Deletion-bias in DNA double-strand break repair differentially contributes to plant genome shrinkage
In order to prevent genome instability, cells need to be protected by a number of repair mechanisms, including DNA double-strand break (DSB) repair. The extent to which DSB repair, biased towards deletions or insertions, contributes to evolutionary diversification of genome size is still under debat...
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Veröffentlicht in: | The New phytologist 2017-06, Vol.214 (4), p.1712-1721 |
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description | In order to prevent genome instability, cells need to be protected by a number of repair mechanisms, including DNA double-strand break (DSB) repair. The extent to which DSB repair, biased towards deletions or insertions, contributes to evolutionary diversification of genome size is still under debate.
We analyzed mutation spectra in Arabidopsis thaliana and in barley (Hordeum vulgare) by PacBio sequencing of three DSB-targeted loci each, uncovering repair via gene conversion, single strand annealing (SSA) or nonhomologous end-joining (NHEJ). Furthermore, phylogenomic comparisons between A. thaliana and two related species were used to detect naturally occurring deletions during Arabidopsis evolution.
Arabidopsis thaliana revealed significantly more and larger deletions after DSB repair than barley, and barley displayed more and larger insertions. Arabidopsis displayed a clear net loss of DNA after DSB repair, mainly via SSA and NHEJ. Barley revealed a very weak net loss of DNA, apparently due to less active break-end resection and easier copying of template sequences into breaks. Comparative phylogenomics revealed several footprints of SSA in the A. thaliana genome.
Quantitative assessment of DNA gain and loss through DSB repair processes suggests deletion-biased DSB repair causing ongoing genome shrinking in A. thaliana, whereas genome size in barley remains nearly constant. |
doi_str_mv | 10.1111/nph.14490 |
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We analyzed mutation spectra in Arabidopsis thaliana and in barley (Hordeum vulgare) by PacBio sequencing of three DSB-targeted loci each, uncovering repair via gene conversion, single strand annealing (SSA) or nonhomologous end-joining (NHEJ). Furthermore, phylogenomic comparisons between A. thaliana and two related species were used to detect naturally occurring deletions during Arabidopsis evolution.
Arabidopsis thaliana revealed significantly more and larger deletions after DSB repair than barley, and barley displayed more and larger insertions. Arabidopsis displayed a clear net loss of DNA after DSB repair, mainly via SSA and NHEJ. Barley revealed a very weak net loss of DNA, apparently due to less active break-end resection and easier copying of template sequences into breaks. Comparative phylogenomics revealed several footprints of SSA in the A. thaliana genome.
Quantitative assessment of DNA gain and loss through DSB repair processes suggests deletion-biased DSB repair causing ongoing genome shrinking in A. thaliana, whereas genome size in barley remains nearly constant.</description><identifier>ISSN: 0028-646X</identifier><identifier>EISSN: 1469-8137</identifier><identifier>DOI: 10.1111/nph.14490</identifier><identifier>PMID: 28245065</identifier><language>eng</language><publisher>England: New Phytologist Trust</publisher><subject>Arabidopsis - genetics ; Barley ; Biological evolution ; Capsella - genetics ; Cells ; Copying ; Deletion ; Deoxyribonucleic acid ; DNA ; DNA Breaks, Double-Stranded ; DNA damage ; DNA End-Joining Repair ; DNA Repair - physiology ; double‐strand break (DSB) repair ; Gene sequencing ; Genetic recombination ; genome shrinkage ; Genome Size ; genome size evolution ; Genome, Plant ; Genomes ; Genomic instability ; Hordeum - genetics ; Instability ; Mutation ; Net losses ; nonhomologous end joining (NHEJ) ; Nucleotide sequence ; Repair ; Sequence Deletion ; Sequencing ; Shrinkage ; single strand annealing (SSA) ; Spectra ; Stability</subject><ispartof>The New phytologist, 2017-06, Vol.214 (4), p.1712-1721</ispartof><rights>2017 New Phytologist Trust</rights><rights>2017 The Authors. New Phytologist © 2017 New Phytologist Trust</rights><rights>2017 The Authors. New Phytologist © 2017 New Phytologist Trust.</rights><rights>Copyright © 2017 New Phytologist Trust</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4760-1f98d2361003ee96b4f67ff73efe4f1904724792f8e3c1f9fb25c353b9a93cb13</citedby><cites>FETCH-LOGICAL-c4760-1f98d2361003ee96b4f67ff73efe4f1904724792f8e3c1f9fb25c353b9a93cb13</cites><orcidid>0000-0002-2521-4000</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.jstor.org/stable/pdf/90010405$$EPDF$$P50$$Gjstor$$H</linktopdf><linktohtml>$$Uhttps://www.jstor.org/stable/90010405$$EHTML$$P50$$Gjstor$$H</linktohtml><link.rule.ids>314,780,784,803,1417,1433,27924,27925,45574,45575,46409,46833,58017,58250</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/28245065$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Vu, Giang T. H.</creatorcontrib><creatorcontrib>Cao, Hieu X.</creatorcontrib><creatorcontrib>Reiss, Bernd</creatorcontrib><creatorcontrib>Schubert, Ingo</creatorcontrib><title>Deletion-bias in DNA double-strand break repair differentially contributes to plant genome shrinkage</title><title>The New phytologist</title><addtitle>New Phytol</addtitle><description>In order to prevent genome instability, cells need to be protected by a number of repair mechanisms, including DNA double-strand break (DSB) repair. The extent to which DSB repair, biased towards deletions or insertions, contributes to evolutionary diversification of genome size is still under debate.
