Mitogenome of Uncaria rhynchophylla: genome structure, characterization, and phylogenetic relationships

Abstract

Background: Uncaria rhynchophylla is listed in the Chinese pharmacopoeia as one of the five botanical sources of the traditional medicine Gou-Teng, which has been utilized for the treatment of mental and cardiovascular disorders. This particular species is well-known in China for its hook-like structures originating from the leaf axils. Despite available reports on its chloroplast genome, there persists a notable lack of understanding concerning the structural variations and evolution of its mitochondrial genome. This knowledge gap hinders our ability to fully comprehend its genetic attributes. Results: We successfully assembled the mitochondrial genome of U. rhynchophylla by seamlessly integrating Illumina short reads with Nanopore long reads, resulting in a non-circular genome comprising 1 circular contig and 2 linear contigs. The total length of this genome is 421,660 bp, encompassing 36 PCGs. The identification of 4 distinct pairs of repeats has unveiled their pivotal role in repeat-mediated recombination. Of the 28 homologous fragments derived from chloroplasts, the majority were observed to have been transferred from the inverted repeat (IR) regions of the chloroplast genome to the mitochondrial genome. The mitochondrial DNA provides a distinctive resolution for the positioning of several species within the Gentianales phylogenetic framework, which remains unresolved by chloroplast DNA. Conclusion: By utilizing a newly assembled, high-quality mitochondrial genome of U. rhynchophylla, we have elucidated its intricate genomic structure, distinctive sequence characteristics, and potential for phylogenetic analysis. These findings mark significant strides in advancing our comprehension of the genetics of Uncaria.