Blackberries with no thorns? Scientist assembles genome of a blackberry in major step to breed better fruit

University of Florida

Facebook

XLinkedInWeChatBlueskyMessageWhatsAppEmail

 

image: 

UF Professor Zhanao Deng examining berries at the UF/IFAS Gulf Coast Research and Education Center 

view more 

Credit: UF/IFAS

Thornless, disease-resistant, and tastier blackberries could be on the horizon — thanks to new genetic research from the University of Florida.

New UF blackberry varieties could provide a boon for farmers looking to rebound after the decline of Florida citrus and who see an opportunity to meet the growing demand for blackberries, which have soared in popularity in recent years.

“Overall, this study not only advances our understanding of blackberry genetics, but it sets the stage for significant improvements in blackberry breeding techniques,” said UF/IFAS researcher Zhanao Deng, who led the study that was recently published in journal Horticulture Research. “The end result could be better, more robust blackberry varieties that benefit both growers and consumers worldwide.”

Over the past 20 years, consumer demand for blackberries has increased, leading to farmers growing more of the flavorful fruit in the United States and across the globe.

The United States produces 37 million pounds of processed blackberries and almost 3 million pounds of fresh fruit annually. In Florida, growers produced blackberries on 277 farms and 702 acres, according to the 2022 U.S. Department of Agriculture Census of Agriculture.

The new study delves into the genetic makeup of blackberries, said Deng, a professor of environmental horticulture at the UF/IFAS Gulf Coast Research and Education Center. He and colleagues have been developing new blackberry varieties using deep insights gained from genome sequencing.

Using a large collection of DNA sequences from an experimental blackberry BL1, the team computationally pieced them together, rebuilding the original sequence of the entire genome of this blackberry.

It starts with understanding that BL1 is a tetraploid fruit, one that comes from a plant with four copies of each chromosome in its cells. That means it has twice the normal number of chromosomes as a typical diploid plant, like a raspberry. Working with a tetraploid is more complex than a diploid, Deng said.

“The release of this tetraploid blackberry genome can contribute to more efficient and targeted breeding, ultimately leading to the development of new cultivars with enhanced fruit quality, and resistance to important diseases,” Deng said. “The reference genome created from this research can be a powerful tool for anyone working with blackberries.”

The genome assembly also uncovers the secrets behind key traits like growing blackberry plants with no thorns and the production of anthocyanin production, which affects the color and health benefits of the fruit.

“This finding can help us understand why blackberries develop their characteristic deep purple/black color over time and how to potentially enhance this process for more nutritious berries” he said.

For Florida, the southeastern United States and regions with similar climates, this research holds huge promise.

By using the genetic insights gained from this study, Deng said it can accelerate the process to create blackberry varieties that are better suited to local growing conditions, enhancing both the yield and the quality of the fruit produced in Florida and globally.

---

Journal

Horticulture Research

DOI

10.1093/hr/uhaf052 

Article Title

A chromosome-scale and haplotype-resolved genome assembly of tetraploid blackberry

First ever global map of fishmeal and fish oil factories exposes industry's footprint

UBC study has revealed the global distribution of FMFO factories for the first time, shedding light on a critical area of the aquaculture supply chain, identifying where these ingredients are being produced, and who controls the industry’s footprint.

University of British Columbia

Facebook

XLinkedInWeChatBlueskyMessageWhatsAppEmail

 

image: 

Spatial distribution of factories

Factories are color-coded by data type. Factories in dark blue represent plants whose locations we were able to verify using satellite imagery and company website information. Green shaded circles represent and are scaled to the number of factories per producing country.

view more 

Credit: Lauren Shea

Around the world, millions of tons of small fish are processed into fishmeal and fish oil (FMFO) each year—key ingredients in aquaculture that helps farmed fish, like salmon, grow. A new University of British Columbia (UBC) study has revealed the global distribution of FMFO factories for the first time, shedding light on a critical area of the aquaculture supply chain, identifying where these ingredients are being produced, and who controls the industry’s footprint.

