1 Introduction

Algae, a diverse group of photosynthetic eukaryotes, play a crucial role in global carbon fixation and primary production in aquatic ecosystems. They exhibit a wide range of adaptations to various environmental conditions, from the harsh tidal zones inhabited by brown algae to the nutrient-poor waters where marine cyanobacteria thrive (Cock et al., 2010; Teng et al., 2017; Chen et al., 2020). The evolutionary history of algae is marked by multiple endosymbiotic events, leading to the acquisition of plastids and the diversification of algal lineages. These adaptations are not only morphological but also genetic, involving complex regulatory mechanisms that enable algae to respond to environmental stresses such as light intensity, salinity, and temperature fluctuations (Raven et al., 2003).

Algal species provides insights into the evolutionary processes that have shaped the diversity and complexity of itselfs (Blaby-Haas and Merchant, 2019). It helps in identifying key genes and pathways that contribute to the resilience and productivity of algae in various habitats. This knowledge is particularly important in the context of climate change, as it can inform strategies for conserving and managing algal populations that are critical for ecosystem stability and carbon cycling. Additionally, the study of algal genomics and transcriptomics can lead to biotechnological applications, such as the development of biofuels and the improvement of algal strains for aquaculture and bioremediation (Matsuzaki et al., 2004).

This study unravel the genetic mechanisms underlying algal adaptation by synthesizing findings from recent genomics and transcriptomics studies. The objectives are to: elucidate the genetic strategies employed by different algal groups to adapt to their environments, highlight the role of horizontal gene transfer and gene regulation in these adaptive processes, and explore the implications of these genetic mechanisms for ecological and biotechnological applications. Integrating data from multiple studies, this study seeks to provide a comprehensive understanding of how genetic diversity and evolutionary pressures shape the adaptability of algae, thereby contributing to the broader field of evolutionary biology and environmental science.

2 Overview of Algal Genomics

Algal genomics is a rapidly advancing field that provides critical insights into the genetic mechanisms underlying the adaptation, evolution, and functional capabilities of algae. With the increasing biotechnological, environmental, and nutraceutical importance of algae, understanding their genomic structure, the techniques used in their study, and key genomic findings is essential.

2.1 Algal genome structure

The structure of algal genomes varies significantly across different species, reflecting their diverse evolutionary histories and ecological niches. For instance, the genome of the polar eukaryotic microalga Coccomyxa subellipsoidea exhibits significant synteny conservation with its relatives, yet shows extensive intra-chromosomal rearrangements, which may contribute to its adaptation to cold environments (Blanc et al., 2012). Similarly, the genomic analysis of Picochlorum species reveals substantial heterozygosity and allelic diversity, which are crucial for their adaptation to variable environments such as salt plains and brackish waters (Foflonker et al., 2018). These structural variations highlight the complex genomic architecture that supports the ecological versatility of algae.

2.2 Techniques in algal genomics

Advancements in sequencing technologies and bioinformatics have revolutionized the study of algal genomics. Whole-genome sequencing, transcriptomics, and comparative genomics are among the key techniques employed. For example, RNA-Seq analysis has been used to assess gene expression patterns in Alexandrium minutum under nutrient-deficient conditions, providing insights into its physiological adaptations and stress responses (Meng et al., 2019). Additionally, the use of population genomics approaches, such as genome-wide association studies (GWAS) and selection scans, has enabled the identification of loci associated with adaptation and speciation in various algal species (Bamba et al., 2018). These techniques facilitate a comprehensive understanding of the genetic basis of algal adaptation and evolution.

