Chloroplast genomic insights into adaptive evolution and rapid radiation in the genus Passiflora (Passifloraceae)

Autores
Cauz Santos, Luiz Augusto; Portugal da Costa, Zirlane; Sader, Mariela Analía; van den Berg, Cássio; Carneiro Vieira, Maria Lucia
Año de publicación
2025
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Chloroplasts are essential organelles in plants and eukaryotic algae, responsible for photosynthesis, fatty acid synthesis, amino acid production, and stress responses. The genus Passiflora, known for its species diversity and dynamic chloroplast (cp) genome evolution, serves as an excellent model for studying structural variations. This study investigates evolutionary relationships within Passiflora by sequencing 11 new chloroplast genomes, assessing selective pressures on cp genes, and comparing plastid and nuclear phylogenies. Passiflora cp genomes showed significant variations in size, gene content, and structure, ranging from 132,736 to 163,292 base pairs, especially in Decaloba. Structural rearrangements and species-specific repeat patterns were identified. Selective pressure tests revealed significant adaptive evolution in certain lineages, with several genes, including clpP and petL, under positive selection. Phylogenetic analyses confirmed the monophyly of subgenera Astrophea, Passiflora, and Decaloba, while Deidamioides appeared polyphyletic. Nuclear phylogenetic analysis based on 35S rDNA sequences supported the monophyly of Astrophea but showed inconsistencies within subgenus Passiflora compared to cp genome data. This study highlights the evolutionary complexity of Passiflora cp genomes, demonstrating significant structural variations and adaptive evolution. The findings underscore the effectiveness of plastid phylogenomics in resolving phylogenetic relationships and provide insights into adaptive mechanisms shaping cp genome diversity in angiosperms.
Fil: Cauz Santos, Luiz Augusto. Universidad de Viena. Instituto de Botanica; Austria
Fil: Portugal da Costa, Zirlane. Universidade do Sao Paulo. Escola Superior de Agricultura Luiz de Queiroz; Brasil
Fil: Sader, Mariela Analía. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; Argentina
Fil: van den Berg, Cássio. Universidade Estadual de Feira de Santana; Brasil
Fil: Carneiro Vieira, Maria Lucia. Universidade do Sao Paulo. Escola Superior de Agricultura Luiz de Queiroz; Brasil
Materia
Chloroplast genome,
Genome rearrangements
Phylogenomics
Adaptive evolution
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/279860
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/279860
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Chloroplast genomic insights into adaptive evolution and rapid radiation in the genus Passiflora (Passifloraceae)Cauz Santos, Luiz AugustoPortugal da Costa, ZirlaneSader, Mariela Analíavan den Berg, CássioCarneiro Vieira, Maria LuciaChloroplast genome,Genome rearrangementsPhylogenomicsAdaptive evolutionhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Chloroplasts are essential organelles in plants and eukaryotic algae, responsible for photosynthesis, fatty acid synthesis, amino acid production, and stress responses. The genus Passiflora, known for its species diversity and dynamic chloroplast (cp) genome evolution, serves as an excellent model for studying structural variations. This study investigates evolutionary relationships within Passiflora by sequencing 11 new chloroplast genomes, assessing selective pressures on cp genes, and comparing plastid and nuclear phylogenies. Passiflora cp genomes showed significant variations in size, gene content, and structure, ranging from 132,736 to 163,292 base pairs, especially in Decaloba. Structural rearrangements and species-specific repeat patterns were identified. Selective pressure tests revealed significant adaptive evolution in certain lineages, with several genes, including clpP and petL, under positive selection. Phylogenetic analyses confirmed the monophyly of subgenera Astrophea, Passiflora, and Decaloba, while Deidamioides appeared polyphyletic. Nuclear phylogenetic analysis based on 35S rDNA sequences supported the monophyly of Astrophea but showed inconsistencies within subgenus Passiflora compared to cp genome data. This study highlights the evolutionary complexity of Passiflora cp genomes, demonstrating significant structural variations and adaptive evolution. The findings underscore the effectiveness of plastid phylogenomics in resolving phylogenetic relationships and provide insights into adaptive mechanisms shaping cp genome diversity in angiosperms.Fil: Cauz Santos, Luiz Augusto. Universidad de Viena. Instituto de Botanica; AustriaFil: Portugal da Costa, Zirlane. Universidade do Sao Paulo. Escola Superior de Agricultura Luiz de Queiroz; BrasilFil: Sader, Mariela Analía. