# 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)

## TL;DR

This study explores how the Hilsa shad adapts to migration by conserving energy through genetic and metabolic changes.

## Contribution

The paper provides a chromosome-level genome and identifies energy conservation as a novel adaptive strategy in anadromous fish.

## Key findings

- Differential gene expression in liver and muscle tissues reveals habitat-specific adaptations.
- Muscle protein catabolism and ubiquitin-proteasomal complexes are hypothesized to fuel migration.
- Fatty acid synthesis and glucose homeostasis genes suggest metabolic adaptations to riverine environments.

## Abstract

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.