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...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2021-01-01
|
| Series: | Frontiers in Genetics |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2020.610838/full |
| _version_ | 1819298689545404416 |
|---|---|
| author | Abdullah Claudia L. Henriquez Thomas B. Croat Peter Poczai Ibrar Ahmed |
| author_facet | Abdullah Claudia L. Henriquez Thomas B. Croat Peter Poczai Ibrar Ahmed |
| author_sort | Abdullah |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-24T05:33:54Z |
| format | Article |
| id | doaj.art-37ee3c5230df4d9ebfc09e763a371e20 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-24T05:33:54Z |
| publishDate | 2021-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-37ee3c5230df4d9ebfc09e763a371e202022-12-21T17:13:04ZengFrontiers Media S.A.Frontiers in Genetics1664-80212021-01-011110.3389/fgene.2020.610838610838Mutational Dynamics of Aroid Chloroplast Genomes II Abdullah0Claudia L. Henriquez1Thomas B. Croat2Peter Poczai3Ibrar Ahmed4Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, PakistanDepartment of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United StatesMissouri Botanical Garden, St. Louis, MO, United StatesFinnish Museum of Natural History, University of Helsinki, Helsinki, FinlandAlpha Genomics Private Limited, Islamabad, PakistanThe 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.https://www.frontiersin.org/articles/10.3389/fgene.2020.610838/fullAraceae (aroid)chloroplast genomecorrelationsrepeatsInDels (insertions/deletions) |
| spellingShingle | Abdullah Claudia L. Henriquez Thomas B. Croat Peter Poczai Ibrar Ahmed Mutational Dynamics of Aroid Chloroplast Genomes II Frontiers in Genetics Araceae (aroid) chloroplast genome correlations repeats InDels (insertions/deletions) |
| 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 | Araceae (aroid) chloroplast genome correlations repeats InDels (insertions/deletions) |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2020.610838/full |
| work_keys_str_mv | AT abdullah mutationaldynamicsofaroidchloroplastgenomesii AT claudialhenriquez mutationaldynamicsofaroidchloroplastgenomesii AT thomasbcroat mutationaldynamicsofaroidchloroplastgenomesii AT peterpoczai mutationaldynamicsofaroidchloroplastgenomesii AT ibrarahmed mutationaldynamicsofaroidchloroplastgenomesii |