RaGOO: fast and accurate reference-guided scaffolding of draft genomes

Autor: Michael Alonge, Sebastian Soyk, Srividya Ramakrishnan, Xingang Wang, Sara Goodwin, Fritz J. Sedlazeck, Zachary B. Lippman, Michael C. Schatz

Publikováno v: Genome Biology, Vol 20, Iss 1, Pp 1-17 (2019)

Abstract We present RaGOO, a reference-guided contig ordering and orienting tool that leverages the speed and sensitivity of Minimap2 to accurately achieve chromosome-scale assemblies in minutes. After the pseudomolecules are constructed, RaGOO ident

Externí odkaz: https://doaj.org/article/d6f1cece618840d8afe7799d28bbb714

Establishing Physalis as a Solanaceae model system enables genetic reevaluation of the inflated calyx syndrome

Autor: Anat Hendelman, Matthias Benoit, Sebastian Soyk, Jia He, Michael Schatz, Michael Alonge, Zachary Lippman, Joyce Van Eck, Srividya Ramakrishnan, Nathan Reem

Publikováno v: The Plant cell. 35(1)

The highly diverse Solanaceae family contains several widely studied models and crop species. Fully exploring, appreciating, and exploiting this diversity requires additional model systems. Particularly promising are orphan fruit crops in the genus P

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a0dd0756ead1b2ffa6b20bb6b0fb3a6b
https://pubmed.ncbi.nlm.nih.gov/36268892

Automated assembly scaffolding elevates a new tomato system for high-throughput genome editing

Autor: Michael C. Schatz, Sebastian Soyk, Zachary B. Lippman, Melanie Kirsche, Ludivine Lebeigle, Michael Alonge, Sergey Aganezov, Xingang Wang

Publikováno v: BioRxiv
bioRxiv

Advancing crop genomics requires efficient genetic systems enabled by high-quality personalized genome assemblies. Here, we introduce RagTag, a toolset for automating assembly scaffolding and patching, and we establish chromosome-scale reference geno

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::97ebce254ea1df9e9021bf15a0ef65c4
https://doi.org/10.1101/2021.11.18.469135

Optimized sample selection for cost-efficient long-read population sequencing

Autor: Fritz J. Sedlazeck, Michael C. Schatz, Sergey Aganezov, Rajiv C. McCoy, Sebastian Soyk, William J Salerno, Zachary B. Lippman, Timothy Rhyker Ranallo-Benavidez, Zachary H. Lemmon

Publikováno v: Genome Res

An increasingly important scenario in population genetics is when a large cohort has been genotyped using a low-resolution approach (e.g., microarrays, exome capture, short-read WGS), from which a few individuals are resequenced using a more comprehe

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::003c278f444f12b800c8eee58c22b67a
https://pubmed.ncbi.nlm.nih.gov/33811084

Major impacts of widespread structural variation on gene expression and crop improvement in tomato

Autor: Melissa Kramer, Michael C. Schatz, Joyce Van Eck, Jesse Gillis, Harry J. Klee, Lei Zhang, Fritz J. Sedlazeck, Zachary B. Lippman, Ziva Amsellem, Sebastian Soyk, Matthias Benoit, Hamid Razifard, Hamsini Suresh, W. Richard McCombie, Esther van der Knaap, Tom Hai Harel, Yuval Levy, Gili Shalev-Schlosser, Xingang Wang, Sergey Aganezov, Gina Robitaille, Samuel F. Hutton, Lara Pereira, Florian Maumus, Melanie Kirsche, Danielle Ciren, Jennifer Kim, Srividya Ramakrishnan, Zachary H. Lemmon, Michael Alonge, Denise M. Tieman, Yuval Eshed, Ana L. Caicedo, Sara Goodwin, T. Rhyker Ranallo-Benavidez

Publikováno v: Cell
Cell, Elsevier, 2020, 182 (1), pp.145-161.e23. ⟨10.1016/j.cell.2020.05.021⟩
Cell, 2020, 182 (1), pp.145-161.e23. ⟨10.1016/j.cell.2020.05.021⟩

Structural variants (SVs) underlie important crop improvement and domestication traits. However, resolving the extent, diversity, and quantitative impact of SVs has been challenging. We used long-read nanopore sequencing to capture 238,490 SVs in 100

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::28692db8b8baf8caa9f0fb8ddadb6f6a
https://europepmc.org/articles/PMC7354227/