International team cracks genomic code for earliest forms of terrestrial plant life
Discovery answers fundamental question of how earliest land plants evolved from aquatic freshwater algae
UNIVERSITY OF NEBRASKA-LINCOLN
Plant life first emerged on land about 550 million years ago, and an international research team co-led by University of Nebraska–Lincoln computational biologist Yanbin Yin has cracked the genomic code of its humble beginnings, which made possible all other terrestrial life on Earth, including humans.
The team — about 50 scientists in eight countries – has generated the first genomic sequence of four strains of Zygnema algae, the closest living relatives of land plants. Their findings shed light on the ability of plants to adjust to the environment and provide a rich basis for future research.
The study was published May 1 in the journal Nature Genetics.
“This is an evolutionary story,” said Yin, who led the research team with a scientist from Germany. “It answers the fundamental question of how the earliest land plants evolved from aquatic freshwater algae.”
Yin’s lab in the Nebraska Food for Health Center and the Department of Food Science and Technology has a long history of studying plant cell wall carbohydrates, a major component of dietary fibers for humans and farm animals; lignocelluloses for biofuel production; and natural barriers to protect crops from pathogens and environmental stresses.
All current plant life on land burst from a one-off evolutionary event known as plant terrestrialization from ancient freshwater algae. The first land plants, known as embryophyta within the clade of streptophyta, emerged on land about 550 million years ago — their arrival fundamentally changing the surface and atmosphere of the planet. They made all other terrestrial life, including humans and animals, possible by serving as an evolutionary foundation for future flora and food for fauna.
The researchers worked with four algal strains from the genus Zygnema — two from a culture collection in the United States and two from Germany. Scientists combined a range of cutting-edge DNA sequencing techniques to determine the entire genome sequences of these algae. These methods enabled scientists to generate complete genomes for these organisms at the level of whole chromosomes — something that had never been done before on this group of algae. Comparing the genomes with those of other plants and algae led to the discovery of specific overabundances of cell wall enzymes, signalling genes and environmental response factors.
A unique feature of these algae revealed by microscopic imaging — performed at the University of Innsbruck in Austria, the Universität Hamburg in Germany and UNL’s Center for Biotechnology — is a thick and highly sticky layer of carbohydrates outside the cell walls, called the mucilage layer. Xuehuan Feng, the first author of the paper and a Husker postdoctoral research associate, developed a new and effective DNA extraction method to remove this mucilage layer for high purity and high molecular DNAs.
“It is fascinating that the genetic building blocks, whose origins predate land plants by millions of years, duplicated and diversified in the ancestors of plants and algae and, in doing so, enabled the evolution of more specialized molecular machinery,” said Iker Irisarri of the Leibniz Institute for the Analysis of Biodiversity Change and co-first author of the paper.
The team’s other co-leader, Jan de Vries of the University of Göttingen, said, “Not only do we present a valuable, high-quality resource for the entire plant scientific community, who can now explore these genome data, our analyses uncovered intricate connections between environmental responses.”
The four multicellular Zygnema algae belong to the class Zygnematophyceae, the closest living relatives of land plants; it is a class of freshwater and semi-terrestrial algae with more than 4,000 described species. Zygnematophyceae possess adaptations to withstand terrestrial stressors, such as desiccation, ultraviolet light, freezing and other abiotic stresses. The key to understanding these adaptations is the genome sequences. Before this paper, genome sequences were only available for four unicellular Zygnematophyceae.
Yin said this research aligns with one of the National Science Foundation’s 10 Big Ideas — “Understanding the Rules of Life” — to address societal challenges, from clean water to climate resilience. The discovery also holds significance in applied sciences, such as bioenergy, water sustainability and carbon sequestration.
“Our gene network analyses reveal co-expression of genes, especially those for cell wall synthesis and remodifications that were expanded and gained in the last common ancestor of land plants and Zygnematophyceae,” Yin said. “We shed light on the deep evolutionary roots of the mechanism for balancing environmental responses and multicellular cell growth.”
