High satellite repeat turnover in great apes studied with short- and long-read technologies.
Identifieur interne : 000538 ( PubMed/Checkpoint ); précédent : 000537; suivant : 000539High satellite repeat turnover in great apes studied with short- and long-read technologies.
Auteurs : Monika Cechova [États-Unis] ; Robert S. Harris [États-Unis] ; Marta Tomaszkiewicz [États-Unis] ; Barbara Arbeithuber [États-Unis] ; Francesca Chiaromonte [États-Unis] ; Kateryna D. Makova [États-Unis]Source :
- Molecular biology and evolution [ 1537-1719 ] ; 2019.
Abstract
Satellite repeats are a structural component of centromeres and telomeres, and in some instances their divergence is known to drive speciation. Due to their highly repetitive nature, satellite sequences have been understudied and underrepresented in genome assemblies. To investigate their turnover in great apes, we studied satellite repeats of unit sizes up to 50 bp in human, chimpanzee, bonobo, gorilla, and Sumatran and Bornean orangutans, using unassembled short and long sequencing reads. The density of satellite repeats, as identified from accurate short reads (Illumina), varied greatly among great ape genomes. These were dominated by a handful of abundant repeated motifs, frequently shared among species, which formed two groups: (1) the (AATGG)n repeat (critical for heat shock response) and its derivatives; and (2) subtelomeric 32-mers involved in telomeric metabolism. Using the densities of abundant repeats, individuals could be classified into species. However clustering did not reproduce the accepted species phylogeny, suggesting rapid repeat evolution. Several abundant repeats were enriched in males vs. females; using Y chromosome assemblies or FIuorescent In Situ Hybridization, we validated their location on the Y. Finally, applying a novel computational tool, we identified many satellite repeats completely embedded within long Oxford Nanopore and Pacific Biosciences reads. Such repeats were up to 59 kb in length and consisted of perfect repeats interspersed with other similar sequences. Our results based on sequencing reads generated with three different technologies provide the first detailed characterization of great ape satellite repeats, and open new avenues for exploring their functions.
DOI: 10.1093/molbev/msz156
PubMed: 31273383
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Harris</name><affiliation wicri:level="2"><nlm:affiliation>Department of Biology, Pennsylvania State University, University Park, PA USA.</nlm:affiliation><country>États-Unis</country><placeName><region type="state">Pennsylvanie</region></placeName><wicri:cityArea>Department of Biology, Pennsylvania State University, University Park</wicri:cityArea></affiliation></author><author><name sortKey="Tomaszkiewicz, Marta" sort="Tomaszkiewicz, Marta" uniqKey="Tomaszkiewicz M" first="Marta" last="Tomaszkiewicz">Marta Tomaszkiewicz</name><affiliation wicri:level="2"><nlm:affiliation>Department of Biology, Pennsylvania State University, University Park, PA USA.</nlm:affiliation><country>États-Unis</country><placeName><region type="state">Pennsylvanie</region></placeName><wicri:cityArea>Department of Biology, Pennsylvania State University, University Park</wicri:cityArea></affiliation></author><author><name sortKey="Arbeithuber, Barbara" sort="Arbeithuber, Barbara" uniqKey="Arbeithuber B" first="Barbara" last="Arbeithuber">Barbara Arbeithuber</name><affiliation wicri:level="2"><nlm:affiliation>Department of Biology, Pennsylvania State University, University Park, PA USA.</nlm:affiliation><country>États-Unis</country><placeName><region type="state">Pennsylvanie</region></placeName><wicri:cityArea>Department of Biology, Pennsylvania State University, University Park</wicri:cityArea></affiliation></author><author><name sortKey="Chiaromonte, Francesca" sort="Chiaromonte, Francesca" uniqKey="Chiaromonte F" first="Francesca" last="Chiaromonte">Francesca Chiaromonte</name><affiliation wicri:level="2"><nlm:affiliation>Department of Statistics, Pennsylvania State University, University Park, PA USA.</nlm:affiliation><country>États-Unis</country><placeName><region type="state">Pennsylvanie</region></placeName><wicri:cityArea>Department of Statistics, Pennsylvania State University, University Park</wicri:cityArea></affiliation></author><author><name sortKey="Makova, Kateryna D" sort="Makova, Kateryna D" uniqKey="Makova K" first="Kateryna D" last="Makova">Kateryna D. Makova</name><affiliation wicri:level="2"><nlm:affiliation>Center for Medical Genomics, Penn State, University Park, PA USA.</nlm:affiliation><country>États-Unis</country><placeName><region type="state">Pennsylvanie</region></placeName><wicri:cityArea>Center for Medical Genomics, Penn State, University Park</wicri:cityArea></affiliation></author></analytic><series><title level="j">Molecular biology and evolution</title><idno type="eISSN">1537-1719</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Satellite repeats are a structural component of centromeres and telomeres, and in some instances their divergence is known to drive speciation. Due to their highly repetitive nature, satellite sequences have been understudied and underrepresented in genome assemblies. To investigate their turnover in great apes, we studied satellite repeats of unit sizes up to 50 bp in human, chimpanzee, bonobo, gorilla, and Sumatran and Bornean orangutans, using unassembled short and long sequencing reads. The density of satellite repeats, as identified from accurate short reads (Illumina), varied greatly among great ape genomes. These were dominated by a handful of abundant repeated motifs, frequently shared among species, which formed two groups: (1) the (AATGG)n repeat (critical for heat shock response) and its derivatives; and (2) subtelomeric 32-mers involved in telomeric metabolism. Using the densities of abundant repeats, individuals could be classified into species. However clustering did not reproduce the accepted species phylogeny, suggesting rapid repeat evolution. Several abundant repeats were enriched in males vs. females; using Y chromosome assemblies or FIuorescent In Situ Hybridization, we validated their location on the Y. Finally, applying a novel computational tool, we identified many satellite repeats completely embedded within long Oxford Nanopore and Pacific Biosciences reads. Such repeats were up to 59 kb in length and consisted of perfect repeats interspersed with other similar sequences. Our results based on sequencing reads generated with three different technologies provide the first detailed characterization of great ape satellite repeats, and open new avenues for exploring their functions.