International Journal of Aquaculture, 2024, Vol.14, No.2, 62-72 http://www.aquapublisher.com/index.php/ija 66 lineage-specific genes associated with ion transport and transmembrane functions. Positive selection on ion transport-related genes further underscores the importance of these mechanisms in salinity tolerance (Tong et al., 2019). 5.2 Transcriptomic responses to temperature changes Temperature fluctuations impose significant stress on algal species, necessitating rapid acclimation and long-term genetic adaptation. The red alga Galdieria sulphuraria, subjected to continuous cold stress, exhibited a 30% increase in growth rate after more than 100 generations. Whole-genome sequencing identified 757 variants in 429 genes involved in cell cycle regulation, gene regulation, signaling, and transmembrane transport, indicating a complex genetic reprogramming in response to cold stress. The accumulation of variants in CpG islands suggests epigenetic remodeling as a component of thermal adaptation (Rossoni and Weber, 2019). Similarly, the brown alga Ectocarpus sp. has been studied for its responses to temperature and salinity stresses. A high-density genetic map with 3,588 SNP markers identified 39 QTLs for growth-related traits under different temperature and salinity conditions, with GO enrichment tests highlighting membrane transport processes (Avia et al., 2017). 5.3 Genetic mechanisms of light adaptation Light is a fundamental environmental factor affecting photosynthetic organisms like algae. The genetic basis of light adaptation has been explored through proteomic comparisons of two Ostreococcus ecotypes. These studies revealed that faster-evolving genes encode membrane or excreted proteins, which are likely involved in cell surface modifications driven by selection for resistance to viruses and grazers. The relationship between GC content and chromosome length suggests recombination events since the divergence of the two strains, contributing to their unique genomic features and light adaptation strategies (Jancek et al., 2008). Additionally, the genome of the polar microalga Coccomyxa subellipsoidea C-169, which exhibits traits of cold adaptation, provides insights into the genetic mechanisms underlying light adaptation in extreme environments. The presence of Zepp retrotransposons and the loss of certain proteins in C-169 suggest evolutionary routes similar to those of psychrophilic microbes, aiding in its adaptation to low light and cold conditions (Blanc et al., 2012). 6 Integration of Genomics and Transcriptomics 6.1 Combined approaches in algal research The integration of genomics and transcriptomics has become a pivotal approach in algal research, providing comprehensive insights into the genetic and functional mechanisms underlying algal adaptation. Genomic data offers a blueprint of the organism's potential, while transcriptomic data reveals the active expression of genes under various conditions. This combined approach allows researchers to correlate genetic information with functional outcomes, thereby enhancing our understanding of how algae respond to environmental changes and stressors. 6.2 Insights gained from integrated studies Integrated genomic and transcriptomic studies have significantly advanced our knowledge of algal biology. For instance, the availability of over 100 whole-genome sequences of algae has opened new avenues for exploring the functional capabilities encoded by algal genomes. These studies have revealed that algae possess a vast array of genes with unknown functions, indicating a rich potential for discovering novel biological processes and pathways. Additionally, population genomics approaches have been instrumental in identifying genes associated with adaptive phenotypic variations and local climatic adaptations (Bernatchez, 2016; Bamba et al., 2018). By combining these genomic insights with transcriptomic data, researchers can pinpoint the specific genes and regulatory networks involved in algal adaptation to diverse environmental conditions. Khan et al. (2020) demonstrated strain engineering in advanced biotechnology processes for industrial applications. The approach starts with strain engineering, using synthetic biology and mutagenesis techniques to tailor organisms for specific traits (Figure 2). The most promising strains are identified through efficient screening methods and then transferred to the high-throughput selection stage. Process development involves optimizing these strains for large-scale production and purification. Finally, these strains are integrated into industrial
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