Published in Science Advances, the study delivers the first-ever open-source global map of FMFO factories—506 in total, spread across 63 countries, with Peru, Mauritania, and Chile hosting the highest numbers.

“Production of fishmeal is a major issue in aquaculture. Understanding where FMFO production occurs is essential for addressing its environmental, social, and economic impacts,” said lead author, Lauren Shea, who conducted this research while a Master’s student at UBC’s Institute for the Oceans and Fisheries. “Knowing that, along with what species are being used and how it affects local environments and economies, can support the development of more transparent and responsible aquaculture practices.”

Over 400 companies operate these factories, with many concentrated in sensitive regions already facing fishery stress. Nearly 40 per cent of FMFO continues to be made from whole wild-caught fish, many of which are critical to marine food webs and human nutrition in low-income coastal communities.

This makes the industry both vital and controversial, according to the study’s authors. On one hand, it supports aquaculture, which is essential for meeting global seafood demand as wild fish stocks decline. On the other hand, its reliance on wild-caught, small-pelagic fish—like anchovies and sardines—which are critical to the dietary backbone for communities in regions like West Africa and Southeast Asia.

“Dependence on the global FMFO trade could undermine food security while fueling unsustainable fishing practices,” explained Dr. Rashid Sumaila, professor at UBC’s Institute for the Oceans and Fisheries and the School of Public Policy and Global Affairs, and senior author on the study. “This is not just an environmental issue—it’s about justice and equity.”

The study used satellite imagery, national databases, and industry certifications to verify factory locations and raw material use. Company websites, government lists, and open-source certification data were also cross-referenced.

The resulting database shows stark patterns. Peru, for example, hosts 125 FMFO factories—the highest in the world—while Mauritania ranks second with 42, many of which have been linked to reduced local fish availability and rising prices. Yet, countries with few factories, like Norway and Denmark, often have disproportionately high production, thanks to better technologies and economies of scale.

The researchers emphasised that the database was just a starting point. Regular updates and deeper dives into factory-level environmental and social impacts are essential next steps, noting that countries like China, a major FMFO player, remain opaque due to language barriers, lack of public reporting, and minimal online presence from producers.

“With more transparent data, governments and organizations can better regulate FMFO sourcing, track environmental impacts, and support alternatives—like plant-based feeds or novel proteins—that reduce pressure on wild fish stocks,” said Shea. “By-products can be a sustainable solution when managed properly. Improved data could further enable traceability, helping ensure that seafood products are sourced responsibly throughout the supply chain.”

Dr. Sumaila agreed, noting that frameworks, like the Fisheries Transparency Initiative (FiTI), which encourages governments to publish key data on fish production and trade, are excellent tools to use in conjunction with this map database. He highlights Mauritania, a FiTI member, for its leadership in its publicly accessible factory list.

“Science can only go so far,” said Sumaila. “We need political will, corporate accountability, and community engagement to drive real change.  If aquaculture is going to be part of a sustainable food future, we need better data, smarter policies, and ethical sourcing of feed ingredients,” he said.

 

Example of factory location verification using the Google Maps satellite layer.

All factories had large warehouses and cylindrical tanks for FMFO processing and storage (highlighted in yellow boxes). Factories were typically located on the waterfront and clustered together in industrial zones.

Credit

Lauren Shea

---

Journal

Science Advances

DOI

10.1126/sciadv.adr6921 

Method of Research

Experimental study

Subject of Research

Animals

Article Title

Spatial distribution of fishmeal and fish oil factories around the globe

Article Publication Date

23-Apr-2025

COI Statement

Competing interests: C.C.C.W. provides scientific support to companies in the seafood sector through the Seafood Business for Ocean Stewardship (SeaBOS) initiative (https://seabos.org/). None of the SeaBOS members had any role in the study design, analysis, interpretation of data, or conclusions drawn in this paper. All other authors declare that they have no competing interests.

