Characterization of the Complete Chloroplast Genome of Acer truncatum Bunge (Sapindales: Aceraceae): A New Woody Oil Tree Species Producing Nervonic Acid
Acer truncatum, which is a new woody oil tree species, is an important ornamental and medicinal plant in China. To assess the genetic diversity and relationships of A. truncatum, we analyzed its complete chloroplast (cp) genome sequence. The A. truncatum cp genome comprises 156,492 bp, with the larg...
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| creator | Li, Qianzhong Yan, Kunyuan Li, Shushun Li, Shuxian Bi, Changwei Zhu, Lu Wang, Yanan Ma, Qiuyue Wen, Jing |
| description | Acer truncatum, which is a new woody oil tree species, is an important ornamental and medicinal plant in China. To assess the genetic diversity and relationships of A. truncatum, we analyzed its complete chloroplast (cp) genome sequence. The A. truncatum cp genome comprises 156,492 bp, with the large single-copy, small single-copy, and inverted repeat (IR) regions consisting of 86,010, 18,050, and 26,216 bp, respectively. The A. truncatum cp genome contains 112 unique functional genes (i.e., 4 rRNA, 30 tRNA, and 78 protein-coding genes) as well as 78 simple sequence repeats, 9 forward repeats, 1 reverse repeat, 5 palindromic repeats, and 7 tandem repeats. We analyzed the expansion/contraction of the IR regions in the cp genomes of six Acer species. A comparison of these cp genomes indicated the noncoding regions were more diverse than the coding regions. A phylogenetic analysis revealed that A. truncatum is closely related to A. miaotaiense. Moreover, a novel ycf4-cemA indel marker was developed for distinguishing several Acer species (i.e., A. buergerianum, A. truncatum, A. henryi, A. negundo, A. ginnala, and A. tonkinense). The results of the current study provide valuable information for future evolutionary studies and the molecular barcoding of Acer species. |
| doi_str_mv | 10.1155/2019/7417239 |
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To assess the genetic diversity and relationships of A. truncatum, we analyzed its complete chloroplast (cp) genome sequence. The A. truncatum cp genome comprises 156,492 bp, with the large single-copy, small single-copy, and inverted repeat (IR) regions consisting of 86,010, 18,050, and 26,216 bp, respectively. The A. truncatum cp genome contains 112 unique functional genes (i.e., 4 rRNA, 30 tRNA, and 78 protein-coding genes) as well as 78 simple sequence repeats, 9 forward repeats, 1 reverse repeat, 5 palindromic repeats, and 7 tandem repeats. We analyzed the expansion/contraction of the IR regions in the cp genomes of six Acer species. A comparison of these cp genomes indicated the noncoding regions were more diverse than the coding regions. A phylogenetic analysis revealed that A. truncatum is closely related to A. miaotaiense. Moreover, a novel ycf4-cemA indel marker was developed for distinguishing several Acer species (i.e., A. buergerianum, A. truncatum, A. henryi, A. negundo, A. ginnala, and A. tonkinense). The results of the current study provide valuable information for future evolutionary studies and the molecular barcoding of Acer species.</description><identifier>ISSN: 2314-6133</identifier><identifier>EISSN: 2314-6141</identifier><identifier>DOI: 10.1155/2019/7417239</identifier><identifier>PMID: 31886246</identifier><language>eng</language><publisher>Cairo, Egypt: Hindawi Publishing Corporation</publisher><subject>Acer - genetics ; Acer truncatum ; Biological evolution ; Chloroplasts ; Comparative analysis ; Contraction ; Deoxyribonucleic acid ; DNA ; Evolution ; Fatty Acids, Monounsaturated - metabolism ; Flowers & plants ; Genes ; Genes, Plant ; Genetic aspects ; Genetic diversity ; Genetic Markers ; Genetic Variation ; Genome, Chloroplast ; Genomes ; Genomics ; Herbal medicine ; Inverted repeat ; Likelihood Functions ; Medicinal plants ; Medicine, Botanic ; Medicine, Herbal ; Microsatellite Repeats - genetics ; Nucleotide sequence ; Ornamental plants ; Phylogenetics ; Phylogeny ; Plant Oils - metabolism ; Plant sciences ; rRNA ; Seeds ; Simple sequence repeats ; Species ; Transfer RNA ; Trees ; Trees - genetics ; tRNA ; Wood - genetics</subject><ispartof>BioMed research international, 2019, Vol.2019 (2019), p.1-13</ispartof><rights>Copyright © 2019 Qiuyue Ma et al.</rights><rights>COPYRIGHT 2019 John Wiley & Sons, Inc.