Yaniv Brandvain
Associate Editor, Empirical Population Genetics section

Yaniv Brandvain is an Associate Professor of Plant and Microbial Biology at the University of Minnesota working in theoretical and empirical population genomics. He received a BA in Human Ecology from the College of the Atlantic and a PhD in Biology from Indiana University, working on the robe of conflict, cooperation, and co-adaptation in plant evolution and speciation. During his postdoc at the University of California, Davis, he developed evolutionary theory concerning meiotic drive, and he developed population genomic approaches to study the evolutionary origins of self-fertilizing plant species. He is interested in understanding how new plant species arise with a particular interest in how mating systems and genomic conflicts shape plant diversity. His lab combines empirical and theoretical population genomic analyses with collaborative work in empirical systems to study the evolutionary forces shaping flowering plant diversity. He was also named McKnight Land-Grant Professor from the University of Minnesota (2017-2019) for his research efforts and received the Stanley Dagley-Samuel Kirkwood Undergraduate Education Award for his efforts in undergraduate instruction in biostatistics. 

A formidable invader of freshwater bodies, duckweed’s ability to thrive in diverse environments is a remarkable display of resilience, especially considering its small genome size and lack of sexual reproduction. Duckweed—the common name for members of the Lemnaceae family of monocots—defies conventional reproductive norms through clonal propagation. New individuals sprout from a single parent, bypassing the need for sexual reproduction and allowing for the fast reproduction that underlies their invasiveness.

Research recently published in G3: Genes|Genomes|Genetics delves into DNA methylation in the duckweed Spirodela polyrhiza, exploring its implications for clonal propagation and shedding light on the intricacies of plant biology.

Duckweed’s resilience hints at the intricate role epigenetic variation plays in shaping the plant kingdom’s evolution. Epigenetic modifications, particularly DNA marks like 5-methylcytosine (5mC), play pivotal roles in regulating gene expression and genome stability in plants. But duckweed deviates from the norm for plants, exhibiting notably low levels of 5mC.

Prompted by this intriguing anomaly, Harkess, Bewick, et al., set out to better understand the genetic and epigenetic impact that clonal propagation has on duckweed.

In plants, DNA methylation occurs in three sequence contexts: CG, CHG, and CHH (where H = A, C, T). It is initiated by the highly conserved RNA-directed DNA methylation (RdDM) pathway, which generates 24-nucleotide heterochromatic siRNAs via processing of double-stranded RNAs by DICER-LIKE 3 (DCL3). Subsequently, maintenance methyltransferases like MET1, CMT2, and CMT3 ensure the preservation of methylation during DNA replication.

However, key players of the RdDM pathway are notably absent in duckweed, as is the CMT2 maintenance methlytransferase. These absences have profound implications, particularly at CHH sites, where methylation is significantly reduced.

Interestingly, this phenomenon extends beyond duckweed, with related species Landoltia punctata, Lemna minor, and the aquatic seagrass Zostera marina exhibiting a similar absence of methylation machinery. The loss of these methylation players may represent a shared evolutionary adaptation among aquatic plants, potentially conferring advantages in varied climates and stresses.

The authors also report the absence of transposon proliferation in the S. polyrhiza genome, despite the loss of highly conserved genes involved in CHH methylation, prompting them to speculate on the role of CHH methylation in silencing transposons in asexual species. They suggest that clonally propagated species may rely more heavily on maintenance methylation mechanisms, rendering CHH methylation unnecessary for transposon suppression. Based on the research, it appears that losing CHH-type methylation and heterochromatic siRNAs may benefit duckweed by facilitating rapid asexual reproduction. The authors suggest that duckweed’s reproductive efficiency through quick clonal propagation might be enhanced by foregoing the RdDM and CMT2 pathway. Duckweed serves as a captivating case study in plant biology, offering invaluable insights into the intricate interplay between epigenetics, evolution, and environmental adaptation. As researchers continue to unravel its mysteries, the implications for agriculture, ecology, and beyond are boundless.