The international research collaboration includes about 50 researchers from 20 research institutions in eight countries — the United States, Germany, France, Austria, Canada, China, Israel and Singapore. Other Husker researchers on the team are Chi Zhang, professor of biological sciences, and Jeffrey Mower, professor of agronomy and horticulture.
Funding for UNL’s portion of the research came primarily from Yin’s NSF CAREER award, the Nebraska Tobacco Settlement Biomedical Research Enhancement Fund, the National Institutes of Health, and the U.S. departments of Agriculture and Energy.
Discovery answers fundamental question of how earliest land plants evolved from aquatic freshwater algae
UNIVERSITY OF NEBRASKA-LINCOLN
Plant life first emerged on land about 550 million years ago, and an international research team co-led by University of Nebraska–Lincoln computational biologist Yanbin Yin has cracked the genomic code of its humble beginnings, which made possible all other terrestrial life on Earth, including humans.
The team — about 50 scientists in eight countries – has generated the first genomic sequence of four strains of Zygnema algae, the closest living relatives of land plants. Their findings shed light on the ability of plants to adjust to the environment and provide a rich basis for future research.
The study was published May 1 in the journal Nature Genetics.
“This is an evolutionary story,” said Yin, who led the research team with a scientist from Germany. “It answers the fundamental question of how the earliest land plants evolved from aquatic freshwater algae.”
Yin’s lab in the Nebraska Food for Health Center and the Department of Food Science and Technology has a long history of studying plant cell wall carbohydrates, a major component of dietary fibers for humans and farm animals; lignocelluloses for biofuel production; and natural barriers to protect crops from pathogens and environmental stresses.
All current plant life on land burst from a one-off evolutionary event known as plant terrestrialization from ancient freshwater algae. The first land plants, known as embryophyta within the clade of streptophyta, emerged on land about 550 million years ago — their arrival fundamentally changing the surface and atmosphere of the planet. They made all other terrestrial life, including humans and animals, possible by serving as an evolutionary foundation for future flora and food for fauna.
The researchers worked with four algal strains from the genus Zygnema — two from a culture collection in the United States and two from Germany. Scientists combined a range of cutting-edge DNA sequencing techniques to determine the entire genome sequences of these algae. These methods enabled scientists to generate complete genomes for these organisms at the level of whole chromosomes — something that had never been done before on this group of algae. Comparing the genomes with those of other plants and algae led to the discovery of specific overabundances of cell wall enzymes, signalling genes and environmental response factors.
A unique feature of these algae revealed by microscopic imaging — performed at the University of Innsbruck in Austria, the Universität Hamburg in Germany and UNL’s Center for Biotechnology — is a thick and highly sticky layer of carbohydrates outside the cell walls, called the mucilage layer. Xuehuan Feng, the first author of the paper and a Husker postdoctoral research associate, developed a new and effective DNA extraction method to remove this mucilage layer for high purity and high molecular DNAs.
“It is fascinating that the genetic building blocks, whose origins predate land plants by millions of years, duplicated and diversified in the ancestors of plants and algae and, in doing so, enabled the evolution of more specialized molecular machinery,” said Iker Irisarri of the Leibniz Institute for the Analysis of Biodiversity Change and co-first author of the paper.
The team’s other co-leader, Jan de Vries of the University of Göttingen, said, “Not only do we present a valuable, high-quality resource for the entire plant scientific community, who can now explore these genome data, our analyses uncovered intricate connections between environmental responses.”
The four multicellular Zygnema algae belong to the class Zygnematophyceae, the closest living relatives of land plants; it is a class of freshwater and semi-terrestrial algae with more than 4,000 described species. Zygnematophyceae possess adaptations to withstand terrestrial stressors, such as desiccation, ultraviolet light, freezing and other abiotic stresses. The key to understanding these adaptations is the genome sequences. Before this paper, genome sequences were only available for four unicellular Zygnematophyceae.