 

Rats are more motivated to help their friends

Rats are more motivated to help distressed peers if they affiliate with them socially, and friendliness between rats may be driven by oxytocin signaling in a reward-related brain region

Society for Neuroscience

Facebook

XLinkedInWeChatBlueskyMessageWhatsAppEmail

Why are some people more helpful than others? In a new JNeurosci paper, Inbal Bartal, from Tel Aviv University, and colleagues used rats to explore why some individuals may be more receptive to the distress of others and how this information leads to helpful behavior. During a task the researchers previously developed, they observed the behaviors and brain activity of helpful rats compared to less helpful rats. In this task that probes helping behavior, rats are given the option to release a distressed peer trapped in a restrainer. Rats were more likely to come to the aid of others that they had previous positive social interactions with. These helpful rats had increased activity in brain regions associated with empathy and motivation compared to less helpful rats.  

The researchers also observed that helper rats had increased oxytocin receptor expression in a brain region that drives motivation compared to the less helpful rats. According to the authors, this could mean that caring for others, more than relating to others’ distresses, contributes to helpfulness. When oxytocin signaling was inhibited, rats were less friendly with others, suggesting oxytocin may support helping by making rats feel attachment to others. “We appear to live in an increasingly polarized society where there is a gap in empathy towards others. This work helps us understand prosocial, or helpful, acts better. We see others in distress all the time but tend to help only certain individuals. The similarity between human and rat brains helps us understand the way our brain mediates prosocial decisions,” says Bartel. 

### 

Please contact media@sfn.org for full-text PDF. 

About JNeurosci 

JNeurosci was launched in 1981 as a means to communicate the findings of the highest quality neuroscience research to the growing field. Today, the journal remains committed to publishing cutting-edge neuroscience that will have an immediate and lasting scientific impact, while responding to authors' changing publishing needs, representing breadth of the field and diversity in authorship. 

About The Society for Neuroscience 

The Society for Neuroscience is the world's largest organization of scientists and physicians devoted to understanding the brain and nervous system. The nonprofit organization, founded in 1969, now has nearly 35,000 members in more than 95 countries. 

---

Journal

JNeurosci

DOI

10.1523/JNEUROSCI.0845-24.2025 

Article Title

Neural and Behavioral Correlates of Individual Variability in Rat Helping Behavior: A Role for Social Affiliation and Oxytocin Receptors

Article Publication Date

28-Apr-2025

 

New research on bird behavior suggests that evolution may repeat itself

Indiana University

Facebook

XLinkedInWeChatBlueskyMessageWhatsAppEmail

Scientists have long wondered whether evolution would follow the same path if history had a chance for a “do-over.” New research suggests that it does, when it comes to the brain and its regulation of behavior — one of nature’s most complex traits. This discovery sheds new light on the origin of behavioral variation.

The study, published in Nature Ecology & Evolution, is led by Kimberly Rosvall, an associate professor in the Indiana University College of Arts and Sciences’ Department of Biology, and Sara Lipshutz, a former postdoctoral fellow at IU and current assistant professor of biology at Duke University.

Together, the team found that bird species who nest in hard-to-get tree cavities have independently evolved heightened aggression, particularly in females. Even more striking, researchers found this behavioral similarity across lineages mirrored molecular similarity in the birds’ brains.

To conduct this work, researchers observed wild birds and measured their aggressive response to a stuffed decoy and a speaker playing aggressive calls. They replicated this territorial challenge for hundreds of birds across five branches of the bird family tree: swallows, wood warblers, sparrows, thrushes and wrens.

In each lineage, they focused on two closely related species: one obligate cavity-nester, and one with a more flexible nesting strategy. Obligate cavity-nesters cannot reproduce without securing a hole in a tree or another similar structure. The team expected that these species would be more aggressive due to their nesting constraints.

“I have been studying cavity-nesters, like tree swallows and bluebirds, for over 20 years,” Rosvall said. “We knew they fiercely defend their nesting territories, including those human-made bird boxes you might see in your local park. Now we know this ever-present competition also shapes their brain evolution.”

