Mutational Dynamics of Aroid Chloroplast Genomes II

Abdullah, Claudia L. Henriquez, Thomas B Croat, Péter Poczai, Ibrar Ahmed

Research output: Contribution to journalArticleScientificpeer-review

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.

Original languageEnglish
Article number610838
JournalFrontiers in Genetics
Volume11
Number of pages10
ISSN1664-8021
DOIs
Publication statusPublished - 20 Jan 2021
MoE publication typeA1 Journal article-refereed

Fields of Science

  • 1184 Genetics, developmental biology, physiology
  • Araceae (aroid)
  • chloroplast genome
  • correlations
  • repeats
  • InDels (insertions deletions)

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