Introduction: Lotus corniculatus is a perennial leguminous herb and serves as a high-quality forage, playing a key role in both grassland ecological restoration and the development of grazing livestock farming.Methods: In this study, we successfully assembled the L. corniculatus mitochondrial genome and investigated various related aspects, including genomic features, RNA editing sites, codon preference, gene transfer events, and phylogeny.Results and discussion: We found that the length of the L. corniculatus mitochondrial genome is 401,301 bp, and its GC content is 45.15%. It consists of 53 genes, comprising 32 protein-coding genes, 3 ribosomal RNA genes, and 18 transfer RNA genes. A total of 146 scattered repeats, 8 tandem repeats, and 124 simple sequence repeats are present in the mitochondrial genome. A thorough examination of all protein-coding genes revealed 485 instances of RNA editing and 9579 codons. Additionally, 57 homologous fragments were identified in L. corniculatus mitochondrial genome and chloroplast genomes, accounting for approximately 4.04% of the L. corniculatus mitochondrial genome. Furthermore, a phylogenetic tree based on mitochondrial genome data from 33 species belonging to four Fabaceae subfamilies and two species from other families validated the evolutionary relationship of Lotus. These findings have significant implications for understanding the organization and evolution of the L. corniculatus mitochondrial genome as well as for the identification of genetic markers. They also offer valuable perspectives relevant to devising strategies for molecular breeding and evolutionary categorization of legumes.

Leymus is a perennial genus that belongs to the tribe Triticeae (Poaceae) which has an adaptive capacity to ecological conditions and strong resistance to cold, drought, and salinity. Most Leymus species are fine herbs that can be used for agriculture, conservation, and landscaping. Due to confusion taxonomy within genera, the complete chloroplast (cp) genome of 13 Leymus species was sequenced, assembled, and compared with those of three other previously published Leymus species (Leymus condensatus, Leymus angustus, and Leymus mollis) to clarify the issue. Overall, the whole cp genome size ranged between 135,057 (L. condensatus) and 136,906 bp (Leymus coreanus) and showed a typical quadripartite structure. All studied species had 129 genes, including 83 protein-coding genes, 38 transfer RNAs, and 8 ribosomal RNAs. In total, 800 tandem repeats and 707 SSR loci were detected, most of which were distributed in the large single-copy region, followed by the inverted repeat (IR) and small single-copy regions. The sequence identity of all sequences was highly similar, especially concerning the protein-coding and IR regions; in particular, the protein-coding regions were significantly similar to those in the IR regions, regardless of small sequence differences in the whole cp genome. Moreover, the coding regions were more conserved than the non-coding regions. Comparisons of the IR boundaries showed that IR contraction and expansion events were reflected in different locations of rpl22, rps19, ndhH, and psbA genes. The close phylogenetic relationship of Leymus and Psathyrostachys indicated that Psathyrostachys possibly is the donor of the Ns genome sequence identified in Leymus. Altogether, the complete cp genome sequence of Leymus will lay a solid foundation for future population genetics and phylogeography studies, as well as for the analysis of the evolution of economically valuable plants.

Corethrodendron fruticosum is an endemic forage grasses in China with high ecological value. In this study, the complete chloroplast genome of C. fruticosum was sequenced using Illumina paired-end sequencing. The C. fruticosum chloroplast genome was 123,100 bp and comprised 105 genes, including 74 protein-coding genes, 4 rRNA-coding genes, and 27 tRNA-coding genes. The genome had a GC content of 34.53%, with 50 repetitive sequences and 63 simple repeat repetitive sequences that did not contain reverse repeats. The simple repeats included 45 single-nucleotide repeats, which accounted for the highest proportion and primarily comprised A/T repeats. A comparative analysis of C. fruticosum, C. multijugum, and four Hedysarum species revealed that the six genomes were highly conserved, with differentials primarily located in the conserved non-coding regions. Moreover, the accD and clpP genes in the coding regions exhibited high nucleotide variability. Accordingly, these genes may serve as molecular markers for the classification and phylogenetic analysis of Corethrodendron species. Phylogenetic analysis further revealed that C. fruticosum and C. multijugum appeared in different clades than the four Hedysarum species. The newly sequenced chloroplast genome provides further insights into the phylogenetic position of C. fruticosum, which is useful for the classification and identification of Corethrodendron.

