Genome skimming allows for assembly of high-copy fractions of the genome into contiguous, complete genomes.
Genome skimming is a sequencing approach that uses low-pass, shallow sequencing of a genome (up to 5%), to generate fragments of DNA, known as genome skims.[1][2] These genome skims contain information about the high-copy fraction of the genome.[2] The high-copy fraction of the genome consists of the ribosomal DNA, plastid genome (plastome), mitochondrial genome (mitogenome), and nuclear repeats such as microsatellites and transposable elements.[3] It employs high-throughput, next generation sequencing technology to generate these skims.[1] Although these skims are merely 'the tip of the genomic iceberg', phylogenomic analysis of them can still provide insights on evolutionary history and biodiversity at a lower cost and larger scale than traditional methods.[2][3][4] Due to the small amount of DNA required for genome skimming, its methodology can be applied in other fields other than genomics. Tasks like this include determining the traceability of products in the food industry, enforcing international regulations regarding biodiversity and biological resources, and forensics.[5]
^ abStraub, Shannon C. K.; Parks, Matthew; Weitemier, Kevin; Fishbein, Mark; Cronn, Richard C.; Liston, Aaron (February 2012). "Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics". American Journal of Botany. 99 (2): 349–364. doi:10.3732/ajb.1100335. PMID 22174336.
^ abcDodsworth, Steven (September 2015). "Genome skimming for next-generation biodiversity analysis". Trends in Plant Science. 20 (9): 525–527. doi:10.1016/j.tplants.2015.06.012. PMID 26205170.
^ abDodsworth, Steven Andrew, author. Genome skimming for phylogenomics. OCLC 1108700470. {{cite book}}: |last= has generic name (help)CS1 maint: multiple names: authors list (link)
^Trevisan, Bruna; Alcantara, Daniel M.C.; Machado, Denis Jacob; Marques, Fernando P.L.; Lahr, Daniel J.G. (2019-09-13). "Genome skimming is a low-cost and robust strategy to assemble complete mitochondrial genomes from ethanol preserved specimens in biodiversity studies". PeerJ. 7: e7543. doi:10.7717/peerj.7543. ISSN 2167-8359. PMC 6746217. PMID 31565556.
^Malé, Pierre-Jean G.; Bardon, Léa; Besnard, Guillaume; Coissac, Eric; Delsuc, Frédéric; Engel, Julien; Lhuillier, Emeline; Scotti-Saintagne, Caroline; Tinaut, Alexandra; Chave, Jérôme (April 2014). "Genome skimming by shotgun sequencing helps resolve the phylogeny of a pantropical tree family". Molecular Ecology Resources. 14 (5): 966–75. doi:10.1111/1755-0998.12246. PMID 24606032. S2CID 26777683.
Genomeskimming is a sequencing approach that uses low-pass, shallow sequencing of a genome (up to 5%), to generate fragments of DNA, known as genome...
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Nolan C.; Ebert, Daniel P.; Rieseberg, Loren H. (18 November 2013). "Genomeskimming reveals the origin of the Jerusalem Artichoke tuber crop species: neither...
classification of Magnolia and Magnoliaceae based on whole plastid genome sequences via genomeskimming". Journal of Systematics and Evolution. 58 (5): 673–695....
classification of Magnolia and Magnoliaceae based on whole plastid genome sequences via genomeskimming", Journal of Systematics and Evolution, 58 (5): 673–695,...
M.; Villanueva, R.; Voight, J. R.; Allcock, A. L. (2023-02-10). "Genomeskimming elucidates the evolutionary history of OctopodA". Molecular Phylogenetics...
Vecchione, M.; Villanueva, R.; Voight, J.R.; Allcock, A.L. (May 2023). "Genomeskimming elucidates the evolutionary history of Octopoda". Molecular Phylogenetics...
List of sequenced eukaryotic genomes List of sequenced bacterial genomes List of sequenced archaeal genomesGenomeskimming Moore MJ, Soltis PS, Bell CD...
Ripma, Lee (December 2017). "Phylogeny of the popcorn flowers: Use of genomeskimming to evaluate monophyly and interrelationships in subtribe Amsinckiinae...
and John S. Sproul. "Species delimitation, classical taxonomy and genomeskimming: a review of the ground beetle genus Lionepha (Coleoptera: Carabidae)...
World milkweed vines (Gonolobinae) and resurrection of Chthamalia: a genomeskimming and targeted enrichment approach. Botany 2017. Fort Worth, TX. Woodson...
alternative genetic analysis in the absence of a reference genome. Other than the multiplex GBS skimming, imputation of missing SNPs has the potential to further...
amounts of memory which makes them impractical for large genomes, such as the human genome. Therefore, tools using Bloom filters have been developed...
whole-genome sequences indicate that the basenji and the dingo are both considered to be basal members of the domestic dog clade. In 2021, the genome of...
h−1 under aerobic conditions. The genome of L. mesenteroides has been successfully mapped, having an average genome size of 1.90138 Mbp and 1762 protein...
of cheilostome bryozoans and their parental care inferred by a new genome-skimmed phylogeny". Science Advances. 8 (13): eabm7452. Bibcode:2022SciA......
genomes in 10 days or less, with less than one error per 100,000 DNA base pairs, covering 98% of the genome and costing less than $10,000 per genome (this...
yoghurt are also used. Analysis of the L. delbrueckii subsp. bulgaricus genome indicates that the bacterium may have originated on the surface of a plant...
yellow-spotted river turtle and the painted turtle may filter feed by skimming the water surface with their mouth and throat open to collect particles...
plates can filter it, and be slow enough so that it cannot escape. The "skimming" may take place on the surface, underwater, or even at the ocean's bottom...
lacks single nucleotide polymorphisms in their genome. After reconstructing the history of the baiji genome for this dolphin species, researchers found that...
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