Complete Chloroplast Genomes of Pterodon emarginatus Vogel and Pterodon pubescens Benth: Comparative and Phylogenetic Analyses
Background: The species Pterodon emarginatus and P. pubescens , popularly known as white sucupira or faveira, are native to the Cerrado biome and have the potential for medicinal use and reforestation. They are sister species with evolutionary proximity. Objective: Considering that the chloroplast g...
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| Veröffentlicht in: | Current genomics 2023-12, Vol.24 (4), p.236-249 |
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| creator | Brito, Juliana Borges Pereira Antunes, Adriana Maria Ferreira, Ramilla Dos Santos Braga de Campos Telles, Mariana Pires Targueta, Cintia Pelegrineti Soares, Thannya Nascimento |
| description | Background: The species Pterodon emarginatus and P. pubescens , popularly known as white sucupira or faveira, are native to the Cerrado biome and have the potential for medicinal use and reforestation. They are sister species with evolutionary proximity.
Objective: Considering that the chloroplast genome exhibits a conserved structure and genes, the analysis of its sequences can contribute to the understanding of evolutionary, phylogenetic, and diversity issues.
Methods: The chloroplast genomes of P. emarginatus and P. pubescens were sequenced on the Illumina MiSeq platform. The genomes were assembled based on the de novo strategy. We performed the annotation of the genes and the repetitive regions of the genomes. The nucleotide diversity and phylogenetic relationships were analyzed using the gene sequences of these species and others of the Leguminosae family, whose genomes are available in databases.
Results: The complete chloroplast genome of P. emarginatus is 159,877 bp, and that of P. pubescens is 159,873 bp. The genomes of both species have circular and quadripartite structures. A total of 127 genes were predicted in both species, including 110 single-copy genes and 17 duplicated genes in the inverted regions. 141 microsatellite regions were identified in P. emarginatus and 140 in P. pubescens . The nucleotide diversity estimates of the gene regions in twenty-one species of the Leguminosae family were 0.062 in LSC, 0.086 in SSC, and 0.036 in IR. The phylogenetic analysis demonstrated the proximity between the genera Pterodon and Dipteryx , both from the clade Dipterygeae. Ten pairs of primers with potential for the development of molecular markers were designed.
Conclusion: The genetic information obtained on the chloroplast genomes of P. emarginatus and P. pubescens presented here reinforces the similarity and evolutionary proximity between these species, with a similarity percentage of 99.8%. |
| doi_str_mv | 10.2174/0113892029244147231016050434 |
| format | Article |
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Objective: Considering that the chloroplast genome exhibits a conserved structure and genes, the analysis of its sequences can contribute to the understanding of evolutionary, phylogenetic, and diversity issues.
Methods: The chloroplast genomes of P. emarginatus and P. pubescens were sequenced on the Illumina MiSeq platform. The genomes were assembled based on the de novo strategy. We performed the annotation of the genes and the repetitive regions of the genomes. The nucleotide diversity and phylogenetic relationships were analyzed using the gene sequences of these species and others of the Leguminosae family, whose genomes are available in databases.
Results: The complete chloroplast genome of P. emarginatus is 159,877 bp, and that of P. pubescens is 159,873 bp. The genomes of both species have circular and quadripartite structures. A total of 127 genes were predicted in both species, including 110 single-copy genes and 17 duplicated genes in the inverted regions. 141 microsatellite regions were identified in P. emarginatus and 140 in P. pubescens . The nucleotide diversity estimates of the gene regions in twenty-one species of the Leguminosae family were 0.062 in LSC, 0.086 in SSC, and 0.036 in IR. The phylogenetic analysis demonstrated the proximity between the genera Pterodon and Dipteryx , both from the clade Dipterygeae. Ten pairs of primers with potential for the development of molecular markers were designed.
Conclusion: The genetic information obtained on the chloroplast genomes of P. emarginatus and P. pubescens presented here reinforces the similarity and evolutionary proximity between these species, with a similarity percentage of 99.8%.</description><identifier>ISSN: 1389-2029</identifier><identifier>EISSN: 1875-5488</identifier><identifier>DOI: 10.2174/0113892029244147231016050434</identifier><identifier>PMID: 38169762</identifier><language>eng</language><publisher>United Arab Emirates: Bentham Science Publishers</publisher><subject>Annotations ; Chloroplasts ; Evolution ; Gene duplication ; Gene sequencing ; Genes ; Genomes ; Leguminosae ; Life Sciences, Genetics & Genomics, Genetics & Heredity ; Nucleotides ; Phylogenetics ; Phylogeny ; Proximity ; Pterodon emarginatus ; Reforestation ; Sibling species ; Similarity</subject><ispartof>Current genomics, 2023-12, Vol.24 (4), p.236-249</ispartof><rights>2023 Bentham Science Publishers.</rights><rights>Copyright Benham Science Publishers 2023</rights><rights>2023 Bentham Science Publishers 2023 Bentham Science Publishers</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-b527t-6aeffec1329a2ec0c1e87ce815759e9c1ae76bcaa2202b836a515f9b378456d73</cites><orcidid>0000-0002-4654-4316</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/PMC10758126/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC10758126/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/38169762$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Brito, Juliana Borges Pereira</creatorcontrib><creatorcontrib>Antunes, Adriana Maria</creatorcontrib><creatorcontrib>Ferreira, Ramilla Dos Santos Braga</creatorcontrib><creatorcontrib>de Campos Telles, Mariana Pires</creatorcontrib><creatorcontrib>Targueta, Cintia Pelegrineti</creatorcontrib><creatorcontrib>Soares, Thannya Nascimento</creatorcontrib><title>Complete Chloroplast Genomes of Pterodon emarginatus Vogel and Pterodon pubescens Benth: Comparative and Phylogenetic Analyses</title><title>Current genomics</title><addtitle>CG</addtitle><description>Background: The species Pterodon emarginatus and P. pubescens , popularly known as white sucupira or faveira, are native to the Cerrado biome and have the potential for medicinal use and reforestation. They are sister species with evolutionary proximity.