Yin said this research aligns with one of the National Science Foundation’s 10 Big Ideas — “Understanding the Rules of Life” — to address societal challenges, from clean water to climate resilience. The discovery also holds significance in applied sciences, such as bioenergy, water sustainability and carbon sequestration.
“Our gene network analyses reveal co-expression of genes, especially those for cell wall synthesis and remodifications that were expanded and gained in the last common ancestor of land plants and Zygnematophyceae,” Yin said. “We shed light on the deep evolutionary roots of the mechanism for balancing environmental responses and multicellular cell growth.”
The international research collaboration includes about 50 researchers from 20 research institutions in eight countries — the United States, Germany, France, Austria, Canada, China, Israel and Singapore. Other Husker researchers on the team are Chi Zhang, professor of biological sciences, and Jeffrey Mower, professor of agronomy and horticulture.
Funding for UNL’s portion of the research came primarily from Yin’s NSF CAREER award, the Nebraska Tobacco Settlement Biomedical Research Enhancement Fund, the National Institutes of Health, and the U.S. departments of Agriculture and Energy.
JOURNAL
Nature Genetics
Nature Genetics
DOI
METHOD OF RESEARCH
Imaging analysis
Imaging analysis
SUBJECT OF RESEARCH
Cells
Cells
ARTICLE TITLE
Genomes of multicellular algal sisters to land plants illuminate signaling network evolution
Genomes of multicellular algal sisters to land plants illuminate signaling network evolution
ARTICLE PUBLICATION DATE
1-May-2024
1-May-2024
Genomes of “star algae” shed light on origin of plants
International research team generates first genomes of complex closest relatives of land plants
Land plants cover the surface of our planet and often tower over us. They form complex bodies with multiple organs that consist of a broad range of cell types. Developing this morphological complexity is underpinned by intricate networks of genes, whose coordinated action shapes plant bodies through various molecular mechanisms. All of these magnificent forms burst forth from a one-off evolutionary event: when plants conquered Earth’s surface, known as plant terrestrialization. Among those algae most closely related to land plants, diverse body types are found – ranging from single-celled algae to more complex cell filaments. From this group of relatives, an international group of researchers led by the Universities of Göttingen and Nebraska–Lincoln has now generated the first genome data of such complex specimens, on four filamentous “star algae” of the genus Zygnema. Their results were published in Nature Genetics.
The researchers worked with four algal strains in total, two from a culture collection in the USA and two that have been kept safe in the Algal Culture Collection at Göttingen University (SAG). The research involved more than 50 scientists from nine countries who combined a range of cutting-edge sequencing techniques to elucidate the entire DNA sequence of these algae. The advanced methods enabled them to generate complete genomes for these organisms at the level of whole chromosomes – something that had never been done before on this group of algae. Comparing the genes on the genomes with those of other plants and algae led to the discovery of specific overabundances of signalling genes and environmental response factors. Dr Iker Irisarri, Leibniz Institute for the Analysis of Biodiversity Change, explains: “Many of these genes underpin molecular functions that were important for the emergence of the first multicellular terrestrial plants. It is fascinating that the genetic building blocks, whose origins predate land plants by millions of years, duplicated and diversified in the ancestors of plants and algae and, in doing so, enabled the evolution of more specialized molecular machinery”.
Professor Jan de Vries, University of Göttingen, says: “Not only do we present a valuable, high-quality resource for the entire plant scientific community, who can now explore these genome data, our analyses uncovered intricate connections between environmental responses. This sheds light on one of land plants’ most important features: their ability to adjust their growth and development so that it aligns with the environment in which they dwell – a process known as developmental plasticity.”