We analyzed mutation spectra in Arabidopsis thaliana and in barley (Hordeum vulgare) by PacBio sequencing of three DSB-targeted loci each, uncovering repair via gene conversion, single strand annealing (SSA) or nonhomologous end-joining (NHEJ). Furthermore, phylogenomic comparisons between A. thaliana and two related species were used to detect naturally occurring deletions during Arabidopsis evolution.
Arabidopsis thaliana revealed significantly more and larger deletions after DSB repair than barley, and barley displayed more and larger insertions. Arabidopsis displayed a clear net loss of DNA after DSB repair, mainly via SSA and NHEJ. Barley revealed a very weak net loss of DNA, apparently due to less active break-end resection and easier copying of template sequences into breaks. Comparative phylogenomics revealed several footprints of SSA in the A. thaliana genome.
Quantitative assessment of DNA gain and loss through DSB repair processes suggests deletion-biased DSB repair causing ongoing genome shrinking in A. thaliana, whereas genome size in barley remains nearly constant.</description><subject>Arabidopsis - genetics</subject><subject>Barley</subject><subject>Biological evolution</subject><subject>Capsella - genetics</subject><subject>Cells</subject><subject>Copying</subject><subject>Deletion</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA Breaks, Double-Stranded</subject><subject>DNA damage</subject><subject>DNA End-Joining Repair</subject><subject>DNA Repair - physiology</subject><subject>double‐strand break (DSB) repair</subject><subject>Gene sequencing</subject><subject>Genetic recombination</subject><subject>genome shrinkage</subject><subject>Genome Size</subject><subject>genome size evolution</subject><subject>Genome, Plant</subject><subject>Genomes</subject><subject>Genomic instability</subject><subject>Hordeum - genetics</subject><subject>Instability</subject><subject>Mutation</subject><subject>Net losses</subject><subject>nonhomologous end joining (NHEJ)</subject><subject>Nucleotide sequence</subject><subject>Repair</subject><subject>Sequence Deletion</subject><subject>Sequencing</subject><subject>Shrinkage</subject><subject>single strand annealing (SSA)</subject><subject>Spectra</subject><subject>Stability</subject><issn>0028-646X</issn><issn>1469-8137</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2017</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp10E1PFTEUBuDGaOSCLvwBmiZucDHQr-m0SwIoJgRcaOJu0s6cQi9z27HthNx_b-ECCxPP5mye8-bkRegDJUe0znGYb4-oEJq8QisqpG4U5d1rtCKEqUYK-XsP7ee8JoToVrK3aI8pJloi2xUaz2CC4mNorDcZ-4DPrk7wGBc7QZNLMmHENoG5wwlm4xMevXOQIBRvpmmLhxhK8nYpkHGJeJ5MKPgGQtwAzrfJhztzA-_QG2emDO-f9gH69fX85-lFc3n97fvpyWUziE6ShjqtRsYlJYQDaGmFk51zHQcHwlFNRMdEp5lTwIeKnWXtwFtutdF8sJQfoMNd7pzinwVy6Tc-DzDVpyAuuaeqY0opydpKP_9D13FJoX5XlZaMad4-qC87NaSYcwLXz8lvTNr2lPQP1fe1-v6x-mo_PSUudgPji3zuuoLjHbj3E2z_n9Rf_bh4jvy4u1jnEtPLhSaEEkFa_hfcQZbl</recordid><startdate>201706</startdate><enddate>201706</enddate><creator>Vu, Giang T. H.</creator><creator>Cao, Hieu X.</creator><creator>Reiss, Bernd</creator><creator>Schubert, Ingo</creator><general>New Phytologist Trust</general><general>Wiley Subscription Services, Inc</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QO</scope><scope>7SN</scope><scope>8FD</scope><scope>C1K</scope><scope>F1W</scope><scope>FR3</scope><scope>H95</scope><scope>L.G</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0002-2521-4000</orcidid></search><sort><creationdate>201706</creationdate><title>Deletion-bias in DNA double-strand break repair differentially contributes to plant genome shrinkage</title><author>Vu, Giang T. H. ; Cao, Hieu X. ; Reiss, Bernd ; Schubert, Ingo</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4760-1f98d2361003ee96b4f67ff73efe4f1904724792f8e3c1f9fb25c353b9a93cb13</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2017</creationdate><topic>Arabidopsis - genetics</topic><topic>Barley</topic><topic>Biological evolution</topic><topic>Capsella - genetics</topic><topic>Cells</topic><topic>Copying</topic><topic>Deletion</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA Breaks, Double-Stranded</topic><topic>DNA damage</topic><topic>DNA End-Joining Repair</topic><topic>DNA Repair - physiology</topic><topic>double‐strand break (DSB) repair</topic><topic>Gene