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Mitochondrial genomes organization in alloplasmic lines of sunflower ( Helianthus annuus L.) with various types of cytoplasmic male sterility
Cytoplasmic male sterility (CMS) is a common phenotype in higher plants, that is often associated with rearrangements in mitochondrial DNA (mtDNA), and is widely used to produce hybrid seeds in a variety of valuable crop species. Investigation of the CMS phenomenon promotes understanding of fundamen...
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description | Cytoplasmic male sterility (CMS) is a common phenotype in higher plants, that is often associated with rearrangements in mitochondrial DNA (mtDNA), and is widely used to produce hybrid seeds in a variety of valuable crop species. Investigation of the CMS phenomenon promotes understanding of fundamental issues of nuclear-cytoplasmic interactions in the ontogeny of higher plants. In the present study, we analyzed the structural changes in mitochondrial genomes of three alloplasmic lines of sunflower (
L.). The investigation was focused on CMS line PET2, as there are very few reports about its mtDNA organization.
The NGS sequencing,
assembly, and annotation of sunflower mitochondrial genomes were performed. The comparative analysis of mtDNA of HA89 fertile line and two HA89 CMS lines (PET1, PET2) occurred.
The mtDNA of the HA89 fertile line was almost identical to the HA412 line (NC_023337). The comparative analysis of HA89 fertile and CMS (PET1) analog mitochondrial genomes revealed 11,852 bp inversion, 4,732 bp insertion, 451 bp deletion and 18 variant sites. In the mtDNA of HA89 (PET2) CMS line we determined 27.5 kb and 106.5 kb translocations, 711 bp and 3,780 bp deletions, as well as, 5,050 bp and 15,885 bp insertions. There are also 83 polymorphic sites in the PET2 mitochondrial genome, as compared with the fertile line.
The observed mitochondrial reorganizations in PET1 resulted in only one new open reading frame formation (
), and PET2 mtDNA rearrangements led to the elimination of
, duplication of
gene and appearance of four new ORFs with transcription activity specific for the HA89 (PET2) CMS line-
,
,
and
.
and
are the
chimeric ORFs, containing transmembrane domains and possibly may impact on mitochondrial membrane potential. So
and
may be the cause for the appearance of the PET2 CMS phenotype, while the contribution of other mtDNA reorganizations in CMS formation is negligible. |
doi_str_mv | 10.7717/peerj.5266 |
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L.). The investigation was focused on CMS line PET2, as there are very few reports about its mtDNA organization.
The NGS sequencing,
assembly, and annotation of sunflower mitochondrial genomes were performed. The comparative analysis of mtDNA of HA89 fertile line and two HA89 CMS lines (PET1, PET2) occurred.
The mtDNA of the HA89 fertile line was almost identical to the HA412 line (NC_023337). The comparative analysis of HA89 fertile and CMS (PET1) analog mitochondrial genomes revealed 11,852 bp inversion, 4,732 bp insertion, 451 bp deletion and 18 variant sites. In the mtDNA of HA89 (PET2) CMS line we determined 27.5 kb and 106.5 kb translocations, 711 bp and 3,780 bp deletions, as well as, 5,050 bp and 15,885 bp insertions. There are also 83 polymorphic sites in the PET2 mitochondrial genome, as compared with the fertile line.
The observed mitochondrial reorganizations in PET1 resulted in only one new open reading frame formation (
), and PET2 mtDNA rearrangements led to the elimination of
, duplication of
gene and appearance of four new ORFs with transcription activity specific for the HA89 (PET2) CMS line-
,
,
and
.