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; ArgentinaFil: van den Berg, Cássio. Universidade Estadual de Feira de Santana; BrasilFil: Carneiro Vieira, Maria Lucia. Universidade do Sao Paulo. Escola Superior de Agricultura Luiz de Queiroz; BrasilBioMed Central2025-02info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/279860Cauz Santos, Luiz Augusto; Portugal da Costa, Zirlane; Sader, Mariela Analía; van den Berg, Cássio; Carneiro Vieira, Maria Lucia; Chloroplast genomic insights into adaptive evolution and rapid radiation in the genus Passiflora (Passifloraceae); BioMed Central; BMC Plant Biology; 25; 1; 2-2025; 1-201471-2229CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://link.springer.com/article/10.1186/s12870-025-06210-9info:eu-repo/semantics/altIdentifier/doi/10.1186/s12870-025-06210-9info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2026-02-26T10:29:25Zoai:ri.conicet.gov.ar:11336/279860instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982026-02-26 10:29:25.676CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Chloroplast genomic insights into adaptive evolution and rapid radiation in the genus Passiflora (Passifloraceae)
title Chloroplast genomic insights into adaptive evolution and rapid radiation in the genus Passiflora (Passifloraceae)
spellingShingle Chloroplast genomic insights into adaptive evolution and rapid radiation in the genus Passiflora (Passifloraceae)
Cauz Santos, Luiz Augusto
Chloroplast genome,
Genome rearrangements
Phylogenomics
Adaptive evolution
title_short Chloroplast genomic insights into adaptive evolution and rapid radiation in the genus Passiflora (Passifloraceae)
title_full Chloroplast genomic insights into adaptive evolution and rapid radiation in the genus Passiflora (Passifloraceae)
title_fullStr Chloroplast genomic insights into adaptive evolution and rapid radiation in the genus Passiflora (Passifloraceae)
title_full_unstemmed Chloroplast genomic insights into adaptive evolution and rapid radiation in the genus Passiflora (Passifloraceae)
title_sort Chloroplast genomic insights into adaptive evolution and rapid radiation in the genus Passiflora (Passifloraceae)
dc.creator.none.fl_str_mv Cauz Santos, Luiz Augusto
Portugal da Costa, Zirlane
Sader, Mariela Analía
van den Berg, Cássio
Carneiro Vieira, Maria Lucia
author Cauz Santos, Luiz Augusto
author_facet Cauz Santos, Luiz Augusto
Portugal da Costa, Zirlane
Sader, Mariela Analía
van den Berg, Cássio
Carneiro Vieira, Maria Lucia
author_role author
author2 Portugal da Costa, Zirlane
Sader, Mariela Analía
van den Berg, Cássio
Carneiro Vieira, Maria Lucia
author2_role author
author
author
author
dc.subject.none.fl_str_mv Chloroplast genome,
Genome rearrangements
Phylogenomics
Adaptive evolution
topic Chloroplast genome,
Genome rearrangements
Phylogenomics
Adaptive evolution
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Chloroplasts are essential organelles in plants and eukaryotic algae, responsible for photosynthesis, fatty acid synthesis, amino acid production, and stress responses. The genus Passiflora, known for its species diversity and dynamic chloroplast (cp) genome evolution, serves as an excellent model for studying structural variations. This study investigates evolutionary relationships within Passiflora by sequencing 11 new chloroplast genomes, assessing selective pressures on cp genes, and comparing plastid and nuclear phylogenies. Passiflora cp genomes showed significant variations in size, gene content, and structure, ranging from 132,736 to 163,292 base pairs, especially in Decaloba. Structural rearrangements and species-specific repeat patterns were identified. Selective pressure tests revealed significant adaptive evolution in certain lineages, with several genes, including clpP and petL, under positive selection. Phylogenetic analyses confirmed the monophyly of subgenera Astrophea, Passiflora, and Decaloba, while Deidamioides appeared polyphyletic. Nuclear phylogenetic analysis based on 35S rDNA sequences supported the monophyly of Astrophea but showed inconsistencies within subgenus Passiflora compared to cp genome data. This study highlights the evolutionary complexity of Passiflora cp genomes, demonstrating significant structural variations and adaptive evolution. The findings underscore the effectiveness of plastid phylogenomics in resolving phylogenetic relationships and provide insights into adaptive mechanisms shaping cp genome diversity in angiosperms.
