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McGrath JM, Funk A, Galewski P, Ou S, Townsend B, Davenport K, Daligault H, Johnson S, Lee J, Hastie A, Darracq A, Willems G, Barnes S, Liachko I, Sullivan S, Koren S, Phillippy A, Wang J, Liu T, Pulman J, Childs K, Shu S, Yocum A, Fermin D, Mutasa-Göttgens E, Stevanato P, Taguchi K, Naegele R, Dorn KM. A contiguous de novo genome assembly of sugar beet EL10 ( Beta vulgaris L.). DNA Res 2022; 30:6748264. [PMID: 36208288 PMCID: PMC9896481 DOI: 10.1093/dnares/dsac033] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/26/2022] [Accepted: 09/12/2022] [Indexed: 02/04/2023] Open
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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Affiliation(s)
| | - Andrew Funk
- Plant Breeding, Genetics, and Biotechnology Program, Michigan State University, East Lansing, MI 48824, USA
| | - Paul Galewski
- Plant Breeding, Genetics, and Biotechnology Program, Michigan State University, East Lansing, MI 48824, USA
| | - Shujun Ou
- Plant Breeding, Genetics, and Biotechnology Program, Michigan State University, East Lansing, MI 48824, USA
| | - Belinda Townsend
- Department of Plant Sciences, Rothamsted Research, West Common, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Karen Davenport
- Los Alamos Nat’l Lab, Biosecurity and Public Health, Los Alamos, NM 87545, USA
| | - Hajnalka Daligault
- Los Alamos Nat’l Lab, Biosecurity and Public Health, Los Alamos, NM 87545, USA
| | - Shannon Johnson
- Los Alamos Nat’l Lab, Biosecurity and Public Health, Los Alamos, NM 87545, USA
| | - Joyce Lee
- BioNano Genomics, 9640 Towne Centre Drive, San Diego, CA 92121, USA
| | - Alex Hastie
- BioNano Genomics, 9640 Towne Centre Drive, San Diego, CA 92121, USA
| | - Aude Darracq
- SESVANDERHAVE N.V., Industriepark Soldatenplein Zone 2 Nr 15, 3300 Tienen, Belgium
| | - Glenda Willems
- SESVANDERHAVE N.V., Industriepark Soldatenplein Zone 2 Nr 15, 3300 Tienen, Belgium
| | - Steve Barnes
- SESVANDERHAVE N.V., Industriepark Soldatenplein Zone 2 Nr 15, 3300 Tienen, Belgium
| | - Ivan Liachko
- Phase Genomics, 4000 Mason Road, Suite 225, Seattle, WA 98195, USA
| | - Shawn Sullivan
- Phase Genomics, 4000 Mason Road, Suite 225, Seattle, WA 98195, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Adam Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Jie Wang
- Center for Genomics-Enabled Plant Science, Plant Biology Department, Michigan State University, East Lansing, MI 48824, USA
| | - Tiffany Liu
- Center for Genomics-Enabled Plant Science, Plant Biology Department, Michigan State University, East Lansing, MI 48824, USA
| | - Jane Pulman
- Center for Genomics-Enabled Plant Science, Plant Biology Department, Michigan State University, East Lansing, MI 48824, USA
| | - Kevin Childs
- Center for Genomics-Enabled Plant Science, Plant Biology Department, Michigan State University, East Lansing, MI 48824, USA
| | - Shengqiang Shu
- United States Department of Energy, Joint Genome Institute, Berkeley, CA, USA
| | | | | | - Effie Mutasa-Göttgens
- University of Hertfordshire, Division of Biosciences, Hatfield, Hertfordshire AL10 9AB, UK
| | | | - Kazunori Taguchi
- Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization, Shinsei Memuro, Hokkaido 082-0081, Japan
| | - Rachel Naegele
- USDA-ARS Sugarbeet and Bean Research Unit, Michigan State University, 1066 Bogue St., East Lansing, MI 48824, USA
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Tandon S, Singh A. Residue Behavior of Clopyralid Herbicide in Soil and Sugar Beet Crop under Subtropical Field Conditions. J Food Prot 2022; 85:735-739. [PMID: 35051274 DOI: 10.4315/jfp-21-355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 01/19/2022] [Indexed: 11/11/2022]
Abstract