and
are the
chimeric ORFs, containing transmembrane domains and possibly may impact on mitochondrial membrane potential. So
and
may be the cause for the appearance of the PET2 CMS phenotype, while the contribution of other mtDNA reorganizations in CMS formation is negligible.</description><identifier>ISSN: 2167-8359</identifier><identifier>EISSN: 2167-8359</identifier><identifier>DOI: 10.7717/peerj.5266</identifier><identifier>PMID: 30057860</identifier><language>eng</language><publisher>United States: PeerJ. Ltd</publisher><subject>Agricultural Science ; ATP6 protein ; Comparative analysis ; Corn ; Cytoplasmic male sterility ; Deoxyribonucleic acid ; DNA ; Genetic aspects ; Genetics ; Genomes ; Genomics ; Helianthus annuus ; Hybridization ; Insertion ; Male sterility ; Membrane potential ; Methods ; Mitochondrial DNA ; Mitochondrial genome rearrangements ; Molecular biology ; mtDNA structure ; Ontogeny ; Phenotypes ; Plant mitochondria ; Plant Science ; Seeds ; Sunflower ; Sunflowers ; Transcription ; Translocation ; Transmembrane domains</subject><ispartof>PeerJ (San Francisco, CA), 2018-07, Vol.6, p.e5266-e5266, Article e5266</ispartof><rights>COPYRIGHT 2018 PeerJ. Ltd.</rights><rights>2018 Makarenko et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2018 Makarenko et al. 2018 Makarenko et al.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c570t-77bfe8c96b9e71461594b406b0df3bab602b7e61144b79ed533b6f75c5a017be3</citedby><cites>FETCH-LOGICAL-c570t-77bfe8c96b9e71461594b406b0df3bab602b7e61144b79ed533b6f75c5a017be3</cites><orcidid>0000-0002-0629-3874</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.proquest.com/docview/2073958591/fulltextPDF?pq-origsite=primo$$EPDF$$P50$$Gproquest$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.proquest.com/docview/2073958591?pq-origsite=primo$$EHTML$$P50$$Gproquest$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,25753,27924,27925,37012,37013,44590,53791,53793,75126</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/30057860$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Makarenko, Maksim S</creatorcontrib><creatorcontrib>Kornienko, Igor V</creatorcontrib><creatorcontrib>Azarin, Kirill V</creatorcontrib><creatorcontrib>Usatov, Alexander V</creatorcontrib><creatorcontrib>Logacheva, Maria D</creatorcontrib><creatorcontrib>Markin, Nicolay V</creatorcontrib><creatorcontrib>Gavrilova, Vera A</creatorcontrib><title>Mitochondrial genomes organization in alloplasmic lines of sunflower ( Helianthus annuus L.) with various types of cytoplasmic male sterility</title><title>PeerJ (San Francisco, CA)</title><addtitle>PeerJ</addtitle><description>Cytoplasmic male sterility (CMS) is a common phenotype in higher plants, that is often associated with rearrangements in mitochondrial DNA (mtDNA), and is widely used to produce hybrid seeds in a variety of valuable crop species. Investigation of the CMS phenomenon promotes understanding of fundamental issues of nuclear-cytoplasmic interactions in the ontogeny of higher plants. In the present study, we analyzed the structural changes in mitochondrial genomes of three alloplasmic lines of sunflower (
L.). The investigation was focused on CMS line PET2, as there are very few reports about its mtDNA organization.
The NGS sequencing,
assembly, and annotation of sunflower mitochondrial genomes were performed. The comparative analysis of mtDNA of HA89 fertile line and two HA89 CMS lines (PET1, PET2) occurred.
The mtDNA of the HA89 fertile line was almost identical to the HA412 line (NC_023337). The comparative analysis of HA89 fertile and CMS (PET1) analog mitochondrial genomes revealed 11,852 bp inversion, 4,732 bp insertion, 451 bp deletion and 18 variant sites. In the mtDNA of HA89 (PET2) CMS line we determined 27.5 kb and 106.5 kb translocations, 711 bp and 3,780 bp deletions, as well as, 5,050 bp and 15,885 bp insertions. There are also 83 polymorphic sites in the PET2 mitochondrial genome, as compared with the fertile line.
The observed mitochondrial reorganizations in PET1 resulted in only one new open reading frame formation (
), and PET2 mtDNA rearrangements led to the elimination of
, duplication of
gene and appearance of four new ORFs with transcription activity specific for the HA89 (PET2) CMS line-
,
,
and
.
