Complete chloroplast genome of Castanopsis sclerophylla (Lindl.) Schott: Genome structure and comparative and phylogenetic analysis
Castanopsis sclerophylla (Lindl.) Schott is an important species of evergreen broad-leaved tree in subtropical areas and has high ecological and economic value. However, there are few studies on its chloroplast genome. In this study, the complete chloroplast genome sequence of C. sclerophylla was de...
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description | Castanopsis sclerophylla (Lindl.) Schott is an important species of evergreen broad-leaved tree in subtropical areas and has high ecological and economic value. However, there are few studies on its chloroplast genome. In this study, the complete chloroplast genome sequence of C. sclerophylla was determined using the Illumina HiSeq 2500 platform. The complete chloroplast genome of C. sclerophylla is 160,497 bp long, including a pair of inverted repeat (IR) regions (25,675 bp) separated by a large single-copy (LSC) region of 90,255 bp and a small single-copy (SSC) region of 18,892 bp. The overall GC content of the chloroplast genome is 36.82%. A total of 131 genes were found; of these, 111 genes are unique and annotated, including 79 protein-coding genes, 27 transfer RNA genes (tRNAs), and four ribosomal RNA genes (rRNAs). Twenty-one genes were found to be duplicated in the IR regions. Comparative analysis indicated that IR contraction might be the reason for the smaller chloroplast genome of C. sclerophylla compared to three congeneric species. Sequence analysis indicated that the LSC and SSC regions are more divergent than IR regions within Castanopsis; furthermore, greater divergence was found in noncoding regions than in coding regions. The maximum likelihood phylogenetic analysis showed that four species of the genus Castanopsis form a monophyletic clade and that C. sclerophylla is closely related to Castanopsis hainanensis with strong bootstrap values. These results not only provide a basic understanding of Castanopsis chloroplast genomes, but also illuminate Castanopsis species evolution within the Fagaceae family. Furthermore, these findings will be valuable for future studies of genetic diversity and enhance our understanding of the phylogenetic evolution of Castanopsis. |
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Schott: Genome structure and comparative and phylogenetic analysis</title><source>MEDLINE</source><source>DOAJ Directory of Open Access Journals</source><source>Public Library of Science (PLoS) Journals Open Access</source><source>EZB-FREE-00999 freely available EZB journals</source><source>PubMed Central</source><source>Free Full-Text Journals in Chemistry</source><creator>Ye, Xuemin ; Hu, Dongnan ; Guo, Yangping ; Sun, Rongxi</creator><contributor>Sun, Genlou</contributor><creatorcontrib>Ye, Xuemin ; Hu, Dongnan ; Guo, Yangping ; Sun, Rongxi ; Sun, Genlou</creatorcontrib><description>Castanopsis sclerophylla (Lindl.) Schott is an important species of evergreen broad-leaved tree in subtropical areas and has high ecological and economic value. However, there are few studies on its chloroplast genome. In this study, the complete chloroplast genome sequence of C. sclerophylla was determined using the Illumina HiSeq 2500 platform. The complete chloroplast genome of C. sclerophylla is 160,497 bp long, including a pair of inverted repeat (IR) regions (25,675 bp) separated by a large single-copy (LSC) region of 90,255 bp and a small single-copy (SSC) region of 18,892 bp. The overall GC content of the chloroplast genome is 36.82%. A total of 131 genes were found; of these, 111 genes are unique and annotated, including 79 protein-coding genes, 27 transfer RNA genes (tRNAs), and four ribosomal RNA genes (rRNAs). Twenty-one genes were found to be duplicated in the IR regions. Comparative analysis indicated that IR contraction might be the reason for the smaller chloroplast genome of C. sclerophylla compared to three congeneric species. Sequence analysis indicated that the LSC and SSC regions are more divergent than IR regions within Castanopsis; furthermore, greater divergence was found in noncoding regions than in coding regions. The maximum likelihood phylogenetic analysis showed that four species of the genus Castanopsis form a monophyletic clade and that C. sclerophylla is closely related to Castanopsis hainanensis with strong bootstrap values. These results not only provide a basic understanding of Castanopsis chloroplast genomes, but also illuminate Castanopsis species evolution within the Fagaceae family. Furthermore, these findings will be valuable for future studies of genetic diversity and enhance our understanding of the phylogenetic evolution of Castanopsis.