Complete chloroplast genomes of six neotropical palm species, structural comparison, and evolutionary dynamic patterns
Abstract The Arecaceae family has a worldwide distribution, especially in tropical and subtropical regions. We sequenced the chloroplast genomes of Acrocomia intumescens and A. totai, widely used in the food and energy industries; Bactris gasipaes, important for palm heart; Copernicia alba and C. pr...
| Main Authors: | , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2023-11-01
|
| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-023-44631-4 |
| _version_ | 1797452635824979968 |
|---|---|
| author | Ana Flávia Francisconi Jonathan Andre Morales Marroquín Luiz Augusto Cauz-Santos Cássio van den Berg Kauanne Karolline Moreno Martins Marcones Ferreira Costa Doriane Picanço-Rodrigues Luciano Delmodes de Alencar Cesar Augusto Zanello Carlos Augusto Colombo Brenda Gabriela Díaz Hernández Danilo Trabuco Amaral Maria Teresa Gomes Lopes Elizabeth Ann Veasey Maria Imaculada Zucchi |
| author_facet | Ana Flávia Francisconi Jonathan Andre Morales Marroquín Luiz Augusto Cauz-Santos Cássio van den Berg Kauanne Karolline Moreno Martins Marcones Ferreira Costa Doriane Picanço-Rodrigues Luciano Delmodes de Alencar Cesar Augusto Zanello Carlos Augusto Colombo Brenda Gabriela Díaz Hernández Danilo Trabuco Amaral Maria Teresa Gomes Lopes Elizabeth Ann Veasey Maria Imaculada Zucchi |
| author_sort | Ana Flávia Francisconi |
| collection | DOAJ |
| description | Abstract The Arecaceae family has a worldwide distribution, especially in tropical and subtropical regions. We sequenced the chloroplast genomes of Acrocomia intumescens and A. totai, widely used in the food and energy industries; Bactris gasipaes, important for palm heart; Copernicia alba and C. prunifera, worldwide known for wax utilization; and Syagrus romanzoffiana, of great ornamental potential. Copernicia spp. showed the largest chloroplast genomes (C. prunifera: 157,323 bp and C. alba: 157,192 bp), while S. romanzoffiana and B. gasipaes var. gasipaes presented the smallest (155,078 bp and 155,604 bp). Structurally, great synteny was detected among palms. Conservation was also observed in the distribution of single sequence repeats (SSR). Copernicia spp. presented less dispersed repeats, without occurrence in the small single copy (SSC). All RNA editing sites were C (cytidine) to U (uridine) conversions. Overall, closely phylogenetically related species shared more sites. Almost all nodes of the phylogenetic analysis showed a posterior probability (PP) of 1.0, reaffirming the close relationship between Acrocomia species. These results elucidate the conservation among palm chloroplast genomes, but point to subtle structural changes, providing support for the evolutionary dynamics of the Arecaceae family. |
| first_indexed | 2024-03-09T15:11:31Z |
| format | Article |
| id | doaj.art-2755e89632de46c7b9b430cf239c3fe0 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-03-09T15:11:31Z |
| publishDate | 2023-11-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-2755e89632de46c7b9b430cf239c3fe02023-11-26T13:18:54ZengNature PortfolioScientific Reports2045-23222023-11-0113111510.1038/s41598-023-44631-4Complete chloroplast genomes of six neotropical palm species, structural comparison, and evolutionary dynamic patternsAna Flávia Francisconi0Jonathan Andre Morales Marroquín1Luiz Augusto Cauz-Santos2Cássio van den Berg3Kauanne Karolline Moreno Martins4Marcones Ferreira Costa5Doriane Picanço-Rodrigues6Luciano Delmodes de Alencar7Cesar Augusto Zanello8Carlos Augusto Colombo9Brenda Gabriela Díaz Hernández10Danilo Trabuco Amaral11Maria Teresa Gomes Lopes12Elizabeth Ann Veasey13Maria Imaculada Zucchi14Programa de Pós-Gradução em Genética e Biologia Molecular, Universidade Estadual de Campinas, R. Monteiro LobatoPrograma de Pós-Gradução em Genética e Biologia Molecular, Universidade Estadual de Campinas, R. Monteiro LobatoDepartment of Botany and Biodiversity Research, University of ViennaDepartamento de Ciências Biológicas, Universidade Estadual de Feira de SantanaPrograma de Pós-Gradução em Genética e Biologia Molecular, Universidade Estadual de Campinas, R. Monteiro LobatoPrograma de Pós-Gradução em Genética e Biologia Molecular, Universidade Estadual de Campinas, R. Monteiro LobatoDepartamento de Biologia, Universidade Federal do AmazonasPrograma de Pós-Gradução em Genética e Biologia Molecular, Universidade Estadual de Campinas, R. Monteiro LobatoPrograma de Pós-Gradução em Genética e Biologia Molecular, Universidade Estadual de Campinas, R. Monteiro LobatoInstituto AgronômicoInstituto AgronômicoDepartamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal do ABCFaculdade de Ciências Agrárias, Universidade Federal do AmazonasDepartamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São