The Complete Chloroplast Genome Sequence of a Relict Conifer Glyptostrobus pensilis: Comparative Analysis and Insights into Dynamics of Chloroplast Genome Rearrangement in Cupressophytes and Pinaceae
Glyptostrobus pensilis, belonging to the monotypic genus Glyptostrobus (Family: Cupressaceae), is an ancient conifer that is naturally distributed in low-lying wet areas. Here, we report the complete chloroplast (cp) genome sequence (132,239 bp) of G. pensilis. The G. pensilis cp genome is similar i...
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| description | Glyptostrobus pensilis, belonging to the monotypic genus Glyptostrobus (Family: Cupressaceae), is an ancient conifer that is naturally distributed in low-lying wet areas. Here, we report the complete chloroplast (cp) genome sequence (132,239 bp) of G. pensilis. The G. pensilis cp genome is similar in gene content, organization and genome structure to the sequenced cp genomes from other cupressophytes, especially with respect to the loss of the inverted repeat region A (IRA). Through phylogenetic analysis, we demonstrated that the genus Glyptostrobus is closely related to the genus Cryptomeria, supporting previous findings based on physiological characteristics. Since IRs play an important role in stabilize cp genome and conifer cp genomes lost different IR regions after splitting in two clades (cupressophytes and Pinaceae), we performed cp genome rearrangement analysis and found more extensive cp genome rearrangements among the species of cupressophytes relative to Pinaceae. Additional repeat analysis indicated that cupressophytes cp genomes contained less potential functional repeats, especially in Cupressaceae, compared with Pinaceae. These results suggested that dynamics of cp genome rearrangement in conifers differed since the two clades, Pinaceae and cupressophytes, lost IR copies independently and developed different repeats to complement the residual IRs. In addition, we identified 170 perfect simple sequence repeats that will be useful in future research focusing on the evolution of genetic diversity and conservation of genetic variation for this endangered species in the wild. |
| doi_str_mv | 10.1371/journal.pone.0161809 |
| format | Article |
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Here, we report the complete chloroplast (cp) genome sequence (132,239 bp) of G. pensilis. The G. pensilis cp genome is similar in gene content, organization and genome structure to the sequenced cp genomes from other cupressophytes, especially with respect to the loss of the inverted repeat region A (IRA). Through phylogenetic analysis, we demonstrated that the genus Glyptostrobus is closely related to the genus Cryptomeria, supporting previous findings based on physiological characteristics. Since IRs play an important role in stabilize cp genome and conifer cp genomes lost different IR regions after splitting in two clades (cupressophytes and Pinaceae), we performed cp genome rearrangement analysis and found more extensive cp genome rearrangements among the species of cupressophytes relative to Pinaceae. Additional repeat analysis indicated that cupressophytes cp genomes contained less potential functional repeats, especially in Cupressaceae, compared with Pinaceae. These results suggested that dynamics of cp genome rearrangement in conifers differed since the two clades, Pinaceae and cupressophytes, lost IR copies independently and developed different repeats to complement the residual IRs. In addition, we identified 170 perfect simple sequence repeats that will be useful in future research focusing on the evolution of genetic diversity and conservation of genetic variation for this endangered species in the wild.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0161809</identifier><identifier>PMID: 27560965</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Analysis ; Biodiversity ; Biological evolution ; Biology and Life Sciences ; Biotechnology ; Chloroplasts ; Comparative analysis ; Coniferophyta - classification ; Coniferophyta - genetics ; Conifers ; Conservation ; Cupressaceae ; Cupressaceae - genetics ; Deoxyribonucleic acid ; DNA ; DNA, Plant - chemistry ; DNA, Plant - genetics ; Earth Sciences ; Education ; Endangered & extinct species ; Endangered species ; Evolution ; Evolution, Molecular ; Forestry ; Gene Rearrangement ; Genes, Chloroplast - genetics ; Genetic aspects ; Genetic diversity ; Genetic Variation ; Genome, Chloroplast - genetics ; Genome, Plant - genetics ; Genomes ; Internet ; Inverted repeat ; Inverted Repeat Sequences - genetics ; Laboratories ; Legumes ; Molecular biology ; Nucleotide sequence ; Phylogenetics ; Phylogeny ; Physiological aspects ; Pinaceae ; Pinaceae - classification ; Pinaceae - genetics ; Plastids ; Repetitive Sequences, Nucleic Acid - genetics ; Research and Analysis Methods ; Sequence Analysis, DNA ; Simple sequence repeats ; Species diversity ; Species Specificity ; Splitting ; Wildlife conservation</subject><ispartof>PloS one, 2016-08, Vol.11 (8), p.e0161809-e0161809</ispartof><rights>COPYRIGHT 2016 Public Library of Science</rights><rights>2016 Hao 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>2016 Hao et al 2016 Hao et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c725t-79edad2ef9cc83577af496d2f833c46193ab500cf8db397ff0fae611c9c6e4b33</citedby><cites>FETCH-LOGICAL-c725t-79edad2ef9cc83577af496d2f833c46193ab500cf8db397ff0fae611c9c6e4b33</cites><orcidid>0000-0002-8466-0561</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/PMC4999192/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4999192/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2095,2914,23846,27903,27904,53769,53771,79346,79347</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/27560965$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Heinze, Berthold</contributor><creatorcontrib>Hao, Zhaodong</creatorcontrib><creatorcontrib>Cheng, Tielong</creatorcontrib><creatorcontrib>Zheng, Renhua</creatorcontrib><creatorcontrib>Xu, Haibin</creatorcontrib><creatorcontrib>Zhou, Yanwei</creatorcontrib><creatorcontrib>Li, Meiping</creatorcontrib><creatorcontrib>Lu, Fengjuan</creatorcontrib><creatorcontrib>Dong, Yini</creatorcontrib><creatorcontrib>Liu, Xin</creatorcontrib><creatorcontrib>Chen, Jinhui</creatorcontrib><creatorcontrib>Shi, Jisen</creatorcontrib><title>The Complete Chloroplast Genome Sequence of a Relict Conifer Glyptostrobus pensilis: Comparative Analysis and Insights into Dynamics of Chloroplast Genome Rearrangement in Cupressophytes and Pinaceae</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Glyptostrobus pensilis, belonging to the monotypic genus Glyptostrobus (Family: Cupressaceae), is an ancient conifer that is naturally distributed in low-lying wet areas. Here, we report the complete chloroplast (cp) genome sequence (132,239 bp) of G. pensilis. The G. pensilis cp genome is similar in gene content, organization and genome structure to the sequenced cp genomes from other cupressophytes, especially with respect to the loss of the inverted repeat region A (IRA). Through phylogenetic analysis, we demonstrated that the genus Glyptostrobus is closely related to the genus Cryptomeria, supporting previous findings based on physiological characteristics. Since IRs play an important role in stabilize cp genome and conifer cp genomes lost different IR regions after splitting in two clades (cupressophytes and Pinaceae), we performed cp genome rearrangement analysis and found more extensive cp genome rearrangements among the species of cupressophytes relative to Pinaceae. Additional repeat analysis indicated that cupressophytes cp genomes contained less potential functional repeats, especially in Cupressaceae, compared with Pinaceae. These results suggested that dynamics of cp genome rearrangement in conifers differed since the two clades, Pinaceae and cupressophytes, lost IR copies independently and developed different repeats to complement the residual IRs. In addition, we identified 170 perfect simple sequence repeats that will be useful in future research focusing on the evolution of genetic diversity and conservation of genetic variation for this endangered species in the wild.</description><subject>Analysis</subject><subject>Biodiversity</subject><subject>Biological evolution</subject><subject>Biology and Life Sciences</subject><subject>Biotechnology</subject><subject>Chloroplasts</subject><subject>Comparative analysis</subject><subject>Coniferophyta - classification</subject><subject>Coniferophyta - genetics</subject><subject>Conifers</subject><subject>Conservation</subject><subject>Cupressaceae</subject><subject>Cupressaceae - genetics</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA, Plant - chemistry</subject><subject>DNA, Plant - genetics</subject><subject>Earth Sciences</subject><subject>Education</subject><subject>Endangered & extinct species</subject><subject>Endangered 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Renhua</au><au>Xu, Haibin</au><au>Zhou, Yanwei</au><au>Li, Meiping</au><au>Lu, Fengjuan</au><au>Dong, Yini</au><au>Liu, Xin</au><au>Chen, Jinhui</au><au>Shi, Jisen</au><au>Heinze, Berthold</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>The