De Novo Assembly and Comparative Analysis of the Mitochondrial Genomes for Six <i>Rubus</i> Species

Abstract

Rubus is a genus of small berry-producing shrubs, valued for their medicinal properties and as a food source. This genus is a large, globally distributed group that includes over 700 species. Despite numerous plastid and nuclear genomes having been reported for Rubus, there is a notable lack of research on its mitogenomes. We utilized PMAT to assemble the mitogenomes of six Rubus species according to long-read HiFi reads and annotated them through homologous alignment. Subsequently, we compared their characteristic differences within Rubus mitogenomes. The complete mitogenomes of R. parviflorus, R. spectabilis, R. idaeus, R. armeniacus, and R. caesius all exhibit master circle structures, with lengths ranging from 360,869 bp to 447,754 bp. However, R. chamaemorus displays a double-circle structure composed of two small circular molecules, spanning 392,134 bp. These mitogenomes encode a total of 54–61 genes, including 33–34 PCGs, 17–24 tRNAs, and 3 rRNA genes. Compared to the other five Rubus species, R. chamaemorus has fewer sequence repeats. These six species exhibit similar codon usage patterns. A large number of gene transfers were detected between organellar genomes of six Rubus species. Additionally, two phylogenetic trees were constructed using 31 mitogenomes and 94 chloroplast genomes, revealing a minor conflict within Rubus. Overall, this study clarifies the mitogenome characteristics of Rubus and provides valuable insights into the evolution of the genus.

Keywords

• mitogenome
• double-circle structure
• phylogeny
• rearrangement
• sequence collinearity