ArticleBMC genomics2007
Global repeat discovery and estimation of genomic copy number in a large, complex genome using a high-throughput 454 sequence survey.
Article in BMC genomics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
49 citing papers in PubMed, 96 citations in OpenAlex.
- Toward a More Just System of Care in Molecular Pathology.The Milbank quarterly · 2022Article
- Satellitome Analysis and Transposable Elements Comparison in Geographically Distant Populations ofLife (Basel, Switzerland) · 2022Article
- Fast neutron mutagenesis in soybean enriches for small indels and creates frameshift mutations.G3 (Bethesda, Md.) · 2022Article
- The Singular Evolution ofFrontiers in plant science · 2022Article
- Genome assembly of the popular Korean soybean cultivar Hwangkeum.G3 (Bethesda, Md.) · 2021Article
- Comparative Analysis of Transposable Elements in GenusInsects · 2021Article
- Integrative genetic map of repetitive DNA in the sole Solea senegalensis genome shows a Rex transposon located in a proto-sex chromosome.Scientific reports · 2019Article
- Specific LTR-Retrotransposons Show Copy Number Variations between Wild and Cultivated Sunflowers.Genes · 2018Article
- Elucidating the major hidden genomic components of the A, C, and AC genomes and their influence on Brassica evolution.Scientific reports · 2017Article
- Genome-wide analysis of LTR-retrotransposon diversity and its impact on the evolution of the genus Helianthus (L.).BMC genomics · 2017Article
- Genome Size in North American Fireflies: Substantial Variation Likely Driven by Neutral Processes.Genome biology and evolution · 2017Article
- Identification and characterisation of Short Interspersed Nuclear Elements in the olive tree (Olea europaea L.) genome.Molecular genetics and genomics : MGG · 2017Article
- Partial sequencing reveals the transposable element composition of Coffea genomes and provides evidence for distinct evolutionary stories.Molecular genetics and genomics : MGG · 2016Article
- Long Terminal Repeat Retrotransposon Content in Eight Diploid Sunflower Species Inferred from Next-Generation Sequence Data.G3 (Bethesda, Md.) · 2016Article
- Independent Domestication of Two Old World Cotton Species.Genome biology and evolution · 2016Article
- A new resource for the development of SSR markers: Millions of loci from a thousand plant transcriptomes.Applications in plant sciences · 2016Article
- Repetitive DNA and Plant Domestication: Variation in Copy Number and Proximity to Genes of LTR-Retrotransposons among Wild and Cultivated Sunflower (Helianthus annuus) Genotypes.Genome biology and evolution · 2015Article
- Repetitive sequences in plant nuclear DNA: types, distribution, evolution and function.Genomics, proteomics & bioinformatics · 2014Review
- Distinct Copy Number, Coding Sequence, and Locus Methylation Patterns Underlie Rhg1-Mediated Soybean Resistance to Soybean Cyst Nematode.Plant physiology · 2014Article
- The peculiar landscape of repetitive sequences in the olive (Olea europaea L.) genome.Genome biology and evolution · 2014Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundExtensive computational and database tools are available to mine genomic and genetic databases for model organisms, but little genomic data is available for many species of ecological or agricultural significance, especially those with large genomes. Genome surveys using conventional sequencing techniques are powerful, particularly for detecting sequences present in many copies per genome. However these methods are time-consuming and have potential drawbacks. High throughput 454 sequencing provides an alternative method by which much information can be gained quickly and cheaply from high-coverage surveys of genomic DNA.
resultsWe sequenced 78 million base-pairs of randomly sheared soybean DNA which passed our quality criteria. Computational analysis of the survey sequences provided global information on the abundant repetitive sequences in soybean. The sequence was used to determine the copy number across regions of large genomic clones or contigs and discover higher-order structures within satellite repeats. We have created an annotated, online database of sequences present in multiple copies in the soybean genome. The low bias of pyrosequencing against repeat sequences is demonstrated by the overall composition of the survey data, which matches well with past estimates of repetitive DNA content obtained by DNA re-association kinetics (Cot analysis).
conclusionThis approach provides a potential aid to conventional or shotgun genome assembly, by allowing rapid assessment of copy number in any clone or clone-end sequence. In addition, we show that partial sequencing can provide access to partial protein-coding sequences.
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