</rights><rights>Copyright © 2019 Qiuyue Ma et al. This is an open access article distributed under the Creative Commons Attribution License (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. http://creativecommons.org/licenses/by/4.0</rights><rights>Copyright © 2019 Qiuyue Ma et al. 2019</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c565t-32c4144c688555bc5535b8f18a066ad30f1da1553f08ab506982742f7523feff3</citedby><cites>FETCH-LOGICAL-c565t-32c4144c688555bc5535b8f18a066ad30f1da1553f08ab506982742f7523feff3</cites><orcidid>0000-0002-6951-2464 ; 0000-0001-9302-7015</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/PMC6925723/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6925723/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,881,4010,27900,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/31886246$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Ono, Shoichiro</contributor><creatorcontrib>Li, Qianzhong</creatorcontrib><creatorcontrib>Yan, Kunyuan</creatorcontrib><creatorcontrib>Li, Shushun</creatorcontrib><creatorcontrib>Li, Shuxian</creatorcontrib><creatorcontrib>Bi, Changwei</creatorcontrib><creatorcontrib>Zhu, Lu</creatorcontrib><creatorcontrib>Wang, Yanan</creatorcontrib><creatorcontrib>Ma, Qiuyue</creatorcontrib><creatorcontrib>Wen, Jing</creatorcontrib><title>Characterization of the Complete Chloroplast Genome of Acer truncatum Bunge (Sapindales: Aceraceae): A New Woody Oil Tree Species Producing Nervonic Acid</title><title>BioMed research international</title><addtitle>Biomed Res Int</addtitle><description>Acer truncatum, which is a new woody oil tree species, is an important ornamental and medicinal plant in China. To assess the genetic diversity and relationships of A. truncatum, we analyzed its complete chloroplast (cp) genome sequence. The A. truncatum cp genome comprises 156,492 bp, with the large single-copy, small single-copy, and inverted repeat (IR) regions consisting of 86,010, 18,050, and 26,216 bp, respectively. The A. truncatum cp genome contains 112 unique functional genes (i.e., 4 rRNA, 30 tRNA, and 78 protein-coding genes) as well as 78 simple sequence repeats, 9 forward repeats, 1 reverse repeat, 5 palindromic repeats, and 7 tandem repeats. We analyzed the expansion/contraction of the IR regions in the cp genomes of six Acer species. A comparison of these cp genomes indicated the noncoding regions were more diverse than the coding regions. A phylogenetic analysis revealed that A. truncatum is closely related to A. miaotaiense. Moreover, a novel ycf4-cemA indel marker was developed for distinguishing several Acer species (i.e., A. buergerianum, A. truncatum, A. henryi, A. negundo, A. ginnala, and A. tonkinense). The results of the current study provide valuable information for future evolutionary studies and the molecular barcoding of Acer species.</description><subject>Acer - genetics</subject><subject>Acer truncatum</subject><subject>Biological evolution</subject><subject>Chloroplasts</subject><subject>Comparative analysis</subject><subject>Contraction</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>Evolution</subject><subject>Fatty Acids, Monounsaturated - metabolism</subject><subject>Flowers & plants</subject><subject>Genes</subject><subject>Genes, Plant</subject><subject>Genetic aspects</subject><subject>Genetic diversity</subject><subject>Genetic Markers</subject><subject>Genetic Variation</subject><subject>Genome, Chloroplast</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Herbal medicine</subject><subject>Inverted repeat</subject><subject>Likelihood Functions</subject><subject>Medicinal plants</subject><subject>Medicine, Botanic</subject><subject>Medicine, Herbal</subject><subject>Microsatellite Repeats - genetics</subject><subject>Nucleotide sequence</subject><subject>Ornamental plants</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>Plant Oils - metabolism</subject><subject>Plant sciences</subject><subject>rRNA</subject><subject>Seeds</subject><subject>Simple sequence repeats</subject><subject>Species</subject><subject>Transfer RNA</subject><subject>Trees</subject><subject>Trees - genetics</subject><subject>tRNA</subject><subject>Wood - genetics</subject><issn>2314-6133</issn><issn>2314-6141</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2019</creationdate><recordtype>article</recordtype><sourceid>RHX</sourceid><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><recordid>eNqN0sFu1DAQBuAIgWhVeuOMLHEpgqWxHTtOD0jLCgpSRZFaxNHyOuNdV4kd7KRVeRPellm6bIETuWSkfPkTz0xRPKXla0qFOGYlbY7ritaMNw-KfcZpNZO0og93Ned7xWHOVyVeisqykY-LPU6VkqyS-8WPxdokY0dI_rsZfQwkOjKugSxiP3QwYrHuYopDZ_JITiHEHjZkbiGRMU3BmnHqydsprIAcXZjBh9Z0kE9-CWPBwAusySe4IV9jbG_Jue_IZQIgFwNYD5l8TrGdrA8rROk6Bm_xXd8-KR4502U43N4Pii_v310uPszOzk8_LuZnMyukGGec2YpWlZVKCSGWVggulspRZUopTctLR1uDreKuVGYpStkoVlfM1YJxB87xg-LNXe4wLXtoLYQxmU4Pyfcm3epovP77SfBrvYrXWjZMYN8x4GgbkOK3CfKoe58tdJ0JEKeskdAKKW-QPv-HXsUpBTweKsZwJI1S92qFndQ-uIjftZtQPcfhSsWZrFG9ulM2xZwTuN0v01JvlkNvlkNvlwP5sz-PucO_VwHByzuw3ozwxv9nHKABZ-41ZTWra_4TQ3XKIg</recordid><startdate>2019</startdate><enddate>2019</enddate><creator>Li, Qianzhong</creator><creator>Yan, Kunyuan</creator><creator>Li, Shushun</creator><creator>Li, Shuxian</creator><creator>Bi, Changwei</creator><creator>Zhu, Lu</creator><creator>Wang, Yanan</creator><creator>Ma, Qiuyue</creator><creator>Wen, Jing</creator><general>Hindawi