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Untangling the Roots of Plant Genomes: Supporting a “Moonshot” for Botany

PNAS Journal Highlights Global Collaborative Efforts

Research from Fort Worth-based Botanical Research Institute of Texas is featured this month in the prestigious journal Proceedings of the National Academy of Sciences. The article, “Green Plant Genomes: What We Know in an Era of Rapidly Expanding Opportunities” highlights the progress of plant genomics and includes a roadmap for the enormous task of sequencing the genomes of plants worldwide.

“Nearly half a million species of plants inhabit the Earth today and the secrets to understanding nearly everything about them is hidden in the sequences of their DNA (the plant genome),” said Dr. W. John Kress, senior author of the paper and Curator Emeritus at the Smithsonian. “Plants are the foundation of environments across the planet and deciphering their genomes will be a game changer for understanding nearly all aspects of our own lives, from improving foods and medicines to inspiring artists and enhancing ecosystem stability.”

FWBG|BRIT Research Botanist Morgan Gostel, Ph.D., is a co-author of the article, which highlights the contributions of the FWBG|BRIT-based and Smithsonian Institution-funded Global Genome Initiative for Gardens (aka GGI-Gardens). Gostel is director of GGI-Gardens and has managed the international partnership since it began in 2015. To date, GGI-Gardens has supported the collection and preservation of genomic tissue from more than 10,000 species of plants.

“The biggest challenge to jumpstarting an ambitious genome sequencing project like the Earth BioGenome Project is getting access to high-quality tissue from almost half a million species of plants on Earth,” Gostel said. “With our current technology and expectations for where sequencing technologies are headed in the future, high-quality plant tissue, either from well-preserved or fresh collections is critical.”

Botanic gardens offer a good starting place for tissue collection. With more than 3,000 botanic gardens around the world, they contain more than a third of all plant species. “This is precisely the role that GGI-Gardens is playing: connecting genome researchers to botanic gardens, advancing our knowledge of the role that plants play in our lives and tapping into the marvelous power of gardens,” Gostel said.

The effort required to sequence plant genomes is no small task, but it is the goal of the Earth BioGenome Project, “a ‘moonshot’ for biology, [that] aims to sequence, catalog, and characterize the genomes of all of Earth’s eukaryotic biodiversity [including plants, animals, and fungi] over a period of ten years.” The article, one of ten published this week in a Special Feature in PNAS, is co-authored by an international group of plant scientists and outlines a map that will help researchers worldwide achieve this ambitious goal.

An organism’s genome contains all the instructions necessary to carry out the processes of life and it should come as no surprise that genomes are extremely complex. Sequencing and assembling whole genomes will allow researchers to understand how species are related to and have evolved from other species; how they perform essential biological functions; and how they interact with and respond to their environments. Sequencing whole plant genomes is especially complicated compared with other groups of organisms for several reasons, but largely because there are so many species of plants and they have highly variable and often extremely complex genomes.

Consider that as of today’s date, there are just 883 whole genome sequences available for green plants compared with 2,019 whole genome sequences available for vertebrates; yet there are more than 400,000 species of green plants compared with just 73,340 species of vertebrates. The variation in genome size among plants is also astounding – some plants have a genome as small as just 65,000 individual nucleotides (the molecules that make up the four ‘base pairs’ in the genetic code) and as large as nearly 150 billion nucleotides. There is incredible complexity involved with understanding plant genomes.

Untangling this complexity is at the root of this article. The authors present a roadmap that will help the global scientific community collect samples using new partnerships such as the Global Genome Initiative for Gardens and Global Genome Biodiversity Network as well as the latest advances in software and technology that will help researchers sequence and assemble highly complex plant genomes. With this new perspective, botanists will be able to advance plant genome sequencing like never before.

Citation:

Title: Green Plant Genomes: What We Know in an Era of Rapidly Expanding Opportunities

Volume 119 (4) e2115640118

https://www.pnas.org/content/119/4/e2115640118?cct=2546

W. John Kress1,2,3,*, Douglas E. Soltis4,5,6, Paul J. Kersey7, Jill L. Wegrzyn8, James H. Leebens-Mack9, Morgan R. Gostel10, Xin Liu11, and Pamela S. Soltis4,5

1National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, Washington, DC 20013-7012, USA. 2Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA. 3The Arnold Arboretum, Harvard University, Boston, MA 02130, USA. 4Florida Museum of Natural History, 5Biodiversity Institute, and 6Department of Biology, University of Florida, Gainesville, FL 32611, USA.  7Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK. 8Department of Ecology and Evolutionary Biology, Institute for Systems Genomics: Computational Biology Core, University of Connecticut, Storrs CT 06269-3214, USA. 9Department of Plant Biology, 2101 Miller Plant Sciences, University of Georgia, Athens, GA 30602-7271, USA. 10Botanical Research Institute of Texas (BRIT), Fort Worth, TX 76107-3400, USA. 11China National GeneBank, BGI-Shenzhen, Shenzhen, China.  

*Corresponding author: W. John Kress

See also:
Earth BioGenome Project Begins Genome Sequencing in Earnest: 3,000 Genomes Expected to Be Sequenced by End of 2022

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