Evolution of small inversions in chloroplast genome: A case study from a recurrent inversion in angiosperms
- Autores
- Catalano, Santiago Andres; Saidman, Beatriz Ofelia; Vilardi, Juan Cesar
- Año de publicación
- 2009
- Idioma
- inglés
- Tipo de recurso
- artículo
- Estado
- versión publicada
- Descripción
- Small inversions (SIs) in the chloroplast genome of angiosperms are ubiquitous. These inversions are always flanked by inverted repeats (palindromes or quasipalindromes) between approximately 8 and 50 bp long that form a hairpin structure when the DNA is single-stranded. We evaluated different methodological and empirical issues about SI evolution. As a case study, we analysed an SI recently discovered in the psbC-trnS intergenic region of Prosopis (Fabaceae). First, we analysed how inversions can be optimized in cases where the inverted segment also shows indels and substitutions, proposing a method based on Fixed States Optimization. Second, we evaluated the occurrence of this inversion on a phylogeny that includes the major lineages of angiosperms. Finally, we assessed whether the occurrence of this inversion was related to the thermodynamic stability of the hairpin structure (measured by its corresponding free energy) and/or the length of the palindromes by using a modified version of Maddison's Concentrated Changes Test. Hairpin structure was conserved in most of the 154 sequences analysed, with the inversion taking place at least 10 times in different lineages (monocots, magnoliids, rosids). As was previously proposed for other SIs, our analysis strongly suggests that the occurrence of this inversion is correlated with higher hairpin stability. In contrast, we found no evidence of a correlation with longer palindromes. Our results are in agreement with the hypothesis that hairpin formation is a requisite for SI occurrence. However, alternative explanations cannot be discarded.
Fil: Catalano, Santiago Andres. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico - Tucumán. Unidad Ejecutora Lillo; Argentina
Fil: Saidman, Beatriz Ofelia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Ecología, Genética y Evolución de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Ecología, Genética y Evolución de Buenos Aires; Argentina
Fil: Vilardi, Juan Cesar. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Ecología, Genética y Evolución de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Ecología, Genética y Evolución de Buenos Aires; Argentina - Materia
-
Small Inversions
Chloroplast Genome
Angiosperms
Prosopis - Nivel de accesibilidad
- acceso abierto
- Condiciones de uso
- https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
- Repositorio
- Institución
- Consejo Nacional de Investigaciones Científicas y Técnicas
- OAI Identificador
- oai:ri.conicet.gov.ar:11336/76155
Ver los metadatos del registro completo
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Evolution of small inversions in chloroplast genome: A case study from a recurrent inversion in angiospermsCatalano, Santiago AndresSaidman, Beatriz OfeliaVilardi, Juan CesarSmall InversionsChloroplast GenomeAngiospermsProsopishttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Small inversions (SIs) in the chloroplast genome of angiosperms are ubiquitous. These inversions are always flanked by inverted repeats (palindromes or quasipalindromes) between approximately 8 and 50 bp long that form a hairpin structure when the DNA is single-stranded. We evaluated different methodological and empirical issues about SI evolution. As a case study, we analysed an SI recently discovered in the psbC-trnS intergenic region of Prosopis (Fabaceae). First, we analysed how inversions can be optimized in cases where the inverted segment also shows indels and substitutions, proposing a method based on Fixed States Optimization. Second, we evaluated the occurrence of this inversion on a phylogeny that includes the major lineages of angiosperms. Finally, we assessed whether the occurrence of this inversion was related to the thermodynamic stability of the hairpin structure (measured by its corresponding free energy) and/or the length of the palindromes by using a modified version of Maddison's Concentrated Changes Test. Hairpin structure was conserved in most of the 154 sequences analysed, with the inversion taking place at least 10 times in different lineages (monocots, magnoliids, rosids). As was previously proposed for other SIs, our analysis strongly suggests that the occurrence of this inversion is correlated with higher hairpin stability. In contrast, we found no evidence of a correlation with longer palindromes. Our results are in agreement with the hypothesis that hairpin formation is a requisite for SI occurrence. However, alternative explanations cannot be discarded.Fil: Catalano, Santiago Andres. