Construction and characterization of a sugar beet (<i>Beta vulgaris</i>) fosmid library

Lange, Cornelia; Holtgräwe, Daniela; Schulz, Britta; Weißhaar, Bernd; Himmelbauer, Heinz

doi:10.1139/g08-071

Cited by 24 publications

(16 citation statements)

References 19 publications

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“…3). First, a super-tree was inferred from all the trees in the phylome (19,747 trees) by using a gene tree parsimony approach as implemented in the DupTree algorithm 35 . This approach is different from other super-tree approaches (such as finding the majority-rule consensus) as it finds the species topology with the minimum total number of RESEARCH LETTER duplications implied when reconciling a collection of gene family trees (that is, the phylome) with that species topology.…”

Section: Methods Summarymentioning

confidence: 99%

The genome of the recently domesticated crop plant sugar beet (Beta vulgaris)

Dohm

Minoche

Holtgräwe

et al. 2013

Nature

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558

586

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Sugar beet (Beta vulgaris ssp. vulgaris) is an important crop of temperate climates which provides nearly 30% of the world's annual sugar production and is a source for bioethanol and animal feed. The species belongs to the order of Caryophylalles, is diploid with 2n 5 18 chromosomes, has an estimated genome size of 714-758 megabases 1 and shares an ancient genome triplication with other eudicot plants 2 . Leafy beets have been cultivated since Roman times, but sugar beet is one of the most recently domesticated crops. It arose in the late eighteenth century when lines accumulating sugar in the storage root were selected from crosses made with chard and fodder beet 3 . Here we present a reference genome sequence for sugar beet as the first non-rosid, non-asterid eudicot genome, advancing comparative genomics and phylogenetic reconstructions. The genome sequence comprises 567 megabases, of which 85% could be assigned to chromosomes. The assembly covers a large proportion of the repetitive sequence content that was estimated 4 to be 63%. We predicted 27,421 protein-coding genes supported by transcript data and annotated them on the basis of sequence homology. Phylogenetic analyses provided evidence for the separation of Caryophyllales before the split of asterids and rosids, and revealed lineage-specific gene family expansions and losses. We sequenced spinach (Spinacia oleracea), another Caryophyllales species, and validated features that separate this clade from rosids and asterids. Intraspecific genomic variation was analysed based on the genome sequences of sea beet (Beta vulgaris ssp. maritima; progenitor of all beet crops) and four additional sugar beet accessions. We identified seven million variant positions in the reference genome, and also large regions of low variability, indicating artificial selection. The sugar beet genome sequence enables the identification of genes affecting agronomically relevant traits, supports molecular breeding and maximizes the plant's potential in energy biotechnology.During the last 200 years of sugar beet breeding, the sugar content has increased from 8% to 18% in today's cultivars. Breeding has also actively selected for traits like resistance to viral and fungal diseases, improved taproot yield, monogermy of the seed and bolting resistance.

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Section: Methods Summarymentioning

confidence: 99%

The genome of the recently domesticated crop plant sugar beet (Beta vulgaris)

Dohm

Minoche

Holtgräwe

et al. 2013

Nature

Self Cite

558

586

View full text Add to dashboard Cite

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“…Isolation of satellite monomers from sugar beet libraries BAC and Fosmid libraries of the sugar beet genome (McGrath et al 2004;Hohmann et al 2003;Lange et al 2008;Holtgräwe et al, in preparation) were screened for pBV and pEV monomers using the stand-alone version of FASTA-Nucleotide (ftp://ftp.ebi.ac.uk/pub/software/unix/ fasta/CURRENT/windows/; default parameters) and previously published pBV (EMBL accession Z22849) and pEV (EMBL accession Z22848) monomer sequences as query (Menzel et al 2008;Dechyeva et al 2003;. Full-length monomers were extracted and sequence alignments were generated using MUSCLE (http://www.drive5.com/muscle/; default parameters) and DNASTAR-SeqMan-NGen (http://www.…”

