Comparative analysis of codon usage patterns in chloroplast genomes of six Euphorbiaceae species.
Identifieur interne : 000510 ( Main/Exploration ); précédent : 000509; suivant : 000511Comparative analysis of codon usage patterns in chloroplast genomes of six Euphorbiaceae species.
Auteurs : Zhanjun Wang [République populaire de Chine] ; Beibei Xu [République populaire de Chine] ; Bao Li [République populaire de Chine] ; Qingqing Zhou [République populaire de Chine] ; Guiyi Wang [République populaire de Chine] ; Xingzhou Jiang [République populaire de Chine] ; Chenchen Wang [République populaire de Chine] ; Zhongdong Xu [République populaire de Chine]Source :
- PeerJ [ 2167-8359 ] ; 2020.
Abstract
Euphorbiaceae plants are important as suppliers of biodiesel. In the current study, the codon usage patterns and sources of variance in chloroplast genome sequences of six different Euphorbiaceae plant species have been systematically analyzed. Our results revealed that the chloroplast genomes of six Euphorbiaceae plant species were biased towards A/T bases and A/T-ending codons, followed by detection of 17 identical high-frequency codons including GCT, TGT, GAT, GAA, TTT, GGA, CAT, AAA, TTA, AAT, CCT, CAA, AGA, TCT, ACT, TAT and TAA. It was found that mutation pressure was a minor factor affecting the variation of codon usage, however, natural selection played a significant role. Comparative analysis of codon usage frequencies of six Euphorbiaceae plant species with four model organisms reflected that Arabidopsis thaliana, Populus trichocarpa, and Saccharomyces cerevisiae should be considered as suitable exogenous expression receptor systems for chloroplast genes of six Euphorbiaceae plant species. Furthermore, it is optimal to choose Saccharomyces cerevisiae as the exogenous expression receptor. The outcome of the present study might provide important reference information for further understanding the codon usage patterns of chloroplast genomes in other plant species.
DOI: 10.7717/peerj.8251
PubMed: 31934501
PubMed Central: PMC6951282
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populaire de Chine</country><wicri:regionArea>College of Life Sciences, Hefei Normal University, Hefei, Anhui</wicri:regionArea><wicri:noRegion>Anhui</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Cyrus Tang Hematology Center, Soochow University, Soochow, Jiangsu, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Cyrus Tang Hematology Center, Soochow University, Soochow, Jiangsu</wicri:regionArea><wicri:noRegion>Jiangsu</wicri:noRegion></affiliation></author><author><name sortKey="Li, Bao" sort="Li, Bao" uniqKey="Li B" first="Bao" last="Li">Bao Li</name><affiliation wicri:level="1"><nlm:affiliation>College of Life Sciences, Hefei Normal University, Hefei, Anhui, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Life Sciences, Hefei Normal University, Hefei, Anhui</wicri:regionArea><wicri:noRegion>Anhui</wicri:noRegion></affiliation></author><author><name sortKey="Zhou, Qingqing" sort="Zhou, Qingqing" uniqKey="Zhou Q" first="Qingqing" last="Zhou">Qingqing Zhou</name><affiliation wicri:level="1"><nlm:affiliation>College of Life Sciences, Hefei Normal University, Hefei, Anhui, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Life Sciences, Hefei Normal University, Hefei, Anhui</wicri:regionArea><wicri:noRegion>Anhui</wicri:noRegion></affiliation></author><author><name sortKey="Wang, Guiyi" sort="Wang, Guiyi" uniqKey="Wang G" first="Guiyi" last="Wang">Guiyi Wang</name><affiliation wicri:level="1"><nlm:affiliation>College of Life Sciences, Hefei Normal University, Hefei, Anhui, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Life Sciences, Hefei Normal University, Hefei, Anhui</wicri:regionArea><wicri:noRegion>Anhui</wicri:noRegion></affiliation></author><author><name sortKey="Jiang, Xingzhou" sort="Jiang, Xingzhou" uniqKey="Jiang X" first="Xingzhou" last="Jiang">Xingzhou Jiang</name><affiliation wicri:level="1"><nlm:affiliation>College of Life Sciences, Hefei Normal University, Hefei, Anhui, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Life Sciences, Hefei Normal University, Hefei, Anhui</wicri:regionArea><wicri:noRegion>Anhui</wicri:noRegion></affiliation></author><author><name sortKey="Wang, Chenchen" sort="Wang, Chenchen" uniqKey="Wang C" first="Chenchen" last="Wang">Chenchen Wang</name><affiliation wicri:level="1"><nlm:affiliation>College of Life Sciences, Hefei Normal University, Hefei, Anhui, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Life Sciences, Hefei Normal University, Hefei, Anhui</wicri:regionArea><wicri:noRegion>Anhui</wicri:noRegion></affiliation></author><author><name sortKey="Xu, Zhongdong" sort="Xu, Zhongdong" uniqKey="Xu Z" first="Zhongdong" last="Xu">Zhongdong Xu</name><affiliation wicri:level="1"><nlm:affiliation>College of Life Sciences, Hefei Normal University, Hefei, Anhui, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Life Sciences, Hefei Normal University, Hefei, Anhui</wicri:regionArea><wicri:noRegion>Anhui</wicri:noRegion></affiliation></author></analytic><series><title level="j">PeerJ</title><idno type="ISSN">2167-8359</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><i>Euphorbiaceae</i> plants are important as suppliers of biodiesel. In the current study, the codon usage patterns and sources of variance in chloroplast genome sequences of six different <i>Euphorbiaceae</i> plant species have been systematically analyzed. Our results revealed that the chloroplast genomes of six <i>Euphorbiaceae</i> plant species were biased towards A/T bases and A/T-ending codons, followed by detection of 17 identical high-frequency codons including GCT, TGT, GAT, GAA, TTT, GGA, CAT, AAA, TTA, AAT, CCT, CAA, AGA, TCT, ACT, TAT and TAA. It was found that mutation pressure was a minor factor affecting the variation of codon usage, however, natural selection played a significant role. Comparative analysis of codon usage frequencies of six <i>Euphorbiaceae</i> plant species with four model organisms reflected that <i>Arabidopsis thaliana</i>, <i>Populus trichocarpa</i>, and <i>Saccharomyces cerevisiae</i> should be considered as suitable exogenous expression receptor systems for chloroplast genes of six <i>Euphorbiaceae</i> plant species. Furthermore, it is optimal to choose <i>Saccharomyces cerevisiae</i> as the exogenous expression receptor. The outcome of the present study might provide important reference information for further understanding the codon usage patterns of chloroplast genomes in other plant species.