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The First Complete Chloroplast Genome Sequences in Actinidiaceae: Genome Structure and Comparative Analysis
Actinidia chinensis is an important economic plant belonging to the basal lineage of the asterids. Availability of a complete Actinidia chloroplast genome sequence is crucial to understanding phylogenetic relationships among major lineages of angiosperms and facilitates kiwifruit genetic improvement...
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| Published in: | PloS one 2015-06, Vol.10 (6), p.e0129347-e0129347 |
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| creator | Yao, Xiaohong Tang, Ping Li, Zuozhou Li, Dawei Liu, Yifei Huang, Hongwen |
| description | Actinidia chinensis is an important economic plant belonging to the basal lineage of the asterids. Availability of a complete Actinidia chloroplast genome sequence is crucial to understanding phylogenetic relationships among major lineages of angiosperms and facilitates kiwifruit genetic improvement. We report here the complete nucleotide sequences of the chloroplast genomes for Actinidia chinensis and A. chinensis var deliciosa obtained through de novo assembly of Illumina paired-end reads produced by total DNA sequencing. The total genome size ranges from 155,446 to 157,557 bp, with an inverted repeat (IR) of 24,013 to 24,391 bp, a large single copy region (LSC) of 87,984 to 88,337 bp and a small single copy region (SSC) of 20,332 to 20,336 bp. The genome encodes 113 different genes, including 79 unique protein-coding genes, 30 tRNA genes and 4 ribosomal RNA genes, with 16 duplicated in the inverted repeats, and a tRNA gene (trnfM-CAU) duplicated once in the LSC region. Comparisons of IR boundaries among four asterid species showed that IR/LSC borders were extended into the 5' portion of the psbA gene and IR contraction occurred in Actinidia. The clap gene has been lost from the chloroplast genome in Actinidia, and may have been transferred to the nucleus during chloroplast evolution. Twenty-seven polymorphic simple sequence repeat (SSR) loci were identified in the Actinidia chloroplast genome. Maximum parsimony analyses of a 72-gene, 16 taxa angiosperm dataset strongly support the placement of Actinidiaceae in Ericales within the basal asterids. |
| doi_str_mv | 10.1371/journal.pone.0129347 |
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Availability of a complete Actinidia chloroplast genome sequence is crucial to understanding phylogenetic relationships among major lineages of angiosperms and facilitates kiwifruit genetic improvement. We report here the complete nucleotide sequences of the chloroplast genomes for Actinidia chinensis and A. chinensis var deliciosa obtained through de novo assembly of Illumina paired-end reads produced by total DNA sequencing. The total genome size ranges from 155,446 to 157,557 bp, with an inverted repeat (IR) of 24,013 to 24,391 bp, a large single copy region (LSC) of 87,984 to 88,337 bp and a small single copy region (SSC) of 20,332 to 20,336 bp. The genome encodes 113 different genes, including 79 unique protein-coding genes, 30 tRNA genes and 4 ribosomal RNA genes, with 16 duplicated in the inverted repeats, and a tRNA gene (trnfM-CAU) duplicated once in the LSC region. Comparisons of IR boundaries among four asterid species showed that IR/LSC borders were extended into the 5' portion of the psbA gene and IR contraction occurred in Actinidia. The clap gene has been lost from the chloroplast genome in Actinidia, and may have been transferred to the nucleus during chloroplast evolution. Twenty-seven polymorphic simple sequence repeat (SSR) loci were identified in the Actinidia chloroplast genome. Maximum parsimony analyses of a 72-gene, 16 taxa angiosperm dataset strongly support the placement of Actinidiaceae in Ericales within the basal asterids.