International Journal of Aquaculture, 2024, Vol.14, No.2, 62-72 http://www.aquapublisher.com/index.php/ija 65 The figure shows a cluster analysis of the expression of genes related to sexual reproduction, covering multiple stages from sex determination to cell wall biosynthesis. These color blocks show the differences in the expression of specific genes in different reproductive stages. Such data emphasize the importance of transcriptome analysis in revealing key regulatory mechanisms in algal reproduction. The gene expression patterns during sex determination and gamete recognition reveal sex-specific regulatory networks, while the expression patterns of cell wall biosynthesis are associated with changes in cell structure after reproduction. These findings not only enhance our understanding of algal biology, but may also guide future biotechnology applications. 4 Genetic Mechanisms of Algal Adaptation 4.1 Stress response genes Algae have developed various genetic mechanisms to adapt to environmental stressors, such as changes in salinity, temperature, and pH. For instance, the adaptation of Alewife populations to freshwater environments involves the transcriptional regulation of osmoregulatory genes. Specifically, genes that regulate gill ion exchange, such as the freshwater paralog of Na+/K+-ATPase α-subunit, are more highly expressed in landlocked populations, facilitating enhanced freshwater tolerance (Velotta et al., 2017). Similarly, in Picochlorumspecies, gene gain and loss, as well as horizontal gene transfer (HGT), play crucial roles in adapting to salinity stress. One notable HGT candidate, indolepyruvate decarboxylase, is differentially expressed under salinity stress, highlighting the importance of gene regulation in stress response (Foflonker et al., 2018). 4.2 Regulatory networks Regulatory networks are essential for coordinating the expression of genes involved in stress responses and adaptation. In the case of acidophilic green algae, such as Chlamydomonas eustigma, higher expression of heat-shock proteins and H+-ATPase, along with the acquisition of metal-detoxifying genes through HGT, are key regulatory mechanisms that facilitate adaptation to acidic environments (Hirooka et al., 2017). Additionally, the genomic analysis of Ostreococcus ecotypes reveals that faster-evolving genes, particularly those encoding membrane or excreted proteins, are subject to selection pressures driven by environmental factors such as resistance to viruses and grazers (Jancek et al., 2008). These regulatory networks enable algae to fine-tune their physiological responses to diverse environmental challenges. 4.3 Evolutionary adaptations Evolutionary adaptations in algae are driven by various genetic mechanisms, including endosymbiotic gene transfer, polygenic adaptation, and balancing selection. The evolutionary history of algae, as revealed by genomic studies, indicates that endosymbiotic gene transfer has played a significant role in the diversification of algal phyla (Khan et al., 2020). In fish, adaptive evolution often involves soft sweeps, where shifts in allele frequencies rather than fixation of beneficial alleles contribute to local adaptation (Bernatchez et al., 2016). This mechanism is also observed in killifish populations that have rapidly adapted to toxic pollution through selective sweeps on existing genetic variation, particularly targeting the aryl hydrocarbon receptor-based signaling pathway (Reid et al., 2016). These evolutionary processes underscore the dynamic nature of genetic adaptation in response to environmental pressures. 5 Case Studies in Algal Genomics and Transcriptomics 5.1 Genomic adaptations to salinity Salinity is a critical environmental factor influencing the survival and distribution of aquatic organisms, including algae. Genomic studies have provided insights into the mechanisms of salinity adaptation. For instance, research on the spotted sea bass (Lateolabrax maculatus) has revealed that alternative splicing (AS) plays a significant role in salinity adaptation. RNA-Seq datasets identified 8618 AS events, with differential alternative splicing (DAS) events characterized in the gill and liver under varying salinity conditions. These DAS genes were enriched in gene ontology (GO) terms related to transcriptional and post-transcriptional regulation, highlighting the complexity of the transcriptome in response to salinity changes (Tian et al., 2020). Additionally, comparative genomics of Schizothoracine fish inhabiting soda lakes on the Tibetan Plateau identified expansions of
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