Out of over 10,000 genes expressed in the brains of all 10 species, the team found a set of genes that were consistently altered in their expression in the cavity-nesters’ brains. Each time a lineage evolved higher aggression, its brain independently had the same changes as other cavity-nesting lineages.

“It’s a small number of genes,” Rosvall said. “But it’s exciting because evolution did repeat itself. We knew this could happen for physical traits but not for a complex behavior like aggression.”

The team also identified a larger set of genes that was associated with aggressiveness along two or three branches of the bird family tree, showing — as Rosvall and Lipshutz like to say — “There may be many ways to build an aggressive bird.”

This study is a major advance because it shows that behavioral evolution can arise from a combination of independent changes in the brain, layered atop re-use of the same genetic toolkit.

“If you asked five artists to paint the same landscape, you might expect to recognize each painting as the same scene, even if they also look a bit different,” Rosvall said. “Our results are like that, except the artist is natural selection, repeatedly dialing up aggression over the last 25 million years.”

The findings highlight both the predictability and creativity of evolution, but they also may inform human health.

“Our results did not flag the stereotypical ‘aggression’ genes, like those related to testosterone,” Rosvall said. “Instead, we saw convergent increases in aggression linked to genes with connections to neurodegenerative disorders.

“This doesn’t mean aggressive birds are going to get Alzheimer’s. It just means evolution has repeatedly tweaked these genes to shift brain function and behavior. And understanding why might help us develop evolution-inspired support for people.”

Rosvall specializes in behavioral ecology, neurobiology and genomics. Her lab uses natural variation to understand how animals solve problems in their environment, including habitat limitation and climate change. Both Rosvall and Lipshutz were supported by the National Science Foundation.

---

Journal

Nature

DOI

10.1038/s41559-025-02675-x 

Method of Research

Observational study

Subject of Research

Animals

Article Title

Repeated behavioural evolution is associated with convergence of gene expression in cavity-nesting songbirds

Article Publication Date

28-Apr-2025

Fungi dwelling on human skin may provide new antibiotics

A yeast known as Malassezia protects skin against bacterial infections — up to a certain point

University of Oregon

Facebook

XLinkedInWeChatBlueskyMessageWhatsAppEmail

University of Oregon researchers have uncovered a molecule produced by yeast living on human skin that showed potent antimicrobial properties against a pathogen responsible for a half-million hospitalizations annually in the United States. 

It’s a unique approach to tackling the growing problem of antibiotic-resistant bacteria. With the global threat of drug-resistant infections, fungi inhabiting human skin are an untapped resource for identifying new antibiotics, said Caitlin Kowalski, a postdoctoral researcher at the UO who led the study. 

Described in a paper published April 14 in Current Biology, the common skin fungus Malassezia gobbles up oil and fats on human skin to produce fatty acids that selectively eliminate Staphylococcus aureus. One out of every three people have Staphylococcus aureus harmlessly dwelling in their nose, but the bacteria are a risk factor for serious infections when given the opportunity: open wounds, abrasions and cuts. They’re the primary cause of skin and soft tissue infections known as staph infections. 

Staphylococcus aureus is also a hospital superbug notorious for being resistant to current antibiotics, elevating the pressing need for new medicines. 

There are lots of studies that identify new antibiotic structures, Kowalski said, “but what was fun and interesting about ours is that we identified (a compound) that is well-known and that people have studied before.” 

The compound is not toxic in normal lab conditions, but it can be potent in conditions that replicate the acidic environment of healthy skin. 

“I think that’s why in some cases we may have missed these kinds of antimicrobial mechanisms,” Kowalski added, “because the pH in the lab wasn’t low enough. But human skin is really acidic.” 

Humans play host to a colossal array of microorganisms, known as the microbiome, but we know little about our resident fungi and their contributions to human health, Kowalski said. The skin microbiome is of special interest to her because while other body parts crowd dozens of different fungi, the skin is dominantly colonized by one kind known as Malassezia. 