Objective: Considering that the chloroplast genome exhibits a conserved structure and genes, the analysis of its sequences can contribute to the understanding of evolutionary, phylogenetic, and diversity issues.
Methods: The chloroplast genomes of P. emarginatus and P. pubescens were sequenced on the Illumina MiSeq platform. The genomes were assembled based on the de novo strategy. We performed the annotation of the genes and the repetitive regions of the genomes. The nucleotide diversity and phylogenetic relationships were analyzed using the gene sequences of these species and others of the Leguminosae family, whose genomes are available in databases.
Results: The complete chloroplast genome of P. emarginatus is 159,877 bp, and that of P. pubescens is 159,873 bp. The genomes of both species have circular and quadripartite structures. A total of 127 genes were predicted in both species, including 110 single-copy genes and 17 duplicated genes in the inverted regions. 141 microsatellite regions were identified in P. emarginatus and 140 in P. pubescens . The nucleotide diversity estimates of the gene regions in twenty-one species of the Leguminosae family were 0.062 in LSC, 0.086 in SSC, and 0.036 in IR. The phylogenetic analysis demonstrated the proximity between the genera Pterodon and Dipteryx , both from the clade Dipterygeae. Ten pairs of primers with potential for the development of molecular markers were designed.
Conclusion: The genetic information obtained on the chloroplast genomes of P. emarginatus and P. pubescens presented here reinforces the similarity and evolutionary proximity between these species, with a similarity percentage of 99.8%.</description><subject>Annotations</subject><subject>Chloroplasts</subject><subject>Evolution</subject><subject>Gene duplication</subject><subject>Gene sequencing</subject><subject>Genes</subject><subject>Genomes</subject><subject>Leguminosae</subject><subject>Life Sciences, Genetics & Genomics, Genetics & Heredity</subject><subject>Nucleotides</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>Proximity</subject><subject>Pterodon emarginatus</subject><subject>Reforestation</subject><subject>Sibling species</subject><subject>Similarity</subject><issn>1389-2029</issn><issn>1875-5488</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2023</creationdate><recordtype>article</recordtype><recordid>eNp9kk1v1DAQhiMEoqXwF1AkOHBZsJ34IwgJlRUUpEpwAK4jxzvZpDh2aju72gsnfjiOtpSPAyePPM87mlfvFMVTSp4zKusXhNJKNYywhtU1rSWrKKGCcFJX9Z3ilCrJV7xW6m6uM7hayJPiQYxXhDCiJLlfnFSKikYKdlp8X_txspiwXPfWBz9ZHVN5gc6PGEvflZ8SBr_xrsRRh-3gdJpj-dVv0ZbabX63p7nFaNDF8g261L8sl8E66DTs8Ej2B5tlDtNgynOn7SFifFjc67SN-OjmPSu-vHv7ef1-dfnx4sP6_HLVcibTSmjsOjS0Yo1maIihqKRBRbnkDTaGapSiNVqz7LZVldCc8q5pK6lqLjayOiteH-fmNUfc5D1T0BamMGRXB_B6gL87buhh63dAieSKMpEnPLuZEPz1jDHBOGS_1mqHfo7AmhxDw3izoE_-Qa_8HLLjhSKVEFxKmqlXR8oEH2PA7nYbSmBJGv6XdJY__tPRrfhXtBn4cQTaJQ89RjOgM3gL9ilNsN_vAeeA33REiyaB8SP4Cd0cbK5dylqY-glycAFBhxyeRRhidLBcGiyXBjtv5xGB1UtjRqghTnqbPypR_QTWEto6</recordid><startdate>20231212</startdate><enddate>20231212</enddate><creator>Brito, Juliana Borges Pereira</creator><creator>Antunes, Adriana Maria</creator><creator>Ferreira, Ramilla Dos Santos Braga</creator><creator>de Campos Telles, Mariana Pires</creator><creator>Targueta, Cintia Pelegrineti</creator><creator>Soares, Thannya Nascimento</creator><general>Bentham Science Publishers</general><general>Benham Science Publishers</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QL</scope><scope>7QO</scope><scope>7QP</scope><scope>7SS</scope><scope>7T7</scope><scope>7TK</scope><scope>7TM</scope><scope>7U9</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0002-4654-4316</orcidid></search><sort><creationdate>20231212</creationdate><title>Complete Chloroplast Genomes of Pterodon emarginatus Vogel and Pterodon pubescens Benth: Comparative and Phylogenetic Analyses</title><author>Brito, Juliana Borges Pereira ; Antunes, Adriana Maria ; Ferreira, Ramilla Dos Santos Braga ; de Campos Telles, Mariana Pires ; Targueta, Cintia Pelegrineti ; Soares, Thannya Nascimento</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-b527t-6aeffec1329a2ec0c1e87ce815759e9c1ae76bcaa2202b836a515f9b378456d73</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2023</creationdate><topic>Annotations</topic><topic>Chloroplasts</topic><topic>Evolution</topic><topic>Gene