Comparative Mitogenomic Analysis Reveals Gene and Intron Dynamics in Rubiaceae and Intra-Specific Diversification in Damnacanthus indicus

Abstract

The dynamic evolution of mitochondrial gene and intron content has been reported across the angiosperms. However, a reference mitochondrial genome (mitogenome) is not available in Rubiaceae. The phylogenetic utility of mitogenome data at a species level is rarely assessed. Here, we assembled mitogenomes of six Damnacanthus indicus (Rubiaceae, Rubioideae) representing two varieties (var. indicus and var. microphyllus). The gene and intron content of D. indicus was compared with mitogenomes from representative angiosperm species and mitochondrial contigs from the other Rubiaceae species. Mitogenome structural rearrangement and sequence divergence in D. indicus were analyzed in six individuals. The size of the mitogenome in D. indicus varied from 417,661 to 419,435 bp. Comparing the number of intact mitochondrial protein-coding genes in other Gentianales taxa (38), D. indicus included 32 genes representing several losses. The intron analysis revealed a shift from cis to trans splicing of a nad1 intron (nad1i728) in D. indicus and it is a shared character with the other four Rubioideae taxa. Two distinct mitogenome structures (type A and B) were identified. Two-step direct repeat-mediated recombination was proposed to explain structural changes between type A and B mitogenomes. The five individuals from two varieties in D. indicus diverged well in the whole mitogenome-level comparison with one exception. Collectively, our study elucidated the mitogenome evolution in Rubiaceae along with D. indicus and showed the reliable phylogenetic utility of the whole mitogenome data at a species-level evolution.

Genomic, transcriptomic, and metabolomic analysis of Oldenlandia corymbosa reveals the biosynthesis and mode of action of anti‐cancer metabolites

“…The plastid genome comprised 152,414 base pairs (bp), in agreement with previously reported Oldenlandia and Hedyotis plastid sequences, which range from 152,327 to 154,560 bp (Zhang et al, 2019; Yik et al, 2021) (Table S3). The mitochondrial genome has a size of 258,274 bp, which is smaller than other species of the family such as Damnacanthus indicus (417,816 bp) (Han et al, 2021) and Scyphiphora hydrophyllacea (354,155 bp) (Chen et al, 2020).…”

“…The mitochondrial genome was extracted from the nuclear assembly in one single contig. Then, it was annotated by BLAST searches against previously annotated mitochondrial genomes: Damnacanthus indicus (Han et al, 2021) (NCBI: MZ285076) and Scyphiphora hydrophyllacea (Chen et al, 2020) (NCBI: MT610041). tRNA genes were annotated using tRNAscan-SE (Schattner et al, 2005).…”

Discrimination of Panax ginseng from counterfeits using single nucleotide polymorphism: A focused review

“…In angiosperms, the mitogenome, compared to the chloroplast genome, was not used to analyze the phylogeny over several decades. In the recent past, researchers have been interested in the potential usefulness of mitochondrial data for phylogenetic data ( Han et al, 2021 ). With regard to differentiating between species or cultivars, much work has been published on the mitogenome in ginseng.…”

The assembled Banana dihaploid mitochondrial genome is compact with a high number of gene copies

“…In Raphanus sativus, L. 40 protein coding genes, three rRNA genes and 23 tRNA genes were found in the mt genome (Peng and Gao 2020). Very recently, six mitogenomes of Damnacanthus indicus was sequenced and found to have 32 protein coding genes after several losses (Han et al 2021). Plant organellar genes undergo post transcriptional modifications such as splicing and editing, among them RNA editing specifically C to U change is found to be evolved during early land plant development (Liu et al 2011).…”