Malassezia can be associated with cases of dandruff and eczema, but it’s considered relatively harmless and a normal part of skin flora. The yeast has evolved to live on mammalian skin, so much so that it can’t make fatty acids without the lipids — oils and fats — secreted by skin. 

Despite the abundance of Malassezia found on us, they remain understudied, Kowalski said. 

“The skin is a parallel system to what’s happening in the gut, which is really well-studied,” she said. “We know that the intestinal microbiome can modify host compounds and make their own unique compounds that have new functions. Skin is lipid-rich, and the skin microbiome processes these lipids to also produce bioactive compounds. So what does this mean for skin health and diseases?” 

Looking at human skin samples from healthy donors and experiments done with skin cells in the lab, Kowalski found that the fungal species Malassezia sympodialis transformed host lipids into antibacterial hydroxy fatty acids. Fatty acids have various functions in cells but are notably the building blocks for cell membranes. 

The hydroxy fatty acids synthesized by Malassezia sympodialis were detergent-like, destroying the membranes of Staphylococcus aureus and causing its internal contents to leak away. The attack prevented the colonization of Staphylococcus aureus on the skin and ultimately killed the bacteria in as little as 15 minutes, Kowalski said. 

But the fungus isn’t a magic bullet. After enough exposure, the staph bacteria eventually became tolerant to the fungus, as they do when clinical antibiotics are overused. 

Looking at their genetics, the researchers found that the bacteria evolved a mutation in the Rel gene, which activates the bacterial stress response. Similar mutations have been previously identified in patients with Staphylococcus aureus infections. 

The findings show that a bacteria’s host environment and interactions with other microbes can influence its susceptibility to antibiotics. 

“There’s growing interest in applying microbes as a therapeutic, such as adding bacteria to prevent the growth of a pathogen,” Kowalski said. “But it can have consequences that we have not yet fully understood. Even though we know antibiotics lead to the evolution of resistance, it hasn’t been considered when we think about the application of microbes as a therapeutic.” 

While the discovery adds a layer of complexity for drug discovery, Kowalski said she is excited about the potential of resident fungi as a new source for future antibiotics. 

Identifying the antimicrobial fatty acids took three years and a cross-disciplinary effort. Kowalski collaborated with chemical microbiologists at McMaster University to track down the compound. 

“It was like finding a needle in a haystack but with molecules you can’t see,” said Kowalski’s adviser, Matthew Barber, an associate professor of biology in the College of Arts and Sciences at the UO. 

Kowalski is working on a follow-up study that goes deeper into the genetic mechanisms that led to the antibiotic tolerance. She is also preparing to launch her own lab to further investigate the overlooked role of the skin microbiome, parting from Barber’s lab after bringing fungi into focus. 

“Antibiotic-resistant bacterial infections are a major human health threat and one that, in some ways, is getting worse,” Barber said. “We still have a lot of work to do in understanding the microorganisms but also finding new ways that we can possibly treat or prevent those infections.” 

— By Leila Okahata, University Communications

This work was supported by the National Science Foundation, National Institutes of Health, L’Oreal USA for Women in Science Fellowship and Helen Hay Whitney Foundation Fellowship. 

About the University of Oregon College of Arts and Sciences 
The University of Oregon College of Arts and Sciences supports the UO’s mission and shapes its identity as a comprehensive research university. With disciplines in humanities and social and natural sciences, the College of Arts and Sciences serves approximately two-thirds of all UO students. The College of Arts and Sciences faculty includes some of the world’s most accomplished researchers, and the more than $75 million in sponsored research activity of the faculty underpins the UO’s status as a Carnegie Research I institution and its membership in the Association of American Universities.

---

Journal

Current Biology

DOI

10.1016/j.cub.2025.03.055 

Article Title

Skin mycobiota-mediated antagonism against Staphylococcus aureus through a modified fatty acid

Article Publication Date

14-Apr-2025