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Mutational Dynamics of Aroid Chloroplast Genomes II

The co-occurrence among single nucleotide polymorphisms (SNPs), insertions-deletions (InDels), and oligonucleotide repeats has been reported in prokaryote, eukaryote, and chloroplast genomes. Correlations among SNPs, InDels, and repeats have been investigated in the plant family Araceae previously u...

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Autores principales: Abdullah, Henriquez, Claudia L., Croat, Thomas B., Poczai, Peter, Ahmed, Ibrar
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7854696/
https://www.ncbi.nlm.nih.gov/pubmed/33552129
http://dx.doi.org/10.3389/fgene.2020.610838
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author Abdullah,
Henriquez, Claudia L.
Croat, Thomas B.
Poczai, Peter
Ahmed, Ibrar
author_facet Abdullah,
Henriquez, Claudia L.
Croat, Thomas B.
Poczai, Peter
Ahmed, Ibrar
author_sort Abdullah,
collection PubMed
description The co-occurrence among single nucleotide polymorphisms (SNPs), insertions-deletions (InDels), and oligonucleotide repeats has been reported in prokaryote, eukaryote, and chloroplast genomes. Correlations among SNPs, InDels, and repeats have been investigated in the plant family Araceae previously using pair-wise sequence alignments of the chloroplast genomes of two morphotypes of one species, Colocasia esculenta belonging to subfamily Aroideae (crown group), and four species from the subfamily Lemnoideae, a basal group. The family Araceae is a large family comprising 3,645 species in 144 genera, grouped into eight subfamilies. In the current study, we performed 34 comparisons using 27 species from 7 subfamilies of Araceae to determine correlation coefficients among the mutational events at the family, subfamily, and genus levels. We express strength of the correlations as: negligible or very weak (0.10–0.19), weak (0.20–0.29), moderate (0.30–0.39), strong (0.40–0.69), very strong (0.70–0.99), and perfect (1.00). We observed strong/very strong correlations in most comparisons, whereas a few comparisons showed moderate correlations. The average correlation coefficient was recorded as 0.66 between “SNPs and InDels,” 0.50 between “InDels and repeats,” and 0.42 between “SNPs and repeats.” In qualitative analyses, 95–100% of the repeats at family and sub-family level, while 36–86% of the repeats at genus level comparisons co-occurred with SNPs in the same bins. Our findings show that such correlations among mutational events exist throughout Araceae and support the hypothesis of distribution of oligonucleotide repeats as a proxy for mutational hotspots.
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spelling pubmed-78546962021-02-04 Mutational Dynamics of Aroid Chloroplast Genomes II Abdullah, Henriquez, Claudia L. Croat, Thomas B. Poczai, Peter Ahmed, Ibrar Front Genet Genetics The co-occurrence among single nucleotide polymorphisms (SNPs), insertions-deletions (InDels), and oligonucleotide repeats has been reported in prokaryote, eukaryote, and chloroplast genomes. Correlations among SNPs, InDels, and repeats have been investigated in the plant family Araceae previously using pair-wise sequence alignments of the chloroplast genomes of two morphotypes of one species, Colocasia esculenta belonging to subfamily Aroideae (crown group), and four species from the subfamily Lemnoideae, a basal group. The family Araceae is a large family comprising 3,645 species in 144 genera, grouped into eight subfamilies. In the current study, we performed 34 comparisons using 27 species from 7 subfamilies of Araceae to determine correlation coefficients among the mutational events at the family, subfamily, and genus levels. We express strength of the correlations as: negligible or very weak (0.10–0.19), weak (0.20–0.29), moderate (0.30–0.39), strong (0.40–0.69), very strong (0.70–0.99), and perfect (1.00). We observed strong/very strong correlations in most comparisons, whereas a few comparisons showed moderate correlations. The average correlation coefficient was recorded as 0.66 between “SNPs and InDels,” 0.50 between “InDels and repeats,” and 0.42 between “SNPs and repeats.” In qualitative analyses, 95–100% of the repeats at family and sub-family level, while 36–86% of the repeats at genus level comparisons co-occurred with SNPs in the same bins. Our findings show that such correlations among mutational events exist throughout Araceae and support the hypothesis of distribution of oligonucleotide repeats as a proxy for mutational hotspots. Frontiers Media S.A. 2021-01-20 /pmc/articles/PMC7854696/ /pubmed/33552129 http://dx.doi.org/10.3389/fgene.2020.610838 Text en Copyright © 2021 Abdullah, Henriquez, Croat, Poczai and Ahmed. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Abdullah,
Henriquez, Claudia L.
Croat, Thomas B.
Poczai, Peter
Ahmed, Ibrar
Mutational Dynamics of Aroid Chloroplast Genomes II
title Mutational Dynamics of Aroid Chloroplast Genomes II
title_full Mutational Dynamics of Aroid Chloroplast Genomes II
title_fullStr Mutational Dynamics of Aroid Chloroplast Genomes II
title_full_unstemmed Mutational Dynamics of Aroid Chloroplast Genomes II
title_short Mutational Dynamics of Aroid Chloroplast Genomes II
title_sort mutational dynamics of aroid chloroplast genomes ii
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7854696/
https://www.ncbi.nlm.nih.gov/pubmed/33552129
http://dx.doi.org/10.3389/fgene.2020.610838
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