About: Coevolution between simple sequence repeats (SSRs) and virus genome size

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An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Coevolution between simple sequence repeats (SSRs) and virus genome size
Creator	Tan, Zhongyang Li, Mingfu Shen, Guoli Yu, Ruqin Feng, Haiping Jiang, Jianhui Niu, Yile Ouyang, Qingjian Tian, Yonglei Tian, You Yang, Ronghua Zhao, Xiangyan
Source	PMC
abstract	BACKGROUND: Relationship between the level of repetitiveness in genomic sequence and genome size has been investigated by making use of complete prokaryotic and eukaryotic genomes, but relevant studies have been rarely made in virus genomes. RESULTS: In this study, a total of 257 viruses were examined, which cover 90% of genera. The results showed that simple sequence repeats (SSRs) is strongly, positively and significantly correlated with genome size. Certain repeat class is distributed in a certain range of genome sequence length. Mono-, di- and tri- repeats are widely distributed in all virus genomes, tetra- SSRs as a common component consist in genomes which more than 100 kb in size; in the range of genome < 100 kb, genomes containing penta- and hexa- SSRs are not more than 50%. Principal components analysis (PCA) indicated that dinucleotide repeat affects the differences of SSRs most strongly among virus genomes. Results showed that SSRs tend to accumulate in larger virus genomes; and the longer genome sequence, the longer repeat units. CONCLUSIONS: We conducted this research standing on the height of the whole virus. We concluded that genome size is an important factor in affecting the occurrence of SSRs; hosts are also responsible for the variances of SSRs content to a certain degree.
has issue date	2012-08-30(xsd:dateTime)
bibo:doi	10.1186/1471-2164-13-435
bibo:pmid	22931422
has license	cc-by
sha1sum (hex)	8c2cab93f7eaa4abbb56f5f2e2b5a173523912d0
schema:url	https://doi.org/10.1186/1471-2164-13-435
resource representing a document's title	Coevolution between simple sequence repeats (SSRs) and virus genome size
has PubMed Central identifier	PMC3585866
has PubMed identifier	22931422
schema:publication	BMC Genomics
resource representing a document's body	covid:8c2cab93f7eaa4abbb56f5f2e2b5a173523912d0#body_text
is schema:about of	named entity 'range' named entity 'genomes' named entity 'repeat units' named entity 'genome size' named entity 'level' named entity 'correlated' named entity 'VIRUS' named entity 'SEQUENCE LENGTH' named entity 'COMPONENT' covid:arg/8c2cab93f7eaa4abbb56f5f2e2b5a173523912d0 named entity 'simple sequence repeats' named entity 'dinucleotide' named entity 'range' named entity 'relative density' named entity 'parasite' named entity 'taxonomic' named entity 'virus' named entity 'virus' named entity 'scatter plots' named entity 'rapid evolution' named entity 'genomes' named entity 'scatter plots' named entity 'selection pressure' named entity 'Nodamura virus' named entity 'genome' named entity '1, 2' named entity 'genome size' named entity 'viruses' named entity 'positive relationship' named entity 'S33' named entity 'genomes' named entity 'genomes' named entity 'genome' named entity 'viruses' named entity 'relative density' named entity 'CRISPR' named entity 'scree plot' named entity 'virus' named entity 'genome size' named entity 'virus' named entity 'genome size' named entity 'viruses' named entity 'genome' named entity 'origin theory' named entity 'ssRNA' named entity 'positive relationship' named entity 'genome' named entity 'Regression analysis' named entity 'genome' named entity 'genome size' named entity 'virus' named entity 'genome size' named entity 'pathogens' named entity 'Genbank' named entity 'genome' named entity 'viruses' named entity 'base pairs' named entity 'goodness of fit' named entity 'hepatitis B virus' named entity 'E. coli' named entity 'genome size' named entity 'CRISPR' named entity 'genomes' named entity 'virus' named entity 'genome' named entity 'entomopoxvirus' named entity 'virus genome' named entity 'recombination' named entity 'genomes' named entity 'archaea'

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