Complete Chloroplast Genome Sequence of a Relict Conifer Glyptostrobus pensilis: Comparative Analysis and Insights into Dynamics of Chloroplast Genome Rearrangement in Cupressophytes and Pinaceae</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2016-08-25</date><risdate>2016</risdate><volume>11</volume><issue>8</issue><spage>e0161809</spage><epage>e0161809</epage><pages>e0161809-e0161809</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Glyptostrobus pensilis, belonging to the monotypic genus Glyptostrobus (Family: Cupressaceae), is an ancient conifer that is naturally distributed in low-lying wet areas. Here, we report the complete chloroplast (cp) genome sequence (132,239 bp) of G. pensilis. The G. pensilis cp genome is similar in gene content, organization and genome structure to the sequenced cp genomes from other cupressophytes, especially with respect to the loss of the inverted repeat region A (IRA). Through phylogenetic analysis, we demonstrated that the genus Glyptostrobus is closely related to the genus Cryptomeria, supporting previous findings based on physiological characteristics. Since IRs play an important role in stabilize cp genome and conifer cp genomes lost different IR regions after splitting in two clades (cupressophytes and Pinaceae), we performed cp genome rearrangement analysis and found more extensive cp genome rearrangements among the species of cupressophytes relative to Pinaceae. Additional repeat analysis indicated that cupressophytes cp genomes contained less potential functional repeats, especially in Cupressaceae, compared with Pinaceae. These results suggested that dynamics of cp genome rearrangement in conifers differed since the two clades, Pinaceae and cupressophytes, lost IR copies independently and developed different repeats to complement the residual IRs. In addition, we identified 170 perfect simple sequence repeats that will be useful in future research focusing on the evolution of genetic diversity and conservation of genetic variation for this endangered species in the wild.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>27560965</pmid><doi>10.1371/journal.pone.0161809</doi><tpages>e0161809</tpages><orcidid>https://orcid.org/0000-0002-8466-0561</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2016-08, Vol.11 (8), p.e0161809-e0161809 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_1814150333 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Public Library of Science (PLoS); EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Analysis Biodiversity Biological evolution Biology and Life Sciences Biotechnology Chloroplasts Comparative analysis Coniferophyta - classification Coniferophyta - genetics Conifers Conservation Cupressaceae Cupressaceae - genetics Deoxyribonucleic acid DNA DNA, Plant - chemistry DNA, Plant - genetics Earth Sciences Education Endangered & extinct species Endangered species Evolution Evolution, Molecular Forestry Gene Rearrangement Genes, Chloroplast - genetics Genetic aspects Genetic diversity Genetic Variation Genome, Chloroplast - genetics Genome, Plant - genetics Genomes Internet Inverted repeat Inverted Repeat Sequences - genetics Laboratories Legumes Molecular biology Nucleotide sequence Phylogenetics Phylogeny Physiological aspects Pinaceae Pinaceae - classification Pinaceae - genetics Plastids Repetitive Sequences, Nucleic Acid - genetics Research and Analysis Methods Sequence Analysis, DNA Simple sequence repeats Species diversity Species Specificity Splitting Wildlife conservation |
| title | The Complete Chloroplast Genome Sequence of a Relict Conifer Glyptostrobus pensilis: Comparative Analysis and Insights into Dynamics of Chloroplast Genome Rearrangement in Cupressophytes and Pinaceae |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-24T03%3A55%3A05IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=The%20Complete%20Chloroplast%20Genome%20Sequence%20of%20a%20Relict%20Conifer%20Glyptostrobus%20pensilis:%20Comparative%20Analysis%20and%20Insights%20into%20Dynamics%20of%20Chloroplast%20Genome%20Rearrangement%20in%20Cupressophytes%20and%20Pinaceae&rft.jtitle=PloS%20one&rft.au=Hao,%20Zhaodong&rft.date=2016-08-25&rft.volume=11&rft.issue=8&rft.spage=e0161809&rft.epage=e0161809&rft.pages=e0161809-e0161809&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0161809&rft_dat=%3Cgale_plos_%3EA461579484%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1814150333&rft_id=info:pmid/27560965&rft_galeid=A461579484&rft_doaj_id=oai_doaj_org_article_f33e0a74553941ed94a7963eb04f869a&rfr_iscdi=true |