and
are the
chimeric ORFs, containing transmembrane domains and possibly may impact on mitochondrial membrane potential. So
and
may be the cause for the appearance of the PET2 CMS phenotype, while the contribution of other mtDNA reorganizations in CMS formation is negligible.</description><subject>Agricultural Science</subject><subject>ATP6 protein</subject><subject>Comparative analysis</subject><subject>Corn</subject><subject>Cytoplasmic male sterility</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>Genetic aspects</subject><subject>Genetics</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Helianthus annuus</subject><subject>Hybridization</subject><subject>Insertion</subject><subject>Male sterility</subject><subject>Membrane potential</subject><subject>Methods</subject><subject>Mitochondrial DNA</subject><subject>Mitochondrial genome rearrangements</subject><subject>Molecular biology</subject><subject>mtDNA structure</subject><subject>Ontogeny</subject><subject>Phenotypes</subject><subject>Plant mitochondria</subject><subject>Plant Science</subject><subject>Seeds</subject><subject>Sunflower</subject><subject>Sunflowers</subject><subject>Transcription</subject><subject>Translocation</subject><subject>Transmembrane domains</subject><issn>2167-8359</issn><issn>2167-8359</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2018</creationdate><recordtype>article</recordtype><sourceid>PIMPY</sourceid><sourceid>DOA</sourceid><recordid>eNptkt-K1DAUh4so7jLujQ8gAUFWYcb0T5LmRlgWdRdGvNHrkKSn0wyZZEzSXcZ38J1Nd9ZxRmyhKaff-Zr-eoriZYkXjJXs_RYgrBekovRJcV6VlM3bmvCnR_dnxUWMa5yPtqK4rZ8XZzXGhLUUnxe_vpjk9eBdF4y0aAXObyAiH1bSmZ8yGe-QcUha67dWxo3RyBo3ET2Ko-utv4eALtENWCNdGsaIpHNjXpaLt-jepAHdyWB8LqTddt-nd-kg20gLKCYIxpq0e1E866WNcPG4zorvnz5-u76ZL79-vr2-Ws41YTjNGVM9tJpTxYGVDS0Jb1SDqcJdXyupKK4UA1qWTaMYh47UtaI9I5pIXDIF9ay43Xs7L9diG8xGhp3w0oiHQv56IUMy2oJgneRYA9FUq4YonhPN9k7LKrtqTrLrw961HdUGOg0uBWlPpKdPnBnEyt8JivMOaZMFl4-C4H-MEJPYmKjBWukg5yYqzDgnuOU8o6__Qdd-DC5HNVF5Ny3h5V9qlcMVxvU-v1dPUnFFKK5p1eTrrFj8h8pnB_nHeAe9yfWThjdHDQNIm4bo7TjNSDwF3-1BHXyMAfpDGCUW09CKh6EV09Bm-NVxfAf0z4jWvwGiGOj1</recordid><startdate>20180723</startdate><enddate>20180723</enddate><creator>Makarenko, Maksim S</creator><creator>Kornienko, Igor V</creator><creator>Azarin, Kirill V</creator><creator>Usatov, Alexander V</creator><creator>Logacheva, Maria D</creator><creator>Markin, Nicolay V</creator><creator>Gavrilova, Vera A</creator><general>PeerJ. Ltd</general><general>PeerJ, Inc</general><general>PeerJ Inc</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7XB</scope><scope>88I</scope><scope>8FE</scope><scope>8FH</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>LK8</scope><scope>M2P</scope><scope>M7P</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>Q9U</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope><orcidid>https://orcid.org/0000-0002-0629-3874</orcidid></search><sort><creationdate>20180723</creationdate><title>Mitochondrial genomes organization in alloplasmic lines of sunflower ( Helianthus annuus L.) with various types of cytoplasmic male sterility</title><author>Makarenko, Maksim S ; Kornienko, Igor V ; Azarin, Kirill V ; Usatov, Alexander V ; Logacheva, Maria D ; Markin, Nicolay V ; Gavrilova, Vera A</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c570t-77bfe8c96b9e71461594b406b0df3bab602b7e61144b79ed533b6f75c5a017be3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2018</creationdate><topic>Agricultural Science</topic><topic>ATP6 protein</topic><topic>Comparative analysis</topic><topic>Corn</topic><topic>Cytoplasmic male sterility</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>Genetic aspects</topic><topic>Genetics</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Helianthus annuus</topic><topic>Hybridization</topic><topic>Insertion</topic><topic>Male sterility</topic><topic>Membrane potential</topic><topic>Methods</topic><topic>Mitochondrial DNA</topic><topic>Mitochondrial genome rearrangements</topic><topic>Molecular biology</topic><topic>mtDNA structure</topic><topic>Ontogeny</topic><topic>Phenotypes</topic><topic>Plant mitochondria</topic><topic>Plant Science</topic><topic>Seeds</topic><topic>Sunflower</topic><topic>Sunflowers</topic><topic>Transcription</topic><topic>Translocation</topic><topic>Transmembrane domains</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Makarenko, Maksim