International Journal of Marine Science, 2024, Vol.14, No.5, 295-303 http://www.aquapublisher.com/index.php/ijms 297 2.3 Comparative genomics: Ascidians and other marine invertebrates Comparative genomic studies between Ascidians and other marine invertebrates reveal both shared and unique adaptive strategies. For instance, the genetic basis of adaptation in Ascidians shows parallels with other marine organisms, such as the presence of genes under positive selection related to stress responses and environmental tolerance (Valero et al., 2021). However, Ascidians also exhibit distinct features, such as the specific expansion of gene families related to their unique tunic structure and the presence of horizontally transferred genes. Additionally, the genomic landscape of adaptation in Ascidians is shaped by both genetic and epigenetic variations, a feature that is increasingly recognized in other marine invertebrates as well (Guo et al., 2022). 3 Molecular Mechanisms of Environmental Adaptation 3.1 Gene families associated with stress response Gene families such as heat shock proteins (HSPs) play a crucial role in the stress response of Ascidians. HSPs are highly conserved proteins that assist in protein folding, repair, and protection against stress-induced damage. In the invasive ascidian Ciona savignyi, a comprehensive study identified 32 HSP-related genes, including HSP20, HSP40, HSP60, HSP70, HSP90, and HSP100, which are differentially expressed in response to temperature and salinity challenges (Huang et al., 2018). These proteins help maintain cellular homeostasis under stress conditions by preventing protein misfolding and aggregation. The expansion of HSPgene families, such as HSP70, has also been observed in other Ascidians like Styela clava, suggesting a genomic basis for their broad environmental adaptability (Wei et al., 2020). 3.2 Epigenetic modifications and adaptation Epigenetic modifications, particularly DNA methylation, are pivotal in the rapid adaptation of Ascidians to environmental changes. In Ciona robusta, significant DNA methylation variations were observed in genes associated with temperature and salinity, such as heat shock protein 90 and Na+-K+-2Cl− cotransporter (Pu and Zhan, 2017). These modifications occur mainly in gene bodies and are correlated with environmental factors, indicating that epigenetic regulation plays a role in local adaptation during biological invasions. Such epigenetic changes can lead to phenotypic plasticity, allowing Ascidians to thrive in diverse and changing environments (Cheaib et al., 2015). 3.3 Transcriptional regulation of adaptation to salinity and temperature 3.3.1 Heat shock proteins and thermal tolerance Heat shock proteins (HSPs) are central to the thermal tolerance of Ascidians. The transcriptional response of HSP genes to heat stress is well-documented, with HSP70 being one of the most responsive genes. In Ciona savignyi, HSP70-4 showed the highest induction after 1 hour of high-temperature treatment, highlighting its role in thermal adaptation (Huang et al., 2018). The regulation of HSPs involves heat shock transcription factors (HSFs), which bind to heat shock elements (HSEs) in the promoters of HSP genes, initiating their transcription in response to heat stress (Rossoni and Weber, 2019). 3.3.2 Ion Transporters in osmoregulation Ion transporters are essential for osmoregulation in Ascidians, enabling them to maintain cellular ion balance under varying salinity conditions. The Na+-K+-2Cl− cotransporter, for instance, is crucial for adapting to salinity changes. In Ciona robusta, DNA methylation of this transporter gene was significantly correlated with salinity levels, suggesting that both transcriptional and epigenetic mechanisms regulate its expression. Additionally, in the fish Cynoglossus semilaevis, HSP70 genes were upregulated under low salinity stress, indicating a potential cross-talk between heat shock proteins and ion transporters in osmoregulation (Deng et al., 2021). 4 Genetic Basis of Habitat Specialization 4.1 Adaptation to intertidal and subtidal zones Ascidians, like many marine organisms, exhibit remarkable adaptations to various environmental conditions, including intertidal and subtidal zones. The leathery sea squirt, Styela clava, provides a compelling example of genomic adaptations that facilitate survival in diverse habitats. The expansion of gene families related to heat-shock proteins and the complement system, as well as the horizontal transfer of cold-shock protein genes,
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