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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.

One of the major challenges in any sustainable aquaculture production systems is the accumulation of nitrogenous waste such as ammonia and its biological nitrification products viz nitrite and nitrate. Considering the bio-security issues, amelioration of these wastes without water exchange can be accomplished only by way of establishing in situ nitrification and denitrification through biofilters/ bioreactors activated with nitrifying/denitrifying bioaugmentors. In such systems, coexistence of aerobic denitrifiers, anaerobic ammonia oxidizers (Anammox) and complete ammonia oxidizers (Comammox) together with the autotrophic nitrifiers enhance the coupled nitrification-denitrification. This promotes total nitrogen removal without external carbon supplements or additional anerobic compartment in the system. Various recirculating aquaculture systems (RAS) comprise diverse nitrifying community in biofilters/bioreactors thereby imparting distinctive nitrogen conversion in the system. Meanwhile, the structure and population dynamics of the nitrifying/denitrifying consortia are influenced by the environmental factors forming the decisive factors of the success of the processes. Accordingly, understanding the complexity of nitrifying/denitrifying community composition turns out to be a requirement to facilitate its improvised performance. In this context, the review addresses different biological nitrogen removal systems, significance of nitrification-denitrification in RAS, genetic diversity of the key players in RAS, methods of analysis of their community structure, current application and prospects of the processes in RAS.

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