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0212325</identifier><identifier>PMID: 31361757</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Amino acids ; Analysis ; Biodiversity ; Biological evolution ; Biology and Life Sciences ; Castanopsis ; Castanopsis sclerophylla ; Chloroplasts ; Chloroplasts - genetics ; Chloroplasts - metabolism ; Comparative analysis ; Computer and Information Sciences ; Contraction ; Deoxyribonucleic acid ; Divergence ; DNA ; Ecological monitoring ; Engineering and Technology ; Evolution ; Fagaceae - genetics ; Fagaceae - metabolism ; Forestry ; Future predictions ; Genes ; Genes, Plant ; Genetic diversity ; Genetic engineering ; Genetic research ; Genome, Chloroplast ; Genomes ; Genomics ; Herbal medicine ; Infrared analysis ; Inverted repeat ; Laboratories ; Nucleotide sequence ; Phylogenetics ; Phylogeny ; Plant sciences ; Proteins ; Ribonucleic acid ; Ribosomal RNA ; RNA ; rRNA ; Species ; Transfer RNA ; Trees ; Whole Genome Sequencing</subject><ispartof>PloS one, 2019-07, Vol.14 (7), p.e0212325-e0212325</ispartof><rights>COPYRIGHT 2019 Public Library of Science</rights><rights>2019 Ye 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>2019 Ye et al 2019 Ye et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c593t-2047cb4f5e95e5fd06b5adffcdd2a0990ed8fa9833d3a50aba952fcafb6cfa1e3</citedby><cites>FETCH-LOGICAL-c593t-2047cb4f5e95e5fd06b5adffcdd2a0990ed8fa9833d3a50aba952fcafb6cfa1e3</cites><orcidid>0000-0002-7820-2468</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6667119/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6667119/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2102,2928,23866,27924,27925,53791,53793,79600,79601</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/31361757$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Sun, Genlou</contributor><creatorcontrib>Ye, Xuemin</creatorcontrib><creatorcontrib>Hu, Dongnan</creatorcontrib><creatorcontrib>Guo, Yangping</creatorcontrib><creatorcontrib>Sun, Rongxi</creatorcontrib><title>Complete chloroplast genome of Castanopsis sclerophylla (Lindl.) Schott: Genome structure and comparative and phylogenetic analysis</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Castanopsis sclerophylla (Lindl.) Schott is an important species of evergreen broad-leaved tree in subtropical areas and has high ecological and economic value. However, there are few studies on its chloroplast genome. In this study, the complete chloroplast genome sequence of C. sclerophylla was determined using the Illumina HiSeq 2500 platform. The complete chloroplast genome of C. sclerophylla is 160,497 bp long, including a pair of inverted repeat (IR) regions (25,675 bp) separated by a large single-copy (LSC) region of 90,255 bp and a small single-copy (SSC) region of 18,892 bp. The overall GC content of the chloroplast genome is 36.82%. A total of 131 genes were found; of these, 111 genes are unique and annotated, including 79 protein-coding genes, 27 transfer RNA genes (tRNAs), and four ribosomal RNA genes (rRNAs). Twenty-one genes were found to be duplicated in the IR regions. Comparative analysis indicated that IR contraction might be the reason for the smaller chloroplast genome of C. sclerophylla compared to three congeneric species. Sequence analysis indicated that the LSC and SSC regions are more divergent than IR regions within Castanopsis; furthermore, greater divergence was found in noncoding regions than in coding regions. The maximum likelihood phylogenetic analysis showed that four species of the genus Castanopsis form a monophyletic clade and that C. sclerophylla is closely related to Castanopsis hainanensis with strong bootstrap values. These results not only provide a basic understanding of Castanopsis chloroplast genomes, but also illuminate Castanopsis species evolution within the Fagaceae family. Furthermore, these findings will be valuable for future studies of genetic diversity and enhance our understanding of the phylogenetic evolution of Castanopsis.