Fil: Cauz Santos, Luiz Augusto. Universidad de Viena. Instituto de Botanica; Austria
Fil: Portugal da Costa, Zirlane. Universidade do Sao Paulo. Escola Superior de Agricultura Luiz de Queiroz; Brasil
Fil: Sader, Mariela Analía. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; Argentina
Fil: van den Berg, Cássio. Universidade Estadual de Feira de Santana; Brasil
Fil: Carneiro Vieira, Maria Lucia. Universidade do Sao Paulo. Escola Superior de Agricultura Luiz de Queiroz; Brasil
description Chloroplasts are essential organelles in plants and eukaryotic algae, responsible for photosynthesis, fatty acid synthesis, amino acid production, and stress responses. The genus Passiflora, known for its species diversity and dynamic chloroplast (cp) genome evolution, serves as an excellent model for studying structural variations. This study investigates evolutionary relationships within Passiflora by sequencing 11 new chloroplast genomes, assessing selective pressures on cp genes, and comparing plastid and nuclear phylogenies. Passiflora cp genomes showed significant variations in size, gene content, and structure, ranging from 132,736 to 163,292 base pairs, especially in Decaloba. Structural rearrangements and species-specific repeat patterns were identified. Selective pressure tests revealed significant adaptive evolution in certain lineages, with several genes, including clpP and petL, under positive selection. Phylogenetic analyses confirmed the monophyly of subgenera Astrophea, Passiflora, and Decaloba, while Deidamioides appeared polyphyletic. Nuclear phylogenetic analysis based on 35S rDNA sequences supported the monophyly of Astrophea but showed inconsistencies within subgenus Passiflora compared to cp genome data. This study highlights the evolutionary complexity of Passiflora cp genomes, demonstrating significant structural variations and adaptive evolution. The findings underscore the effectiveness of plastid phylogenomics in resolving phylogenetic relationships and provide insights into adaptive mechanisms shaping cp genome diversity in angiosperms.
publishDate 2025
dc.date.none.fl_str_mv 2025-02
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/279860
Cauz Santos, Luiz Augusto; Portugal da Costa, Zirlane; Sader, Mariela Analía; van den Berg, Cássio; Carneiro Vieira, Maria Lucia; Chloroplast genomic insights into adaptive evolution and rapid radiation in the genus Passiflora (Passifloraceae); BioMed Central; BMC Plant Biology; 25; 1; 2-2025; 1-20
1471-2229
CONICET Digital
CONICET
url http://hdl.handle.net/11336/279860
identifier_str_mv Cauz Santos, Luiz Augusto; Portugal da Costa, Zirlane; Sader, Mariela Analía; van den Berg, Cássio; Carneiro Vieira, Maria Lucia; Chloroplast genomic insights into adaptive evolution and rapid radiation in the genus Passiflora (Passifloraceae); BioMed Central; BMC Plant Biology; 25; 1; 2-2025; 1-20
1471-2229
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://link.springer.com/article/10.1186/s12870-025-06210-9
info:eu-repo/semantics/altIdentifier/doi/10.1186/s12870-025-06210-9
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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score 12.665996

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