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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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Abou-Elwafa SF, Büttner B, Chia T, Schulze-Buxloh G, Hohmann U, Mutasa-Göttgens E, Jung C, Müller AE. Conservation and divergence of autonomous pathway genes in the flowering regulatory network of Beta vulgaris. J Exp Bot 2011; 62:3359-74. [PMID: 20974738 PMCID: PMC3130164 DOI: 10.1093/jxb/erq321] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [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] [Received: 07/20/2010] [Revised: 09/13/2010] [Accepted: 09/15/2010] [Indexed: 05/19/2023]
Abstract
The transition from vegetative growth to reproductive development is a complex process that requires an integrated response to multiple environmental cues and endogenous signals. In Arabidopsis thaliana, which has a facultative requirement for vernalization and long days, the genes of the autonomous pathway function as floral promoters by repressing the central repressor and vernalization-regulatory gene FLC. Environmental regulation by seasonal changes in daylength is under control of the photoperiod pathway and its key gene CO. The root and leaf crop species Beta vulgaris in the caryophyllid clade of core eudicots, which is only very distantly related to Arabidopsis, is an obligate long-day plant and includes forms with or without vernalization requirement. FLC and CO homologues with related functions in beet have been identified, but the presence of autonomous pathway genes which function in parallel to the vernalization and photoperiod pathways has not yet been reported. Here, this begins to be addressed by the identification and genetic mapping of full-length homologues of the RNA-regulatory gene FLK and the chromatin-regulatory genes FVE, LD, and LDL1. When overexpressed in A. thaliana, BvFLK accelerates bolting in the Col-0 background and fully complements the late-bolting phenotype of an flk mutant through repression of FLC. In contrast, complementation analysis of BvFVE1 and the presence of a putative paralogue in beet suggest evolutionary divergence of FVE homologues. It is further shown that BvFVE1, unlike FVE in Arabidopsis, is under circadian clock control. Together, the data provide first evidence for evolutionary conservation of components of the autonomous pathway in B. vulgaris, while also suggesting divergence or subfunctionalization of one gene. The results are likely to be of broader relevance because B. vulgaris expands the spectrum of evolutionarily diverse species which are subject to differential developmental and/or environmental regulation of floral transition.
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Affiliation(s)
- Salah F. Abou-Elwafa
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, D-24098 Kiel, Germany
| | - Bianca Büttner
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, D-24098 Kiel, Germany
| | - Tansy Chia
- Broom's Barn Research Centre, Higham, Bury St. Edmunds, Suffolk IP28 6NP, UK
| | - Gretel Schulze-Buxloh
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, D-24098 Kiel, Germany
| | - Uwe Hohmann
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, D-24098 Kiel, Germany
| | | | - Christian Jung
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, D-24098 Kiel, Germany
| | - Andreas E. Müller
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, D-24098 Kiel, Germany
- To whom correspondence should be addressed. E-mail:
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Abstract
Gibberellins (GAs) function not only to promote the growth of plant organs, but also to induce phase transitions during development. Their involvement in flower initiation in long-day (LD) and biennial plants is well established and there is growing insight into the mechanisms by which floral induction is achieved. The extent to which GAs mediate the photoperiodic stimulus to flowering in LD plants is, with a few exceptions, less clear. Despite evidence for photoperiod-enhanced GA biosynthesis in leaves of many LD plants, through up-regulation of GA 20-oxidase gene expression, a function for GAs as transmitted signals from leaves to apices in response to LD has been demonstrated only in Lolium species. In Arabidopsis thaliana, as one of four quantitative floral pathways, GA signalling has a relatively minor influence on flowering time in LD, while in SD, in the absence of the photoperiod flowering pathway, the GA pathway assumes a major role and becomes obligatory. Gibberellins promote flowering in Arabidopsis through the activation of genes encoding the floral integrators SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1), LEAFY (LFY), and FLOWERING LOCUS T (FT) in the inflorescence and floral meristems, and in leaves, respectively. Although GA signalling is not required for floral organ specification, it is essential for the normal growth and development of these organs. The sites of GA production and action within flowers, and the signalling pathways involved are beginning to be revealed.
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Affiliation(s)
- Effie Mutasa-Göttgens
- Broom's Barn Research Centre, Rothamsted Research Department of Applied Crop Science, Higham, Bury St Edmunds, Suffolk IP28 6NP, UK
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Dimmer E, Roden L, Cai D, Kingsnorth C, Mutasa-Göttgens E. Transgenic analysis of sugar beet xyloglucan endo-transglucosylase/hydrolase Bv-XTH1 and Bv-XTH2 promoters reveals overlapping tissue-specific and wound-inducible expression profiles. Plant Biotechnol J 2004; 2:127-39. [PMID: 17147605 DOI: 10.1046/j.1467-7652.2004.00056.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The identification and analysis of tissue-specific gene regulatory elements will improve our knowledge of the molecular mechanisms that control the growth and development of different plant tissues and offer potentially useful tools for the genetic engineering of plants. A polymerase chain reaction (PCR)-based 5'-genome walk from sequences of an isolated sugar beet xyloglucan endo-transglucosylase hydrolase (XTH) gene led to the isolation of two independent upstream fragments. They were 1332 and 2163 base pairs upstream of the XTH ATG start site, respectively. In vivo transgenic assays in sugar beet hairy roots and Arabidopsis thaliana revealed that both fragments had promoter function and, in A. thaliana, directed expression in vascular tissues within the root, leaves and petals. Promoter activity was also observed in the leaf trichomes and within rapidly expanding stem internodes. Expression driven by both promoters was found to be wound inducible. Overall, the spatial and temporal expression pattern of these promoters suggested that the corresponding Bv-XTH genes (designated Bv-XTH1 and Bv-XTH2) may be involved in secondary cell wall formation. This work provides new insights on molecular mechanisms that could be exploited for the genetic engineering of sugar beet crops.
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Affiliation(s)
- Emily Dimmer
- Broom's Barn Research Station, Higham, Bury St Edmunds, Suffolk, IP28 6NP, UK
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