Horizontal Gene Transfer in Eukaryotes: Key Insights

Genes are typically passed from parent to offspring, but they can also be acquired from unrelated organisms through horizontal gene transfer (HGT). While well-documented in bacteria and archaea, research increasingly shows that eukaryotes also experience HGT, influencing their evolution in unexpected ways.

Understanding how foreign genes integrate into eukaryotic genomes sheds light on adaptation, symbiosis, and disease resistance. Scientists continue to uncover new examples across diverse lineages, challenging traditional views of inheritance.

Mechanisms Within Eukaryotic Cells

Unlike prokaryotes, which readily exchange genes through plasmids and transduction, eukaryotic cells must navigate additional barriers, including nuclear compartmentalization and chromatin organization. Despite these challenges, HGT occurs in diverse eukaryotic lineages through mechanisms that allow foreign DNA to bypass cellular defenses and become functionally incorporated.

One primary route involves endosymbiosis, where intracellular organelles such as mitochondria and plastids contribute genetic material to the host genome. This process, known as endosymbiotic gene transfer (EGT), has been extensively studied in plants and protists, where organelle-derived genes relocate to the nuclear genome over evolutionary timescales. Non-homologous recombination facilitates this transfer, allowing sequences to integrate into chromosomal DNA. Some of these transferred genes acquire regulatory elements that enable their expression, contributing to metabolic adaptations.

Another mechanism involves the uptake of environmental DNA, observed in certain unicellular eukaryotes. Phagocytosis, typically associated with nutrient acquisition, can introduce foreign genetic material into the cytoplasm. If this DNA escapes degradation and reaches the nucleus, it may integrate into the genome through double-strand break repair pathways. Bdelloid rotifers, for example, have incorporated extensive foreign genes, likely facilitated by their ability to survive desiccation, which increases DNA fragmentation and uptake.

Viruses also play a significant role in HGT. Retrotransposons, mobile genetic elements derived from ancient viral infections, facilitate gene movement between species. Endogenous viral elements (EVEs) in eukaryotic genomes provide evidence of past viral-mediated transfers, some of which have been co-opted for host functions. For instance, syncytin, derived from an endogenous retrovirus, is essential for placental development in mammals, illustrating how viral sequences can be repurposed for new biological roles.

Examples in Various Organisms

HGT has been identified in a range of eukaryotic organisms, influencing genetic diversity and functional capabilities. While the extent and frequency of HGT vary, certain groups exhibit a higher propensity for acquiring foreign genes. Examining specific cases in protists, fungi, and plants provides insight into how these transfers contribute to evolutionary innovation.

Protists

Protists, a diverse group of mostly unicellular eukaryotes, exhibit extensive HGT, particularly in species that engage in phagotrophy or symbiosis. The dinoflagellate Karlodinium veneficum has acquired bacterial genes that enhance its ability to produce toxic polyketides, compounds that aid in predation and defense. Similarly, Euglena gracilis, a photosynthetic protist, has incorporated numerous genes from prokaryotic sources, particularly those involved in carbohydrate metabolism. A 2019 study in Nature Communications identified over 30 bacterial-derived genes in Euglena, many contributing to its ability to utilize diverse carbon sources. These findings suggest that HGT has expanded the metabolic flexibility of protists, enabling adaptation to variable environments.

Fungi

Fungal genomes contain numerous instances of HGT, often involving genes that enhance survival in specific ecological niches. Rhizopus delemar, a zygomycete fungus associated with plant decomposition, has integrated genes encoding carbohydrate-active enzymes from Actinobacteria, enabling more efficient degradation of complex plant polymers. Research published in PLOS Genetics (2020) highlighted this bacterial gene acquisition. Similarly, Aspergillus species have acquired bacterial-derived genes related to secondary metabolism, contributing to the production of bioactive compounds like mycotoxins and antibiotics. These horizontally acquired genes shape fungal metabolic pathways, conferring advantages in nutrient acquisition and microbial competition.

Plants

HGT in plants, though less frequent, has been documented in species engaged in parasitism or symbiosis. The parasitic plant Cuscuta (dodder) has acquired functional genes from its hosts, enhancing nutrient transport and defense suppression. A 2022 study in Current Biology demonstrated how these transfers improve the parasite’s ability to extract resources. Another example is Amborella trichopoda, an early-diverging angiosperm that has incorporated entire mitochondrial genomes from bacterial and algal sources. A 2013 study in Science found that while many of these foreign sequences appear non-functional, some have been repurposed for cellular processes, showing how plants integrate and utilize foreign genetic material.

Investigative Techniques in Genomics

Advancements in genomic sequencing have transformed the study of HGT in eukaryotes, enabling precise detection of foreign genetic material. High-throughput sequencing technologies, particularly whole-genome sequencing (WGS) and transcriptome analysis, provide comprehensive datasets that help identify transferred genes. By comparing genomic sequences across taxa, scientists can pinpoint anomalies in gene composition—such as discrepancies in GC content, codon usage biases, or phylogenetic incongruences—often signaling foreign origin.

Beyond sequence comparisons, functional validation techniques confirm the biological relevance of acquired genes. RNA sequencing (RNA-seq) determines whether transferred genes are actively transcribed. Combined with proteomics, which identifies and quantifies expressed proteins, researchers can assess whether these genes contribute to metabolism or structural functions. Gene knockout experiments using CRISPR-Cas9 further validate functionality by selectively disabling transferred genes and observing phenotypic consequences.

Phylogenetic methods help distinguish true HGT events from gene loss or convergent evolution. By constructing gene trees and comparing them with species trees, researchers can identify instances where a gene’s evolutionary trajectory deviates from expected lineage relationships. If a gene clusters more closely with homologs from distantly related organisms rather than its own lineage, it suggests horizontal acquisition. This technique has been particularly effective in identifying bacterial-derived genes in eukaryotic genomes, as seen in studies of plant mitochondrial DNA. Machine learning algorithms further refine these analyses, automating the detection of HGT signatures in large genomic datasets.

Convergence With Microbial Pathways

The acquisition of foreign genes through HGT has allowed eukaryotes to integrate microbial-derived pathways into their biochemical networks, enhancing metabolic versatility. This is particularly evident in organisms reliant on complex ecological interactions, where microbial genes provide adaptive advantages. Certain fungi and protists have incorporated bacterial genes involved in carbohydrate metabolism, enabling more efficient degradation of plant-derived polysaccharides. These enzymes, originally exclusive to prokaryotes, have been successfully integrated into eukaryotic genomes, expanding metabolic capabilities.

Beyond metabolism, microbial genes have influenced cellular signaling and stress responses in eukaryotes. Some horizontally acquired genes encode proteins that regulate oxidative stress, crucial for survival under fluctuating environmental conditions. Studies on extremophilic protists reveal bacterial-derived antioxidant enzymes that enhance resilience against reactive oxygen species, facilitating colonization of harsh habitats. Similarly, genes encoding transport proteins, such as ATP-binding cassette (ABC) transporters, have transferred from bacteria to certain eukaryotic lineages, improving their ability to handle toxic compounds and antimicrobial agents. These genetic acquisitions show how microbial pathways, once foreign, become integral to eukaryotic physiology.