DNA sequence organization in the genomes of five marine invertebrates

Goldberg, Robert B.; Crain, William R.; Ruderman, Joan V.; Moore, George T.; Barnett, Thomas; Higgins, R. C.; Gelfand, R; Galau, Glenn A.; Britten, Roy J.; Davidson, Eric H.

doi:10.1007/bf00284817

Cited by 98 publications

(35 citation statements)

References 19 publications

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“…The genome sequence depth for all three species is around sixfold, recovering~1.5 Gbp per species. This is lower than the previously estimated genome sizes of these species of~2.8 Gbp (Goldberg et al, 1975), which together with CEGMA data suggest the assembled genome data sets are biased towards coding sequence to the exclusion of longer repeat sequences, or perhaps that previous calculations were overestimates. A L. polyphemus genome has been noted online (Nossa et al, 2014), but the data presented here represents a large increase in publically available sequence data for the Xiphosura clade, particularly by including Southeast Asian species.…”

Section: Resultscontrasting

confidence: 67%

Ancestral whole-genome duplication in the marine chelicerate horseshoe crabs

et al. 2015

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Whole-genome duplication (WGD) results in new genomic resources that can be exploited by evolution for rewiring genetic regulatory networks in organisms. In metazoans, WGD occurred before the last common ancestor of vertebrates, and has been postulated as a major evolutionary force that contributed to their speciation and diversification of morphological structures. Here, we have sequenced genomes from three of the four extant species of horseshoe crabs-Carcinoscorpius rotundicauda, Limulus polyphemus and Tachypleus tridentatus. Phylogenetic and sequence analyses of their Hox and other homeobox genes, which encode crucial transcription factors and have been used as indicators of WGD in animals, strongly suggests that WGD happened before the last common ancestor of these marine chelicerates 4135 million years ago. Signatures of subfunctionalisation of paralogues of Hox genes are revealed in the appendages of two species of horseshoe crabs. Further, residual homeobox pseudogenes are observed in the three lineages. The existence of WGD in the horseshoe crabs, noted for relative morphological stasis over geological time, suggests that genomic diversity need not always be reflected phenotypically, in contrast to the suggested situation in vertebrates. This study provides evidence of ancient WGD in the ecdysozoan lineage, and reveals new opportunities for studying genomic and regulatory evolution after WGD in the Metazoa.

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Section: Resultscontrasting

confidence: 67%

Ancestral whole-genome duplication in the marine chelicerate horseshoe crabs

et al. 2015

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“…DNA was sheared to different singlestrand sizes in the Virtis 60 homogenizer (15,16). The modal single-strand fragment lengths were ascertained by analytical alkaline band sedimentation velocity in the model E ultracentrifuge (17) or by alkaline sucrose density centrifugation (2).…”

Section: Methodsmentioning

confidence: 99%

“…Size distribution of S1 nuclease-resistant repetitive duplexes. DNA fragments (7500 Nt) were reassociated to a Cot of 0.3 (a Cot at which over 75% of Achlya repetitive sequences form duplex structures but only 3% of single copy sequences can react) at 600 in 0.18 M NaCl/6 mM 1,4-piperazinediethanesulfonic acid (Pipes), pH 6.7, directly treated with S1 nuclease according to the mild conditions of Britten et al (19), and collected by HAP chromatography (13,16). Approximately 15% of the DNA was resistant to S1 nuclease.…”

Section: Methodsmentioning

confidence: 99%

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DNA sequence organization in the water mold Achlya

Hudspeth

Timberlake

Goldberg

1977

Proc. Natl. Acad. Sci. U.S.A.

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Experiments are described that characterize the organization of DNA sequences in the water mold Achlya bisexualis . These experiments demonstrate that repetitive and single copy sequences in the Achlya genome are arranged in a long-period interspersion pattern. Estimates of the spacing intervals between repetitive and single copy DNA indicate, however, that the interspersion pattern in Achlya is longer than has been previously reported in other eukaryotes. These data and measurements of structural gene expression in Achlya [Timberlake, W.E., Shumard, D. S. & Goldberg, R. B. (1977) Cell 10, 623-632] make it difficult to propose a regulatory function for repeated DNA in this eukaryote.

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“…Mathematical analysis of a Cot curve permits estimation of genome size, the proportion of the genome contained in the single-copy and repetitive DNA components, and the kinetic complexity of each component. Interspecific comparison of Cot data has provided considerable insight into the structure and evolution of eukaryotic genomes (e.g., Britten and Kohne 1968;Davidson et al 1975;Goldberg et al 1975;Galau et al 1976;Hake and Walbot 1980;Geever et al 1989).…”

mentioning

confidence: 99%

Integration of Cot Analysis, DNA Cloning, and High-Throughput Sequencing Facilitates Genome Characterization and Gene Discovery

Peterson¹,

Schulze²,

Sciara³

et al. 2002

Genome Res.

175

153

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Cot-based sequence discovery represents a powerful means by which both low-copy and repetitive sequences can be selectively and efficiently fractionated, cloned, and characterized. Based upon the results of a Cot analysis, hydroxyapatite chromatography was used to fractionate sorghum (Sorghum bicolor) genomic DNA into highly repetitive (HR), moderately repetitive (MR), and single/low-copy (SL) sequence components that were consequently cloned to produce HRCot, MRCot, and SLCot genomic libraries. Filter hybridization (blotting) and sequence analysis both show that the HRCot library is enriched in sequences traditionally found in high-copy number (e.g., retroelements, rDNA, centromeric repeats), the SLCot library is enriched in low-copy sequences (e.g., genes and “nonrepetitive ESTs”), and the MRCot library contains sequences of moderate redundancy. The Cot analysis suggests that the sorghum genome is approximately 700 Mb (in agreement with previous estimates) and that HR, MR, and SL components comprise 15%, 41%, and 24% of sorghum DNA, respectively. Unlike previously described techniques to sequence the low-copy components of genomes, sequencing of Cot components is independent of expression and methylation patterns that vary widely among DNA elements, developmental stages, and taxa. High-throughput sequencing of Cot clones may be a means of “capturing” the sequence complexity of eukaryotic genomes at unprecedented efficiency

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DNA sequence organization in the genomes of five marine invertebrates

Cited by 98 publications

References 19 publications

Ancestral whole-genome duplication in the marine chelicerate horseshoe crabs

Ancestral whole-genome duplication in the marine chelicerate horseshoe crabs

DNA sequence organization in the water mold Achlya

Integration of Cot Analysis, DNA Cloning, and High-Throughput Sequencing Facilitates Genome Characterization and Gene Discovery

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