Publishing Corporation</general><general>Hindawi</general><general>John Wiley & Sons, Inc</general><general>Hindawi Limited</general><scope>ADJCN</scope><scope>AHFXO</scope><scope>RHU</scope><scope>RHW</scope><scope>RHX</scope><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>7QL</scope><scope>7QO</scope><scope>7T7</scope><scope>7TK</scope><scope>7U7</scope><scope>7U9</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>CWDGH</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>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0002-6951-2464</orcidid><orcidid>https://orcid.org/0000-0001-9302-7015</orcidid></search><sort><creationdate>2019</creationdate><title>Characterization of the Complete Chloroplast Genome of Acer truncatum Bunge (Sapindales: Aceraceae): A New Woody Oil Tree Species Producing Nervonic Acid</title><author>Li, Qianzhong ; Yan, Kunyuan ; Li, Shushun ; Li, Shuxian ; Bi, Changwei ; Zhu, Lu ; Wang, Yanan ; Ma, Qiuyue ; Wen, Jing</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c565t-32c4144c688555bc5535b8f18a066ad30f1da1553f08ab506982742f7523feff3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2019</creationdate><topic>Acer - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>BioMed research international</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Li, Qianzhong</au><au>Yan, Kunyuan</au><au>Li, Shushun</au><au>Li, Shuxian</au><au>Bi, Changwei</au><au>Zhu, Lu</au><au>Wang, Yanan</au><au>Ma, Qiuyue</au><au>Wen, Jing</au><au>Ono, Shoichiro</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Characterization of the Complete Chloroplast Genome of Acer truncatum Bunge (Sapindales: Aceraceae): A New Woody Oil Tree Species Producing Nervonic Acid</atitle><jtitle>BioMed research international</jtitle><addtitle>Biomed Res Int</addtitle><date>2019</date><risdate>2019</risdate><volume>2019</volume><issue>2019</issue><spage>1</spage><epage>13</epage><pages>1-13</pages><issn>2314-6133</issn><eissn>2314-6141</eissn><abstract>Acer truncatum, which is a new woody oil tree species, is an important ornamental and medicinal plant in China. To assess the genetic diversity and relationships of A. truncatum, we analyzed its complete chloroplast (cp) genome sequence. The A. truncatum cp genome comprises 156,492 bp, with the large single-copy, small single-copy, and inverted repeat (IR) regions consisting of 86,010, 18,050, and 26,216 bp, respectively. The A. truncatum cp genome contains 112 unique functional genes (i.e., 4 rRNA, 30 tRNA, and 78 protein-coding genes) as well as 78 simple sequence repeats, 9 forward repeats, 1 reverse repeat, 5 palindromic repeats, and 7 tandem repeats. We analyzed the expansion/contraction of the IR regions in the cp genomes of six Acer species. A comparison of these cp genomes indicated the noncoding regions were more diverse than the coding regions. A phylogenetic analysis revealed that A. truncatum is closely related to A. miaotaiense. Moreover, a novel ycf4-cemA indel marker was developed for distinguishing several Acer species (i.e., A. buergerianum, A. truncatum, A. henryi, A. negundo, A. ginnala, and A. tonkinense). The results of the current study provide valuable information for future evolutionary studies and the molecular barcoding of Acer species.</abstract><cop>Cairo, Egypt</cop><pub>Hindawi Publishing Corporation</pub><pmid>31886246</pmid><doi>10.1155/2019/7417239</doi><tpages>13</tpages><orcidid>https://orcid.org/0000-0002-6951-2464</orcidid><orcidid>https://orcid.org/0000-0001-9302-7015</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Acer - genetics Acer truncatum Biological evolution Chloroplasts Comparative analysis Contraction Deoxyribonucleic acid DNA Evolution Fatty Acids, Monounsaturated - metabolism Flowers & plants Genes Genes, Plant Genetic aspects Genetic diversity Genetic Markers Genetic Variation Genome, Chloroplast Genomes Genomics Herbal medicine Inverted repeat Likelihood Functions Medicinal plants Medicine, Botanic Medicine, Herbal Microsatellite Repeats - genetics Nucleotide sequence Ornamental plants Phylogenetics Phylogeny Plant Oils - metabolism Plant sciences rRNA Seeds Simple sequence repeats Species Transfer RNA Trees Trees - genetics tRNA Wood - genetics |
| title | Characterization of the Complete Chloroplast Genome of Acer truncatum Bunge (Sapindales: Aceraceae): A New Woody Oil Tree Species Producing Nervonic Acid |
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