Yao-Wu Yuan
Associate Editor, Complex Traits

Yao-Wu Yuan is an Associate Professor at the University of Connecticut, Storrs. He is interested in understanding how and why organisms evolve so many beautiful forms in nature. His lab primarily studies floral trait diversification in the wildflower genus Mimulus (monkeyflowers) and aims to uncover the genes, pathways, and principles that explain the tremendous diversity of flowers by integrating genetics, genomics, development, mathematical modeling, and pollination ecology.

Why Publish in GENETICS?

Pears are big business in the United States’ Pacific Northwest. But did you know that traditional pear breeding has remained largely unchanged for centuries? This slow process is difficult and costly, requiring the long-term commitment of labor, materials, and land-space resources. However, traditional pear breeding might get some help from genomics, thanks to a unique collaboration between students, scientists, and the pear industry fostered through an initiative called the American Campus Tree Genomes (ACTG) Project.

ACTG was born from two professors’ desire to memorialize Auburn University’s iconic Toomer’s Oak trees that were poisoned during the 2010 Auburn University football season. Their plan: sequence the oak’s DNA and create the first-ever live-oak reference genome. To sweeten the pot, they decided to create a semester-long course so that actual Auburn students could take part in sequencing the Auburn oak trees.

“ACTG leverages iconic and economically valuable trees to bridge the gap between students and cutting-edge genomics,” says ACTG co-founder Alex Harkess, PhD. “Students collaboratively assemble, analyze, and publish tree genomes in prestigious journals, gaining invaluable experience.”

The first semester was a success despite most of the students having never written a manuscript, performed command line bioinformatics, or engaged in plant genomics molecular work. It sparked a nationwide initiative, which was officially founded in 2021 by Alex Harkess, PhD, Faculty Investigator at HudsonAlpha Institute for Biotechnology, and Les Goertzen, PhD, Director of the John D. Freeman Herbarium at Auburn University. Other institutions can replicate the experience using their own campus trees as a springboard for scientific and educational endeavors.

ACTG is disrupting traditional academic models, offering students a unique entry point into the world of genomic research. The initiative transcends textbook learning, immersing participants in the actual process of assembling, analyzing, and publishing tree genomes in esteemed scientific journals. Students in this course have access to cutting-edge genome sequencing techniques and bioinformatic skills through experts at HudsonAlpha. By working on genuine research projects with tangible outcomes, students gain confidence and experience, shaping their trajectories toward successful careers in the ever-evolving field of genomics.

“This course is a welcoming opportunity for students and trainees to not just interact with a completely new idea but become proficient in it no matter their skill level. I had no previous experience with bioinformatics, and I came out with an entirely new, highly marketable skill set,” says Harrison Estes, an Auburn University ‘23 grad who participated in the pear genome class. He is currently a graduate student at the University of Wisconsin and credits the ACTG class as helping him achieve this goal.

The emphasis on student participation extends beyond technical training. ACTG actively addresses barriers to STEM entry and persistence, providing valuable opportunities for individuals without access to advanced technologies. The ACTG team seeks out participation from small universities and colleges, community and junior colleges, and HBCUs that lack mature genetics and bioinformatics training pipelines.

The transformative power of ACTG goes beyond equipping students with invaluable skills and experience. By delving into real-world research projects, ACTG participants translate their knowledge into tangible applications that directly benefit the scientific community and economically important industries.

In the case of the pear industry, a cohort of Auburn students in the ACTG initiative worked with pear experts at Washington State University and the USDA Agricultural Research Service to create a high-quality pear genome. The meticulous work of the ACTG students yielded a fully phased, chromosome-scale assembly, a significant advancement over previous efforts.