sequencing</topic><topic>Genetic recombination</topic><topic>genome shrinkage</topic><topic>Genome Size</topic><topic>genome size evolution</topic><topic>Genome, Plant</topic><topic>Genomes</topic><topic>Genomic instability</topic><topic>Hordeum - genetics</topic><topic>Instability</topic><topic>Mutation</topic><topic>Net losses</topic><topic>nonhomologous end joining (NHEJ)</topic><topic>Nucleotide sequence</topic><topic>Repair</topic><topic>Sequence Deletion</topic><topic>Sequencing</topic><topic>Shrinkage</topic><topic>single strand annealing (SSA)</topic><topic>Spectra</topic><topic>Stability</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Vu, Giang T. H.</creatorcontrib><creatorcontrib>Cao, Hieu X.</creatorcontrib><creatorcontrib>Reiss, Bernd</creatorcontrib><creatorcontrib>Schubert, Ingo</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Biotechnology Research Abstracts</collection><collection>Ecology Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ASFA: Aquatic Sciences and Fisheries Abstracts</collection><collection>Engineering Research Database</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) 1: Biological Sciences & Living Resources</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) Professional</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>The New phytologist</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Vu, Giang T. H.</au><au>Cao, Hieu X.</au><au>Reiss, Bernd</au><au>Schubert, Ingo</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Deletion-bias in DNA double-strand break repair differentially contributes to plant genome shrinkage</atitle><jtitle>The New phytologist</jtitle><addtitle>New Phytol</addtitle><date>2017-06</date><risdate>2017</risdate><volume>214</volume><issue>4</issue><spage>1712</spage><epage>1721</epage><pages>1712-1721</pages><issn>0028-646X</issn><eissn>1469-8137</eissn><abstract>In order to prevent genome instability, cells need to be protected by a number of repair mechanisms, including DNA double-strand break (DSB) repair. The extent to which DSB repair, biased towards deletions or insertions, contributes to evolutionary diversification of genome size is still under debate.
We analyzed mutation spectra in Arabidopsis thaliana and in barley (Hordeum vulgare) by PacBio sequencing of three DSB-targeted loci each, uncovering repair via gene conversion, single strand annealing (SSA) or nonhomologous end-joining (NHEJ). Furthermore, phylogenomic comparisons between A. thaliana and two related species were used to detect naturally occurring deletions during Arabidopsis evolution.
Arabidopsis thaliana revealed significantly more and larger deletions after DSB repair than barley, and barley displayed more and larger insertions. Arabidopsis displayed a clear net loss of DNA after DSB repair, mainly via SSA and NHEJ. Barley revealed a very weak net loss of DNA, apparently due to less active break-end resection and easier copying of template sequences into breaks. Comparative phylogenomics revealed several footprints of SSA in the A. thaliana genome.
Quantitative assessment of DNA gain and loss through DSB repair processes suggests deletion-biased DSB repair causing ongoing genome shrinking in A. thaliana, whereas genome size in barley remains nearly constant.</abstract><cop>England</cop><pub>New Phytologist Trust</pub><pmid>28245065</pmid><doi>10.1111/nph.14490</doi><tpages>10</tpages><orcidid>https://orcid.org/0000-0002-2521-4000</orcidid><oa>free_for_read</oa></addata></record> |
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subjects | Arabidopsis - genetics Barley Biological evolution Capsella - genetics Cells Copying Deletion Deoxyribonucleic acid DNA DNA Breaks, Double-Stranded DNA damage DNA End-Joining Repair DNA Repair - physiology double‐strand break (DSB) repair Gene sequencing Genetic recombination genome shrinkage Genome Size genome size evolution Genome, Plant Genomes Genomic instability Hordeum - genetics Instability Mutation Net losses nonhomologous end joining (NHEJ) Nucleotide sequence Repair Sequence Deletion Sequencing Shrinkage single strand annealing (SSA) Spectra Stability |
title | Deletion-bias in DNA double-strand break repair differentially contributes to plant genome shrinkage |
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