Exploring the science of plants, from the field to the lab

One Thousand Plant Genomes: Understanding One Billion Years of Evolution

Posted in Applied Science on October 25, 2019 by Samantha Frangos

Samantha Frangos is a Laboratory Technician in the Pfizer Plant Research Laboratory of The New York Botanical Garden.

Mosaic of diverse plant speciesThe green plant tree of life is built upon many evolutionary innovations. Plants have come a long way since they began as single-celled organisms one billion years ago. They have transitioned from water to land and managed to become the beautiful, towering, flowering and fruiting beings that are the backbone of life on earth. They have complex life histories—creating vascular systems, waxy cuticles, spores, seeds and flowers. These innovations define key turning points in the history of green plants, and they are what separate the major plant groups: green algae, mosses and liverworts, ferns, gymnosperms and flowering plants.

The One Thousand Plant Transcriptomes Initiative, also known as the 1KP initiative, is a global collaboration of nearly 200 plant scientists, including NYBG’s Dr. Dennis Stevenson. “This long term project integrates field work, herbarium research, and living collections with the latest in laboratory and information sciences as an international collaboration,” Dr Stevenson said. For almost 10 years, this group has been attempting to sequence the genes of one thousand plants, spanning every plant family on the tree of life. The publication of these sequences, 1,147 in total, brings science significantly closer to understanding how the tree of life works in the plant kingdom. By examining the similarities and differences in genes, we can more fully understand how plants created evolutionarily significant transitions. For example: we can use this data to understand how conifers, which disperse their seeds in cones, are related to flowering plants, which disperse their seeds in fruit and only appeared in the fossil record about 200 million years ago.

Several plants from the New York Botanical Garden’s living collections were included in the project, including the Sequoiadendron giganteum, which was planted in front of the Everett Children’s Adventure Garden in 1965. Dr. Stevenson, along with his associates, contributed almost 100 of the over 1,000 plants sequenced for this project, the majority representing the gymnosperm, fern and moss plant groups. Over 100 specialists contributed material from both the field and living collections that include the Central Collection of Algal Cultures; Royal Botanic Gardens, KewRoyal Botanic Garden Edinburgh; Atlanta Botanical Garden; Fairylake Botanical Garden, Shenzhen; the Florida Museum of Natural History; Duke University; University of British Columbia Botanical Garden; and the University of Alberta.

Diagram of the Tree of Life

In addition to the taxonomic expertise that was required to assure that the 1,000 plants chosen were an equal sampling across every branch of the tree of life, computational expertise was also required to tackle the amount of data created by such an endeavor. The efforts of the 1KP project resulted in the creation of approximately two orders of magnitude more genetic data than the totality of current plant databases. Not only botanists, but bioinformatics experts and computer scientists from across the globe developed new computational tools that can be used for the analysis of genetic data and the creation of plant family trees.

Plant scientists have long thought that plant evolution came as a result of plant genes, or in some cases whole genomes, being duplicated. These duplications allow a plant to keep one functioning version of a gene while the duplicated gene may result in a beneficial (or detrimental) mutation. A surprising result of this paper was that there was very little genome duplication seen in the chlorophyte (or green algae) plant group. That leads to the question, how did algae make the leap to land? There are an estimated 500,000 plant species in the world that have gone through almost one billion years of evolution. The diversity of the plant kingdom comes from the different ways in which plants figured out how to adapt to their very specific environments. This project will provide new hypotheses about the evolution and subsequent genetic diversity of green plants.  Following the success of this project, the 1KP team has already started thinking about their next endeavor: 10,000 genomes!

 For more information and to read the 1KP capstone paper, please head to Nature. Sequences, sequence alignments, and tree data are available through the CyVerse Data Commons.