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Chloroplast genome characterization of Uncaria guianensis and Uncaria tomentosa and evolutive dynamics of the Cinchonoideae subfamily
Uncaria species are used in traditional medicine and are considered of high therapeutic value and economic importance. This work describes the assembly and annotation of the chloroplast genomes of U. guianensis and U. tomentosa, as well as a comparative analysis. The genomes were sequenced on MiSeq...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10209157/ https://www.ncbi.nlm.nih.gov/pubmed/37225737 http://dx.doi.org/10.1038/s41598-023-34334-1 |
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author | Castro, Andrezza Arantes Nunes, Rhewter Carvalho, Larissa Resende Targueta, Cíntia Pelegrineti dos Santos Braga-Ferreira, Ramilla de Melo-Ximenes, Amanda Alves Corvalán, Leonardo Carlos Jeronimo Bertoni, Bianca Waleria Pereira, Ana Maria Soares de Campos Telles, Mariana Pires |
author_facet | Castro, Andrezza Arantes Nunes, Rhewter Carvalho, Larissa Resende Targueta, Cíntia Pelegrineti dos Santos Braga-Ferreira, Ramilla de Melo-Ximenes, Amanda Alves Corvalán, Leonardo Carlos Jeronimo Bertoni, Bianca Waleria Pereira, Ana Maria Soares de Campos Telles, Mariana Pires |
author_sort | Castro, Andrezza Arantes |
collection | PubMed |
description | Uncaria species are used in traditional medicine and are considered of high therapeutic value and economic importance. This work describes the assembly and annotation of the chloroplast genomes of U. guianensis and U. tomentosa, as well as a comparative analysis. The genomes were sequenced on MiSeq Illumina, assembled with NovoPlasty, and annotated using CHLOROBOX GeSeq. Addictionaly, comparative analysis were performed with six species from NCBI databases and primers were designed in Primer3 for hypervariable regions based on the consensus sequence of 16 species of the Rubiaceae family and validated on an in-silico PCR in OpenPrimeR. The genome size of U. guianensis and U. tomentosa was 155,505 bp and 156,390 bp, respectively. Both Species have 131 genes and GC content of 37.50%. The regions rpl32-ccsA, ycf1, and ndhF-ccsA showed the three highest values of nucleotide diversity within the species of the Rubiaceae family and within the Uncaria genus, these regions were trnH-psbA, psbM-trnY, and rps16-psbK. Our results indicates that the primer of the region ndhA had an amplification success for all species tested and can be promising for usage in the Rubiaceae family. The phylogenetic analysis recovered a congruent topology to APG IV. The gene content and the chloroplast genome structure of the analyzed species are conserved and most of the genes are under negative selection. We provide the cpDNA of Neotropical Uncaria species, an important genomic resource for evolutionary studies of the group. |
format | Online Article Text |
id | pubmed-10209157 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-102091572023-05-26 Chloroplast genome characterization of Uncaria guianensis and Uncaria tomentosa and evolutive dynamics of the Cinchonoideae subfamily Castro, Andrezza Arantes Nunes, Rhewter Carvalho, Larissa Resende Targueta, Cíntia Pelegrineti dos Santos Braga-Ferreira, Ramilla de Melo-Ximenes, Amanda Alves Corvalán, Leonardo Carlos Jeronimo Bertoni, Bianca Waleria Pereira, Ana Maria Soares de Campos Telles, Mariana Pires Sci Rep Article Uncaria species are used in traditional medicine and are considered of high therapeutic value and economic importance. This work describes the assembly and annotation of the chloroplast genomes of U. guianensis and U. tomentosa, as well as a comparative analysis. The genomes were sequenced on MiSeq Illumina, assembled with NovoPlasty, and annotated using CHLOROBOX GeSeq. Addictionaly, comparative analysis were performed with six species from NCBI databases and primers were designed in Primer3 for hypervariable regions based on the consensus sequence of 16 species of the Rubiaceae family and validated on an in-silico PCR in OpenPrimeR. The genome size of U. guianensis and U. tomentosa was 155,505 bp and 156,390 bp, respectively. Both Species have 131 genes and GC content of 37.50%. The regions rpl32-ccsA, ycf1, and ndhF-ccsA showed the three highest values of nucleotide diversity within the species of the Rubiaceae family and within the Uncaria genus, these regions were trnH-psbA, psbM-trnY, and rps16-psbK. Our results indicates that the primer of the region ndhA had an amplification success for all species tested and can be promising for usage in the Rubiaceae family. The phylogenetic analysis recovered a congruent topology to APG IV. The gene content and the chloroplast genome structure of the analyzed species are conserved and most of the genes are under negative selection. We provide the cpDNA of Neotropical Uncaria species, an important genomic resource for evolutionary studies of the group. Nature Publishing Group UK 2023-05-24 /pmc/articles/PMC10209157/ /pubmed/37225737 http://dx.doi.org/10.1038/s41598-023-34334-1 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Castro, Andrezza Arantes Nunes, Rhewter Carvalho, Larissa Resende Targueta, Cíntia Pelegrineti dos Santos Braga-Ferreira, Ramilla de Melo-Ximenes, Amanda Alves Corvalán, Leonardo Carlos Jeronimo Bertoni, Bianca Waleria Pereira, Ana Maria Soares de Campos Telles, Mariana Pires Chloroplast genome characterization of Uncaria guianensis and Uncaria tomentosa and evolutive dynamics of the Cinchonoideae subfamily |
title | Chloroplast genome characterization of Uncaria guianensis and Uncaria tomentosa and evolutive dynamics of the Cinchonoideae subfamily |
title_full | Chloroplast genome characterization of Uncaria guianensis and Uncaria tomentosa and evolutive dynamics of the Cinchonoideae subfamily |
title_fullStr | Chloroplast genome characterization of Uncaria guianensis and Uncaria tomentosa and evolutive dynamics of the Cinchonoideae subfamily |
title_full_unstemmed | Chloroplast genome characterization of Uncaria guianensis and Uncaria tomentosa and evolutive dynamics of the Cinchonoideae subfamily |
title_short | Chloroplast genome characterization of Uncaria guianensis and Uncaria tomentosa and evolutive dynamics of the Cinchonoideae subfamily |
title_sort | chloroplast genome characterization of uncaria guianensis and uncaria tomentosa and evolutive dynamics of the cinchonoideae subfamily |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10209157/ https://www.ncbi.nlm.nih.gov/pubmed/37225737 http://dx.doi.org/10.1038/s41598-023-34334-1 |
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