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0129347</identifier><identifier>PMID: 26046631</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Actinidia ; Actinidia - genetics ; Actinidia chinensis ; Actinidiaceae ; Actinidiaceae - classification ; Actinidiaceae - genetics ; Analysis ; Angiosperms ; Botanical gardens ; Camellia sinensis ; Chloroplast Proteins - classification ; Chloroplast Proteins - genetics ; Chloroplasts ; Comparative analysis ; Contraction ; Deoxyribonucleic acid ; DNA ; DNA sequencing ; DNA, Chloroplast - chemistry ; DNA, Chloroplast - genetics ; Economic analysis ; Economic planning ; Evolution ; Flowers & plants ; Gene duplication ; Gene sequencing ; Genes ; Genes, Chloroplast - genetics ; Genetic engineering ; Genetic improvement ; Genome, Chloroplast - genetics ; Genome, Plant - genetics ; Genomes ; Genomics ; Germplasm ; Inverted repeat ; Kiwifruit ; Laboratories ; Molecular Sequence Data ; Mutation ; Nuclei ; Nucleotide sequence ; Phylogenetics ; Phylogeny ; PsbA gene ; Repetitive Sequences, Nucleic Acid - genetics ; Reproduction (copying) ; Ribonucleic acid ; RNA ; rRNA ; Sequence Analysis, DNA ; Transfer RNA ; tRNA</subject><ispartof>PloS one, 2015-06, Vol.10 (6), p.e0129347-e0129347</ispartof><rights>COPYRIGHT 2015 Public Library of Science</rights><rights>2015 Yao 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, and reproduction in any medium, provided the original author and source are credited Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2015 Yao et al 2015 Yao et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-bf486d22e5bd1962c3f555126adc6cbf5e627ba12cc1f8994b3bf8ada393887a3</citedby><cites>FETCH-LOGICAL-c692t-bf486d22e5bd1962c3f555126adc6cbf5e627ba12cc1f8994b3bf8ada393887a3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.proquest.com/docview/1686215130/fulltextPDF?pq-origsite=primo$$EPDF$$P50$$Gproquest$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.proquest.com/docview/1686215130?pq-origsite=primo$$EHTML$$P50$$Gproquest$$Hfree_for_read</linktohtml><link.rule.ids>230,315,730,783,787,888,25765,27936,27937,37024,37025,44602,53804,53806,75454</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/26046631$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Chen, Zhong-Hua</contributor><creatorcontrib>Yao, Xiaohong</creatorcontrib><creatorcontrib>Tang, Ping</creatorcontrib><creatorcontrib>Li, Zuozhou</creatorcontrib><creatorcontrib>Li, Dawei</creatorcontrib><creatorcontrib>Liu, Yifei</creatorcontrib><creatorcontrib>Huang, Hongwen</creatorcontrib><title>The First Complete Chloroplast Genome Sequences in Actinidiaceae: Genome Structure and Comparative Analysis</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Actinidia chinensis is an important economic plant belonging to the basal lineage of the asterids. Availability of a complete Actinidia chloroplast genome sequence is crucial to understanding phylogenetic relationships among major lineages of angiosperms and facilitates kiwifruit genetic improvement. We report here the complete nucleotide sequences of the chloroplast genomes for Actinidia chinensis and A. chinensis var deliciosa obtained through de novo assembly of Illumina paired-end reads produced by total DNA sequencing. The total genome size ranges from 155,446 to 157,557 bp, with an inverted repeat (IR) of 24,013 to 24,391 bp, a large single copy region (LSC) of 87,984 to 88,337 bp and a small single copy region (SSC) of 20,332 to 20,336 bp. The genome encodes 113 different genes, including 79 unique protein-coding genes, 30 tRNA genes and 4 ribosomal RNA genes, with 16 duplicated in the inverted repeats, and a tRNA gene (trnfM-CAU) duplicated once in the LSC region. Comparisons of IR boundaries among four asterid species showed that IR/LSC borders were extended into the 5' portion of the psbA gene and IR contraction occurred in Actinidia. The clap gene has been lost from the chloroplast genome in Actinidia, and may have been transferred to the nucleus during chloroplast evolution. Twenty-seven polymorphic simple sequence repeat (SSR) loci were identified in the Actinidia chloroplast genome. Maximum parsimony analyses of a 72-gene, 16 taxa angiosperm dataset strongly support the placement of Actinidiaceae in Ericales within the basal asterids.