2.3 Key genomic findings in algal research

Several key findings have emerged from genomic studies of algae, shedding light on their adaptive strategies and evolutionary processes. The genomic analysis of Picochlorum species has revealed that gene gain, loss, and horizontal gene transfer (HGT) play significant roles in their adaptation to salinity stress. In Coccomyxa subellipsoidea, the presence of unique gene clusters and the loss of certain proteins suggest specific adaptations to low temperatures. Furthermore, the study of Galdieria sulphuraria under continuous cold stress has identified numerous genetic variants and candidate genes involved in thermal adaptation, highlighting the complexity of the adaptive response at the genetic level (Rossoni and Weber, 2019). These findings underscore the dynamic nature of algal genomes and their capacity for rapid adaptation to changing environmental conditions.

3 Transcriptomics in Algal Research

3.1 Principles of transcriptomics

Transcriptomics is the study of the complete set of RNA transcripts produced by the genome under specific circumstances or in a specific cell. This field provides insights into gene expression patterns and regulatory mechanisms, which are crucial for understanding the functional elements of the genome and the molecular constituents of cells and tissues. In algal research, transcriptomics helps elucidate how algae respond to environmental changes, stress conditions, and nutrient availability, thereby revealing the underlying genetic mechanisms of adaptation and survival.

3.2 Techniques in transcriptome analysis

Several advanced techniques are employed in transcriptome analysis, including RNA sequencing (RNA-Seq), quantitative real-time PCR (qRT-PCR), and microarray analysis. RNA-Seq is a powerful and widely used method that allows for the comprehensive analysis of the transcriptome, providing both qualitative and quantitative data on RNA expression levels (Morse et al., 2018). This technique involves the conversion of RNA into complementary DNA (cDNA), which is then sequenced using high-throughput sequencing technologies. qRT-PCR is often used to validate RNA-Seq results by quantifying the expression levels of specific genes. Microarray analysis, although less commonly used today, involves hybridizing cDNA to a grid of DNA probes, allowing for the simultaneous measurement of the expression levels of thousands of genes.

3.3 Key transcriptomic findings in algal research

Recent transcriptomic studies have provided significant insights into the physiological and molecular responses of algae to various environmental conditions. For instance, a study on the marine toxic dinoflagellate Alexandrium minutum revealed that nutrient deficiencies (specifically nitrogen and phosphorus) significantly affect gene expression related to photosynthesis, metabolism, and toxin biosynthesis. The study found that under nutrient stress, A. minutum shifts its trophic mode to facultative mixotrophy, indicating an ecological adaptation strategy to survive in nutrient-poor environments (Figure 1) (Meng et al., 2019).

Figure 1 Cluster analysis of reproductive degree related to sexual reproduction (Adopted from Meng et al., 2019) Image caption: (A) Sex determination., (B) Sperm-egg recognition., (C) Sex differentiation., (D) Mating., (E) Fertilization., (F) Cell wall biogenesis. Specific colors represent different expression levels. Red, high expression; blue, low expression (Adopted from Meng et al., 2019)

Another key finding from transcriptomic research is the identification of genes involved in sexual reproduction in algae. In A. minutum, several unigenes related to sex determination, sperm-egg recognition, and mating were differentially expressed under nutrient stress conditions. This suggests that nutrient availability can influence reproductive processes, which may have implications for population dynamics and bloom formation in marine environments.

The figure 1 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 Picochlorum species, 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 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 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 evolutionary relationships among algal species. For instance, bioinformatics analyses have revealed that over half of the proteins encoded by algal genomes are of unknown function, highlighting the need for further functional characterization (López et al., 2011). Gene Ontology databases and similarity searches have been used to investigate the function of species-specific genes in Ostreococcus ecotypes, providing insights into their ecological adaptations (Jancek et al., 2008). Moreover, bioinformatics tools have been crucial in identifying the extent and impact of HGT in algal genomes, which plays a significant role in their adaptation to variable environments.

7.3 High-throughput functional genomics

High-throughput functional genomics approaches, such as transcriptomics and proteomics, complement genomic data by providing insights into gene expression and protein function. These methodologies have been used to study the coordinated gene regulation involved in algal adaptation to environmental stresses, such as salinity (Bian et al., 2019). Comparative proteomics has also been employed to analyze the genetic basis of adaptation in different algal ecotypes, revealing species-specific functions and the evolutionary rates of orthologous genes. These high-throughput techniques are essential for understanding the functional capabilities of algae and their responses to environmental changes.

