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Horizontal genetic transfer (HGT) is a common phenomenon in eukaryotic genomes. However, the mechanisms by which HGT-derived genes persist and integrate into other pathways remain unclear. This topic is of significant interest because, over time, the stressors that initially favoured the fixation of HGT may diminish or disappear. Despite this, the foreign genes may continue to exist if they become part of a broader stress response or other pathways. The conventional model suggests that the acquisition of HGT equates to adaptation. However, this model may evolve into more complex interactions between gene products, a concept we refer to as the 'Integrated HGT Model' (IHM). To explore this concept further, we studied specialized HGT-derived genes that encode heavy metal detoxification functions. The recruitment of these genes into other pathways could provide clear examples of IHM. In our study, we exposed two anciently diverged species of polyextremophilic red algae from the Galdieria genus to arsenic and mercury stress in laboratory cultures. We then analysed the transcriptome data using differential and coexpression analysis. Our findings revealed that mercury detoxification follows a 'one gene-one function' model, resulting in an indivisible response. In contrast, the arsH gene in the arsenite response pathway demonstrated a complex pattern of duplication, divergence and potential neofunctionalization, consistent with the IHM. Our research sheds light on the fate and integration of ancient HGTs, providing a novel perspective on the ecology of extremophiles.

Prior to fertilization, mothers provision their oocytes with mRNA that regulates the early stages of development and may additionally include transcripts for proteins that support embryonic stress response early on. At some point during embryogenesis, however, these maternal transcripts are degraded as zygotic transcription activates and intensifies during a phenomenon known as the maternal-to-zygotic transition (MZT). Some evidence suggests that as the MZT progresses, and the effects of maternal transcripts are waning while the zygotic expression is being established, offspring of marine broadcast spawners become more vulnerable to environmental perturbations. In light of escalating threats to marine broadcast spawners, it is critical to understand their reproduction and development, which are essential processes for species resilience by repopulating and replenishing existing populations. Reef building corals, in particular, are under threat from multiple stressors at the local and global scales. Mass mortality has occurred in recent years due to a series of marine heatwaves. In addition, there is chronic stress occurring in the form of ocean acidification, or the decline in pH in surface waters due to the uptake of atmospheric carbon dioxide of anthropogenic origin. Here, we characterize the function of maternal mRNAs, the timeline of the MZT, and sensitivity of gene expression to ocean acidification (OA) in the reef- building coral, Montipora capitata to investigate role of the MZT in embryonic stress response in reef-building corals. In Manuscript 1, we examine gene expression over nine developmental stages in Montipora capitata from eggs and embryos at 1, 4, 9, 14, 22, and 36 hours-post-fertilization (hpf), as well as swimming larvae (9d), and adult colonies. Weighted Gene Coexpression Network Analysis revealed four expression peaks, identifying the maternal complement, two waves of the MZT, and adult expression. Gene ontology enrichment revealed maternal mRNA