The Plant Press

Untangling the roots of plant genomes: Supporting a 'moonshot' for botany

From Plant Press, Vol. 25, No. 2, April 2022.

Adapted from the Botanical Research Institute of Texas

Research featured in Proceedings of the National Academy of Sciences (119: e2115640118; http://doi.org/10.1073/pnas.2115640118) highlights the progress of plant genomics and includes a roadmap for the enormous task of sequencing the genomes of plants worldwide.

The article, titled "Green plant genomes: What we know in an era of rapidly expanding opportunities," underscores the significance of this massive endeavor.

"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 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."

The article highlights the contributions of Global Genome Initiative for Gardens (aka GGI-Gardens), based at the Fort Worth Botanic Garden and Botanical Research Institute of Texas (FWBG|BRIT) and funded by the Smithsonian Institution. Co-author of the article, Morgan Gostel, is the 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.”

Women support staff of the US National Herbarium 2022

From Plant Press, Vol. 25, No. 2, April 2022.

Historically women have had a heavy presence in museum work most notably in illustration, research assistance, and collection management. More recently collections work has expanded to include digitization, outreach, administration, and library and information resourcing, as well as fulfilling everyday department tasks. Today, women comprise 67% of the support staff in the Department of Botany, while holding only 25% of the curatorial positions. During National Women's History month, we highlight the women support staff of the US National Herbarium.

Ancient hybridization and genome doubling explain the origin of the apple tribe

From Plant Press, Vol. 25, No. 2, April 2022.

In the 1930s, biologists studying chromosomes in the rose family (Rosaceae) noticed that species in the apple tribe (Maleae) had approximately twice as many chromosomes (base chromosome number = 17) as every other species in the rose family (base chromosome number = 7, 8, or 9). Over the ensuing decades, researchers proposed hypotheses of hybridization and/or genome doubling to explain the evolutionary origin of the apple tribe and the unusually high chromosome counts in the apple tribe.

There were two competing hypotheses explaining the evolutionary origin of the apple tribe, but it was difficult to test them rigorously with the data available at the time. For many years, botanists tested these hypotheses using morphological characters, chromosome count data, and more recently, single-locus genetic data. Until a few years ago, researchers did not have access to genome-scale genetic data to test hypotheses of ancient hybridization and/or genome doubling.

An ancient hybridization event gave rise to the apple tribe (Maleae) in the rose family, Rosaceae. Maleae taxa include (from left) sweet crabapple (Malus coronaria), Callery pear (Pyrus calleryana), and Canadian serviceberry (Amelanchier canadensis). (photos by Richie Hodel and Jun Wen)

Smithsonian scientists Richie Hodel, Liz Zimmer, Bin-Bin Liu, and Jun Wen synthesized recently published phylogenomic data from the nuclear and chloroplast genomes of multiple species in the rose family, and applied novel phylogenetic network and multiply-labeled tree analyses to resolve the origin of the apple tribe. They found that an ancient hybridization event occurred between ancestors of the Rosaceae tribes Sorbarieae and Spiraeeae, likely between approximately 65-50 million years ago. Phylogenetic network analyses indicated this hybridization event gave rise to the clade Gillenieae + Maleae. The tribe Gillenieae is a small clade with follicular fruit sister to the larger pome-bearing apple tribe. In contrast to the Maleae, the Gillenieae do not have elevated chromosome counts, indicating that this hybridization event promoted the diversification of the clade Gillenieae + Maleae, but does not explain the high chromosome number in Maleae.

Another key result was that subsequent allopolyploidy (genome doubling involving two distinct species) between ancestors of the apple tribe likely occurred between approximately 50-35 million years ago. Multiply-labeled tree analyses indicated this event probably followed the divergence of the Gillenieae and Maleae lineages. This genome doubling event explains the elevated chromosome numbers observed in the Maleae by researchers over the past century. The research is published in Frontiers in Plant Science (https://doi.org/10.3389/fpls.2021.820997).

Rosaceae tribe, Amygdaleae, which includes (from left) Japanese apricot (Prunus mume) and almond (Prunus dulcis), was once hypothesized to have played a role in a hybridization event leading to the apple tribe, but recent research indicates the participants in the ancient hybridization event were likely ancestors of the tribes Spiraeeae and Sorbarieae. (photos by Richie Hodel and Jun Wen)

Explosive fossil fruit found buried beneath ancient Indian lava flows

From Plant Press, Vol. 25, No. 2, April 2022.

