Search Results - "Soyk, Sebastian"

RaGOO: fast and accurate reference-guided scaffolding of draft genomes by Alonge, Michael, Soyk, Sebastian, Ramakrishnan, Srividya, Wang, Xingang, Goodwin, Sara, Sedlazeck, Fritz J, Lippman, Zachary B, Schatz, Michael C

“…We present RaGOO, a reference-guided contig ordering and orienting tool that leverages the speed and sensitivity of Minimap2 to accurately achieve…”
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Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing by Alonge, Michael, Lebeigle, Ludivine, Kirsche, Melanie, Jenike, Katie, Ou, Shujun, Aganezov, Sergey, Wang, Xingang, Lippman, Zachary B, Schatz, Michael C, Soyk, Sebastian

“…Advancing crop genomics requires efficient genetic systems enabled by high-quality personalized genome assemblies. Here, we introduce RagTag, a toolset for…”
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Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato by Alonge, Michael, Wang, Xingang, Benoit, Matthias, Soyk, Sebastian, Pereira, Lara, Zhang, Lei, Suresh, Hamsini, Ramakrishnan, Srividya, Maumus, Florian, Ciren, Danielle, Levy, Yuval, Harel, Tom Hai, Shalev-Schlosser, Gili, Amsellem, Ziva, Razifard, Hamid, Caicedo, Ana L., Tieman, Denise M., Klee, Harry, Kirsche, Melanie, Aganezov, Sergey, Ranallo-Benavidez, T. Rhyker, Lemmon, Zachary H., Kim, Jennifer, Robitaille, Gina, Kramer, Melissa, Goodwin, Sara, McCombie, W. Richard, Hutton, Samuel, Van Eck, Joyce, Gillis, Jesse, Eshed, Yuval, Sedlazeck, Fritz J., van der Knaap, Esther, Schatz, Michael C., Lippman, Zachary B.

“…Structural variants (SVs) underlie important crop improvement and domestication traits. However, resolving the extent, diversity, and quantitative impact of…”
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Variation in the flowering gene SELF PRUNING 5G promotes day-neutrality and early yield in tomato by Soyk, Sebastian, Müller, Niels A, Park, Soon Ju, Schmalenbach, Inga, Jiang, Ke, Hayama, Ryosuke, Zhang, Lei, Van Eck, Joyce, Jiménez-Gómez, José M, Lippman, Zachary B

“…Zachary Lippman, José Jiménez-Gómez and colleagues show that cultivated tomatoes have lost day-length-sensitive flowering, compared to their wild relatives, as…”
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PROTEIN TARGETING TO STARCH is required for localising GRANULE-BOUND STARCH SYNTHASE to starch granules and for normal amylose synthesis in Arabidopsis by Seung, David, Soyk, Sebastian, Coiro, Mario, Maier, Benjamin A, Eicke, Simona, Zeeman, Samuel C

“…The domestication of starch crops underpinned the development of human civilisation, yet we still do not fully understand how plants make starch. Starch is…”
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Duplication of a domestication locus neutralized a cryptic variant that caused a breeding barrier in tomato by Soyk, Sebastian, Lemmon, Zachary H., Sedlazeck, Fritz J., Jiménez-Gómez, José M., Alonge, Michael, Hutton, Samuel F., Van Eck, Joyce, Schatz, Michael C., Lippman, Zachary B.

“…Genome editing technologies are being widely adopted in plant breeding 1 . However, a looming challenge of engineering desirable genetic variation in diverse…”
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Rapid improvement of domestication traits in an orphan crop by genome editing by Lemmon, Zachary H., Reem, Nathan T., Dalrymple, Justin, Soyk, Sebastian, Swartwood, Kerry E., Rodriguez-Leal, Daniel, Van Eck, Joyce, Lippman, Zachary B.

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Non-invasive topology analysis of membrane proteins in the secretory pathway by Brach, Thorsten, Soyk, Sebastian, Müller, Christopher, Hinz, Giselbert, Hell, Rüdiger, Brandizzi, Federica, Meyer, Andreas J

“…We present a novel method to experimentally visualize in vivo the topology of transmembrane proteins residing in the endoplasmic reticulum (ER) membrane or…”
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Meristem transitions and plant architecture-learning from domestication for crop breeding by Gaarslev, Natalia, Swinnen, Gwen, Soyk, Sebastian

“…Genetic networks that regulate meristem transitions were recurrent targets of selection during crop domestication and allow fine-tuning of plant architecture…”
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New Horizons for Dissecting Epistasis in Crop Quantitative Trait Variation by Soyk, Sebastian, Benoit, Matthias, Lippman, Zachary B

“…Uncovering the genes, variants, and interactions underlying crop diversity is a frontier in plant genetics. Phenotypic variation often does not reflect the…”
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New Horizons for Dissecting Epistasis in Crop Quantitative Trait Variation by Soyk, Sebastian, Benoit, Matthias, Lippman, Zachary B

“…Uncovering the genes, variants, and interactions underlying crop diversity is a frontier in plant genetics. Phenotypic variation often does not reflect the…”
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Bypassing Negative Epistasis on Yield in Tomato Imposed by a Domestication Gene by Soyk, Sebastian, Lemmon, Zachary H., Oved, Matan, Fisher, Josef, Liberatore, Katie L., Park, Soon Ju, Goren, Anna, Jiang, Ke, Ramos, Alexis, van der Knaap, Esther, Van Eck, Joyce, Zamir, Dani, Eshed, Yuval, Lippman, Zachary B.