The d’anjou genome assembly, recently published as a featured article in G3: Genes|Genomes|Genetics, reveals thousands of genomic variants which are of great importance to pear breeding efforts. This high-quality resource unlocks a treasure trove of information for pear breeders. The new genome assembly is also an important tool for studies on the evolution, domestication, and molecular breeding of pear.

“The ACTG: American Campus Tree Genomes program not only built high-quality genomic resources for a valuable pear cultivar that will ultimately benefit growers and consumers alike, but it educated nearly 20 students and scientists in the needs of the apple and pear industry,” said Ines Hanrahan, PhD, Executive Director, Washington Tree Fruit Research Commission.

The pear is only one of many important tree species in the ACTG pipeline. Learn more about the American Campus Tree Genomes project here.

We’re taking time to get to know the members of the GSA’s Early Career Scientist Committees. Join us to learn more about our early career scientist advocates.

Aishwarya Kothari

Community and Membership Engagement Subcommittee

Montana State University

Research interest

I am a fourth-year PhD student at Montana State University studying plant genetics. My interests are in the fields of epigenetics and molecular biology as I work toward improving human health and nutrition through increased access to quality food.

As a small step to this ambitious goal, I study the effects of heat stress in wheat at the molecular level. My current research objective is to use functional genomics—specifically ChIP, ATAC-Seq, and RNA-Seq—to identify molecular mechanisms of wheat grain development in response to heat stress. The complexity of the wheat genome makes it difficult to identify stress-tolerant genes and incorporate them into breeding. However, determining the effects of heat stress on transcriptome and chromatin accessibility in developing wheat spikes will potentially enhance cereal breeding. My research also involves the use of a class of plant growth regulators, brassinosteroids, to improve stress tolerance by altering plant response to stress during development. Brassinosteroids have a significant role in plant growth and development and in stress-response regulation. In the future, I want to study the effects of these plant hormones in conjunction with whole genome sequencing to better understand chromatin dynamics and the internal mechanisms of hormonal action in plant systems towards stress-tolerance.

As a PhD-trained scientist, you have many career options. What interests you the most?

After graduating, I am interested in doing research in industry—preferably related to sustainability and environmental effects. To protect our planet, we must take steps to slow down and control climate change.

I am specifically interested in sustainably growing crops with high nutritional quality that can cope with climate change without loss in yield. As the population increases, so does the demand for more food and better health; these increases then cause food prices to skyrocket, making healthy-eating and better-quality food very expensive.

My main goal is to provide research support to agriculture industries by establishing various methods to develop new, tolerant plant varieties without impacting the environment. Growing up in India, an agriculture-based country where nearly 50 percent of the farmers face issues pertaining to crop health and yield losses, greatly influenced this goal. The farmers struggle each year to get their crops to the market and suffer huge losses due to natural disasters. Additionally, the agriculture sector in India is not fully equipped with highly sophisticated techniques in molecular breeding, and I wish to fill that gap.

My undergraduate degree in biotechnology cultivated my passion for research. As an undergraduate student, I worked on diverse projects involving plant tissue culture, food quality, and genetics. Being a plant scientist will help me hone my skills in sophisticated molecular techniques and in visualizing agronomic characteristics of vigorous plants, which will guide me on proper management, breeding, and engineering practices.

In addition to your research, how do you want to advance the scientific enterprise?

I am a strong advocate for promoting science communication, especially to the general public. There have been many instances where information was poorly communicated and misconstrued, causing a lot of panic. Effectively sharing scientific findings with the public will promote scientific advancements at a faster pace. Additionally, instilling scientific knowledge in children at an early age may encourage them to pursue science in the future.

My personal ambition is to help international students and scientists. Being one myself, I know the hardships we must face to fit into the scientific community outside of our home countries. Also, not all countries have the resources required to enhance the abilities of their early career scientists, limiting their potential. Having forums like the Early Career Leadership Program makes it easier to connect with scientists all over the world and share our experiences. Making such forums more widespread and accessible to everyone is the next step.