Section: Methodsmentioning

confidence: 99%

Epigenetic profiling of heterochromatic satellite DNA

Zakrzewski¹,

Weißhaar

Fuchs

et al. 2011

Chromosoma

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Sugar beet (Beta vulgaris) chromosomes consist of large heterochromatic blocks in pericentromeric, centromeric, and intercalary regions comprised of two different highly abundant DNA satellite families. To investigate DNA methylation at single base resolution at heterochromatic regions, we applied a method for strand-specific bisulfite sequencing of more than 1,000 satellite monomers followed by statistical analyses. As a result, we uncovered diversity in the distribution of different methylation patterns in both satellite families. Heavily methylated CG and CHG (H=A, T, or C) sites occur more frequently in intercalary heterochromatin, while CHH sites, with the exception of CAA, are only sparsely methylated, in both intercalary and pericentromeric/centromeric heterochromatin. We show that the difference in DNA methylation intensity is correlated to unequal distribution of heterochromatic histone H3 methylation marks. While clusters of H3K9me2 were absent from pericentromeric heterochromatin and restricted only to intercalary heterochromatic regions, H3K9me1 and H3K27me1 were observed in all types of heterochromatin. By sequencing of a small RNA library consisting of 6.76 million small RNAs, we identified small interfering RNAs (siRNAs) of 24 nucleotides in size which originated from both strands of the satellite DNAs. We hypothesize an involvement of these siRNAs in the regulation of DNA and histone methylation for maintaining heterochromatin.

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“…Especially elements of the highly repetitive Cotzilla family contribute significantly to the B. vulgaris genome size and thus have a major evolutionary impact. The sequencing of the B. vulgaris genome by nextgeneration sequencing technologies is currently underway (Lange et al 2008). Knowledge about the molecular structure of retrotransposons and their heterogeneity will not only be critical for the annotation of the B. vulgaris genome sequence but also for the understanding of their evolution and significance in plant genomes.…”

Section: Evolutionarily Young Cotzilla and Ancient Salire Retrotranspmentioning

confidence: 99%

The Ty1-copia families SALIRE and Cotzilla populating the Beta vulgaris genome show remarkable differences in abundance, chromosomal distribution, and age

Weber¹,

Wenke²,

Frömmel³

et al. 2009

Chromosome Res

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Long terminal repeat (LTR) retrotransposons are major components of plant genomes influencing genome size and evolution. Using two separate approaches, we identified the Ty1-copia retrotransposon families Cotzilla and SALIRE in the Beta vulgaris (sugar beet) genome. While SALIRE elements are similar to typical Ty1-copia retrotransposons, Cotzilla elements belong to a lineage called Sireviruses. Hallmarks of Cotzilla retrotransposons are the existence of an additional putative env-like open reading frame upstream of the 3'LTR, an extended gag region, and a frameshift separating the gag and pol genes. Detected in a c ( 0 ) t-1 DNA library, Cotzilla elements belong to the most abundant retrotransposon families in B. vulgaris and are relatively homogenous and evolutionarily young. In contrast, the SALIRE family has relatively few copies, is diverged, and most likely ancient. As revealed by fluorescent in situ hybridization, SALIRE elements target predominantly gene-rich euchromatic regions, while Cotzilla retrotransposons are abundant in the intercalary and pericentromeric heterochromatin. The analysis of two retrotransposons from the same subclass contrasting in abundance, age, sequence diversity, and localization gives insight in the heterogeneity of LTR retrotransposons populating a plant genome.

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Construction and characterization of a sugar beet (Beta vulgaris) fosmid library

Cited by 24 publications

References 19 publications

The genome of the recently domesticated crop plant sugar beet (Beta vulgaris)

The genome of the recently domesticated crop plant sugar beet (Beta vulgaris)

Epigenetic profiling of heterochromatic satellite DNA

The Ty1-copia families SALIRE and Cotzilla populating the Beta vulgaris genome show remarkable differences in abundance, chromosomal distribution, and age

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