Evolution of small inversions in chloroplast genome: A case study from a recurrent inversion in angiosperms

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 metho...

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Detalles Bibliográficos
Autores principales: Catalano, S.A., Saidman, B.O., Vilardi, J.C.
Formato: JOUR
Materias:
chloroplast
DNA
evolutionary biology
genome
hypothesis testing
legume
optimization
phylogeny
Fabaceae
Liliopsida
magnoliids
Magnoliophyta
Prosopis
rosids
Acceso en línea:http://hdl.handle.net/20.500.12110/paper_07483007_v25_n1_p93_Catalano
Aporte de:
Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) de Universidad de Buenos Aires
id todo:paper_07483007_v25_n1_p93_Catalano
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spelling todo:paper_07483007_v25_n1_p93_Catalano2023-10-03T15:39:03Z Evolution of small inversions in chloroplast genome: A case study from a recurrent inversion in angiosperms Catalano, S.A. Saidman, B.O. Vilardi, J.C. chloroplast DNA evolutionary biology genome hypothesis testing legume optimization phylogeny Fabaceae Liliopsida magnoliids Magnoliophyta Prosopis rosids 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. © The Willi Hennig Society 2008. JOUR info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by/2.5/ar http://hdl.handle.net/20.500.12110/paper_07483007_v25_n1_p93_Catalano
institution Universidad de Buenos Aires
institution_str I-28
repository_str R-134
collection Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA)
topic chloroplast
DNA
evolutionary biology
genome
hypothesis testing
legume
optimization
phylogeny
Fabaceae
Liliopsida
magnoliids
Magnoliophyta
Prosopis
rosids
spellingShingle chloroplast
DNA
evolutionary biology
genome
hypothesis testing
legume
optimization
phylogeny
Fabaceae
Liliopsida
magnoliids
Magnoliophyta
Prosopis
rosids
Catalano, S.A.
Saidman, B.O.
Vilardi, J.C.
Evolution of small inversions in chloroplast genome: A case study from a recurrent inversion in angiosperms
topic_facet chloroplast
DNA
evolutionary biology
genome
hypothesis testing
legume
optimization
phylogeny
Fabaceae
Liliopsida
magnoliids
Magnoliophyta
Prosopis
rosids
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. © The Willi Hennig Society 2008.
format JOUR
author Catalano, S.A.
Saidman, B.O.
Vilardi, J.C.
author_facet Catalano, S.A.
Saidman, B.O.
Vilardi, J.C.
author_sort Catalano, S.A.
title Evolution of small inversions in chloroplast genome: A case study from a recurrent inversion in angiosperms
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
url http://hdl.handle.net/20.500.12110/paper_07483007_v25_n1_p93_Catalano
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AT saidmanbo evolutionofsmallinversionsinchloroplastgenomeacasestudyfromarecurrentinversioninangiosperms
AT vilardijc evolutionofsmallinversionsinchloroplastgenomeacasestudyfromarecurrentinversioninangiosperms
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