Original publication: Feng X et al: “Genomes of multicellular algal sisters to land plants illuminate signaling network evolution”, Nature Genetics 2024. Doi: 10.1038/s41588-024-01737-3
www.uni-goettingen.de/en/613776.html
Land plants cover the surface of our planet and often tower over us. They form complex bodies with multiple organs that consist of a broad range of cell types. Developing this morphological complexity is underpinned by intricate networks of genes, whose coordinated action shapes plant bodies through various molecular mechanisms. All of these magnificent forms burst forth from a one-off evolutionary event: when plants conquered Earth’s surface, known as plant terrestrialization. Among those algae most closely related to land plants, diverse body types are found – ranging from single-celled algae to more complex cell filaments. From this group of relatives, an international group of researchers led by the Universities of Göttingen and Nebraska–Lincoln has now generated the first genome data of such complex specimens, on four filamentous “star algae” of the genus Zygnema. Their results were published in Nature Genetics.
The researchers worked with four algal strains in total, two from a culture collection in the USA and two that have been kept safe in the Algal Culture Collection at Göttingen University (SAG). The research involved more than 50 scientists from nine countries who combined a range of cutting-edge sequencing techniques to elucidate the entire DNA sequence of these algae. The advanced methods enabled them to generate complete genomes for these organisms at the level of whole chromosomes – something that had never been done before on this group of algae. Comparing the genes on the genomes with those of other plants and algae led to the discovery of specific overabundances of signalling genes and environmental response factors. Dr Iker Irisarri, Leibniz Institute for the Analysis of Biodiversity Change, explains: “Many of these genes underpin molecular functions that were important for the emergence of the first multicellular terrestrial plants. It is fascinating that the genetic building blocks, whose origins predate land plants by millions of years, duplicated and diversified in the ancestors of plants and algae and, in doing so, enabled the evolution of more specialized molecular machinery”.
Professor Jan de Vries, University of Göttingen, says: “Not only do we present a valuable, high-quality resource for the entire plant scientific community, who can now explore these genome data, our analyses uncovered intricate connections between environmental responses. This sheds light on one of land plants’ most important features: their ability to adjust their growth and development so that it aligns with the environment in which they dwell – a process known as developmental plasticity.”
Original publication: Feng X et al: “Genomes of multicellular algal sisters to land plants illuminate signaling network evolution”, Nature Genetics 2024. Doi: 10.1038/s41588-024-01737-3
Microscope image of Zygnema circumcarinatum, a filamentous alga with a star-shaped chloroplast. Because of this feature, algae of the genus Zygnema are also called "star algae" (scale is 50 µm, corresponding to 0.05 mm)
CREDIT
Dr Tatyana Darienko
JOURNAL
Nature Genetics
METHOD OF RESEARCH
Experimental study
SUBJECT OF RESEARCH
Not applicable
ARTICLE TITLE
Genomes of multicellular algal sisters to land plants illuminate signaling network evolution
ARTICLE PUBLICATION DATE
1-May-2024
Plants utilize drought stress hormone to block snacking spider mites
Spider mite infestation induces a rapid stomatal closure response
UNIVERSITY OF CAMBRIDGE
Recent findings that plants employ a drought-survival mechanism to also defend against nutrient-sucking pests could inform future crop breeding programmes aimed at achieving better broadscale pest control.
Using an advanced fluorescent biosensor (ABACUS2) that can detect tiny changes in plant hormone concentrations at the cellular scale, scientists saw that abscisic acid (ABA), usually linked with drought response, started closing the plant’s entry gates within 5 hours of being infested with spider mites.
Microscopic leaf pores (stomata) are important for gas exchange but are also the major sites for water loss. When there is a water shortage, plants act to conserve water by producing the drought stress hormone ABA to close their stomata.