“…Selection for inflorescence architecture with improved flower production and yield is common to many domesticated crops. However, tomato inflorescences…”
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Rapid improvement of domestication traits in an orphan crop by genome editing by Lemmon, Zachary H., Reem, Nathan T., Dalrymple, Justin, Soyk, Sebastian, Swartwood, Kerry E., Rodriguez-Leal, Daniel, Van Eck, Joyce, Lippman, Zachary B.

“…Genome editing holds great promise for increasing crop productivity, and there is particular interest in advancing breeding in orphan crops, which are often…”
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Establishing Physalis as a Solanaceae model system enables genetic reevaluation of the inflated calyx syndrome by He, Jia, Alonge, Michael, Ramakrishnan, Srividya, Benoit, Matthias, Soyk, Sebastian, Reem, Nathan T, Hendelman, Anat, Van Eck, Joyce, Schatz, Michael C, Lippman, Zachary B

“…The highly diverse Solanaceae family contains several widely studied models and crop species. Fully exploring, appreciating, and exploiting this diversity…”
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The Starch Granule-Associated Protein EARLY STARVATION1 Is Required for the Control of Starch Degradation in Arabidopsis thaliana Leaves by Feike, Doreen, Seung, David, Graf, Alexander, Bischof, Sylvain, Ellick, Tamaryn, Coiro, Mario, Soyk, Sebastian, Eicke, Simona, Mettler-Altmann, Tabea, Lu, Kuan Jen, Trick, Martin, Zeeman, Samuel C., Smith, Alison M.

“…To uncover components of the mechanism that adjusts the rate of leaf starch degradation to the length of the night, we devised a screen for mutant Arabidopsis…”
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Optimized sample selection for cost-efficient long-read population sequencing by Ranallo-Benavidez, T Rhyker, Lemmon, Zachary, Soyk, Sebastian, Aganezov, Sergey, Salerno, William J, McCoy, Rajiv C, Lippman, Zachary B, Schatz, Michael C, Sedlazeck, Fritz J

“…An increasingly important scenario in population genetics is when a large cohort has been genotyped using a low-resolution approach (e.g., microarrays, exome…”
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β-Amylase–Like Proteins Function as Transcription Factors in Arabidopsis, Controlling Shoot Growth and Development by Reinhold, Heike, Soyk, Sebastian, Šimková, Klára, Hostettler, Carmen, Marafino, John, Mainiero, Samantha, Vaughan, Cara K., Monroe, Jonathan D., Zeeman, Samuel C.

“…Plants contain β-amylase-like proteins (BAMs; enzymes usually associated with starch breakdown) present in the nucleus rather than targeted to the chloroplast…”
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The Enzyme-Like Domain of Arabidopsis Nuclear β-Amylases Is Critical for DNA Sequence Recognition and Transcriptional Activation by Soyk, Sebastian, Šimková, Klára, Zürcher, Evelyne, Luginbühl, Leonie, Brand, Luise H., Vaughan, Cara K., Wanke, Dierk, Zeeman, Samuel C.

“…Plant BZR1-BAM transcription factors contain a β-amylase (BAM)-like domain, characteristic of proteins involved in starch breakdown. The enzyme-derived domains…”
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PROTEIN TARGETING TO STARCH Is Required for Localising GRANULE-BOUND STARCH SYNTHASE to Starch Granules and for Normal Amylose Synthesis in Arabidopsis: e1002080 by Seung, David, Soyk, Sebastian, Coiro, Mario, Maier, Benjamin A, Eicke, Simona, Zeeman, Samuel C

“…The domestication of starch crops underpinned the development of human civilisation, yet we still do not fully understand how plants make starch. Starch is…”
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Author Correction: Duplication of a domestication locus neutralized a cryptic variant that caused a breeding barrier in tomato by Soyk, Sebastian, Lemmon, Zachary H., Sedlazeck, Fritz J., Jiménez-Gómez, José M., Alonge, Michael, Hutton, Samuel F., Van Eck, Joyce, Schatz, Michael C., Lippman, Zachary B.

“…An amendment to this paper has been published and can be accessed via a link at the top of the paper…”
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