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[学术文献 ] Genome assembly of two allotetraploid cotton germplasms reveals mechanisms of somatic embryogenesis and enables precise genome editing 进入全文
nature genetics
Somatic embryogenesis is crucial for plant genetic engineering, yet the underlying mechanisms in cotton remain poorly understood. Here we present a telomere-to-telomere assembly of Jin668 and a high-quality assembly of YZ1, two highly regenerative allotetraploid cotton germplasms. The completion of the Jin668 genome enables characterization of ~30.1 Mb of centromeric regions invaded by centromeric retrotransposon of maize and Tekay retrotransposons, an ~8.1 Mb 5S rDNA array containing 25,190 copies and a ~75.1 Mb major 45S rDNA array with 8,131 copies. Comparative analyses of regenerative and recalcitrant genotypes reveal dynamic transcriptional patterns and chromatin accessibility during the initial regeneration process. A hierarchical gene regulatory network identifies AGL15 as a contributor to regeneration. Additionally, we demonstrate that genetic variation affects sgRNA target sites, while the Jin668 genome assembly reduces the risk of off-target effects in CRISPR-based genome editing. Together, the complete Jin668 genome reveals the complexity of genomic regions and cotton regeneration, and improves the precision of genome editing.
[前沿资讯 ] European boost for global food security: Dutch biotech Solynta gets €20 million EIB backing for highly disease resistant potato varieties 进入全文
Solynta
EIB lends €20 million to Dutch biotechnology company Solynta to develop potato seeds with strong resistance to disease and resilience to climate change. The focus of the EIB loan, which is supported under the European Commission’s InvestEU programme, is on the use of true potato seeds instead of traditional tubers for cultivation. Solynta’s technology holds promise of securing successful potato harvests and enhancing food supplies worldwide. Through proven hybrid breeding technology, Solynta has been able to create more robust potato varieties that require much fewer crop protection inputs. Solynta’s breeding method, which excludes genetically modified organisms (GMOs), can adapt potato characteristics relatively quickly to different needs including resistance to diseases such as late blight – a destructive fungal illness – and adaptation to climate change. As a result, the company’s potato varieties contribute to the United Nations sustainable-development goals (SDGs) such as ending poverty and hunger and promoting responsible consumption and production.
[学术文献 ] Natural variation of an E3 ubiquitin ligase encoding gene Chalk9 regulates grain chalkiness in rice 进入全文
nature communications
Grain chalkiness is an undesirable trait affecting rice quality, concerning both consumers and breeders. However, the genetic mechanisms underlying rice chalkiness remain largely elusive. Here, we identify Chalk9 as a major gene associated with grain chalkiness in a natural population. Chalk9 encodes an E3 ubiquitin ligase that targets OsEBP89 for its ubiquitination and degradation. Low expression of Chalk9 results in excessive accumulation of OsEBP89, disrupting the homeostasis of storage components and leading to the chalkiness phenotype. A 64-bp insertion/deletion in the Chalk9 promoter contributes to its differential transcriptional levels, thus causing chalkiness variation among rice varieties. Moreover, the elite allele Chalk9-L reduces grain chalkiness, without compromising yield. Chalk9-L is strongly selected in japonica but exhibits a complex evolutionary trajectory in indica. Our findings reveal the molecular and genetic mechanisms underlying chalkiness and provide a potential strategy for breeding rice varieties with improved quality.
[学术文献 ] A generalized platform for artificial intelligence-powered autonomous enzyme engineering 进入全文
nature communications
Proteins are the molecular machines of life with numerous applications in energy, health, and sustainability. However, engineering proteins with desired functions for practical applications remains slow, expensive, and specialist-dependent. Here we report a generally applicable platform for autonomous enzyme engineering that integrates machine learning and large language models with biofoundry automation to eliminate the need for human intervention, judgement, and domain expertise. Requiring only an input protein sequence and a quantifiable way to measure fitness, this automated platform can be applied to engineer a wide array of proteins. As a proof of concept, we engineer Arabidopsis thaliana halide methyltransferase (AtHMT) for a 90-fold improvement in substrate preference and 16-fold improvement in ethyltransferase activity, along with developing a Yersinia mollaretii phytase (YmPhytase) variant with 26-fold improvement in activity at neutral pH. This is accomplished in four rounds over 4 weeks, while requiring construction and characterization of fewer than 500 variants for each enzyme. This platform for autonomous experimentation paves the way for rapid advancements across diverse industries, from medicine and biotechnology to renewable energy and sustainable chemistry.
[前沿资讯 ] The convergence of AI and synthetic biology: the looming deluge 进入全文
npj biomedical innovations
The convergence of AI and synthetic biology is revolutionizing biological discovery and engineering. This manuscript examines how AI-driven tools accelerate bioengineering workflows, unlocking innovations in medicine, agriculture, and sustainability. It also addresses dual-use risks, governance gaps, and ethical dilemmas posed by these advancements, proposing strategies for oversight and updated regulations. By exploring opportunities and risks, this work highlights the transformative potential of AI-driven synthetic biology and pathways for responsible development.
[前沿资讯 ] Reverse evolution? These wild tomatoes are turning back time 进入全文
University of California, Riverside
Evolution is taking an unexpected turn on the volcanic islands of the western Galápagos. Wild tomato plants are producing a toxic blend of chemicals that hasn’t existed in their species for millions of years. Somehow, these plants have started making molecules more like eggplants than the modern tomato. This bizarre twist in evolution is being studied by scientists at the University of California, Riverside. The research team describes this phenomenon as a rare case of “reverse evolution.” That term raises eyebrows in the world of biology, where evolution is typically seen as a one-way street – not a boomerang.