Along with that, promoting mental well-being among students is one of my recent goals. Research has shown that almost 40 percent of graduate students deal with depression and anxiety. This was especially prevalent during the pandemic. The uncertainty during these times—mixed with the competitive nature of the scientific enterprise—takes a toll on the mental well-being of students, affecting their performance, academically and beyond. Therefore, supervisors, faculty, and higher management need to recognize their influence on the overall well-being of graduate students and postdocs. They can help enhance the graduate student experience by promoting a healthy work-life balance.

As a leader within the Genetics Society of America, what do you hope to accomplish?

I have wanted to engage in professional career development activities since I was an undergrad. Now as a graduate student, I feel strongly that we need to invest in career development workshops and events for early career scientists. Being an Early Career Leader at GSA will expand my network and knowledge; everything I learn here I can bring back to my institution and work toward implementing it. The demand for professional development workshops for scientists is increasing. Hence, it is imperative that we bring this much-needed content to early career scientists.

Ultimately, through my efforts to engage early career scientists in various opportunities of professional and personal development, I want to foster a healthy and inclusive culture of welfare in scientific communities.

Previous leadership experience

• Graduate Wellness Champion, Montana State University, 2020–2022
• International Peer Advisor, Montana State University, 2017–2018
• Student Engagement Global Ambassador, Montana State University, 2017–2018
• Orientation Leader, Montana State University, 2016–2018

Researchers identified dozens of quantitative trait loci controlling important traits in Cannabis sativa.

In 2014, United States federal law changed to allow scientific research on Cannabis sativa in states with regulated hemp programs. This legal shift opened the door to research that had previously been slow and difficult due to regulatory hurdles and funding challenges.

A new study published in GENETICS capitalized on this new opportunity and identified 69 quantitative trait loci (QTLs) that are responsible for variation in key agronomic and biochemical traits in C. sativa. This research is a step towards understanding the genetic control of complex traits in hemp and will inform future investigations into the overall evolution and function of complex traits across multiple species.

Hemp is grown for a wide range of commercial uses, including in building materials, textiles, and composite plastics, food and drink, animal feed, and pharmaceutical cannabinoid products, says study leader John McKay of Colorado State University. “It’s important to understand the genes controlling this plant as a crop, and it’s also interesting from a fundamental evolutionary standpoint.”

Identifying QTLs in a non-model species

“Scientists have previously made progress in identifying the genetic basis of complex traits in model and crop species—our team wanted to ask those questions in C. sativa because it’s an understudied species,” says McKay.

Today’s genome sequencing and assembly technologies are largely species-agnostic. As a result, scientists can now take bioinformatic and statistical genetic tools that were initially developed and tested in fruit flies and Arabidopsis and increasingly apply them to non-model species.

McKay and his team developed an F₂ hemp population by crossing two phenotypically distinct varieties—a tall, late-flowering cultivar bred for fiber production and a shorter, early maturing hemp that was bred for both fiber and grain crops. They then used whole genome sequencing to map QTLs associated with traits of interest, such as grain yield and stem biomass, along with 17 biochemical traits. These included levels of cannabidiol and terpenes, which have medical uses, and THC, which is the psychoactive component of marijuana. THC is strictly regulated in the US, and THC levels in industrial hemp must be below 0.3% to remain legal crops.

Most QTLs they identified clustered into one of four genomic regions, suggesting that much of the difference between the two varieties is due to a small number of genes that have large pleiotropic effects. Two candidate genes emerged that may underlie some of these clusters: the homolog of an Arabidopsis transcription factor gene called TINY may be associated with a cluster of agronomic traits, and the gene for olivetol synthase appears to underlie variation in a cluster of biochemical traits, consistent with the enzyme’s role in cannabinoid synthesis. The researchers functionally validated the olivetol synthase candidate by expressing the two hemp alleles in yeast. They found that the allele from the low-cannabinoid cultivar produced less olivetol in the yeast expression system, supporting the hypothesis that allelic variation at this gene plays a role in the observed phenotypic variation.

