Revolutionary progress in understanding plant biology is being driven through advances in DNA sequencing technology. Carnegie plant scientists have played a key role in the sequencing and genome annotation efforts of the model plant Arabidopsis thaliana and the soil alga Chlamydomonas reinhardtii. Now that many genomes from algae to mosses and trees are publicly available, this information can be mined using bioinformatics to build models to understand gene function and ultimately for designing plants for a wide spectrum of applications.

 Carnegie researchers have pioneered a genome-wide gene association network Aranet that can assign functions to genes for which no function had previously been assigned (to date about 50% of the plant genome) by their associations with genes of known function. They are also building protein interaction and metabolic pathway networks in plants to systematically identify signaling and metabolic pathways and relationships among these pathways.

Investigators also develop and apply mining methods to capture biological knowledge about the function of plant genes and maintain and improve the Arabidopsis genome annotation and provide online bioinformatics tools for use by plant biologists worldwide.Other researchers use algal genomes to identify genes that are specific to the green lineage, the so-called Greencut, to uncover the yet unknown regulatory systems critical for photosynthesis.

The objective of this computational work is to understand the evolution of multicellularity and sexual reproduction in the plant lineage, and the evolution of plant- specific characters, and the interactions between plants and other organisms.

Scientific Area: 
Plant Science
Reference to Person: 
Sue Rhee
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Moises Exposito-Alonso
Exposito-Alonso recognized for early career excellence by American Society of Naturalists
February 28, 2020

Palo Alto, CA— Carnegie’s Moises Exposito-Alonso is one of four recipients of the American Society of Naturalists’ Jasper Loftus-Hills Young Investigator Award in recognition of “outstanding and promising work” by individuals who are within three years of completing their Ph.D or in their final year of graduate school.

Exposito-Alonso is an evolutionary geneticist who joined Carnegie last September as a staff associate, a prestigious position designed for early career scientists who are ready to independently deploy creative approaches to challenging research projects. 

His lab is pioneering the use of genomics to ask whether species will

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A fluorescence image of the sea anemone Exaiptasia, courtesy of Tingting Xiang
How do corals make the most of their symbiotic algae?
January 8, 2020

Stanford, CA— Corals depend on their symbiotic relationships with the algae that they host. But how do they keep algal population growth in check? The answer to this fundamental question could help reefs survive in a changing climate.

New work published in Nature Communications by a team including Carnegie’s Tingting Xiang, Sophie Clowez, Rick Kim, and Arthur Grossman indicates how sea anemones, which are closely related to coral, control the size of the algal populations that reside within their tissue.  

Like corals, anemones host photosynthetic algae, which can convert the Sun’s energy into chemical energy. An alga shares some of the sugars

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Researchers in Tübingen courtesy of Moises Exposito-Alonso.
Predicting the mutations plants need to survive climate change
August 28, 2019

Palo Alto, CA— Plant genetic diversity in Central Europe could collapse due to temperature extremes and drought brought on by climate change, according to a new paper in Nature led by Moises Exposito-Alonso, who joins Carnegie next month from the Max Planck Institute for Developmental Biology and UC Berkeley. Because only a few individuals of a species are already adapted to extreme climate conditions, the overall species genetic diversity could be greatly diminished, according to the findings. 

A team of researchers from the Max Planck institute, University of Tübingen, Technical University of Madrid, and UC Berkeley analyzed variants of the mustard plant

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Octopus Spring in Yellowstone National Park courtesy of Devaki Bhaya
Carnegie researchers receive joint U.K.-U.S. grant to study hot spring microbes
August 23, 2019

Palo Alto, CA— Carnegie plant scientists Devaki Bhaya and Arthur Grossman received a nearly $2 million grant from the U.S. National Science Foundation and the U.K. Biotechnology and Biological Sciences Research Council to study photosynthetic microbes from Yellowstone National Park’s Octopus Spring.

Together with Seppe Kuehn of the University of Illinois at Urbana-Champaign and Alison Smith and Chris Howe from the University of Cambridge, Bhaya and Grossman plan to use samples from the field to reconstruct in the lab the highly organized communities of bacteria that carpet the hot springs in a mat-like structure.

They will deploy sophisticated techniques to

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Moises Exposito-Alonso

Evolutionary geneticist Moises Exposito-Alonso joined the Department of Plant Biology as a staff associate in September 2019. He investigates whether and how plants will evolve to keep pace with climate change by conducting large-scale ecological and genome sequencing experiments. He also develops computational methods to derive fundamental principles of evolution, such as how fast natural populations acquire new mutations and how past climates shaped continental-scale biodiversity patterns. His goal is to use these first principles and computational approaches to forecast evolutionary outcomes of populations under climate change to anticipate potential future

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Kamena Kostova

Staff Associate Kamena Kostova joined the Department of Embryology in November 2018. She studies ribosomes, the factory-like structures inside cells that produce proteins. Scientists have known about ribosome structure, function, and biogenesis for some time. But, a major unanswered question is how cells monitor the integrity of the ribosome itself. Problems with ribosomes have been associated with diseases including neurodegeneration and cancer. The Kostova lab investigates the fundamental question of how cells respond when their ribosomes break down using mass spectrometry, functional genomics methods, and CRISPR genome editing.

Kostova received a B.S. in Biology from the

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Sally June Tracy

Sally June Tracy applies cutting-edge experimental and analytical techniques to understand the fundamental physical behavior of materials at extreme conditions. She uses dynamic compression techniques with high-flux X-ray sources to probe the structural changes and phase transitions in materials at conditions that mimic impacts and the interiors of terrestrial and exoplanets. She is also an expert in nuclear resonant scattering and synchrotron X-ray diffraction. She uses these techniques to understand novel behavior at the electronic level.  Tracy received her Ph.D. from the California Institute of

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William Ludington

The Ludington lab investigates complex ecological dynamics from microbial community interactions using the fruit fly  Drosophila melanogaster. The fruit fly gut carries numerous microbial species, which can be cultured in the lab. The goal is to understand the gut ecology and how it relates to host health, among other questions, by taking advantage of the fast time-scale and ease of studying the fruit fly in controlled experiments. 
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