Complete mitochondrial genome of Medicago sativa ssp. falcata (Papilionoideae, Fabaceae): characterization and phylogenetic analysis.

Main conclusion: The first mitogenome of Medicago sativa ssp. falcata complete assembly and a comparative analysis of the four Medicago species base on mitogenome reveal taxonomic insights. Medicago sativa ssp. falcata is primarily distributed in the northern part of the geographical range where alfalfa grows and is a subspecies of the Medicago sativa complex (also called Mediacago falacta). However, compared to M. sativa, M. falcata has better performance in cold resistance and drought tolerance, making it a high-quality gene source for the breeding improvement of Medicago species. We sequenced and assembled the mitochondrial genome of M. falcata with a length of 307,026 bp and successfully annotated 50 genes, of which nad2 exhibited high nucleotide polymorphism in four Medicago species. A total of 197 RNA-editing sites were predicted across 24 protein-coding genes, with alterations at these editing sites resulting in a substantial number of leucine-coding sites, which is consistent with the results of codon usage bias. In addition, we conducted a horizontal comparison of four types of Medicago, including Medicago truncatula, and found that repetitive sequences in their mitogenomes exhibited consistent distribution characteristics. Phylogenetic trees generated through two methods indicated the independent genetic status of M. falcata within the Medicago genus and its partial kinship relationships within the Fabaceae family. The analysis of non-synonymous and synonymous substitution rates of shared protein-coding genes in different plants, along with gene transfer results, suggests that the mitogenome of M. falcata evolved smoothly without showing phases of intense change. This study provides useful information for further understanding the genetic background of M. falcata, with the expectation of contributing to the genomic mining and utilization of germplasm resources in the Medicago genus.