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A Collaboration to Improve Plant Genome Annotations Across Species
… Atlas in  Nucleic Acids Research . The project spans 15 years and involves more than 17 research groups. The team … Having a better handle on the gene function helps identify the molecular targets for plant improvement. … we are looking at 18 different species, which included over 2000 RNA Seq libraries. As I previously mentioned, this is …
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Secrets of the Needles: What Microbes do on Conifer Leaves
… summer project in the JGI-UC Merced Internship Program. In 2023, Shayna Bennett, a UC Merced graduate student in …
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New Research Sheds Light on Diversity in the Deep Sea
… OCE-0728391, OCE-0937404, OCE-1558795 to A-L.R, and OCE-2049478 and DBI-2047598 to K.A. We thank the Department of Energy Joint …
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Olpidium, The Key to the Origin of Terrestrial Fungi
… Before 2006, Olpidium was one of the many obscure fungi of … Olpidium zoospores remained largely untouched until seven years later. In 2018, as members of the ZyGoLife consortium … to the sequencing effort by the JGI and ZyGoLife in recent years. With the much more extensive taxonomic and genetic …
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The More the Merrier: Making the Case for Plant Pan-genomes
… more than once, and these events took place a million years apart: the individual with a maternal  B. distachyon parent (D plastotype) some 1.4 million years ago (Mya), while the S plastotype was a more recent … anticipated with only minor gene loss even after a million years.” Reference genomes for  B. distachyon ,  B. stacei …
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Fields of Breeders’ Dreams: A Team Effort Toward Targeted Crop Improvements
… are often very different than those bred for Texas. Identifying and breeding varieties that have high productivity … from half of the United States. As  reported January 27, 2021 in  Nature , the team led by researchers at the … set up these gardens, we have them to study for a number of years. And that’s a real benefit for the research program.” …
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Pinning Down a Piece of Photosynthesis
… light, transport molecules and regulate reactions. Identifying these proteins and then figuring out what they are … and longtime JGI collaborator Sabeeha Merchant’s group. In 2011, they inventoried a swath of blueprints to find parts … set out to tackle some of these genes, expressing and purifying the range of proteins these genes produced, to …
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Mapping the Earth’s Hidden Fungal Kingdom
… and lay a future-ready foundation     Over the past billion years, fungi have spread quietly throughout our planet. From … origins, fungi remain largely mysterious. Only about 200,000 fungal species have been named. Among those … from diverse fungi, researchers struggle to identify and classify new species from environmental samples. …
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Improving the Cacao Genome and Phytozome
… Cocoa Organization (ICCO), global cocoa bean production in 2017-2018  was 4.6 million metric tons . The global chocolate … why Mars, Inc., a maker of chocolate for more than 100 years and one of the world’s largest buyers of cocoa, is …
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Len Pennacchio
… In 2003, Dr. Pennacchio joined the DOE Joint Genome Institute … 2021-  NLM Board of Regents Working Group on “NIH Comparative Genomics Resource” 2021-  Co-Chair, “Advances in Genome Biology & Technology- Agriculture” 2021-  Weill Neurohub Investigator 2020   Elected Fellow of …
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Leo Baumgart
… Dr. Baumgart joined the DOE Joint Genome Institute in 2018, following his doctoral research in synthetic biology … flowering plant gene regulation." Nature Plants 11, no. 8 (2025): 1514-1527. Lax, Carlos, Stephen J. Mondo, José F. … DNA affinity purification sequencing (DAP-seq) to identify in vitro binding sites of potential Novosphingobium …
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The Power of One, Amplified
… in, on, and around the planet remain unknown. In recent years, advances in sequencing technologies and bioinformatic … diverse than those within more moderate ecosystems. A few years ago, a candidate bacterial lineage was identified from … Research Council of Canada (NSERC) Discovery Grant to PFD (2019-06265). This work was also sponsored by NSF grants …
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