-Adapted from Jerald Pinson (The Florida Museum of Natural History).

Just before the closing scenes of the Cretaceous Period, India was a rogue subcontinent on a collision course with Asia. Before the two landmasses merged, however, India rafted over a “hot spot” within the Earth’s crust, triggering one of the largest volcanic eruptions in Earth’s history, which likely contributed to the extinction of the dinosaurs.

In a recent study published in the International Journal of Plant Sciences (183: 128-138; 2022 https://doi.org/10.1086/717691) scientists excavating the fossilized remains of plant material wedged between layers of volcanic rock describe a new plant species based on the presence of distinctive fruit capsules that likely exploded to disperse their seeds. The fossils may be the oldest fruit discovered to date of the spurge family (Euphorbiaceae), a group of plants with more than 7,000 species, with well-known representatives that include poinsettia, castor oil plant, rubber trees, and crotons.

The fruit of Euphorbiotheca deccanensis is potentially the oldest ever discovered of the spurge family (Euphorbiaceae). Based on the preserved fibers within the fossilized fruit, researchers think it likely exploded to disperse its seeds. (photo by Kristen Grace, Florida Museum of Natural History)

The fossilized fruits were discovered near the village of Mohgaon Kalan in central India, where the remains of the once-widespread volcanic rock lie just beneath the surface in a complex mosaic.

Living in harmony with nature: Winners, losers, and the Convention on Biological Diversity

From Plant Press, Vol. 25, No. 2, April 2022.

By W. John Kress.

A recently published scientific paper documents the imminent decline of thousands of species of plants as a result of the degradation and deterioration of natural environments caused by human greed and recklessness (Plants People Planet; https://doi.org/10.1002/ppp3.10252). As coauthors of that paper, Gary Krupnick and I worked to compile and analyze mountains of data on every species of plant for which we could find information about its current status on the planet.

We categorized each species as a “winner” or “loser” according to how it has responded to the “Lords of the Biosphere,” as our own species has been called by Professor John McNeill of Georgetown University. Plants that are useful to people, such as crops and plantation timber trees, or take advantage of environments altered by humans, such as invasive species, stand a good chance of surviving the current perils facing the planet, which include unrelentless habitat destruction, out-of-control climate change, rampant pollution, and escalating diseases. Such species will be the winners that survive the hazards of the Anthropocene to flourish once again in a future, perhaps hundreds or thousands of years from now, when humans will have less impact. Species that are not useful to people and inhabit threatened ecosystems or are exploited for their useful properties, such as wild medicinal plants, will be the losers. These species will succumb to human-dominated habitats, will decline in number, and may eventually go extinct.

Losers that are useful to humans tend to be overexploited wild species that may be medicinal, ornamental or used for timber. One such species is Ceratozamia kuesteriana, is a cycad threatened by habitat loss and over-collecting. Endemic to the Sierra Madre Oriental of Mexico, the one remaining population of this species numbers less than 300 plants. Credit: this image is in the public domain.

Although our conclusions were not what we were hoping for, we were not surprised by the results: among the tens of thousands of plant species we analyzed, the losers by far outnumbered the winners. No, it was not a good outcome. In fact, the result is extremely discouraging, and another indicator that humans, the world’s biodiversity, and the planet are on a dangerous and tragic trajectory if we do not change fast.

It is no coincidence that a week after this publication went to press (although certainly not because of this paper) thousands of international delegates and concerned observers met in Geneva, Switzerland, to prepare for the 15^th meeting of the Conference of the Parties of the United Nations Convention on Biological Diversity (CBD), which will convene in Kunming, China, later this year. The long-anticipated meeting in Geneva, which is really three separate meetings taking place at the same time: SBSTTA-24 (called the Twenty-fourth meeting of the Subsidiary Body on Scientific, Technical and Technological Advice), SBI-03 (Third meeting of the Subsidiary Body on Implementation), and WG2020-03 (Third meeting of the Open-ended Working Group on the Post-2020 Global Biodiversity Framework), took place over a two-week period, from March 14 -29, to facilitate long-term discussions on how to prevent further loss of biodiversity while at the same time making the benefits of Nature available for human well-being. I participated in the Geneva meetings over those 16 long days as a virtual official Observer representing the Earth BioGenome Project.