8 Applications and Implications

8.1 Algal biotechnology

The advancements in algal genomics and transcriptomics have profound implications for algal biotechnology. The comprehensive genomic analysis of algae, such as the model organism Chlamydomonas reinhardtii, has revealed critical biological processes that can be harnessed for biotechnological applications (Khan et al., 2020). The genomic insights into Picochlorum species have demonstrated how gene regulation and horizontal gene transfer (HGT) contribute to environmental adaptation, which can be leveraged to engineer algae for specific biotechnological purposes, such as biofuel production and bioremediation (Stapley et al., 2010). Additionally, the proteomic comparison of Ostreococcus ecotypes has identified species-specific genes and functions (Table 1) that could be critical for developing algae-based products with enhanced resistance to environmental stressors.

Table 1 Biological functions of algal CRYs, including comparative data from transgenic lines (Adopted from Petersen et al., 2021) Table caption: a: Photoreceptor network; b: weak CPD activity; c: growth curve; Cr, Chlamydomonas reinhardti; Ot, Ostreococcus tauri; Pt, Phaeodactylum tricormutum (Adopted from Petersen et al., 2021)

8.2 Environmental impact and conservation

Understanding the genetic mechanisms of algal adaptation is crucial for assessing the environmental impact of climate change on primary producers. The genomic analysis of Picochlorum species has elucidated how these microalgae adapt to variable environments, providing insights into the resilience of algal populations under changing climatic conditions. This knowledge can inform conservation strategies aimed at preserving algal biodiversity and maintaining ecosystem stability. Furthermore, the evolutionary insights gained from algal genomics can help predict how algal communities might shift in response to environmental stressors, aiding in the development of conservation policies that mitigate the adverse effects of climate change.

8.3 Future prospects in algal research

The future of algal research is promising, with the potential for significant advancements in both fundamental and applied sciences. The ongoing sequencing and analysis of algal genomes will continue to uncover the genetic basis of adaptation and evolution, providing a deeper understanding of algal biology. Future research should focus on exploring the functional capabilities encoded by algal genomes, particularly in the context of environmental stress adaptation and interspecies interactions (Bonin et al., 2006). Additionally, the integration of multi-omics approaches, including genomics, transcriptomics, and proteomics, will enhance our ability to dissect complex biological processes and develop innovative biotechnological applications (Bamba et al., 2018). The continued study of algal genomics holds the promise of unlocking new avenues for sustainable development and environmental conservation.

9 Challenges and Future Directions

9.1 Technical challenges

The field of algal genomics and transcriptomics faces several technical challenges that hinder the comprehensive understanding of genetic mechanisms underlying algal adaptation. One significant issue is the quality and completeness of genome assemblies. As sequencing technologies have become more accessible, there has been a noticeable decline in the quality of genomic resources, including assembly quality, gene annotation quality, and genome completeness. This decline can be attributed to the lack of standardized practices for sequencing, assembly, and annotation, which complicates the cataloging and comparison of sequenced organisms (Hanschen and Starkenburg, 2020). Additionally, the presence of robust cell walls in many algal species poses a challenge for genetic manipulation and the extraction of bio-products, as seen in the case of Galdieria. Furthermore, the need for high-quality biochemical and molecular characterization of predicted proteins to verify their functions remains a critical bottleneck in understanding lipid-biosynthesis pathways in microalgae.

