Plants spend their entire lifetime rooted to one spot. When faced with a bad situation, such as a swarm¹ of hungry herbivores（食草动物） or a viral（滤过性毒菌的） outbreak, they have no option to flee but instead must fight to survive. What is the key to their defense²? Chemistry. Thanks to this ongoing³ conflict, plants have evolved into amazing chemists, capable of synthesizing tens of thousands of compounds from thousands of genes⁴. These chemicals, known as specialized⁵ metabolites, allow plants to withstand transient（短暂的） threats from their environment. What's more, some of the same compounds benefit humans, with more than a third of medicinal drugs derived⁶ from plant specialized metabolites.

 

Understanding how plants evolved this prodigious⁷（惊人的） chemical vocabulary has been a longstanding goal in plant biology. A team of Carnegie scientists led by Seung Yon Rhee and Lee Chae undertook a large-scale comparative analysis of plant genomes to investigate how specialized metabolism⁸ evolved. Their findings, as reported in Science, have major implications for the way scientists search for novel beneficial metabolites in plants.

 

To perform the study, the team developed a computational pipeline⁹ system that can transform a sequenced plant genome into a representation of the organism's metabolism. This is known as a metabolic¹⁰ network.

 

"The key to our analysis, or any comparative genome analysis, is the consistency¹¹ and quality of the data across species," says Chae. "Our pipeline ensures this consistency with validated¹² levels of accuracy and coverage¹³."

 

Importantly, the pipeline allows the team to produce a reliable metabolic network for any sequenced genome in about two days or less--a vast savings¹⁴ in time and resources when compared to the previously¹⁵ months-long process, notes Chae.

 

Using the pipeline, the team reconstructed and analyzed¹⁶ metabolic networks for 16 species in the green plant lineage, including flowering plants, algae¹⁷, and mosses¹⁸. They found that genes producing specialized metabolites exhibit unusual properties in the way they evolved, including their number and organization within each genome, the genetic¹⁹ mechanisms²⁰ by which they form, and their tendency to be simultaneously²¹ activated²².

 

Collectively, these properties represent a distinct signature of specialized metabolic genes that offers an innovative²³ strategy for the discovery of novel specialized metabolites from various plant species. Such discoveries could have wide-ranging implications for many research fields, including agriculture, biotechnology, drug discovery, and synthetic²⁴ biology.

 

"Despite our reliance on plant compounds for health and well-being²⁵, we know very little about how they are produced or the true extent of their diversity in nature," says Rhee. "We hope that our findings will enable researchers to use these signatures as a tool to discover previously unknown specialized metabolites, to investigate how they benefit the plant, and to determine how they might benefit us."

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