Genome size and the proportion of repeated nucleotide sequence DNA in plants

Flavell, R. B.; Bennett, M. D.; Smith, James B.; Smith, D. B.

doi:10.1007/bf00485947

Cited by 543 publications

(277 citation statements)

References 29 publications

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“…Sequences with similarity either by BLASTX to known or predicted genes or by BLASTN to maize ESTs represented 5.4% of the library. This observation is consistent with models of the maize genome that predict a small proportion of the maize genome is devoted to the genic regions (Flavell et al 1974).…”

Section: Sample Sequencing Indicates the Maize Genome Is Highly Repetsupporting

confidence: 90%

Abundance, Distribution, and Transcriptional Activity of Repetitive Elements in the Maize Genome

Meyers

Tingey²,

Morgante³

2001

Genome Res.

372

313

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Long terminal repeat (LTR) retrotransposons have been shown to make up much of the maize genome. Although these elements are known to be prevalent in plant genomes of a middle-to-large size, little information is available on the relative proportions composed by specific families of elements in a single genome. We sequenced a library of randomly sheared genomic DNA from maize to characterize this genome. BLAST analysis of these sequences demonstrated that the maize genome is composed of diverse sequences that represent numerous families of retrotransposons. The largest families contain the previously described elements Huck, Ji, and Opie. Approximately 5% of the sequences are predicted to encode proteins. The genomic abundance of 16 families of elements was estimated by hybridization to an array of 10,752 maize bacterial artificial chromosome (BAC) clones. Comparisons of the number of elements present on individual BACs indicated that retrotransposons are in general randomly distributed across the maize genome. A second library was constructed that was selected to contain sequences hypomethylated in the maize genome. Sequence analysis of this library indicated that retroelements abundant in the genome are poorly represented in hypomethylated regions. Fifty-six retroelement sequences corresponding to the integrase and reverse transcriptase domains were isolated from ∼407,000 maize expressed sequence tags (ESTs). Phylogenetic analysis of these and the genomic retroelement sequences indicated that elements most abundant in the genome are less abundant at the transcript level than are more rare retrotransposons. Additional phylogenies also demonstrated that rice and maize retrotransposon families are frequently more closely related to each other than to families within the same species. An analysis of the GC content of the maize genomic library and that of maize ESTs did not support recently published data that the gene space in maize is found within a narrow GC range, but does indicate that genic sequences have a higher GC content than intergenic sequences (52% vs. 47% GC).

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Section: Sample Sequencing Indicates the Maize Genome Is Highly Repetsupporting

confidence: 90%

Abundance, Distribution, and Transcriptional Activity of Repetitive Elements in the Maize Genome

Meyers

Tingey²,

Morgante³

2001

Genome Res.

372

313

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“…Under the increase-only model, the ancestral genome size for T. monococcum must be no larger than 7.9 pg DNN2C nucleus. Because T. monococcum and T. urartu, which are both A-genome wheats (Kimber and Feldman, 1987), are descended from a single ancestor, that ancestor must also have Numerical values indicate pg DNA per 2C nucleus and are taken from Bennett andSmith (1976, 1991), Bennett et al (1982), andBennett andLeitch (1995). Note that some species have more than one value reported, and that we have included only species with diploid chromosome numbers to avoid complications caused by polyploidy.…”

Section: Letter To the Editormentioning

confidence: 99%

“…Some of this genome-size variation is due to the polyploidy commonly found in the angiosperms or to tandemly repeated satellite sequences (Peacock et al, 1981), but most is associated with ill-defined classes of interspersed highly repetitive and middle repetitive DNAs (Flavell et al, 1974). Recent studies have indicated that the majority of this reiterated DNA is composed of retroelements, severa1 classes of mobile DNA that transpose through an RNA intermediate (Smyth et al, 1989;Moore et al, 1991;Pearce et al, 1996;SanMiguel et al, 1996;Suoniemi et al, 1996).…”

mentioning

confidence: 99%

Do Plants Have a One-Way Ticket to Genomic Obesity?

Bennetzen¹,

Kellogg²

1997

Plant Cell

312

146

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“…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.…”

mentioning

confidence: 99%

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

Dohm

Minoche

Holtgräwe

et al. 2013

Nature

526

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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Genome size and the proportion of repeated nucleotide sequence DNA in plants

Cited by 543 publications

References 29 publications

Abundance, Distribution, and Transcriptional Activity of Repetitive Elements in the Maize Genome

Abundance, Distribution, and Transcriptional Activity of Repetitive Elements in the Maize Genome

Do Plants Have a One-Way Ticket to Genomic Obesity?

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

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