The really big book of plants

After nine years of work, an international consortium of scientists has released gene sequences for more than 1100 plant species.

The massive undertaking – described in a paper in the journal Nature – is part of the One Thousand Plant Transcriptomes Initiative (1KP), a global collaboration to examine the diversification of plant species, genes and genomes back to the ancestors of flowering plants and green algae.

It reveals the timing of whole genome duplications and the origins, expansions and contractions of gene families contributing to fundamental genetic innovations enabling the evolution of algae, mosses, ferns, conifer trees, flowering plants and all other green plant lineages.

“In the tree of life, everything is interrelated, and if we want to understand how the tree of life works we need to examine the relationships between species,” says lead investigator Gane Ka-Shu Wong, from the University of Alberta, Canada. “That’s where genetic sequencing comes in.” 

By sequencing and analysing genes from a broad sampling of species, the researchers say, they are better able to reconstruct gene content in the ancestors of all crops, model plant species, and gain a more complete picture of the gene and genome duplications that enabled evolutionary innovations.

More than 100 taxonomic specialists contributed material from field and living collections, including Germany’s Central Collection of Algal Cultures; the Royal Botanic Gardens in London and Edinburgh; Atlanta Botanical Garden, New York Botanical Garden and Florida Museum of Natural History in the US; Fairylake Botanical Garden in Shenzhen, China; and the University of British Columbia Botanical Garden and University of Alberta in Canada. 

The size and scope of the project also required the development and refinement of new computational tools for sequence assembly and phylogenetic analysis.

The timing of 244 whole genome duplications across the green plant tree of life was of particular interest to the researchers.

“Perhaps the biggest surprise of our analyses was the near absence of whole genome duplications in the algae,” says Mike Barker, from University of Arizona, US. 

“Building on nearly 20 years of research on plant genomes, we found that the average flowering plant genome has nearly four rounds of ancestral genome duplication dating as far back as the common ancestor of all seed plants more than 300 million years ago. 

“We also find multiple rounds of genome duplication in fern lineages, but there is little evidence of genome doubling in algal lineages.”

In addition to genome duplications, the expansion of key gene families has contributed to the evolution of multicellularity and complexity in green plants, adds co-author Marcel Quint, from Germany’s Halle University.

“Gene family expansions through duplication events catalysed diversification of plant form and function across the green tree of life,” he says. 

“Such expansions unleashed during terrestrialisation or even before set the stage for evolutionary innovations including the origin of the seed and later the origin of the flower.”