</description><subject>Amino acids</subject><subject>Analysis</subject><subject>Biodiversity</subject><subject>Biological evolution</subject><subject>Biology and Life Sciences</subject><subject>Castanopsis</subject><subject>Castanopsis sclerophylla</subject><subject>Chloroplasts</subject><subject>Chloroplasts - genetics</subject><subject>Chloroplasts - metabolism</subject><subject>Comparative analysis</subject><subject>Computer and Information Sciences</subject><subject>Contraction</subject><subject>Deoxyribonucleic acid</subject><subject>Divergence</subject><subject>DNA</subject><subject>Ecological monitoring</subject><subject>Engineering and Technology</subject><subject>Evolution</subject><subject>Fagaceae - genetics</subject><subject>Fagaceae - metabolism</subject><subject>Forestry</subject><subject>Future predictions</subject><subject>Genes</subject><subject>Genes, Plant</subject><subject>Genetic diversity</subject><subject>Genetic engineering</subject><subject>Genetic research</subject><subject>Genome, Chloroplast</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Herbal medicine</subject><subject>Infrared analysis</subject><subject>Inverted repeat</subject><subject>Laboratories</subject><subject>Nucleotide sequence</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>Plant sciences</subject><subject>Proteins</subject><subject>Ribonucleic acid</subject><subject>Ribosomal RNA</subject><subject>RNA</subject><subject>rRNA</subject><subject>Species</subject><subject>Transfer RNA</subject><subject>Trees</subject><subject>Whole Genome Sequencing</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2019</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>DOA</sourceid><recordid>eNptUstu1DAUjRCItgN_gCASm7KYwY5jO-4CqRpBqTQSC2Bt3fgxk5ETBzupNGt-HE-TVh1UeWH7-pxzHz5Z9g6jFSYcf977MXTgVr3vzAoVuCAFfZGdY0GKJSsQefnkfJZdxLhHiJKKsdfZGcGEYU75efZ37dvemcHkaud88L2DOORb0_nW5N7m63SFzvexiXlUziTE7uAc5JebptNu9Sn_qXZ-GK7ym4kThzCqYQwmh07nKqlDgKG5m-5Hsk_qZmhUCoA7JOE32SsLLpq3877Ifn_7-mv9fbn5cXO7vt4sFRVkWBao5KouLTWCGmo1YjUFba3SugAkBDK6siAqQjQBiqAGQQurwNZMWcCGLLIPk27vfJTz_KIsCsYR4hxXCXE7IbSHvexD00I4SA-NvA_4sJUQUunOSFvpslKYCq1pqUkpFIWKlZqzGmlTHbN9mbONdWu0Mt0QwJ2Inr50zU5u_Z1kjHGcvm6RXc4Cwf8ZTRxk20Rl0vA748ep7hIRIniCfvwP-nx3M2oLqYGmsz7lVUdReU1FKSrMCUuo1TOotLRpG5XMZpsUPyGUE0EFH2Mw9rFHjOTRqg_FyKNV5WzVRHv_dD6PpAdvkn8Ssupz</recordid><startdate>20190730</startdate><enddate>20190730</enddate><creator>Ye, Xuemin</creator><creator>Hu, Dongnan</creator><creator>Guo, Yangping</creator><creator>Sun, Rongxi</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>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>PRINS</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope><orcidid>https://orcid.org/0000-0002-7820-2468</orcidid></search><sort><creationdate>20190730</creationdate><title>Complete chloroplast genome of Castanopsis sclerophylla (Lindl.) Schott: Genome structure and comparative and phylogenetic analysis</title><author>Ye, Xuemin ; Hu, Dongnan ; Guo, Yangping ; Sun, Rongxi</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c593t-2047cb4f5e95e5fd06b5adffcdd2a0990ed8fa9833d3a50aba952fcafb6cfa1e3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2019</creationdate><topic>Amino acids</topic><topic>Analysis</topic><topic>Biodiversity</topic><topic>Biological evolution</topic><topic>Biology and Life Sciences</topic><topic>Castanopsis</topic><topic>Castanopsis sclerophylla</topic><topic>Chloroplasts</topic><topic>Chloroplasts - genetics</topic><topic>Chloroplasts - metabolism</topic><topic>Comparative analysis</topic><topic>Computer and Information Sciences</topic><topic>Contraction</topic><topic>Deoxyribonucleic acid</topic><topic>Divergence</topic><topic>DNA</topic><topic>Ecological monitoring</topic><topic>Engineering and Technology</topic><topic>Evolution</topic><topic>Fagaceae - genetics</topic><topic>Fagaceae - metabolism</topic><topic>Forestry</topic><topic>Future predictions</topic><topic>Genes</topic><topic>Genes, Plant</topic><topic>Genetic diversity</topic><topic>Genetic engineering</topic><topic>Genetic research</topic><topic>Genome, Chloroplast</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Herbal medicine</topic><topic>Infrared analysis</topic><topic>Inverted repeat</topic><topic>Laboratories</topic><topic>Nucleotide sequence</topic><topic>Phylogenetics</topic><topic>Phylogeny</topic><topic>Plant sciences</topic><topic>Proteins</topic><topic>Ribonucleic acid</topic><topic>Ribosomal