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">31934501</PMID><DateRevised><Year>2020</Year><Month>09</Month><Day>30</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">2167-8359</ISSN><JournalIssue CitedMedium="Print"><Volume>8</Volume><PubDate><Year>2020</Year></PubDate></JournalIssue><Title>PeerJ</Title><ISOAbbreviation>PeerJ</ISOAbbreviation></Journal><ArticleTitle>Comparative analysis of codon usage patterns in chloroplast genomes of six <i>Euphorbiaceae</i> species.</ArticleTitle><Pagination><MedlinePgn>e8251</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.7717/peerj.8251</ELocationID><Abstract><AbstractText><i>Euphorbiaceae</i> plants are important as suppliers of biodiesel. In the current study, the codon usage patterns and sources of variance in chloroplast genome sequences of six different <i>Euphorbiaceae</i> plant species have been systematically analyzed. Our results revealed that the chloroplast genomes of six <i>Euphorbiaceae</i> plant species were biased towards A/T bases and A/T-ending codons, followed by detection of 17 identical high-frequency codons including GCT, TGT, GAT, GAA, TTT, GGA, CAT, AAA, TTA, AAT, CCT, CAA, AGA, TCT, ACT, TAT and TAA. It was found that mutation pressure was a minor factor affecting the variation of codon usage, however, natural selection played a significant role. Comparative analysis of codon usage frequencies of six <i>Euphorbiaceae</i> plant species with four model organisms reflected that <i>Arabidopsis thaliana</i>, <i>Populus trichocarpa</i>, and <i>Saccharomyces cerevisiae</i> should be considered as suitable exogenous expression receptor systems for chloroplast genes of six <i>Euphorbiaceae</i> plant species. Furthermore, it is optimal to choose <i>Saccharomyces cerevisiae</i> as the exogenous expression receptor. The outcome of the present study might provide important reference information for further understanding the codon usage patterns of chloroplast genomes in other plant species.</AbstractText><CopyrightInformation>©2020 Wang et al.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y" EqualContrib="Y"><LastName>Wang</LastName><ForeName>Zhanjun</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>College of Life Sciences, Hefei Normal University, Hefei, Anhui, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y" EqualContrib="Y"><LastName>Xu</LastName><ForeName>Beibei</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>College of Life Sciences, Hefei Normal University, Hefei, Anhui, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Cyrus Tang Hematology Center, Soochow University, Soochow, Jiangsu, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Bao</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>College of Life Sciences, Hefei Normal University, Hefei, Anhui, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhou</LastName><ForeName>Qingqing</ForeName><Initials>Q</Initials><AffiliationInfo><Affiliation>College of Life Sciences, Hefei Normal University, Hefei, Anhui, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Guiyi</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>College of Life Sciences, Hefei Normal University, Hefei, Anhui, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jiang</LastName><ForeName>Xingzhou</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>College of Life Sciences, Hefei Normal University, Hefei, Anhui, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Chenchen</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>College of Life Sciences, Hefei Normal University, Hefei, Anhui, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Xu</LastName><ForeName>Zhongdong</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>College of Life Sciences, Hefei Normal University, Hefei, Anhui, China.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>01</Month><Day>06</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>PeerJ</MedlineTA><NlmUniqueID>101603425</NlmUniqueID><ISSNLinking>2167-8359</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Chloroplast genome</Keyword><Keyword MajorTopicYN="N">Codon usage bias</Keyword><Keyword MajorTopicYN="N">Euphorbiaceae plants</Keyword></KeywordList><CoiStatement>The authors declare there are no competing interests.</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2019</Year><Month>06</Month><Day>26</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2019</Year><Month>11</Month><Day>20</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>1</Month><Day>15</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>1</Month><Day>15</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>1</Month><Day>15</Day><Hour>6</Hour><Minute>1</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">31934501</ArticleId><ArticleId IdType="doi">10.7717/peerj.8251</ArticleId><ArticleId 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sort="Xu, Beibei" uniqKey="Xu B" first="Beibei" last="Xu">Beibei Xu</name><name sortKey="Xu, Beibei" sort="Xu, Beibei" uniqKey="Xu B" first="Beibei" last="Xu">Beibei Xu</name><name sortKey="Xu, Zhongdong" sort="Xu, Zhongdong" uniqKey="Xu Z" first="Zhongdong" last="Xu">Zhongdong Xu</name><name sortKey="Zhou, Qingqing" sort="Zhou, Qingqing" uniqKey="Zhou Q" first="Qingqing" last="Zhou">Qingqing Zhou</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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