duplication</topic><topic>Gene sequencing</topic><topic>Genes</topic><topic>Genomes</topic><topic>Leguminosae</topic><topic>Life Sciences, Genetics & Genomics, Genetics & Heredity</topic><topic>Nucleotides</topic><topic>Phylogenetics</topic><topic>Phylogeny</topic><topic>Proximity</topic><topic>Pterodon emarginatus</topic><topic>Reforestation</topic><topic>Sibling species</topic><topic>Similarity</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Brito, Juliana Borges Pereira</creatorcontrib><creatorcontrib>Antunes, Adriana Maria</creatorcontrib><creatorcontrib>Ferreira, Ramilla Dos Santos Braga</creatorcontrib><creatorcontrib>de Campos Telles, Mariana Pires</creatorcontrib><creatorcontrib>Targueta, Cintia Pelegrineti</creatorcontrib><creatorcontrib>Soares, Thannya Nascimento</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Current genomics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Brito, Juliana Borges Pereira</au><au>Antunes, Adriana Maria</au><au>Ferreira, Ramilla Dos Santos Braga</au><au>de Campos Telles, Mariana Pires</au><au>Targueta, Cintia Pelegrineti</au><au>Soares, Thannya Nascimento</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Complete Chloroplast Genomes of Pterodon emarginatus Vogel and Pterodon pubescens Benth: Comparative and Phylogenetic Analyses</atitle><jtitle>Current genomics</jtitle><addtitle>CG</addtitle><date>2023-12-12</date><risdate>2023</risdate><volume>24</volume><issue>4</issue><spage>236</spage><epage>249</epage><pages>236-249</pages><issn>1389-2029</issn><eissn>1875-5488</eissn><abstract>Background: The species Pterodon emarginatus and P. pubescens , popularly known as white sucupira or faveira, are native to the Cerrado biome and have the potential for medicinal use and reforestation. They are sister species with evolutionary proximity.
Objective: Considering that the chloroplast genome exhibits a conserved structure and genes, the analysis of its sequences can contribute to the understanding of evolutionary, phylogenetic, and diversity issues.
Methods: The chloroplast genomes of P. emarginatus and P. pubescens were sequenced on the Illumina MiSeq platform. The genomes were assembled based on the de novo strategy. We performed the annotation of the genes and the repetitive regions of the genomes. The nucleotide diversity and phylogenetic relationships were analyzed using the gene sequences of these species and others of the Leguminosae family, whose genomes are available in databases.
Results: The complete chloroplast genome of P. emarginatus is 159,877 bp, and that of P. pubescens is 159,873 bp. The genomes of both species have circular and quadripartite structures. A total of 127 genes were predicted in both species, including 110 single-copy genes and 17 duplicated genes in the inverted regions. 141 microsatellite regions were identified in P. emarginatus and 140 in P. pubescens . The nucleotide diversity estimates of the gene regions in twenty-one species of the Leguminosae family were 0.062 in LSC, 0.086 in SSC, and 0.036 in IR. The phylogenetic analysis demonstrated the proximity between the genera Pterodon and Dipteryx , both from the clade Dipterygeae. Ten pairs of primers with potential for the development of molecular markers were designed.
Conclusion: The genetic information obtained on the chloroplast genomes of P. emarginatus and P. pubescens presented here reinforces the similarity and evolutionary proximity between these species, with a similarity percentage of 99.8%.</abstract><cop>United Arab Emirates</cop><pub>Bentham Science Publishers</pub><pmid>38169762</pmid><doi>10.2174/0113892029244147231016050434</doi><tpages>14</tpages><orcidid>https://orcid.org/0000-0002-4654-4316</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Annotations Chloroplasts Evolution Gene duplication Gene sequencing Genes Genomes Leguminosae Life Sciences, Genetics & Genomics, Genetics & Heredity Nucleotides Phylogenetics Phylogeny Proximity Pterodon emarginatus Reforestation Sibling species Similarity |
| title | Complete Chloroplast Genomes of Pterodon emarginatus Vogel and Pterodon pubescens Benth: Comparative and Phylogenetic Analyses |
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