RNA</topic><topic>RNA</topic><topic>rRNA</topic><topic>Species</topic><topic>Transfer RNA</topic><topic>Trees</topic><topic>Whole Genome Sequencing</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Ye, Xuemin</creatorcontrib><creatorcontrib>Hu, Dongnan</creatorcontrib><creatorcontrib>Guo, Yangping</creatorcontrib><creatorcontrib>Sun, Rongxi</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Animal Behavior Abstracts</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Nursing & Allied Health Database</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>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>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 Edition)</collection><collection>ProQuest Central UK/Ireland</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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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Ye, Xuemin</au><au>Hu, Dongnan</au><au>Guo, Yangping</au><au>Sun, Rongxi</au><au>Sun, Genlou</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Complete chloroplast genome of Castanopsis sclerophylla (Lindl.) Schott: Genome structure and comparative and phylogenetic analysis</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2019-07-30</date><risdate>2019</risdate><volume>14</volume><issue>7</issue><spage>e0212325</spage><epage>e0212325</epage><pages>e0212325-e0212325</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Castanopsis sclerophylla (Lindl.) Schott is an important species of evergreen broad-leaved tree in subtropical areas and has high ecological and economic value. However, there are few studies on its chloroplast genome. In this study, the complete chloroplast genome sequence of C. sclerophylla was determined using the Illumina HiSeq 2500 platform. The complete chloroplast genome of C. sclerophylla is 160,497 bp long, including a pair of inverted repeat (IR) regions (25,675 bp) separated by a large single-copy (LSC) region of 90,255 bp and a small single-copy (SSC) region of 18,892 bp. The overall GC content of the chloroplast genome is 36.82%. A total of 131 genes were found; of these, 111 genes are unique and annotated, including 79 protein-coding genes, 27 transfer RNA genes (tRNAs), and four ribosomal RNA genes (rRNAs). Twenty-one genes were found to be duplicated in the IR regions. Comparative analysis indicated that IR contraction might be the reason for the smaller chloroplast genome of C. sclerophylla compared to three congeneric species. Sequence analysis indicated that the LSC and SSC regions are more divergent than IR regions within Castanopsis; furthermore, greater divergence was found in noncoding regions than in coding regions. The maximum likelihood phylogenetic analysis showed that four species of the genus Castanopsis form a monophyletic clade and that C. sclerophylla is closely related to Castanopsis hainanensis with strong bootstrap values. These results not only provide a basic understanding of Castanopsis chloroplast genomes, but also illuminate Castanopsis species evolution within the Fagaceae family. Furthermore, these findings will be valuable for future studies of genetic diversity and enhance our understanding of the phylogenetic evolution of Castanopsis.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>31361757</pmid><doi>10.1371/journal.pone.0212325</doi><orcidid>https://orcid.org/0000-0002-7820-2468</orcidid><oa>free_for_read</oa></addata></record> |
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subjects | Amino acids Analysis Biodiversity Biological evolution Biology and Life Sciences Castanopsis Castanopsis sclerophylla Chloroplasts Chloroplasts - genetics Chloroplasts - metabolism Comparative analysis Computer and Information Sciences Contraction Deoxyribonucleic acid Divergence DNA Ecological monitoring Engineering and Technology Evolution Fagaceae - genetics Fagaceae - metabolism Forestry Future predictions Genes Genes, Plant Genetic diversity Genetic engineering Genetic research Genome, Chloroplast Genomes Genomics Herbal medicine Infrared analysis Inverted repeat Laboratories Nucleotide sequence Phylogenetics Phylogeny Plant sciences Proteins Ribonucleic acid Ribosomal RNA RNA rRNA Species Transfer RNA Trees Whole Genome Sequencing |
title | Complete chloroplast genome of Castanopsis sclerophylla (Lindl.) Schott: Genome structure and comparative and phylogenetic analysis |
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