Tree fern genome provides insight into its e

image: Alsophila spinulosa in a forest
vision Lake

Credit: Quanzi Li

Land plants originated from algae 470 million years ago and have been reshaping our world ever since. Throughout their evolution, ferns have undergone a series of changes that have helped them survive on land. For the first time, researchers have characterized the genome arrangement of tree ferns, providing new insight into how ferns evolved.

An important event in the evolution of land plants was the invention of their vascular systems, which help them carry water, nutrients and food through their bodies. These systems are made up of two tissues: xylem and phloem. While the xylem allows the transport of water to the stems and leaves, the phloem helps to transport sugars made by photosynthesis to the rest of the plant. In addition, only xylem cells are lined with lignin-supporting structural materials that give wood and bark sturdiness. The researchers wanted to understand how these vascular systems evolved in ferns and how lignin is made.

“Ferns are the earliest vascular plants, and lignified cell walls were an important innovation during the evolution of these plants,” said Ray Ming (GEGC), a professor of plant biology. “This study has improved our understanding of how vascular tissues evolved in ferns and other types of land plants.”

For this study, the researchers sequenced the genome of flying spider monkey tree fern Alsophila spinulosa and examined how the vascular tissues are constructed. They found that two vascular-related Mac-Domain genes were highly expressed in xylem compared to other tissues, indicating that these may be important regulators in the formation of xylem-specific cells.

Using microscopy and biochemical methods, the researchers also measured the levels of lignin and secondary metabolites — compounds that aren’t necessary for growth or reproduction, but provide certain benefits — in ferns. They discovered that lignin made up 40% of the stem cell wall. In comparison, wood generally contains 25%. They also discovered a new secondary metabolite, made primarily in the xylem, which they named “alsophilin.”

“This new compound is abundant in the xylem, probably as one of the compounds that fill the cavity of non-functional tracheid cells. We also identified the genes involved in alsophilin biosynthesis in the genome,” said Ming.

To understand how ferns evolved, the researchers compared the genomic sequence of A. spinulosa to other members of the same species at nine locations in China. To their surprise, they found that there were six distinct populations, differing in their genomic sequences. Based on their sequencing results, the researchers reconstructed the history of the fern population and saw that on two occasions these species experienced a drastic decline in population numbers. The first occurred 35.6 – 34.5 million years ago and the second occurred 2.5 – 0.7 million years ago.

“This analysis of genomes and lignin composition from a broader collection of ferns will help us understand the role of lignin in the early lineage of vascular plants,” Ming said. “In our future studies, we hope to increase the number of sites and sample size for the genomic analysis.”

The article “The flying spider-monkey tree fern genome provides insight into the evolution and arborescence of ferns” was published in Nature Plants and can be found at

The biochemical analysis was conducted in collaboration with Quanzi Li’s group at the State Key Laboratory of Tree Genetics and Breeding, Beijing, China.

The study was funded by the Fundamental Research Funds of the Chinese Academy of Forestry; the National Natural Science Foundation of China; the Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University; CAMS Innovation Fund for Medical Sciences; PUMC disciplinary development of synthetic biology; and the DOE Great Lakes Bioenergy Research Center.

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