Coincidentally, the closure of stomata also obstructs the preferred entry points for nutrient-sucking pests like spider mites. The two-spotted spider mite is one of the most economically damaging pests – it’s not fussy and attacks a broad range of more than 1000 plants, including 150 crops. Barely visible to the naked eye, these tiny pests pierce and then suck dry plant cells. They can build up to enormous numbers very quickly and can be one of the most destructive pests in the garden and horticulture industry, spoiling house plants and reducing yields of vegetables, fruit and salad crops.
There has been debate about ABA's role in pest resistance. Initially, it was noticed that stomata close when plants are attacked by nutrient-sucking pests, leading to various hypotheses, including that this closure could be a plant response to losing water due to the pests' feeding or even that the pests act to close stomata to prevent plants from sending distress volatiles to pest predators.
In a collaboration between the Centre for Plant Biotechnology and Genomics (CBGP) in Spain and Sainsbury Laboratory Cambridge University (SLCU), researchers studying how thale cress (Arabidopsis thaliana) responds to the two-spotted spider mite (Tetranychus urticae) have determined the plant leaps into action almost immediately, employing the same hormone as for drought to also block spider mites from penetrating plant tissues and, as a result, significantly reducing pest damage.
The findings published in Plant Physiology found the peak closure of stomata is achieved within a time frame of 24 to 30 hours.
“Open stomata are natural apertures where pests like aphids and mites insert their specialised feeding structures, called stylets, to pierce and then suck out the nutrient rich contents from individual sub-epidermal cells”, said Irene Rosa-Díaz, who carried out the spider mite experiments at SLCU and CBGP during her PhD with Professor Isabel Diaz at the Centro de Biotecnología y Genómica de Plantas, Universidad Polytécnica de Madrid, and National Institute of Agricultural and Food Research and Technology (UPM-INIA) .
The plant leaps into action almost immediately, employing the same hormone as for drought to also block spider mites from penetrating plant tissues and, as a result, significantly reducing pest damage.
“We were able to show mite infestation induced a rapid stomatal closure response, with the plant hormone ABA rising in the leaf tissues – highest in stomatal and vascular cells, but also all other leaf cells measured. We showed through multiple different experiments that stomatal closure hinders mites. Plants that were pre-treated with ABA to induce stomatal closure and then infested with mites showed decreased mite damage, while ABA-deficient mutant plants where stomata cannot close well and plants that have a more stomata are more susceptible to mites.”
Alexander Jones’ research group at SLCU develops in vivo biosensors that are revealing hormone dynamics in plants at unprecedented resolution, including ABACUS2 that quantified cellular ABA in these mite experiments.
Dr Jones said the study highlights the important interactions between biotic and abiotic stresses in plants: “Early warning cues from mite feeding induces a cascade of immune signalling molecules, including jasmonic acid (JA) and salicylic acid (SA), among other chemical responses. Together, these results show that ABA accumulation and stomatal closure are also key defence mechanisms employed to reduce mite damage.
“The next step is to investigate what the initial mite-produced signal is that the plant is detecting that then results in ABA accumulation. The biochemical mechanisms being used by the plant as signals of pest attack could be anything, including mite feeding vibrations, mite salivary proteins, chemicals produced by the mites or mite activity, direct cell damage (wounds) or other molecules associated with the mites.
“Identifying the initial triggers could potentially be used to develop new crop treatments to arm the plants ahead of predicted pest infestations. Importantly, efforts to select for plants with altered stomatal traits, which already must balance a photosynthesis vs water conservation trade-off, could also consider resistance to damaging pests.”
Reference
Irene Rosa-Díaz, James Rowe, Ana Cayuela-Lopez, Vicent Arbona, Isabel Díaz, Alexander M. Jones (2024) Spider mite herbivory induces an abscisic acid-driven stomatal defense. Plant Physiology
https://doi.org/10.1093/plphys/kiae215
JOURNAL
PLANT PHYSIOLOGY
METHOD OF RESEARCH
Experimental study
SUBJECT OF RESEARCH
Cells
ARTICLE TITLE
Spider mite herbivory induces an abscisic acid-driven stomatal defense