Medicago ruthenica is a well-known high-quality forage due to its good palatability and strong tolerance to drought, cold and saline-alkali stress. Here, the complete chloroplast genome sequence of M. ruthenica was reported. The chloroplast genome is 126,939 bp in length. This chloroplast genome has no inverted repeat (IR) regions, which is very common in the family Fabaceae. The M. ruthenica chloroplast genome encodes 107 genes, including 73 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Phylogenetic analysis result strongly suggested that M. ruthenica is a distinct lineage in Medicago, being sister to highly supported clade composed of three species (M. hybrida, M. papillosa and M. sativa).

Objectives: Codon usage bias is a fundamental feature of gene expression that can influence evolutionary processes and genetic diversity. This study aimed to investigate the mitochondrial codon usage characteristics and their driving forces in three Medicago species: Medicago polymorpha, Medicago sativa, and Medicago truncatula. Methods: The complete mitochondrial genome sequences of the three species were downloaded from GenBank, and 21 shared coding sequences were screened. Codon usage patterns were analyzed using CodonW 1.4.2 and CUSP software. Key parameters, including the relative synonymous codon usage (RSCU), effective number of codons (ENC), codon adaptation index (CAI), codon bias index (CBI), and frequency of optimal codons (Fop), were calculated. Phylogenetic trees and RSCU clustering maps were constructed to explore evolutionary relationships. Results: The GC contents of the mitochondrial genomes followed the order of GC1 > GC2 > GC3. ENC values averaged above 35, while CAI, CBI, and Fop values ranged from 0.160 to 0.161, −0.078 to −0.076, and 0.362 to 0.363, respectively, indicating a weak preference for codons ending with A/U. Correlation and neutrality analyses suggested that codon usage bias was influenced by both mutation pressure and natural selection, with natural selection being the dominant factor. Fifteen optimal codons, predominantly ending with A/U, were identified. Phylogenetic analysis confirmed the close relationship among the three Medicago species, consistent with traditional taxonomy, whereas the RSCU clustering did not align with the phylogenetic relationships. Conclusions: This study provides insights into the mitochondrial codon usage patterns and their evolutionary determinants in Medicago species, highlighting the predominant role of natural selection in shaping codon usage bias. The findings offer a foundation for comparative genomic studies and evolutionary analyses and may be beneficial for improving genetic engineering and breeding programs of Medicago species.

Medicago ruthenica L., a superior forage crop within the genus Medicago (Fabaceae), is endowed with remarkable stress tolerance and an abundance of bioactive compounds, conferring significant ecological and forage value. Existing reviews primarily focus on a single research direction, and the most recent findings are dated, failing to cover breakthroughs at the molecular level. This paper systematically synthesizes the latest research progress in five key areas: genetic diversity and genomic studies, biotic stress responses, abiotic stress tolerance mechanisms (drought, salinity, and low temperature, etc.), utilization (including genetic breeding, ecological restoration, and forage development), and future research prospects. This review addresses critical gaps in existing literature, particularly regarding advances in genomic sequencing, biotic stresses, and research on stress-associated microorganisms. Research indicates that M. ruthenica exhibits extensive genetic diversity, and its genome contains numerous positive selection signals associated with stress resistance. It can tolerate multiple abiotic and biotic stresses through morphoplasticity, physiological metabolic regulation, and transcriptional regulation. Furthermore, its symbiosis with microorganisms such as rhizobia significantly enhances its stress tolerance. M. ruthenica demonstrates outstanding application potential in degraded grassland restoration and high-quality forage production. Future research should focus on mining stress-resistant genes, optimizing molecular breeding techniques, and integrating artificial intelligence into breeding practices. That will facilitate its transformation from a regional endemic resource to a commercially viable functional species, thereby providing robust support for ecological security and the sustainable development of grassland-based livestock husbandry in cold and arid regions.

Cotyledon tomentosa Harv. is a well-known succulent plant that have important ornamental and economic value. In this study, we release and detail the complete chloroplast genome sequences of C. tomentosa. The whole chloroplast genome was 149,729 bp in length and comprised 131 genes, including 84 protein-coding genes, 37 tRNA genes, eight rRNA genes. The C. tomentosa. chloroplast genome had a GC content of 38.23%. Phylogenetic analysis based on the complete chloroplast genomes showed that C. tomentosa had a close relationship with Kalanchoe tomentosa, Bryophyllum daigremontianum and Kalanchoe fedtschenkoi.