At Del-Bem Lab, we study how genomes evolve, how molecular innovations emerge, and how these innovations shape the biology of plants and other complex biological systems. Our research combines comparative genomics, phylogenomics, evolutionary biology, bioinformatics, and large-scale data analysis to investigate the genomic mechanisms behind major evolutionary transitions.
Our central interest is understanding how new biological functions arise. We ask how genes are born, duplicated, lost, transferred, repurposed, or incorporated into older cellular systems. Although plants are the main focus of the lab, we also investigate broader patterns of genome evolution across cellular life and viruses, using them as comparative systems to understand general principles of genomic innovation.
Plant genome evolution and the origin of terrestrial life
Plants transformed the surface of the Earth. By becoming the dominant primary producers in terrestrial ecosystems, land plants reshaped atmospheric chemistry, soils, freshwater systems, animal evolution, and the structure of most habitats we know today. Understanding plant evolution is therefore essential for understanding the history of life on land.
One of our main research questions is how green plants became terrestrial organisms. We are especially interested in the evolutionary transition from streptophyte algae, the closest algal relatives of land plants, to the first embryophytes. This transition required profound innovations in development, reproduction, stress tolerance, mineral nutrition, cell wall biology, and interactions with microorganisms.
We investigate which genomic changes allowed early plants and their algal relatives to survive outside aquatic environments. How did they tolerate desiccation, temperature variation, UV radiation, salinity, mineral limitation, and toxic elements? How did they interact with early soils and microbial communities? How did they acquire nutrients from heterogeneous terrestrial substrates? How did their cells evolve the structural and regulatory systems required for growth without the buoyancy of water?
Cell wall evolution, soil interactions, and plant terrestrialization
The plant cell wall is one of the most important innovations in the evolution of green plants. It is not only a structural component; it is also a dynamic interface between the plant and the environment. Cell walls mediate growth, defense, water relations, cell-cell communication, microbial interactions, and the physical contact between plants and soils.
Our lab has a long-standing interest in the evolution of cell wall-related gene families. We investigate the origin and diversification of enzymes involved in the synthesis, remodeling, and degradation of plant polysaccharides, with special attention to xyloglucan and other wall-associated carbohydrates. This work connects molecular evolution to major ecological transitions, including the emergence of terrestrial plants, the evolution of roots and rhizoids, and the capacity of plants to modify and stabilize soils.
More recently, we have expanded this framework to study how horizontal gene transfer contributed to the diversity of plant carbohydrate-active enzymes. These analyses suggest that plant genomes did not evolve only by vertical inheritance, duplication, and divergence. They also incorporated genes from other organisms, including fungi and bacteria, which may have contributed to new biochemical capacities during plant evolution.
Horizontal gene transfer and the origin of molecular novelty
A major theme in the lab is the origin of novelty. We study how new genes and new gene families become integrated into pre-existing biological systems. This includes gene duplication, horizontal gene transfer, de novo gene birth, changes in domain architecture, and shifts in gene regulation.
In plants, we are particularly interested in how horizontally acquired genes became functional components of plant metabolism, defense, development, and environmental adaptation. Rather than treating horizontal gene transfer as an evolutionary curiosity, we investigate it as a potentially important source of biochemical innovation in Archaeplastida and land plants.
These questions are also connected to broader issues in genome evolution. Why do some gene families expand dramatically while others remain constrained? Why do some newly acquired genes become central to cellular functions, whereas others are rapidly lost? What genomic, ecological, and biochemical conditions favor the retention of new genes?
Mineral nutrition, stress adaptation, and plant environmental responses
The conquest of land required plants to solve new nutritional problems. In aquatic environments, nutrients are often directly available in solution. On land, plants had to interact with complex mineral substrates, variable water availability, and chemically heterogeneous soils.
We investigate the evolution of gene families involved in nutrient acquisition and environmental responses, including transporters and signaling components. A central question is how ancestral proteins with broad or poorly specialized activities became recruited into more specific functions during plant evolution.
