High-Quality Assembly and Analysis of the Complete Mitogenomes of German Chamomile (Matricaria recutita) and Roman Chamomile (Chamaemelum nobile)

Abstract

German chamomile (Matricaria chamomilla L.) and Roman chamomile (Chamaemelum nobile) are the two well-known chamomile species from the Asteraceae family. Owing to their essential oils and higher medicinal value, these have been cultivated widely across Europe, Northwest Asia, North America, and Africa. Regarding medicinal applications, German chamomile is the most commonly utilized variety and is frequently recognized as the "star among medicinal species". The insufficient availability of genomic resources may negatively impact the progression of chamomile industrialization. Chamomile's mitochondrial genome is lacking in extensive empirical research. In this study, we achieved the successful sequencing and assembly of the complete mitochondrial genome of M. chamomilla and C. nobile for the first time. An analysis was conducted on codon usage, sequence repeats within the mitochondrial genome of M. chamomilla and C. nobile. The phylogenetic analysis revealed a consistent positioning of M. chamomilla and C. nobile branches within both mitochondrial and plastid-sequence-based phylogenetic trees. Furthermore, the phylogenetic analysis also showed a close relationship between M. chamomilla and C. nobile within the clade comprising species from the Asteraceae family. The results of our analyses provide valuable resources for evolutionary research and molecular barcoding in chamomile.

Keywords: Chamaemelum nobile; Matricaria chamomilla; mitochondrial genome; phylogenetic analysis; repetitive sequence analysis.

Figure 1

The circular maps of mitogenomes. (A) The circular diagram illustrating the mitochondrial genome of M. chamomilla. (B) The circular diagram illustrating the mitochondrial genome of C. nobile. The genomic characteristics transcribed in the clockwise and counterclockwise directions are depicted on the inner and outer regions of the circular map, respectively. The functional classification of genes in the mitochondrial genome is visually represented by color-coding. The GC content is visually represented in the inner circle using a dark gray plot.

Figure 2

The repeats analysis of the M. chamomilla and C. nobile chamomile mitochondrial genomes. (A) The repeat sequences detected in the mitochondrial genome of M. chamomilla. (B) The repeat sequences detected in the mitochondrial genome of C. nobile. The dispersed repeats, indicated by green, blue, or pink arcs, are represented in the C1 circle. Tandem repeats are depicted as short bars in the C2 circle. The C3 circle illustrates the microsatellite sequences detected.

Figure 3

The homologous DNA sequences between the chloroplast genome and mitogenome of M. chamomilla and C. nobile. (A) The conserved DNA sequences shared between the chloroplast and mitochondrial genomes of M. chamomilla. (B) The conserved DNA sequences shared between the chloroplast and mitochondrial genomes of C. nobile. The inner green arcs illustrate the homologous DNA fragments. The visualization of homologous sequences between the organelle genomes was performed using the TBtools software (v2.012) with incorporation of the Circos package.

Figure 4

Relative synonymous codon usage (RSCU) in mitochondrial protein-coding genes in the mitogenome of M. chamomilla and C. nobile. The value for RSCU is represented on the y-axis. (A) The RSCU value of M. chamomilla. (B) The RSCU value of C. nobile.

Figure 5

The maximum likelihood (ML) analysis was utilized to investigate the phylogenetic relationships among M. chamomilla, C. nobile, and nine other species belonging to the Asteraceae family. The sequence obtained in this study has been distinguished by highlighting it in red. The GenBank accession numbers for the chloroplast genomes and mitochondrial genomes are provided next to the corresponding Latin names of the species.