Abstract
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.
Highlights
The chloroplast is a double-membrane bound organelle in plants, which plays an important role in photosynthesis (Daniell et al, 2016)
Among 22 comparisons at the family level, the correlations between SNPs and InDels were strong for Symplocarpus renifolius and Zamioculcas zamiifolia (Lodd.) Engl., whereas were categorized as very strong in the remaining 20 comparisons (Figure 1A)
We determined the extent of correlations among SNPs, InDels, and repeats in cp genomes using 27 species from 23 genera, distributed among seven of the eight subfamilies of Araceae
Summary
The chloroplast (cp) is a double-membrane bound organelle in plants, which plays an important role in photosynthesis (Daniell et al, 2016). Co-existence of mutations was observed among SNPs, InDels, and repeats in prokaryotic and eukaryotic genomes (Silva and Kondrashov, 2002; Hardison et al, 2003; Tian et al, 2008; Chen et al, 2009; Zhu et al, 2009; McDonald et al, 2011). The “regional difference hypothesis” suggests that certain regions are more prone to mutations in comparison to other regions (Silva and Kondrashov, 2002; Hardison et al, 2003). The third hypothesis suggests high frequency of oligonucleotide repeats in a region of the genome generates InDels and substitutions (McDonald et al, 2011). Instead of InDel per se, this hypothesis places more importance on “regional difference hypothesis.”
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