ABSTRACT Sugar beet is a major crop for the sugar industry. With growing awareness of unsystematic use of pesticides, health problem, and environmental issues, assessment of pesticide residues in soil and crops has become necessary. Studies of subtropical conditions on dissipation and residue analysis of clopyralid have not yet been reported. Therefore, dissipation kinetics and terminal residues of clopyralid for two cropping seasons in the soil and the sugar beet crop were studied under field conditions. An experiment was laid out in a randomized block design, and a herbicide was applied as a postemergent. Clopyralid was extracted from the matrix by basic water, subjected to solid phase extraction cleanup, and quantified by high-pressure liquid chromatography-UV. The method was validated, and recovery percentage of pesticide ranged from 81 to 88, 77 to 85, 78 to 86, and 89 to 94% in the soil, sugar beet roots, sugar beet leaves, and water, respectively. After application in the soil, clopyralid dissipated rapidly following monophasic first-order kinetics, with a half-life of 13.39 days. Limits of detection and quantitation were 0.007 and 0.02 μg g-1, respectively. Clopyralid does not persist long in soil, and residues were below the European Union's maximum residue levels (0.5 mg kg-1) in the roots and leaves of sugar beet. Residues were also not detected in the groundwater. It can be concluded that clopyralid could be considered a safe herbicide from the environmental aspect due to its nonpersistence and that it would not have an adverse effect on human or animal health. HIGHLIGHTS
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Affiliation(s)
- Shishir Tandon
- Department of Chemistry (Agricultural Chemicals Division), College of Basic Sciences and Humanities, G. B. Pant University of Agriculture & Technology, Pantnagar 263 145, Udham Singh Nagar (Uttarakhand), India
| | - Anand Singh
- Department of Chemistry (Agricultural Chemicals Division), College of Basic Sciences and Humanities, G. B. Pant University of Agriculture & Technology, Pantnagar 263 145, Udham Singh Nagar (Uttarakhand), India
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Hanson SJ, Dawson JC, Goldman IL. Beta vulgaris ssp. vulgaris chromosome 8 shows significant association with geosmin concentration in table beet. G3 (Bethesda) 2021; 11:jkab344. [PMID: 34586384 PMCID: PMC8664477 DOI: 10.1093/g3journal/jkab344] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 09/20/2021] [Indexed: 11/29/2022]
Abstract
Geosmin, a degraded sesquiterpene molecule with earthy and musty odor, imbues table beet with its characteristic aroma. Geosmin is heritable and endogenously produced in table beet; its earthy aroma is sought by some consumers but deters others. Geosmin biosynthesis is catalyzed by a bifunctional geosmin synthase enzyme in diverse bacteria and fungi, but a mechanism for geosmin biosynthesis in plants has not been reported. This work employed association analysis and selective genotyping of a segregating F2:3 mapping population to seek QTL associated with geosmin concentration in table beet. GBS reads were aligned to sugar beet reference genome EL10.2, and association analysis revealed two QTL for geosmin concentration on Beta vulgaris ssp. vulgaris chromosome 8. QTL at EL10.2 positions 28,017,624 and 38,488,687 each show effect size 8.7 μg·kg-1 geosmin and explain 8.5% and 6.4% of total variation in geosmin concentration, respectively. Resolution was low due to large recombination bin size and imperfect alignment between the reference genome and mapping population, but population size and selection proportion were sufficient to detect moderate to large effect QTL. This study, the first molecular genetic mapping experiment in table beet, succeeded in finding QTL for geosmin concentration in table beet, and it provides the basis for fine mapping or candidate gene investigation of functional loci for this distinctive sensory trait.