</description><subject>Actinidia</subject><subject>Actinidia - genetics</subject><subject>Actinidia chinensis</subject><subject>Actinidiaceae</subject><subject>Actinidiaceae - classification</subject><subject>Actinidiaceae - genetics</subject><subject>Analysis</subject><subject>Angiosperms</subject><subject>Botanical gardens</subject><subject>Camellia sinensis</subject><subject>Chloroplast Proteins - classification</subject><subject>Chloroplast Proteins - genetics</subject><subject>Chloroplasts</subject><subject>Comparative analysis</subject><subject>Contraction</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA sequencing</subject><subject>DNA, Chloroplast - chemistry</subject><subject>DNA, Chloroplast - genetics</subject><subject>Economic analysis</subject><subject>Economic planning</subject><subject>Evolution</subject><subject>Flowers & plants</subject><subject>Gene duplication</subject><subject>Gene sequencing</subject><subject>Genes</subject><subject>Genes, Chloroplast - genetics</subject><subject>Genetic engineering</subject><subject>Genetic improvement</subject><subject>Genome, Chloroplast - genetics</subject><subject>Genome, Plant - genetics</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Germplasm</subject><subject>Inverted repeat</subject><subject>Kiwifruit</subject><subject>Laboratories</subject><subject>Molecular Sequence Data</subject><subject>Mutation</subject><subject>Nuclei</subject><subject>Nucleotide sequence</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>PsbA gene</subject><subject>Repetitive Sequences, Nucleic Acid - genetics</subject><subject>Reproduction (copying)</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>rRNA</subject><subject>Sequence Analysis, DNA</subject><subject>Transfer RNA</subject><subject>tRNA</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>PIMPY</sourceid><sourceid>DOA</sourceid><recordid>eNqNk11v0zAUhiMEYmPwDxBEQkJw0RJ_xEm4QKoqNipNmsQGt5ZjH7cuqV1sZ2L_HnfNqgbtAvnC1vFz3vNhnyx7jYopIhX6tHa9t6Kbbp2FaYFwQ2j1JDtFDcEThgvy9Oh8kr0IYV0UJakZe56dYFZQxgg6zX7drCA_Nz7EfO422w4i5PNV57zbdiIZL8C6DeTX8LsHKyHkxuYzGY01yggJAj4fkOh7GXsPubDqXkx4Ec0t5LOU5l0w4WX2TIsuwKthP8t-nH-9mX-bXF5dLOazy4lkDY6TVtOaKYyhbBVqGJZEl2WJMBNKMtnqEhiuWoGwlEjXTUNb0upaKEEaUteVIGfZ273utnOBD30KHLGaYVQiUiRisSeUE2u-9WYj_B13wvB7g_NLLnw0sgPeSk2xBs0qpiiVslVKawKtJgILinTS-jJE69sNKAk2etGNRMc31qz40t1ySsuK1SgJfBgEvEtdDpFvTJDQdcKC6_d5N01T4V3e7_5BH69uoJYiFWCsdimu3InyGUWMMdo0LFHTR6i0FGyMTJ9Km2QfOXwcOSQmwp-4FH0IfHH9_f_Zq59j9v0RuwLRxVVwXR-Ns2EM0j0ovQvBgz40GRV8NxMP3eC7meDDTCS3N8cPdHB6GALyF3EACRo</recordid><startdate>20150605</startdate><enddate>20150605</enddate><creator>Yao, Xiaohong</creator><creator>Tang, Ping</creator><creator>Li, Zuozhou</creator><creator>Li, Dawei</creator><creator>Liu, Yifei</creator><creator>Huang, Hongwen</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</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>IOV</scope><scope>ISR</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20150605</creationdate><title>The First Complete Chloroplast Genome Sequences in Actinidiaceae: Genome Structure and Comparative Analysis</title><author>Yao, Xiaohong ; Tang, Ping ; Li, Zuozhou ; Li, Dawei ; Liu, Yifei ; Huang, Hongwen</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c692t-bf486d22e5bd1962c3f555126adc6cbf5e627ba12cc1f8994b3bf8ada393887a3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>Actinidia</topic><topic>Actinidia - genetics</topic><topic>Actinidia chinensis</topic><topic>Actinidiaceae</topic><topic>Actinidiaceae - classification</topic><topic>Actinidiaceae - genetics</topic><topic>Analysis</topic><topic>Angiosperms</topic><topic>Botanical gardens</topic><topic>Camellia sinensis</topic><topic>Chloroplast Proteins - classification</topic><topic>Chloroplast Proteins - genetics</topic><topic>Chloroplasts</topic><topic>Comparative analysis</topic><topic>Contraction</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA sequencing</topic><topic>DNA, Chloroplast - chemistry</topic><topic>DNA, Chloroplast - genetics</topic><topic>Economic analysis</topic><topic>Economic planning</topic><topic>Evolution</topic><topic>Flowers & plants</topic><topic>Gene duplication</topic><topic>Gene sequencing</topic><topic>Genes</topic><topic>Genes, Chloroplast - genetics</topic><topic>Genetic engineering</topic><topic>Genetic improvement</topic><topic>Genome, Chloroplast - genetics</topic><topic>Genome, Plant - genetics</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Germplasm</topic><topic>Inverted repeat</topic><topic>Kiwifruit</topic><topic>Laboratories</topic><topic>Molecular Sequence Data</topic><topic>Mutation</topic><topic>Nuclei</topic><topic>Nucleotide sequence</topic><topic>Phylogenetics</topic><topic>Phylogeny</topic><topic>PsbA gene</topic><topic>Repetitive Sequences, Nucleic Acid - genetics</topic><topic>Reproduction (copying)</topic><topic>Ribonucleic acid</topic><topic>RNA</topic><topic>rRNA</topic><topic>Sequence Analysis, DNA</topic><topic>Transfer