The researchers also observed epistatic interactions between some of the QTL clusters, further complicating attempts to elucidate any one trait’s exact genetic underpinnings.

“This study definitely adds to the broader conversation about complex traits,” says McKay. “For example, everyone agrees epistasis exists, but breeders and geneticists like to argue about whether it’s important to include in prediction models. Documenting additional cases like this in which epistasis contributes to variation adds to our understanding of the basis of complex traits.”

Traits are complicated but still predictable

The results of this latest study contradict a paper from 2003 that concluded that variation in cannabinoid production is controlled by a single genetic locus. The team from Colorado State University identified at least four loci controlling variation in these chemotypes.

“The field of genetics has always been a friendly place to hypothesize that something—anything—is polygenic,” laughs McKay. “Finding multiple loci controlling a single biochemical trait wasn’t surprising to me, because the abundance of any molecule can be influenced not only by the pathway that makes that molecule but also the ones that influence the cells and machinery that contribute to the process.”

However, despite overturning assumptions of one-to-one genotype-phenotype interactions, McKay emphasizes that he still views the hemp traits in the study as predictable. Future grants would allow research groups like his to dive deeper into the adaptive value of cannabinoids in hemp plants and create more precise genetic manipulations of key traits of interest. Researchers are eager to see policy informed by scientific understanding of the factors that predictably affect cannabinoid content and other traits in hemp crops.

CITATION:
Quantitative Trait Loci Controlling Agronomic and Biochemical Traits in Cannabis sativa
Patrick Woods, Brian J. Campbell, Timothy J. Nicodemus, Edgar B. Cahoon, Jack L. Mullen, and John K. McKay
GENETICS 2021; iyab099
https://doi.org/10.1093/genetics/iyab099

Tissue culture causes heritable methylation changes in plants.

Tissue culture is a useful tool for plant scientists and horticulturalists in large part because it allows them to produce clones. Inconveniently, however, these clones are not always identical to the original, as one might expect them to be. In a report in GENETICS, Han et al. examined how propagation by tissue culture induces heritable epigenomic changes in maize.

When a portion of a plant is grown in tissue culture, it de-differentiates into an amorphous callus. This deprogrammed tissue can be induced to form roots or shoots or even to regenerate an entire plant—but this complex process can leave its marks on the genome and epigenome of the progeny. To get a picture of how tissue culture affects the epigenome, the authors compared methylation patterns in parental plants, plants that had been cultured, and the progeny of those cultured plants.

They found that most methylation was highly stable; it was consistent among all plants and unaffected by culturing. However, a subset of the methylome was variable between cultured and uncultured plants.  Many of these DNA methylation differences were passed on to the progeny of the cultured plants. Importantly, some of the changes the authors identified were shared among independently regenerated progeny, suggesting that tissue culture can prompt consistent, heritable epigenetic effects in maize.

In theory, these epigenetic changes might be due to general stress; for example, the culture process might cause the methylation machinery to become dysregulated. However, since most methylation in the genome was largely unaffected, and many changes were consistent among cultured plants, it’s more likely that these changes are targeted, with certain alleles being more sensitive than others to heritable epigenetic changes during culture. The mechanisms that lead to methylation modifications and the genetic and phenotypic consequences of those changes will be interesting avenues for further study; however, since most plant genome editing requires a culture step, researchers should be cautious about unintended epigenetic consequences.

CITATION:

Heritable Epigenomic Changes to the Maize Methylome Resulting from Tissue Culture

Zhaoxue Han, Peter A. Crisp, Scott Stelpflug, Shawn M. Kaeppler, Qing Li, Nathan M. Springer

GENETICS August 2018 209: 983-995; https://doi.org/10.1534/genetics.118.300987

http://www.genetics.org/content/209/4/983

Crop properties improved by point mutation in microRNA binding domain of Q gene.

