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Industry Engagement Program
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First Monoploid Reference Sequence of Sugarcane
… modern sugarcane cultivars are hybrids, each with more than 100 chromosomes; assembling a sugarcane genome is incredibly complex given its estimated size of 10 billion bases (more than three times the size of the … The final sugarcane sequence generated is 382 Mb; 25,316 protein-coding gene models were predicted with more than …
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Calculating the Costs of Multiple Switchgrass Gene Copies
… (in this case, a plant’s complete genetic makeup) and 10 common gardens. We discovered that 8X populations have …
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Doubling Down on Known Protein Families
… families. From there they focused on families with at least 100 members.  “If you have 100 sequences, the quality of the cluster is significantly higher because it is very hard to have 100 sequences from different locations or habitats that …
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Fungal & Algal Program
… biocontrol agents dramatically affect plant health. The  1000 Fungal Genomes Project is a five-year project to sequence 1000 fungal genomes from across the Fungal Tree of Life, …
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Trent Northen
… starvation modulate root exudation. Science Advances, 2024 10(1), Schadt, C., Martin, S., Carrell, A. et al. An … p.eadg7888. DOI: 10.1126/sciadv.adg7888 Treen D, et al.  SIMILE enables alignment … through standardized fabricated ecosystems. Nature Methods (16), 567–571 (2019) doi: 10.1038/s41592-019-0465-0. …
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Getting to the Bottom of Fungal Functions Across Earth’s Forests
… four forests, researchers have leveraged data from the 1000 Fungal Genomes project to form new connections between … Science Program proposal that Martin submitted in 2012. At that time, the field had surveyed many different soil … when we mapped the first sequenced RNA from the soil, only 10% of them were mapping to the fungal genomes at the JGI,” …
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Nitrosococcus watsonii sp. nov., a new species of marine obligate ammonia‐oxidizing bacteria that is not omnipresent in the world's oceans: calls to validate the names ‘Nitrosococcus halophilus’ and ‘Nitrosomonas mobilis’
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Progress Reports: 2002–2020
… FY16 Progress Report … FY12 Progress Report … FY10 Progress Report …
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Environmental Genomics Group
… microbiomes. mSystems0:e01744-24. https://doi.org/10.1128/msystems.01744-24 Oliver, T., Varghese, N., Roux, S. … Lake Mendota. Sci Data 11 , 966 (2024). https://doi.org/10.1038/s41597-024-03826-8 Nayfach, S., Roux, S., Seshadri, …
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Giant Bacteria Found in Guadeloupe Mangroves Challenge Traditional Concepts
… Antilles and a co-first author on the study, performed the 16S rRNA gene sequencing to identify and classify the … look at carbon storage, you’ll find that they contribute 10-15% of the carbon stored in coastal sediments,” said …
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Picking Up Threads of Cotton Genomics
… out of the green pods in every direction. There are 100 million families around the world whose livelihoods … these things take not five or eight years, but sometimes 10 or 15 years, because the technology develops over time.” …
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