Transcriptomics in aquaculture: current status and applications

Abstract

Transcriptomics is the analysis of total RNA transcript in a cell, which gives a broad idea of cellular processes that are active and dormant. Recent advancement in next-generation sequencing technologies like high-throughput mRNA sequencing (RNA-seq) facilitates in deciphering the functional complexity of the whole transcriptome of an organism. In the recent past, transcriptome profiling has been widely used in aquaculture for effective identification and expression analysis of candidate genes involved in growth, reproduction, development, immunity, disease, stress and toxicology. On the paucity of a comprehensive genome sequence, transcriptomics enables the detection of molecular markers such as simple sequence repeats and single-nucleotide polymorphism associated with the trait of interest. This review summarizes the process of transcriptome analysis and the current state of transcriptomics in aquaculture related to diseases and immunity, reproduction and development, growth and nutrition, toxicology and stress. Further, this review highlights the application of transcriptomics, including generation of genetic resources, differential gene expression, analysis of molecular pathways and development of molecular markers.

Status of genetic and genomic approaches for delineating biological information and improving aquaculture production of farmed rohu, Labeo rohita (Ham, 1822)

“…Rohu research is still ongoing, but aquaculture faces numerous problems. High‐throughput sequencing platforms such as Illumina, ABI, 454, Ion‐torrent and PacBio have been widely used in model and non‐model fish to decipher the genomic information via genome/transcriptome sequencing (Qian et al, 2014; Yanez et al, 2015; Chandhini & Rejish Kumar, 2019). The affordable costs of sequencing and advances in the computational analyses have enabled tremendous progress in fish‐based genomic research (Bernatchez et al, 2017).…”

Protein–protein interaction network: an emerging tool for understanding fish disease in aquaculture

“…For any treatment to be effective, in-depth understanding of the pathogenic mechanisms of disease and immune system of fish is required (Sudhagar et al 2018), and this often involves studying the transcriptomic and proteomic changes and dynamics (for review on the role of transcriptomics in aquaculture, see Chandhini & Kumar 2019; for review on the role of proteomics in disease pathogenesis in aquaculture, see Ahmed et al 2019). However, as described in the works of Chandhini and Kumar (2019) and Ahmed et al (2019), the use of genomics and proteomics in disease management of aquaculture species allows direct prediction or identification of the involved proteins, but not the interactions with other proteins, and this greatly hinders the in-depth understanding of disease pathogenesis and subsequent management. Therefore, the application of the PPI network in aquaculture species may offer new insights into their defence mechanisms against incoming stressors.…”

“…For any treatment to be effective, in‐depth understanding of the pathogenic mechanisms of disease and immune system of fish is required (Sudhagar et al . 2018), and this often involves studying the transcriptomic and proteomic changes and dynamics (for review on the role of transcriptomics in aquaculture, see Chandhini & Kumar 2019; for review on the role of proteomics in disease pathogenesis in aquaculture, see Ahmed et al . 2019).…”

Fish Transcriptomics: Applied to Our Understanding of Aquaculture

“…next-generation sequencing, NGS) and computational methods, we can use genomic and transcriptomic information to better understand the biology of our source of nutrition (production of aquaculture) and improve production. Also, advancements in technology and bioinformatic tools have bolstered many "omic" fields which include transcriptomics but also genomics, metabolomics, proteomics and metagenomics (Chandhini and Kumar, 2019). All "omic" fields including transcriptomics provide extensive amounts of data and the opportunity to understand aquaculture from a holistic approach and address the issues associated with growth, nutrition, disease, and conservation.…”

“…In the past couple of years, there has been extensive amount of research to develop fast and reliable software needed for genomic sequencing on "single node" computers which contain multi-threaded processors (Martinez et al 2018). The transcriptome can be used in a wide range of applications such as identifying a collection of protein encoding genes, the composition of a gene with alternative splicing and post translation modifications, and lastly measure differential expression of hundreds to thousands of genes within a given individual (Chandhini and Kumar, 2019). Transcriptomic studies allow us to better understand gene expression within a temporal framework, where we can ask questions about how gene expression changes during different time periods.…”