International Journal of Aquaculture, 2024, Vol.14, No.2, 62-72 http://www.aquapublisher.com/index.php/ija 67 applications, emphasizing the importance of scalability and cost-effectiveness. Integrating genomics and transcriptomics into algal biology research has significantly expanded our understanding of algal bioprocesses, enabling targeted manipulation of their metabolic pathways to optimize product yields. This systematic approach not only simplifies the development of bioproducts, but also ensures that enhancement measures are economically feasible, thereby pushing the application of algal biotechnology into a practical and scalable category. Figure 2 The key steps in bioengineered green algae production (Adapted from Khan et al., 2020) 6.3 Case study: integrated analysis of algal adaptation A notable example of the power of integrated genomic and transcriptomic analysis is the study of the unicellular green algae Chlamydomonas reinhardtii. This model organism has been extensively used to elucidate biological processes critical to both plants and animals, as well as to develop commercial bio-products (Blaby-Haas and Merchant, 2019). Through the integration of genomic and transcriptomic data, researchers have been able to map out the evolutionary history of C. reinhardtii and identify key genes involved in its adaptation to various environmental stressors. This integrated approach has not only enhanced our understanding of the genetic mechanisms underlying algal adaptation but also provided valuable insights for future biotechnological applications (Khan et al., 2020). 7 Technological Advances and Methodologies 7.1 Next-generation sequencing Next-generation sequencing (NGS) has revolutionized the field of algal genomics by enabling the rapid and cost-effective sequencing of entire genomes. This technology has facilitated the publication of over 100 whole-genome sequences of algae, providing a comprehensive resource for understanding the genetic basis of algal diversity and adaptation. NGS has been instrumental in uncovering the evolutionary history of algae, revealing that they evolved through endosymbiotic gene transfer, which gave rise to multiple algal phyla (Khan et al., 2020). Additionally, NGS has allowed for the detailed analysis of specific algal species, such as Picochlorum, to elucidate their strategies for environmental adaptation, including gene gain and loss, and horizontal gene transfer (HGT) (Foflonker et al., 2018). 7.2 Bioinformatics tools The vast amount of genomic data generated by NGS requires sophisticated bioinformatics tools for analysis and interpretation. These tools are essential for annotating genomes, predicting gene functions, and understanding the
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