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

Abstract

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.

Effects of ammonia on the cellular, physiological, biochemical and genetic traits of Indian major carp (Labeo rohita) fry in artisanal Bangladeshi aquaculture

“…Five different genes with different functional roles were used for gene expression analysis; these included genes related to growth and metabolism (GH, IGF‐I and G‐3‐P) and immunity (hepcidin and interleukin‐1). We chose elongation factor 1 alpha as the reference gene because its suitability has been well documented in numerous aquatic species (Chowdhury et al., 2023; Moshtaghi et al., 2018; Sahu et al., 2015; Zeynali et al., 2020). The candidate genes were selected due to their inferred functional roles in several earlier studies (Aziz et al., 2017; Moshtaghi et al., 2016; Rogl et al., 2018; Sahu et al., 2015).…”

“…glycerol‐3‐phosphate [G‐3‐P]) and immune (e.g. hepcidin, interleukin‐1) genes, among others (Chowdhury et al., 2023; Rahi et al., 2023). Testing the effects of different doses of ammonia on these biological markers in Rohu will help to measure the level of imposed stress and the mechanisms (how ammonia affects the production of Rohu) involved in the loss or failure of aquaculture production.…”

Cellular, Physiological, and Biochemical Basis of Adaptive Response to Variable Osmotic Environments by the River Shad, Tenualosa ilisha

“…It is an anadromous and important transboundary fsh that lives in the Bay of Bengal and migrates to the upstream rivers of Bangladesh (86% share), India (8% share), and Myanmar (4% share) for breeding, and the nursing of ofspring [1,2]. Since 2016, the annual capture of hilsa has increased to 0.5 million tones and this single species alone contributes ≈12% (0.53 million MT) of the total fsh production in Bangladesh [3]. Besides, hilsa contributes approximately 1.15% to the total gross domestic product (GDP) of Bangladesh.…”

“…Terefore, migratory fsh (hilsa) must deploy an appropriate adaptation mechanism to counteract these challenges in hypertonic to hypotonic medium [27]. Te hyperosmoregulatory mechanisms compensate with a low water intake, active absorption of ions by the gills and production of hypotonic urine by kidney [3,20,25]. In sea water, hypo-osmoregulatory mechanisms compensate for water loss and ionic invasion.…”