Multi-chromosomal mitochondrial genome architecture in Crotalaria (Leguminosae): The first complete mitochondrial genome of C. ferruginea

Crotalaria L. (Papilionoideae, Leguminosae) is one of the 86 big angiosperm genera with agronomic and industrial importance. Prevalent polyploidy enhances genetic variation and phenotypic plasticity of Crotalaria. This study assembled the mitochondrial genome (mitogenome) of hexaploid C. ferruginea using Oxford Nanopore Technology sequencing data and that of diploid C. pallida from publicly available whole genome sequencing data. Multi-chromosomal mitogenome architecture in Crotalaria was firstly reported, and hexaploid C. ferruginea displayed a more complex structure compared with diploid C. pallida. The mitogenome of C. ferruginea comprised of two circular (368,906 bp and 83,303 bp) and one linear (82,302 bp) chromosomes, while C. pallida contained one circular (402,601 bp) and one linear (134,427 bp) chromosomes. Five and six long repeats were detected in C. ferruginea (1300–5357 bp) and C. pallida (1033–10436 bp), respectively, likely playing a dominant role in shaping the multi-chromosomal mitogenome architecture. Mitochondrial plastid DNAs (MTPTs) were observed, with total lengths of 7236 bp (C. ferruginea) and 6126 bp (C. pallida). MTPTs in C. ferruginea included partial rrn16S and rrn23S, and those of C. pallida included partial rrn16S and psbB. RNA editing events (C-to-U) in mitochondrial protein-coding genes (PCGs) showed 95.37% and 95.65% non-synonymous substitutions in C. ferruginea and C. pallida, respectively. Phylogenetic analysis indicated that C. ferruginea and C. pallida were clustered into a monophyletic clade closely related to Genista pilosa and Lupinus luteus within Genisteae. Our findings provide valuable insights into mitogenome evolution of Crotalaria and enrich understanding of organelle genomes in Fabaceae.