Humans have been cultivating wheat for ten thousand years, transforming it from an unruly grass into a useful crop highly adapted to our needs. But even after millennia, there are still new avenues for improving this staple food.

A new type of common bread wheat (Triticum aestivum L.) was recently discovered that has properties that could improve the way it bakes, such as an elevated grain protein content. Researchers at Sichuan Agricultural University found that the new variety has a mutation in the gene Q, which was already identified as an important player in wheat’s domestication.

Q’s expression is normally negatively regulated by an miRNA that binds and cleaves its mRNA, preventing it from being translated into protein. The new type of wheat has a point mutation in Q’s miRNA binding domain, which disrupts normal regulation. A good match between the miRNA sequence and its target sequence in the mRNA is needed for binding and, thus, cleavage, so this single mutation in the binding site can have major consequences. Xu et al. confirmed that the mutant plants do, in fact, overexpress Q for this very reason.

Left: Bread made with the new wheat variety. Right: Bread made with wild-type wheat.

These results are an important step toward a better grasp on how Q can be manipulated to improve one of the world’s most important crops. The mutant wheat has a substantial advantage over wild-type wheat; for example, the loaf volume of bread produced with the mutant wheat was 37% greater. This work is also significant because it adds another example to the growing list of miRNA functions in plants. These regulators are now thought to be critical for a huge variety of biological processes in plants, but for many miRNAs, we lack the type of mechanistic information this study provides.

CITATION:

An Overexpressed Q Allele Leads to Increased Spike Density and Improved Processing Quality in Common Wheat (Triticum aestivum)
Bin-Jie Xu, Qing Chen, Ting Zheng, Yun-Feng Jiang, Yuan-Yuan Qiao, Zhen-Ru Guo, Yong-Li Cao, Yan Wang, Ya-Zhou Zhang, Lu-Juan Zong, Jing Zhu, Cai-Hong Liu, Qian-Tao Jiang, Xiu-Jin Lan, Jian Ma, Ji-Rui Wang, You-Liang Zheng, Yu-Ming Wei, Peng-Fei Qi
G3: Genes|Genomes|Genetics 2018 8: 771-778; https://doi.org/10.1534/g3.117.300562
http://www.g3journal.org/content/8/3/771

Recent evolution of simple germ–soma division in a green alga sheds light on the early stages of complex multicellular life.

Among evolution’s greatest innovations are germ cells. These specialized reproductive cells—familiar to us as sperm and eggs in humans—set the stage for complex multicellular life because they free up all the other cells in the body (known as somatic cells) to specialize for many other functions. Because they appeared so long ago in our evolutionary history, the way our germ cells emerged has been obscured, leaving many questions about this momentous biological turning point.

We may never know precisely how the germ–soma dichotomy arose in our lineage, but scientists are still searching for clues. In a report in G3, researchers Gavriel Matt and James Umen describe their work on the green alga Volvox carteri, an intriguing species that has recently and independently evolved a simple germ–soma division. In this alga, a spheroid composed of somatic cells and extracellular matrix surrounds germ cells called gonidia. The gonidial cells undergo embryogenesis to produce new juvenile spheroids that hatch from their mother spheroid, whereas the somatic cells that are left behind eventually senesce and die. This system offers a unique opportunity to explore the early evolution of germ cells.

By comparing the V. carteri germ and somatic cell transcriptomes, Matt and Umen found that the somatic cells had more transcripts from young, lineage-specific genes, whereas the germ cells had more transcripts from ancient genes that are similar to those expressed in stem cells from animals and land plants. The germ cells also expressed more genes overall than the somatic cells did, despite being specialized for reproduction. Although counterintuitive, this is reminiscent of the way certain pluripotent stem cells in other systems express a greater number of genes—including more ancient genes—than their somatic daughter cells do.