S</creatorcontrib><creatorcontrib>Kornienko, Igor V</creatorcontrib><creatorcontrib>Azarin, Kirill V</creatorcontrib><creatorcontrib>Usatov, Alexander V</creatorcontrib><creatorcontrib>Logacheva, Maria D</creatorcontrib><creatorcontrib>Markin, Nicolay V</creatorcontrib><creatorcontrib>Gavrilova, Vera A</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Science Database (Alumni Edition)</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Biological Science Collection</collection><collection>Science Database</collection><collection>Biological Science Database</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>ProQuest Central Basic</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>Directory of Open Access Journals</collection><jtitle>PeerJ (San Francisco, CA)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Makarenko, Maksim S</au><au>Kornienko, Igor V</au><au>Azarin, Kirill V</au><au>Usatov, Alexander V</au><au>Logacheva, Maria D</au><au>Markin, Nicolay V</au><au>Gavrilova, Vera A</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Mitochondrial genomes organization in alloplasmic lines of sunflower ( Helianthus annuus L.) with various types of cytoplasmic male sterility</atitle><jtitle>PeerJ (San Francisco, CA)</jtitle><addtitle>PeerJ</addtitle><date>2018-07-23</date><risdate>2018</risdate><volume>6</volume><spage>e5266</spage><epage>e5266</epage><pages>e5266-e5266</pages><artnum>e5266</artnum><issn>2167-8359</issn><eissn>2167-8359</eissn><abstract>Cytoplasmic male sterility (CMS) is a common phenotype in higher plants, that is often associated with rearrangements in mitochondrial DNA (mtDNA), and is widely used to produce hybrid seeds in a variety of valuable crop species. Investigation of the CMS phenomenon promotes understanding of fundamental issues of nuclear-cytoplasmic interactions in the ontogeny of higher plants. In the present study, we analyzed the structural changes in mitochondrial genomes of three alloplasmic lines of sunflower (
L.). The investigation was focused on CMS line PET2, as there are very few reports about its mtDNA organization.
The NGS sequencing,
assembly, and annotation of sunflower mitochondrial genomes were performed. The comparative analysis of mtDNA of HA89 fertile line and two HA89 CMS lines (PET1, PET2) occurred.
The mtDNA of the HA89 fertile line was almost identical to the HA412 line (NC_023337). The comparative analysis of HA89 fertile and CMS (PET1) analog mitochondrial genomes revealed 11,852 bp inversion, 4,732 bp insertion, 451 bp deletion and 18 variant sites. In the mtDNA of HA89 (PET2) CMS line we determined 27.5 kb and 106.5 kb translocations, 711 bp and 3,780 bp deletions, as well as, 5,050 bp and 15,885 bp insertions. There are also 83 polymorphic sites in the PET2 mitochondrial genome, as compared with the fertile line.
The observed mitochondrial reorganizations in PET1 resulted in only one new open reading frame formation (
), and PET2 mtDNA rearrangements led to the elimination of
, duplication of
gene and appearance of four new ORFs with transcription activity specific for the HA89 (PET2) CMS line-
,
,
and
.
and
are the
chimeric ORFs, containing transmembrane domains and possibly may impact on mitochondrial membrane potential. So
and
may be the cause for the appearance of the PET2 CMS phenotype, while the contribution of other mtDNA reorganizations in CMS formation is negligible.</abstract><cop>United States</cop><pub>PeerJ. Ltd</pub><pmid>30057860</pmid><doi>10.7717/peerj.5266</doi><orcidid>https://orcid.org/0000-0002-0629-3874</orcidid><oa>free_for_read</oa></addata></record> |
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subjects | Agricultural Science ATP6 protein Comparative analysis Corn Cytoplasmic male sterility Deoxyribonucleic acid DNA Genetic aspects Genetics Genomes Genomics Helianthus annuus Hybridization Insertion Male sterility Membrane potential Methods Mitochondrial DNA Mitochondrial genome rearrangements Molecular biology mtDNA structure Ontogeny Phenotypes Plant mitochondria Plant Science Seeds Sunflower Sunflowers Transcription Translocation Transmembrane domains |
title | Mitochondrial genomes organization in alloplasmic lines of sunflower ( Helianthus annuus L.) with various types of cytoplasmic male sterility |
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