PauloAgência Paulista de Tecnologia dos Agronegócios (APTA)Abstract The Arecaceae family has a worldwide distribution, especially in tropical and subtropical regions. We sequenced the chloroplast genomes of Acrocomia intumescens and A. totai, widely used in the food and energy industries; Bactris gasipaes, important for palm heart; Copernicia alba and C. prunifera, worldwide known for wax utilization; and Syagrus romanzoffiana, of great ornamental potential. Copernicia spp. showed the largest chloroplast genomes (C. prunifera: 157,323 bp and C. alba: 157,192 bp), while S. romanzoffiana and B. gasipaes var. gasipaes presented the smallest (155,078 bp and 155,604 bp). Structurally, great synteny was detected among palms. Conservation was also observed in the distribution of single sequence repeats (SSR). Copernicia spp. presented less dispersed repeats, without occurrence in the small single copy (SSC). All RNA editing sites were C (cytidine) to U (uridine) conversions. Overall, closely phylogenetically related species shared more sites. Almost all nodes of the phylogenetic analysis showed a posterior probability (PP) of 1.0, reaffirming the close relationship between Acrocomia species. These results elucidate the conservation among palm chloroplast genomes, but point to subtle structural changes, providing support for the evolutionary dynamics of the Arecaceae family.https://doi.org/10.1038/s41598-023-44631-4 |
| spellingShingle | Ana Flávia Francisconi Jonathan Andre Morales Marroquín Luiz Augusto Cauz-Santos Cássio van den Berg Kauanne Karolline Moreno Martins Marcones Ferreira Costa Doriane Picanço-Rodrigues Luciano Delmodes de Alencar Cesar Augusto Zanello Carlos Augusto Colombo Brenda Gabriela Díaz Hernández Danilo Trabuco Amaral Maria Teresa Gomes Lopes Elizabeth Ann Veasey Maria Imaculada Zucchi Complete chloroplast genomes of six neotropical palm species, structural comparison, and evolutionary dynamic patterns Scientific Reports |
| title | Complete chloroplast genomes of six neotropical palm species, structural comparison, and evolutionary dynamic patterns |
| title_full | Complete chloroplast genomes of six neotropical palm species, structural comparison, and evolutionary dynamic patterns |
| title_fullStr | Complete chloroplast genomes of six neotropical palm species, structural comparison, and evolutionary dynamic patterns |
| title_full_unstemmed | Complete chloroplast genomes of six neotropical palm species, structural comparison, and evolutionary dynamic patterns |
| title_short | Complete chloroplast genomes of six neotropical palm species, structural comparison, and evolutionary dynamic patterns |
| title_sort | complete chloroplast genomes of six neotropical palm species structural comparison and evolutionary dynamic patterns |
| url | https://doi.org/10.1038/s41598-023-44631-4 |
| work_keys_str_mv | AT anaflaviafrancisconi completechloroplastgenomesofsixneotropicalpalmspeciesstructuralcomparisonandevolutionarydynamicpatterns AT jonathanandremoralesmarroquin completechloroplastgenomesofsixneotropicalpalmspeciesstructuralcomparisonandevolutionarydynamicpatterns AT luizaugustocauzsantos completechloroplastgenomesofsixneotropicalpalmspeciesstructuralcomparisonandevolutionarydynamicpatterns AT cassiovandenberg completechloroplastgenomesofsixneotropicalpalmspeciesstructuralcomparisonandevolutionarydynamicpatterns AT kauannekarollinemorenomartins completechloroplastgenomesofsixneotropicalpalmspeciesstructuralcomparisonandevolutionarydynamicpatterns AT marconesferreiracosta completechloroplastgenomesofsixneotropicalpalmspeciesstructuralcomparisonandevolutionarydynamicpatterns AT dorianepicancorodrigues completechloroplastgenomesofsixneotropicalpalmspeciesstructuralcomparisonandevolutionarydynamicpatterns AT lucianodelmodesdealencar completechloroplastgenomesofsixneotropicalpalmspeciesstructuralcomparisonandevolutionarydynamicpatterns AT cesaraugustozanello completechloroplastgenomesofsixneotropicalpalmspeciesstructuralcomparisonandevolutionarydynamicpatterns AT carlosaugustocolombo completechloroplastgenomesofsixneotropicalpalmspeciesstructuralcomparisonandevolutionarydynamicpatterns AT brendagabrieladiazhernandez completechloroplastgenomesofsixneotropicalpalmspeciesstructuralcomparisonandevolutionarydynamicpatterns AT danilotrabucoamaral completechloroplastgenomesofsixneotropicalpalmspeciesstructuralcomparisonandevolutionarydynamicpatterns AT mariateresagomeslopes completechloroplastgenomesofsixneotropicalpalmspeciesstructuralcomparisonandevolutionarydynamicpatterns AT elizabethannveasey completechloroplastgenomesofsixneotropicalpalmspeciesstructuralcomparisonandevolutionarydynamicpatterns AT mariaimaculadazucchi completechloroplastgenomesofsixneotropicalpalmspeciesstructuralcomparisonandevolutionarydynamicpatterns |