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A contiguous de novo genome assembly of sugar beet EL10 (Beta vulgaris L.).
McGrath, J Mitchell; Funk, Andrew; Galewski, Paul; Ou, Shujun; Townsend, Belinda; Davenport, Karen; Daligault, Hajnalka; Johnson, Shannon; Lee, Joyce; Hastie, Alex; Darracq, Aude; Willems, Glenda; Barnes, Steve; Liachko, Ivan; Sullivan, Shawn; Koren, Sergey; Phillippy, Adam; Wang, Jie; Liu, Tiffany; Pulman, Jane; Childs, Kevin; Shu, Shengqiang; Yocum, Anastasia; Fermin, Damian; Mutasa-Göttgens, Effie; Stevanato, Piergiorgio; Taguchi, Kazunori; Naegele, Rachel; Dorn, Kevin M.
  • McGrath JM; USDA-ARS Sugarbeet and Bean Research Unit, Michigan State University, 1066 Bogue St., East Lansing, MI 48824, USA.
  • Funk A; Plant Breeding, Genetics, and Biotechnology Program, Michigan State University, East Lansing, MI 48824, USA.
  • Galewski P; Plant Breeding, Genetics, and Biotechnology Program, Michigan State University, East Lansing, MI 48824, USA.
  • Ou S; Plant Breeding, Genetics, and Biotechnology Program, Michigan State University, East Lansing, MI 48824, USA.
  • Townsend B; Department of Plant Sciences, Rothamsted Research, West Common, Harpenden, Hertfordshire AL5 2JQ, UK.
  • Davenport K; Los Alamos Nat'l Lab, Biosecurity and Public Health, Los Alamos, NM 87545, USA.
  • Daligault H; Los Alamos Nat'l Lab, Biosecurity and Public Health, Los Alamos, NM 87545, USA.
  • Johnson S; Los Alamos Nat'l Lab, Biosecurity and Public Health, Los Alamos, NM 87545, USA.
  • Lee J; BioNano Genomics, 9640 Towne Centre Drive, San Diego, CA 92121, USA.
  • Hastie A; BioNano Genomics, 9640 Towne Centre Drive, San Diego, CA 92121, USA.
  • Darracq A; SESVANDERHAVE N.V., Industriepark Soldatenplein Zone 2 Nr 15, 3300 Tienen, Belgium.
  • Willems G; SESVANDERHAVE N.V., Industriepark Soldatenplein Zone 2 Nr 15, 3300 Tienen, Belgium.
  • Barnes S; SESVANDERHAVE N.V., Industriepark Soldatenplein Zone 2 Nr 15, 3300 Tienen, Belgium.
  • Liachko I; Phase Genomics, 4000 Mason Road, Suite 225, Seattle, WA 98195, USA.
  • Sullivan S; Phase Genomics, 4000 Mason Road, Suite 225, Seattle, WA 98195, USA.
  • Koren S; Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA.
  • Phillippy A; Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA.
  • Wang J; Center for Genomics-Enabled Plant Science, Plant Biology Department, Michigan State University, East Lansing, MI 48824, USA.
  • Liu T; Center for Genomics-Enabled Plant Science, Plant Biology Department, Michigan State University, East Lansing, MI 48824, USA.
  • Pulman J; Center for Genomics-Enabled Plant Science, Plant Biology Department, Michigan State University, East Lansing, MI 48824, USA.
  • Childs K; Center for Genomics-Enabled Plant Science, Plant Biology Department, Michigan State University, East Lansing, MI 48824, USA.
  • Shu S; United States Department of Energy, Joint Genome Institute, Berkeley, CA, USA.
  • Yocum A; A2IDEA, 674 S. Wagner Rd., Ann Arbor, MI 48103, USA.
  • Fermin D; A2IDEA, 674 S. Wagner Rd., Ann Arbor, MI 48103, USA.
  • Mutasa-Göttgens E; University of Hertfordshire, Division of Biosciences, Hatfield, Hertfordshire AL10 9AB, UK.
  • Stevanato P; DAFNAE, University of Padova, Viale Università 16, 35020 Legnaro (PD), Italy.
  • Taguchi K; Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization, Shinsei Memuro, Hokkaido 082-0081, Japan.
  • Naegele R; USDA-ARS Sugarbeet and Bean Research Unit, Michigan State University, 1066 Bogue St., East Lansing, MI 48824, USA.
  • Dorn KM; USDA-ARS Soil Management and Sugarbeet Research Unit, Crops Research Laboratory, 1701 Centre Ave, Fort Collins, CO 80526, USA.
DNA Res ; 30(1)2023 Feb 01.
Article en En | MEDLINE | ID: mdl-36208288
ABSTRACT
A contiguous assembly of the inbred 'EL10' sugar beet (Beta vulgaris ssp. vulgaris) genome was constructed using PacBio long-read sequencing, BioNano optical mapping, Hi-C scaffolding, and Illumina short-read error correction. The EL10.1 assembly was 540 Mb, of which 96.2% was contained in nine chromosome-sized pseudomolecules with lengths from 52 to 65 Mb, and 31 contigs with a median size of 282 kb that remained unassembled. Gene annotation incorporating RNA-seq data and curated sequences via the MAKER annotation pipeline generated 24,255 gene models. Results indicated that the EL10.1 genome assembly is a contiguous genome assembly highly congruent with the published sugar beet reference genome. Gross duplicate gene analyses of EL10.1 revealed little large-scale intra-genome duplication. Reduced gene copy number for well-annotated gene families relative to other core eudicots was observed, especially for transcription factors. Variation in genome size in B. vulgaris was investigated by flow cytometry among 50 individuals producing estimates from 633 to 875 Mb/1C. Read-depth mapping with short-read whole-genome sequences from other sugar beet germplasm suggested that relatively few regions of the sugar beet genome appeared associated with high-copy number variation.
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Texto completo: 1 Banco de datos: MEDLINE Asunto principal: Beta vulgaris Tipo de estudio: Prognostic_studies Límite: Humans Idioma: En Año: 2023 Tipo del documento: Article
Texto completo
Imprimir
XML
PubMed Links
Search on Google

Texto completo: 1 Banco de datos: MEDLINE Asunto principal: Beta vulgaris Tipo de estudio: Prognostic_studies Límite: Humans Idioma: En Año: 2023 Tipo del documento: Article