The duo also investigated the idea that V. carteri evolved its germ–soma division by repurposing genes initially used for the transition to a simpler form of multicellularity without a germ–soma dichotomy, but found little support for this hypothesis. Genes exclusive to V. carteri and one of its close multicellular algal relatives that does not have differentiated cell types, Gonium pectorale, were not specifically enriched in either V. carteri cell type. Instead, they discovered that each V. carteri cell type expresses orthologs of genes from different temporal phases of the light–dark cycle in a related unicellular alga, Chlamydomonas reinhardtii, with somatic cells enriched for expression of dark-phase genes, and gonidial cells enriched for expression of light-phase genes. These results suggest that V. carteri cell types may have evolved through cooption of temporal gene regulation in an ancestor whose different phases were converted into germ- and soma-specific expression programs.

Notably, the researchers also found increased expression of genes involved in anabolic pathways in gonidial cells, which contrasts with the upregulation of genes involved in catabolic pathways found in somatic cells. Specifically, somatic cells preferentially expressed genes involved in breaking down carbon stores into sugars, which are important building blocks for the extracellular matrix that surrounds gonidia and provides a structural scaffold that maintains organismal shape and integrity. These observations suggest that the somatic cells sacrifice themselves for the multicellular collective, contributing stored resources at their own expense. With such an investment in the next generation, it’s no surprise that germ–soma dichotomies have evolved repeatedly, giving researchers fertile ground to explore the rise of complex lifeforms.

CITATION:

Cell-Type Transcriptomes of the Multicellular Green Alga Volvox carteri Yield Insights into the Evolutionary Origins of Germ and Somatic Differentiation Programs
Gavriel Y. Matt and James G. Umen
G3: GENES|GENOMES|GENETICS 2018 8: 531-550; https://doi.org/10.1534/g3.117.300253
http://www.g3journal.org/content/8/2/531

Shrub rich in potentially anticancer and antimalarial cardenolide compounds is sequenced in search of biosynthetic pathways.

The giant milkweed Calotropis gigantea, a flowering shrub that can grow to 13 feet tall, produces a multitude of chemicals that have possible anticancer and antimalarial properties. A new Genome Report published in G3 describes the plant’s genome, providing a crucial tool for engineering the production of these potential drugs.

Parts of C. gigantea have long been used to treat everything from pain to malaria, and naturopaths and practitioners of some types of traditional medicine continue to employ it today. Despite its continued use, however, the plant itself isn’t a suitable medicine—in part because it contains toxic substances that can cause tissue irritation and even poisoning.

Among the chemicals C. gigantea synthesizes are cardenolides, a group that includes some chemicals used to treat congestive heart failure and others that are being investigated for their suggested anticancer and antimalarial properties. One way to optimize the yield of these cardenolides for research would be to produce them en masse in an organism that’s easy to grow and manipulate in the lab—but that requires knowing how C. gigantea makes them.

Hoopes et al. report an annotated whole-genome sequence of the plant, along with transcriptomic data, which together will help reveal how the plant synthesizes cardenolides. Their work also confirmed the evolutionary relationships between C. gigantea and two related plants that don’t produce cardenolides. Comparing the already-sequenced genomes of these two plants with the C. gigantea genome will help narrow down which genes are involved in the biosynthesis of cardenolides—an essential step toward large-scale production of the drug candidates.

CITATION:

Genome Assembly and Annotation of the Medicinal Plant Calotropis gigantea, a Producer of Anticancer and Antimalarial Cardenolides
Genevieve M. Hoopes, John P. Hamilton, Jeongwoon Kim, Dongyan Zhao, Krystle Wiegert-Rininger, Emily Crisovan and C. Robin Buell
G3: GENES|GENOMES|GENETICS 2018 8: 385-391; https://doi.org/10.1534/g3.117.300331
http://www.g3journal.org/content/8/2/385