RNA</topic><topic>tRNA</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Yao, Xiaohong</creatorcontrib><creatorcontrib>Tang, Ping</creatorcontrib><creatorcontrib>Li, Zuozhou</creatorcontrib><creatorcontrib>Li, Dawei</creatorcontrib><creatorcontrib>Liu, Yifei</creatorcontrib><creatorcontrib>Huang, Hongwen</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Opposing Viewpoints Resource Center</collection><collection>Gale In Context: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Animal Behavior Abstracts</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Proquest Nursing & Allied Health Source</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Immunology Abstracts</collection><collection>Meteorological & Geoastrophysical Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Agricultural Science Collection</collection><collection>ProQuest_Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>ProQuest Public Health Database</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Materials Science & Engineering Collection</collection><collection>ProQuest Central (Alumni)</collection><collection>ProQuest Central</collection><collection>Advanced Technologies & Aerospace Collection</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Materials Science Collection</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Materials Science Database</collection><collection>Nursing & Allied Health Database (Alumni Edition)</collection><collection>Meteorological & Geoastrophysical Abstracts - 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Availability of a complete Actinidia chloroplast genome sequence is crucial to understanding phylogenetic relationships among major lineages of angiosperms and facilitates kiwifruit genetic improvement. We report here the complete nucleotide sequences of the chloroplast genomes for Actinidia chinensis and A. chinensis var deliciosa obtained through de novo assembly of Illumina paired-end reads produced by total DNA sequencing. The total genome size ranges from 155,446 to 157,557 bp, with an inverted repeat (IR) of 24,013 to 24,391 bp, a large single copy region (LSC) of 87,984 to 88,337 bp and a small single copy region (SSC) of 20,332 to 20,336 bp. The genome encodes 113 different genes, including 79 unique protein-coding genes, 30 tRNA genes and 4 ribosomal RNA genes, with 16 duplicated in the inverted repeats, and a tRNA gene (trnfM-CAU) duplicated once in the LSC region. Comparisons of IR boundaries among four asterid species showed that IR/LSC borders were extended into the 5' portion of the psbA gene and IR contraction occurred in Actinidia. The clap gene has been lost from the chloroplast genome in Actinidia, and may have been transferred to the nucleus during chloroplast evolution. Twenty-seven polymorphic simple sequence repeat (SSR) loci were identified in the Actinidia chloroplast genome. Maximum parsimony analyses of a 72-gene, 16 taxa angiosperm dataset strongly support the placement of Actinidiaceae in Ericales within the basal asterids.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>26046631</pmid><doi>10.1371/journal.pone.0129347</doi><oa>free_for_read</oa></addata></record> |
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| issn | 1932-6203 1932-6203 |
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| subjects | Actinidia Actinidia - genetics Actinidia chinensis Actinidiaceae Actinidiaceae - classification Actinidiaceae - genetics Analysis Angiosperms Botanical gardens Camellia sinensis Chloroplast Proteins - classification Chloroplast Proteins - genetics Chloroplasts Comparative analysis Contraction Deoxyribonucleic acid DNA DNA sequencing DNA, Chloroplast - chemistry DNA, Chloroplast - genetics Economic analysis Economic planning Evolution Flowers & plants Gene duplication Gene sequencing Genes Genes, Chloroplast - genetics Genetic engineering Genetic improvement Genome, Chloroplast - genetics Genome, Plant - genetics Genomes Genomics Germplasm Inverted repeat Kiwifruit Laboratories Molecular Sequence Data Mutation Nuclei Nucleotide sequence Phylogenetics Phylogeny PsbA gene Repetitive Sequences, Nucleic Acid - genetics Reproduction (copying) Ribonucleic acid RNA rRNA Sequence Analysis, DNA Transfer RNA tRNA |
| title | The First Complete Chloroplast Genome Sequences in Actinidiaceae: Genome Structure and Comparative Analysis |
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