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
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/76155

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spelling 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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