9.2 Research gaps and opportunities

Despite the progress made in algal genomics, several research gaps and opportunities remain. One major gap is the limited understanding of the evolutionary processes and genetic mechanisms that enable algae to adapt to extreme environments, such as polar regions and variable salinity conditions (Blanc et al., 2012). The role of horizontal gene transfer (HGT) in algal adaptation is an emerging area of interest, with studies showing that HGT contributes to the acquisition of novel functions and environmental stress responses (Foflonker et al., 2018). Additionally, the genetic basis of adaptation in nonmodel species, such as the common frog, highlights the need for genome-wide surveys to reveal selection signatures and confirm the footprints of selection (Bonin et al., 20006). Integrative studies combining genome-wide association studies (GWAS), selection scans, functional studies, and fitness measurements in the field are essential to identify loci for adaptation and understand the molecular basis of genetic trade-offs.

9.3 Emerging trends and innovations

Emerging trends and innovations in algal genomics and transcriptomics are poised to address some of the existing challenges and research gaps. The use of long-read sequencing and scaffolding technologies can significantly improve genome assembly quality and completeness, providing more accurate and comprehensive genomic resources (Hanschen and Starkenburg, 2020). Advances in gene prediction and genome assessment software, along with the implementation of standards for assembly quality and evidence-based gene annotation, are crucial for enhancing the reliability of genomic data. Additionally, the discovery of sexual cycles in extremophilic algae, such as Galdieria, opens new avenues for genetic manipulation and the study of haploid/diploid transitions (Goodenough, 2022). The integration of transcriptomic analyses to compare gene expression profiles between different cell types and environmental conditions can further elucidate the genetic mechanisms of adaptation. Overall, these innovations hold promise for advancing our understanding of algal adaptation and unlocking their potential for biotechnological applications.

10 Concluding Remarks

The exploration of algal genomics and transcriptomics has provided significant insights into the genetic mechanisms underlying algal adaptation. Key findings from the reviewed literature include: Algal genomics has revealed that algae evolved through endosymbiotic gene transfer, resulting in the formation of approximately eight distinct phyla. The model organism Chlamydomonas reinhardtii has been instrumental in elucidating biological processes critical to both plants and animals, as well as in the production of various bio-products. Studies on Picochlorum species have shown that gene gain and loss, along with horizontal gene transfer (HGT), play crucial roles in adaptation to variable environments, such as salinity stress. This highlights the dynamic nature of HGT in driving adaptation and expanding habitat ranges. Comparative genomic analyses between acidophilic and neutrophilic algae have identified key genetic adaptations, such as the high expression of heat-shock proteins and H+-ATPase, loss of certain metabolic pathways, and acquisition of metal-detoxifying genes through HGT, which facilitate survival in extremely acidic environments. The availability of complete genome sequences for various algal species has catalyzed the development of recombinant techniques. This has led to significant progress in the genetic engineering of both microalgae and macroalgae, with potential commercial applications in producing recombinant proteins and valuable algal products.

Genomics and transcriptomics are pivotal in advancing our understanding of algal biology and their adaptive mechanisms. These fields provide comprehensive insights into the genetic and molecular bases of algal evolution, environmental adaptation, and metabolic processes. The integration of genomic data with transcriptomic analyses allows researchers to identify key regulatory networks and gene functions that are essential for adaptation to diverse and often extreme environments. This knowledge is crucial for harnessing the biotechnological potential of algae, including the development of sustainable biofuels, bioproducts, and environmental remediation strategies.

The future of algal research lies in the continued integration of genomics and transcriptomics with other omics technologies, such as proteomics and metabolomics. This holistic approach will provide a more detailed understanding of the complex biological systems within algae. Additionally, advancements in CRISPR and other gene-editing technologies hold promise for precise genetic modifications, enabling the development of algae with enhanced traits for industrial applications. Future research should also focus on exploring the genetic diversity of lesser-studied algal species and their potential applications in biotechnology. Collaborative efforts across disciplines will be essential to fully exploit the genetic resources of algae and address global challenges such as climate change, food security, and sustainable energy production.

Acknowledgments

The publisher acknowledges the two anonymous peer reviewers for their careful examination and useful feedback on the initial draft of this study.

Conflict of Interest Disclosure

The author affirm that This study was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest.

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