Not the genes, but how they work together makes a tree a tree

Eduardo Rodriguez Soldado has always been fascinated by DNA and how a single molecule holds the key to all known life.

“I wanted to understand how a sequence of A, C, T and G can lead to a living ecosystem,” he says.

That curiosity eventually led him to one of nature’s most imposing life forms: the tree. In his PhD thesis in the group of Nathaniel Street at Umeå Plant Science Centre and Umeå University, he set out to uncover the genetic mechanisms behind wood formation in both conifers and flowering trees, and to tackle a deceptively simple question.

A question hidden in plain sight

At first glance, the main question of his PhD thesis seems almost naive: What makes a tree a tree?

“It is easy to look at trees and think they are part of a single group of species that all came from one ancestor and then diverged. But that is not the case,” he explains. “Trees are not a single evolutionary group - they are a phenotype, a growth form that has evolved several times in different plant clades.”

Biologically speaking, a tree is a plant that can form and maintain woody tissue - specialized cell layers with strong, lignin-rich cell walls. They provide strength and allow height and longevity.

“The taller a plant grows, the more sunlight it can capture - and the more it can shade competitors,” he says. “This innovation enabled the formation of forests and the richest ecosystems on land.”

The real key innovation is the developmental programme that produces wood, and this is what he wanted to understand.

Scots pine was one of the six different tree species that Eduardo Rodriguez Soldado investigated in his PhD thesis.

Image Sonali Ranade

Six species, hundreds of samples

To do so, he compared gene activity and genomic data from six tree species: Norway spruce, Scots pine and lodgepole pine among the conifers, and aspen, birch and cherry among the flowering trees. Working with samples taken from tree trunks during peak growing season, he created detailed series of developing wood tissues, from the inner layers of the trunk to the outer ones.

“In total, we generated more than 400 samples and produced a large amount of data that we are still exploring,” he says.

By combining these datasets with comparative genomics and validation methods optimised for woody tissues, he was able to map how gene networks operate across species separated by hundreds of millions of years of evolution.

Not new genes - but rewired networks

What he found confirmed what previous research already suggested. There are no “tree genes” that switch on wood formation. It is about how they are regulated.

“Core wood programmes are conserved among species,” he says. “The evolutionary innovation lies in how each lineage rewires its regulators.”

It is like different symphonies played with the same set of instruments.

In other words, trees do not rely on unique sets of genes that suddenly appeared during evolution. Instead, they use largely shared genetic toolkits - but organize them differently. The crucial differences lie in regulatory networks: how genes are activated, how they interact with each other, and how these interactions shape development.

“It is like different symphonies played with the same set of instruments,” he explains.

The degree of conservation across such distant lineages surprised him and his colleagues. Even between conifers and flowering trees, separated by deep evolutionary time, many gene activity patterns were remarkably similar.

One of biology’s toughest tissues

The insights did not come easily. Wood is particularly difficult to analyse at the molecular level. Mature woody tissues are heavily lignified, which makes it extremely challenging to extract high-quality RNA and DNA.

Many sample series had to be repeated several times. Even standard extraction methods and advanced techniques used to study how proteins interact with DNA had to be adapted for woody species.

“I can barely think of a more difficult tissue to work with,” he says. “A significant part of my PhD thesis involved optimising techniques and adapting molecular protocols. It was a challenging detour, but it ultimately led to more robust methods.”

Working through these challenges also resulted in improved protocols and genomic resources that can help other researchers study wood formation in trees.

Eduardo Rodriguez Soldado during his PhD defence at Umeå University.

Image Zeynep Yağmur Karova

Understanding trees for future forests

Although his work is fundamentally driven by curiosity, its implications reach far beyond the lab. Trees are central to carbon storage, forestry and bio-based industries. Understanding how regulatory networks control wood formation may help breeders select trees better adapted to future climates or optimize traits such as wood density and composition.

“Our work provides comparative genomic resources, particularly for conifers, where such data are still limited. These resources may help support bioenergy development, improve breeding strategies and contribute to more resilient forests,” he says.

For Eduardo Rodriguez Soldado, the project has also shaped the direction of his own future work. As he completes his PhD, he is finalising the analyses, side projects and manuscripts that emerged from his thesis. With a background in biochemistry, plant biotechnology and bioinformatics, he feels ready for new challenges, possibly outside academia.

“I am eager to see where the resources we have produced will lead and what other branches of research might grow from them,” he says. “I would like to keep developing genomic tools – perhaps in industry, where I can explore practical applications.”