,042 protein coding genes were predicted, among these, 512 genes were classified under 61 Gene Ontology (GO) terms, associated with various homeostasis processes. Highest number of genes belongs to cellular calcium ion homeostasis, followed by tissue homeostasis. A total of 97 genes were identified, with 16 GO terms related to water homeostasis. Claudins, Aquaporins, Connexins/Gap junctions, Adenylate cyclase, Solute carriers and Voltage gated potassium channel genes were observed to be higher in number in T. ilisha, as compared to that in other teleost species. Seven novel gene variants, in addition to claudin gene (CLDZ), were found in T. ilisha. The present study also identified two putative novel genes, NKAIN3 and L4AM1, for the first time in fish, for which further studies are required for pinpointing their functions in fish. In addition, 1.6 million simple sequence repeats were mined from draft genome assembly. The study provides a valuable genomic resource for the anadromous Hilsa. It will form a basis for future studies, pertaining to its adaptation mechanisms to different salinity levels during migration, which in turn would facilitate in its domestication.