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Affiliation(s)
- Solveig J Hanson
- Centre for Sustainable Food Systems, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Julie C Dawson
- Department of Horticulture, University of Wisconsin—Madison, Madison, WI 53706, USA
| | - Irwin L Goldman
- Department of Horticulture, University of Wisconsin—Madison, Madison, WI 53706, USA
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Schmidt N, Seibt KM, Weber B, Schwarzacher T, Schmidt T, Heitkam T. Broken, silent, and in hiding: tamed endogenous pararetroviruses escape elimination from the genome of sugar beet ( Beta vulgaris). Ann Bot 2021; 128:281-299. [PMID: 33729490 PMCID: PMC8389469 DOI: 10.1093/aob/mcab042] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 03/16/2021] [Indexed: 05/13/2023]
Abstract
BACKGROUND AND AIMS Endogenous pararetroviruses (EPRVs) are widespread components of plant genomes that originated from episomal DNA viruses of the Caulimoviridae family. Due to fragmentation and rearrangements, most EPRVs have lost their ability to replicate through reverse transcription and to initiate viral infection. Similar to the closely related retrotransposons, extant EPRVs were retained and often amplified in plant genomes for several million years. Here, we characterize the complete genomic EPRV fraction of the crop sugar beet (Beta vulgaris, Amaranthaceae) to understand how they shaped the beet genome and to suggest explanations for their absent virulence. METHODS Using next- and third-generation sequencing data and genome assembly, we reconstructed full-length in silico representatives for the three host-specific EPRVs (beetEPRVs) in the B. vulgaris genome. Focusing on the endogenous caulimovirid beetEPRV3, we investigated its chromosomal localization, abundance and distribution by fluorescent in situ and Southern hybridization. KEY RESULTS Full-length beetEPRVs range between 7.5 and 10.7 kb in size, are heterogeneous in structure and sequence, and occupy about 0.3 % of the beet genome. Although all three beetEPRVs were assigned to the florendoviruses, they showed variably arranged protein-coding domains, different fragmentation, and preferences for diverse sequence contexts. We observed small RNAs that specifically target the individual beetEPRVs, indicating stringent epigenetic suppression. BeetEPRV3 sequences occur along all sugar beet chromosomes, preferentially in the vicinity of each other and are associated with heterochromatic, centromeric and intercalary satellite DNAs. BeetEPRV3 members also exist in genomes of related wild species, indicating an initial beetEPRV3 integration 13.4-7.2 million years ago. CONCLUSIONS Our study in beet illustrates the variability of EPRV structure and sequence in a single host genome. Evidence of sequence fragmentation and epigenetic silencing implies possible plant strategies to cope with long-term persistence of EPRVs, including amplification, fixation in the heterochromatin, and containment of EPRV virulence.
