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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2009
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| Acceso en línea: | https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_07483007_v25_n1_p93_Catalano http://hdl.handle.net/20.500.12110/paper_07483007_v25_n1_p93_Catalano |
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paper:paper_07483007_v25_n1_p93_Catalano2023-06-08T15:45:14Z Evolution of small inversions in chloroplast genome: A case study from a recurrent inversion in angiosperms 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. 2009 https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_07483007_v25_n1_p93_Catalano 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 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. |
| 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 |
| publishDate |
2009 |
| url |
https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_07483007_v25_n1_p93_Catalano http://hdl.handle.net/20.500.12110/paper_07483007_v25_n1_p93_Catalano |
| _version_ |
1768542041081380864 |