</div></front></TEI><pubmed><MedlineCitation Status="Publisher" Owner="NLM"><PMID Version="1">31273383</PMID><DateRevised><Year>2019</Year><Month>12</Month><Day>18</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1537-1719</ISSN><JournalIssue CitedMedium="Internet"><PubDate><Year>2019</Year><Month>Jul</Month><Day>02</Day></PubDate></JournalIssue><Title>Molecular biology and evolution</Title><ISOAbbreviation>Mol. Biol. Evol.</ISOAbbreviation></Journal><ArticleTitle>High satellite repeat turnover in great apes studied with short- and long-read technologies.</ArticleTitle><ELocationID EIdType="pii" ValidYN="Y">msz156</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.1093/molbev/msz156</ELocationID><Abstract><AbstractText>Satellite repeats are a structural component of centromeres and telomeres, and in some instances their divergence is known to drive speciation. Due to their highly repetitive nature, satellite sequences have been understudied and underrepresented in genome assemblies. To investigate their turnover in great apes, we studied satellite repeats of unit sizes up to 50 bp in human, chimpanzee, bonobo, gorilla, and Sumatran and Bornean orangutans, using unassembled short and long sequencing reads. The density of satellite repeats, as identified from accurate short reads (Illumina), varied greatly among great ape genomes. These were dominated by a handful of abundant repeated motifs, frequently shared among species, which formed two groups: (1) the (AATGG)n repeat (critical for heat shock response) and its derivatives; and (2) subtelomeric 32-mers involved in telomeric metabolism. Using the densities of abundant repeats, individuals could be classified into species. However clustering did not reproduce the accepted species phylogeny, suggesting rapid repeat evolution. Several abundant repeats were enriched in males vs. females; using Y chromosome assemblies or FIuorescent In Situ Hybridization, we validated their location on the Y. Finally, applying a novel computational tool, we identified many satellite repeats completely embedded within long Oxford Nanopore and Pacific Biosciences reads. Such repeats were up to 59 kb in length and consisted of perfect repeats interspersed with other similar sequences. Our results based on sequencing reads generated with three different technologies provide the first detailed characterization of great ape satellite repeats, and open new avenues for exploring their functions.</AbstractText><CopyrightInformation>© The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Cechova</LastName><ForeName>Monika</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Biology, Pennsylvania State University, University Park, PA USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Harris</LastName><ForeName>Robert S</ForeName><Initials>RS</Initials><AffiliationInfo><Affiliation>Department of Biology, Pennsylvania State University, University Park, PA USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tomaszkiewicz</LastName><ForeName>Marta</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Biology, Pennsylvania State University, University Park, PA USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Arbeithuber</LastName><ForeName>Barbara</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>Department of Biology, Pennsylvania State University, University Park, PA USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chiaromonte</LastName><ForeName>Francesca</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>Department of Statistics, Pennsylvania State University, University Park, PA USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>EMbeDS, Sant'Anna School of Advanced Studies, Pisa, Italy.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Center for Medical Genomics, Penn State, University Park, PA USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Makova</LastName><ForeName>Kateryna D</ForeName><Initials>KD</Initials><AffiliationInfo><Affiliation>Center for Medical Genomics, Penn State, University Park, PA USA.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>R01 GM130691</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2019</Year><Month>07</Month><Day>02</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Mol Biol Evol</MedlineTA><NlmUniqueID>8501455</NlmUniqueID><ISSNLinking>0737-4038</ISSNLinking></MedlineJournalInfo></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2019</Year><Month>03</Month><Day>12</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2019</Year><Month>06</Month><Day>12</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2019</Year><Month>06</Month><Day>13</Day></PubMedPubDate><PubMedPubDate 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Francesca" uniqKey="Chiaromonte F" first="Francesca" last="Chiaromonte">Francesca Chiaromonte</name><name sortKey="Harris, Robert S" sort="Harris, Robert S" uniqKey="Harris R" first="Robert S" last="Harris">Robert S. Harris</name><name sortKey="Makova, Kateryna D" sort="Makova, Kateryna D" uniqKey="Makova K" first="Kateryna D" last="Makova">Kateryna D. Makova</name><name sortKey="Tomaszkiewicz, Marta" sort="Tomaszkiewicz, Marta" uniqKey="Tomaszkiewicz M" first="Marta" last="Tomaszkiewicz">Marta Tomaszkiewicz</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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