Mitochondrial genome variation between different accessions of Matricaria chamomilla L. (Asteraceae) based on SNP mutation analysis

Matricaria chamomilla L. (chamomile, Asteraceae) (GRIN, The Plant List 2013) has a long history of usage in traditional herbal medicine and is still today amongst the most important medicinal plants. Despite this importance, genetic diversity of cultivated and wild germplasm of M. chamomilla was rarely investigated so far. The objective of this study was to estimate the mitochondrial (mt) diversity of various cultivated M. chamomilla genotypes by determining point mutations in the mt genome. 89 SNPs (single nucleotide polymorphisms) were identified in the next generation sequencing data of 33 genotypes from 11 di- and tetraploid chamomile accessions representing a sequence diversity of 0.32 SNPs/kb. Based on the SNP analysis 19 mitochondrial haplotypes (mitotypes) could be specified with genetic distances ranging between 0.011 and 0.851. The examined mt variability within the accessions was higher than expected; only one monomorphic accession (variety 'Camoflora') was identified. Diploid accessions exhibited with 1.9 mitotypes per accession a higher variability than tetraploid accessions with a ratio of 1.3. Although some of the mitotypes were distributed over different accessions, identical mitotypes within di- and tetraploid accessions could not be determined. Furthermore, the mitotypes did not correspond to the geographical origin of the accessions. Although not the whole mt genome could be assembled in this study, the substitutions identified represent a valuable tool for further investigations of maternal phylogenetic relationships within M. chamomilla.