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico - Tucumán. Unidad Ejecutora Lillo; ArgentinaFil: Saidman, Beatriz Ofelia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Ecología, Genética y Evolución de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Ecología, Genética y Evolución de Buenos Aires; ArgentinaFil: Vilardi, Juan Cesar. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Ecología, Genética y Evolución de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Ecología, Genética y Evolución de Buenos Aires; ArgentinaWiley Blackwell Publishing, Inc2009-02info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/76155Catalano, Santiago Andres; Saidman, Beatriz Ofelia; Vilardi, Juan Cesar; Evolution of small inversions in chloroplast genome: A case study from a recurrent inversion in angiosperms; Wiley Blackwell Publishing, Inc; Cladistics; 25; 1; 2-2009; 93-1040748-3007CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1111/j.1096-0031.2008.00236.xinfo:eu-repo/semantics/altIdentifier/url/https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1096-0031.2008.00236.xinfo:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T09:36:43Zoai:ri.conicet.gov.ar:11336/76155instacron: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:34982025-09-29 09:36:43.899CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse |
dc.title.none.fl_str_mv |
Evolution of small inversions in chloroplast genome: A case study from a recurrent inversion in angiosperms |
title |
Evolution of small inversions in chloroplast genome: A case study from a recurrent inversion in angiosperms |
spellingShingle |
Evolution of small inversions in chloroplast genome: A case study from a recurrent inversion in angiosperms Catalano, Santiago Andres Small Inversions Chloroplast Genome Angiosperms Prosopis |
title_short |
Evolution of small inversions in chloroplast genome: A case study from a recurrent inversion in angiosperms |
title_full |
Evolution of small inversions in chloroplast genome: A case study from a recurrent inversion in angiosperms |
title_fullStr |
Evolution of small inversions in chloroplast genome: A case study from a recurrent inversion in angiosperms |
title_full_unstemmed |
Evolution of small inversions in chloroplast genome: A case study from a recurrent inversion in angiosperms |
title_sort |
Evolution of small inversions in chloroplast genome: A case study from a recurrent inversion in angiosperms |
dc.creator.none.fl_str_mv |
Catalano, Santiago Andres Saidman, Beatriz Ofelia Vilardi, Juan Cesar |
author |
Catalano, Santiago Andres |
author_facet |
Catalano, Santiago Andres Saidman, Beatriz Ofelia Vilardi, Juan Cesar |
author_role |
author |
author2 |
Saidman, Beatriz Ofelia Vilardi, Juan Cesar |
author2_role |
author author |
dc.subject.none.fl_str_mv |
Small Inversions Chloroplast Genome Angiosperms Prosopis |
topic |
Small Inversions Chloroplast Genome Angiosperms Prosopis |
purl_subject.fl_str_mv |
https://purl.org/becyt/ford/1.6 https://purl.org/becyt/ford/1 |
dc.description.none.fl_txt_mv |
Small inversions (SIs) in the chloroplast genome of angiosperms are ubiquitous. These inversions are always flanked by inverted repeats (palindromes or quasipalindromes) between approximately 8 and 50 bp long that form a hairpin structure when the DNA is single-stranded. We evaluated different methodological and empirical issues about SI evolution. As a case study, we analysed an SI recently discovered in the psbC-trnS intergenic region of Prosopis (Fabaceae). First, we analysed how inversions can be optimized in cases where the inverted segment also shows indels and substitutions, proposing a method based on Fixed States Optimization. Second, we evaluated the occurrence of this inversion on a phylogeny that includes the major lineages of angiosperms. Finally, we assessed whether the occurrence of this inversion was related to the thermodynamic stability of the hairpin structure (measured by its corresponding free energy) and/or the length of the palindromes by using a modified version of Maddison's Concentrated Changes Test. Hairpin structure was conserved in most of the 154 sequences analysed, with the inversion taking place at least 10 times in different lineages (monocots, magnoliids, rosids). As was previously proposed for other SIs, our analysis strongly suggests that the occurrence of this inversion is correlated with higher hairpin stability. In contrast, we found no evidence of a correlation with longer palindromes. Our results are in agreement with the hypothesis that hairpin formation is a requisite for SI occurrence. However, alternative explanations cannot be discarded. Fil: Catalano, Santiago Andres. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico - Tucumán. Unidad Ejecutora Lillo; Argentina Fil: Saidman, Beatriz Ofelia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Ecología, Genética y Evolución de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Ecología, Genética y Evolución de Buenos Aires; Argentina Fil: Vilardi, Juan Cesar. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Ecología, Genética y Evolución de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Ecología, Genética y Evolución de Buenos Aires; Argentina |
description |
Small inversions (SIs) in the chloroplast genome of angiosperms are ubiquitous. These inversions are always flanked by inverted repeats (palindromes or quasipalindromes) between approximately 8 and 50 bp long that form a hairpin structure when the DNA is single-stranded. We evaluated different methodological and empirical issues about SI evolution. As a case study, we analysed an SI recently discovered in the psbC-trnS intergenic region of Prosopis (Fabaceae). First, we analysed how inversions can be optimized in cases where the inverted segment also shows indels and substitutions, proposing a method based on Fixed States Optimization. Second, we evaluated the occurrence of this inversion on a phylogeny that includes the major lineages of angiosperms. Finally, we assessed whether the occurrence of this inversion was related to the thermodynamic stability of the hairpin structure (measured by its corresponding free energy) and/or the length of the palindromes by using a modified version of Maddison's Concentrated Changes Test. Hairpin structure was conserved in most of the 154 sequences analysed, with the inversion taking place at least 10 times in different lineages (monocots, magnoliids, rosids). As was previously proposed for other SIs, our analysis strongly suggests that the occurrence of this inversion is correlated with higher hairpin stability. In contrast, we found no evidence of a correlation with longer palindromes. Our results are in agreement with the hypothesis that hairpin formation is a requisite for SI occurrence. However, alternative explanations cannot be discarded. |
publishDate |
2009 |
dc.date.none.fl_str_mv |
2009-02 |
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/11336/76155 Catalano, Santiago Andres; Saidman, Beatriz Ofelia; Vilardi, Juan Cesar; Evolution of small inversions in chloroplast genome: A case study from a recurrent inversion in angiosperms; Wiley Blackwell Publishing, Inc; Cladistics; 25; 1; 2-2009; 93-104 0748-3007 CONICET Digital CONICET |
url |
http://hdl.handle.net/11336/76155 |
identifier_str_mv |
Catalano, Santiago Andres; Saidman, Beatriz Ofelia; Vilardi, Juan Cesar; Evolution of small inversions in chloroplast genome: A case study from a recurrent inversion in angiosperms; Wiley Blackwell Publishing, Inc; Cladistics; 25; 1; 2-2009; 93-104 0748-3007 CONICET Digital CONICET |
dc.language.none.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
info:eu-repo/semantics/altIdentifier/doi/10.1111/j.1096-0031.2008.00236.x info:eu-repo/semantics/altIdentifier/url/https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1096-0031.2008.00236.x |
dc.rights.none.fl_str_mv |
info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by-nc-sa/2.5/ar/ |
eu_rights_str_mv |
openAccess |
rights_invalid_str_mv |
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/ |
dc.format.none.fl_str_mv |
application/pdf application/pdf application/pdf application/pdf |
dc.publisher.none.fl_str_mv |
Wiley Blackwell Publishing, Inc |
publisher.none.fl_str_mv |
Wiley Blackwell Publishing, Inc |
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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1844613153689698304 |
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13.070432 |