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Affiliation(s)
- Nicola Schmidt
- Faculty of Biology, Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Kathrin M Seibt
- Faculty of Biology, Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Beatrice Weber
- Faculty of Biology, Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Trude Schwarzacher
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Xingke Road 723, Tianhe District, Guangzhou, PR China
| | - Thomas Schmidt
- Faculty of Biology, Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Tony Heitkam
- Faculty of Biology, Institute of Botany, Technische Universität Dresden, Dresden, Germany
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Kovarik A, Hemleben V. A commentary on: 'Broken, silent and in hiding: tamed endogenous pararetroviruses escape elimination from the genome of sugar beet ( Beta vulgaris)'. Ann Bot 2021; 128:iii-iv. [PMID: 34350938 PMCID: PMC8389174 DOI: 10.1093/aob/mcab068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
This article comments on: Nicola Schmidt, Kathrin M. Seibt, Beatrice Weber, Trude Schwarzacher, Thomas Schmidt, and Tony Heitkam, Broken, silent, and in hiding: tamed endogenous pararetroviruses escape elimination from the genome of sugar beet (Beta vulgaris), Annals of Botany Volume 128, Issue 3, 26 August 2021, Pages 281–291, https://doi.org/10.1093/aob/mcab042
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Affiliation(s)
- Ales Kovarik
- Laboratory of Molecular Epigenetics, Intitute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, Brno, Czech Republic
| | - Vera Hemleben
- Center of Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle, Tübingen, Germany
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Vu DP, Martins Rodrigues C, Jung B, Meissner G, Klemens PAW, Holtgräwe D, Fürtauer L, Nägele T, Nieberl P, Pommerrenig B, Neuhaus HE. Vacuolar sucrose homeostasis is critical for plant development, seed properties, and night-time survival in Arabidopsis. J Exp Bot 2020; 71:4930-4943. [PMID: 32361766 DOI: 10.1093/jxb/eraa205] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 04/23/2020] [Indexed: 05/12/2023]
Abstract
Most cellular sucrose is present in the cytosol and vacuoles of plant cells; however, little is known about the effect of this sucrose compartmentation on plant properties. Here, we examined the effects of altered intracellular sucrose compartmentation in Arabidopsis thaliana leaves by heterologously expressing the sugar beet (Beta vulgaris) vacuolar sucrose loader BvTST2.1 and by generating lines with reduced vacuolar invertase activity (amiR vi1-2). Heterologous expression of BvTST2.1 led to increased monosaccharide levels in leaves, whereas sucrose levels remained constant, indicating that vacuolar invertase activity in mesophyll vacuoles exceeds sucrose uptake. This notion was supported by analysis of tobacco (Nicotiana benthamiana) leaves transiently expressing BvTST2.1 and the invertase inhibitor NbVIF. However, sucrose levels were strongly elevated in leaf extracts from amiR vi1-2 lines, and experiments confirmed that sucrose accumulated in the corresponding vacuoles. The amiR vi1-2 lines exhibited impaired early development and reduced seed weight. When germinated in the dark, amiR vi1-2 seedlings were less able to convert sucrose into monosaccharides than the wild type. Cold temperatures strongly down-regulated both VI genes, but the amiR vi1-2 lines showed normal frost tolerance. These observations indicate that increased vacuolar sucrose levels fully compensate for the effects of low monosaccharide concentrations on frost tolerance.
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Affiliation(s)
- Duc Phuong Vu
- Universität Kaiserslautern, Fachbereich Biologie, Pflanzenphysiologie, Kaiserslautern, Germany
| | | | - Benjamin Jung
- Universität Kaiserslautern, Fachbereich Biologie, Pflanzenphysiologie, Kaiserslautern, Germany
| | - Garvin Meissner
- Universität Kaiserslautern, Fachbereich Biologie, Pflanzenphysiologie, Kaiserslautern, Germany
| | - Patrick A W Klemens
- Universität Kaiserslautern, Fachbereich Biologie, Pflanzenphysiologie, Kaiserslautern, Germany
| | - Daniela Holtgräwe
- Universität Bielefeld, Fakultät für Biologie, Genetik & Genomik der Pflanzen, Bielefeld, Germany
| | - Lisa Fürtauer
- Ludwig-Maximilians-Universität München, Biologie I, Evolutionäre Zellbiologie der Pflanzen, Planegg-Martinsried, Germany
| | - Thomas Nägele
- Ludwig-Maximilians-Universität München, Biologie I, Evolutionäre Zellbiologie der Pflanzen, Planegg-Martinsried, Germany
| | - Petra Nieberl
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Fakultät für Biologie, Molekulare Pflanzenphysiologie, Erlangen, Germany
| | - Benjamin Pommerrenig
- Universität Kaiserslautern, Fachbereich Biologie, Pflanzenphysiologie, Kaiserslautern, Germany
| | - H Ekkehard Neuhaus
- Universität Kaiserslautern, Fachbereich Biologie, Pflanzenphysiologie, Kaiserslautern, Germany
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