Our work on iron uptake illustrates this broader interest. Iron is essential but chemically challenging, especially in terrestrial environments where its availability depends strongly on soil chemistry. By studying the evolution of metal transporters across green plants, we aim to understand how nutrient acquisition systems emerged, diversified, and became linked to the ecological expansion of plants on land.
Genome architecture, non-coding genes, and regulatory evolution
Plant genomes are large, dynamic, and often highly complex. They contain not only protein-coding genes, but also large repertoires of regulatory sequences, repetitive elements, non-coding RNAs, small RNAs, and multicopy gene families. Understanding plant evolution therefore requires looking beyond protein-coding genes alone.
We study how genome size, gene number, non-coding DNA, and RNA gene repertoires evolve across lineages. This includes questions about the relationship between genome expansion and functional capacity, the evolution of tRNA gene copy number and diversity, and the organization of repetitive and multicopy elements in genomes.
We are also interested in how genes enter and leave regulatory circuits. How does a gene become responsive to hormones, sugars, stress, development, or environmental signals? How do regulatory networks change over deep evolutionary time? These questions connect molecular evolution to plant physiology and development.
Comparative genomics and computational evolutionary biology
Most of our research relies on comparative approaches. We analyze genomes, transcriptomes, gene families, protein domains, phylogenies, orthology relationships, molecular functions, and quantitative traits across large evolutionary scales.
We use and develop computational strategies to connect genomic variation with biological phenotypes. This includes phylogeny-aware comparative methods, large-scale annotation pipelines, statistical modeling, and integrative analyses of public genomic databases. The goal is not only to describe gene families, but to infer the evolutionary processes that shaped them and to generate testable hypotheses about biological function.
Our comparative framework allows us to ask questions across different levels of biological organization: from individual domains and gene families to whole genomes, from molecular functions to organismal traits, and from specific plant adaptations to general principles of genome evolution.
Genome evolution beyond plants: viruses, mitochondria, and cellular life
Although plants remain the core biological system of the lab, we also study genome evolution in other organisms and genetic systems. These projects broaden our comparative perspective and allow us to test whether similar evolutionary processes operate across very different forms of life.
We have investigated the evolution of mitochondrial genomes, tRNA repertoires, eukaryotic gene families, and viral genomes. Our work on giant viruses and Asfarviridae-related viruses explores how gene duplication, genome expansion, gene gain and loss, and deep phylogenetic structure shape viral diversity. These systems are especially useful for understanding how genomes can expand, reorganize, and generate new functional repertoires over evolutionary time.
By comparing plants, microbes, organelles, and viruses, we aim to identify both lineage-specific innovations and broader genomic principles that apply across biological systems.
Current research directions
Current projects in the lab are organized around four main directions:
- Plant terrestrialization and Archaeplastida evolution: the genomic changes associated with the transition from aquatic green algae to land plants.
- Plant cell wall and carbohydrate-active enzymes: the evolution of polysaccharide-related gene families, with emphasis on xyloglucan, glycosyl hydrolases, glycosyltransferases, and horizontal gene transfer.
- Genome architecture and regulatory complexity: the evolution of genome size, non-coding DNA, tRNA genes, de novo genes, and regulatory circuits in eukaryotes.
- Comparative genomics across life: the use of plants, fungi, organelles, and viruses to understand general mechanisms of gene family evolution, genome expansion, and molecular innovation.
Our broader goal
The broader goal of Del-Bem Lab is to understand how genomes generate biological complexity. We are especially interested in the evolutionary events that changed the trajectory of life on Earth: the origin of plant terrestriality, the diversification of cell wall systems, the emergence of new regulatory layers, the expansion of genome architecture, and the repeated invention of molecular functions through duplication, transfer, and repurposing.
By combining evolutionary theory, genomics, and computational biology, we aim to reconstruct how past genomic innovations shaped present-day biodiversity and how these insights can help us understand plant biology, adaptation, and the long-term evolution of life.