Genome microsatellite diversity within the Apicomplexa phylum.
Identifieur interne : 001086 ( PubMed/Checkpoint ); précédent : 001085; suivant : 001087Genome microsatellite diversity within the Apicomplexa phylum.
Auteurs : Juan Pablo Isaza [Colombie] ; Juan Fernando Alzate [Colombie]Source :
- Molecular genetics and genomics : MGG [ 1617-4623 ] ; 2016.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- genetics : Apicomplexa.
- Exons, Genetic Variation, Genome Size, Genome, Protozoan, Introns, Microsatellite Repeats.
Abstract
The Apicomplexa phylum groups include unicellular and obligate intracellular protozoan parasites with an apical complex used for attachment and invasion to host cells. In this study, we analyze single sequence repeats (SSRs) in the whole genome of 20 apicomplexan organisms that represent four different lineages within the phylum. Only perfect SSRs with at least 12 nucleotides and composed of 2-6 mers were included. To better understand the association of SSR types with the genomic regions, the SSRs were classified accordingly with the genomic location into exon, intron and intergenic categories. Our results showed heterogeneous SSRs density within the studied genomes. However, the most frequent SSRs types were di- and tri-nucleotide repeats. The former was associated with intergenic regions, while the latter was associated with exon regions.
DOI: 10.1007/s00438-016-1244-6
PubMed: 27590734
Affiliations:
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In this study, we analyze single sequence repeats (SSRs) in the whole genome of 20 apicomplexan organisms that represent four different lineages within the phylum. Only perfect SSRs with at least 12 nucleotides and composed of 2-6 mers were included. To better understand the association of SSR types with the genomic regions, the SSRs were classified accordingly with the genomic location into exon, intron and intergenic categories. Our results showed heterogeneous SSRs density within the studied genomes. However, the most frequent SSRs types were di- and tri-nucleotide repeats. The former was associated with intergenic regions, while the latter was associated with exon regions.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">27590734</PMID><DateCompleted><Year>2017</Year><Month>01</Month><Day>30</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1617-4623</ISSN><JournalIssue CitedMedium="Internet"><Volume>291</Volume><Issue>6</Issue><PubDate><Year>2016</Year><Month>Dec</Month></PubDate></JournalIssue><Title>Molecular genetics and genomics : MGG</Title><ISOAbbreviation>Mol. Genet. Genomics</ISOAbbreviation></Journal><ArticleTitle>Genome microsatellite diversity within the Apicomplexa phylum.</ArticleTitle><Pagination><MedlinePgn>2117-2129</MedlinePgn></Pagination><Abstract><AbstractText>The Apicomplexa phylum groups include unicellular and obligate intracellular protozoan parasites with an apical complex used for attachment and invasion to host cells. In this study, we analyze single sequence repeats (SSRs) in the whole genome of 20 apicomplexan organisms that represent four different lineages within the phylum. Only perfect SSRs with at least 12 nucleotides and composed of 2-6 mers were included. To better understand the association of SSR types with the genomic regions, the SSRs were classified accordingly with the genomic location into exon, intron and intergenic categories. Our results showed heterogeneous SSRs density within the studied genomes. However, the most frequent SSRs types were di- and tri-nucleotide repeats. The former was associated with intergenic regions, while the latter was associated with exon regions.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Isaza</LastName><ForeName>Juan Pablo</ForeName><Initials>JP</Initials><AffiliationInfo><Affiliation>Grupo de Parasitología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Centro Nacional de Secuenciación Genómica, Sede de Investigación Universitaria, Universidad de Antioquia, Medellín, Colombia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Alzate</LastName><ForeName>Juan Fernando</ForeName><Initials>JF</Initials><Identifier Source="ORCID">http://orcid.org/0000-0003-2578-4609</Identifier><AffiliationInfo><Affiliation>Grupo de Parasitología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia. jfernando.alzate@udea.edu.co.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Centro Nacional de Secuenciación Genómica, Sede de Investigación Universitaria, Universidad de Antioquia, Medellín, Colombia. jfernando.alzate@udea.edu.co.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2016</Year><Month>09</Month><Day>02</Day></ArticleDate></Article><MedlineJournalInfo><Country>Germany</Country><MedlineTA>Mol Genet Genomics</MedlineTA><NlmUniqueID>101093320</NlmUniqueID><ISSNLinking>1617-4623</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D016782" MajorTopicYN="N">Apicomplexa</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005091" MajorTopicYN="N">Exons</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014644" MajorTopicYN="Y">Genetic Variation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D059646" MajorTopicYN="N">Genome Size</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018503" MajorTopicYN="N">Genome, Protozoan</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D007438" MajorTopicYN="N">Introns</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018895" MajorTopicYN="Y">Microsatellite Repeats</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Apicomplexa</Keyword><Keyword MajorTopicYN="N">Comparative genomics</Keyword><Keyword MajorTopicYN="N">Microsatellites</Keyword><Keyword MajorTopicYN="N">Parasite genomics</Keyword><Keyword MajorTopicYN="N">Single sequence repeats</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate 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