Introduction: Medicago ruthenica, an essential wild perennial relative of Medicago sativa, is distributed across Eurasia, with good palatability and strong tolerance to drought, cold, and saline-alkali stress. It is exhibits wide adaptability, and its morphology varies greatly under different environmental conditions. Owing to this rich morphological diversity, the inference of its phylogeny has been controversial. Extensive studies have been conducted on the nuclear and chloroplast genomes of M. ruthenica; however, because of the complexity of the mitochondrial genome, the M. ruthenica mitochondrial genome has not been systematically described.Methods: In this study, we successfully assembled the M. ruthenica mitochondrial genome and investigated various related aspects, including genomic features, RNA editing sites, codon preference, gene transfer events, phylogeny, selective pressure, nucleotide diversity analysis and collinearity analysis.Results and discussion: The mitogenome of M. ruthenica is a circular DNA molecule measuring 354,988 base pairs (bp) in length and has a GC content of 45.13%. The mitochondrial genome of M. ruthenica includes 55 genes, with 34 being unique protein-coding genes (PCGs) (excluding three likely pseudogenes), along with three ribosomal RNA genes and 18 transfer RNA genes. The mitogenome is abundant with repetitive sequences; a total of 148 dispersed repeats were identified, including 79 palindromic repeats (53%) and 69 forward repeats (47%), without inverted or complementary repeats. Leucine (Leu) was the most frequently occurring amino acid in PCGs at 10.63%, while tryptophan (Trp) was the least frequent at 1.46%. The codon AUU (Ile) had the highest frequency of use, with the relative synonymous codon usage (RSCU) value of 1.29. atp8, atp4, rps4, nad4, ccmB, ccmFc and nad9 showed significant positive selection pressure in multiple legumes (Ka/Ks > 1) Additionally, M. ruthenica’s phylogenetic relationship was categorized under Medicago, supported by mitogenome data from 33 other legume species. Understanding the mitochondrial genome characteristics of M. ruthenica is critical for elucidating its genetic background. The results of this study serve as a basis for the genetic breeding of M. ruthenica.

Background: Bromus inermis is a high-quality perennial forage grass in the Poaceae family, with significant ecological and economic value. While its chloroplast genome has been sequenced, the mitochondrial genome of this species remains poorly understood due to the inherent complexity and frequent recombination of plant mitochondrial genomes. Methods: We sequenced the complete mitochondrial genome of B. inermis using both Illumina Novaseq6000 and Oxford Nanopore PromethION platforms. Subsequently, comprehensive bioinformatics analyses were performed, including genome assembly and annotation, repetitive sequence identification, codon usage analysis, RNA editing site prediction, the detection of chloroplast-derived sequences, and phylogenetic reconstruction. Results: The mitochondrial genome of B. inermis was determined to be 515,056 bp in length, with a GC content of 44.34%, similar to other Poaceae species. This genome encodes 35 protein-coding genes, 22 tRNA genes, and 10 rRNA genes. Repetitive sequences account for 16.2% of the genome, totaling 83,528 bp, including 124 simple sequence repeats, 293 dispersed repeats, and 31 tandem repeats. A total of 460 RNA editing sites were identified, among which 430 were nonsynonymous. Additionally, 110 putative chloroplast-derived sequences were detected. A phylogenetic analysis based on mitochondrial genome data clarified the species’ evolutionary position within Poaceae. Conclusions: This study provides genetic resources for evolutionary research on and the communication of organelle genomes. Meanwhile, it also lays a solid foundation for the better development and utilization of the germplasm resources of B. inermis.

Thymus mongolicus (Lamiaceae) is a plant commonly found throughout China, in which it is widely used in chemical products for daily use, traditional medicinal preparations, ecological management, and cooking. In this study, we have assembled and annotated for the first time the entire mitochondrial genome (mitogenome) of T. mongolicus. The mitochondrial genome of T. mongolicus is composed in a monocyclic structure, with an overall size of 450,543 base pairs (bp) and a GC composition of 45.63%. It contains 32 unique protein-encoding genes. The repetitive sequences of the T. mongolicus mitogenome include 165 forward repetitive sequences and 200 palindromic repetitive sequences, in addition to 88 simple sequence repeats, of which tetramers accounted for the highest proportion (40.91%). An analysis of the mitogenome codons revealed that synonymous codons generally end with A/U. With the exception of nad4L, which uses ACG/ATG as an initiation codon, all other genes begin with the ATG start codon. Codon analysis of the mitogenome also showed that leucine (909) are the most abundant amino acid, while tryptophan (134) are the least prevalent. In total, 374 RNA editing sites were detected. Moreover, 180 homologous segments totaling 105,901 bp were found when the mitochondrial and chloroplast genomes of T. mongolicus were compared. Phylogenetic analysis further indicated that T. mongolicus is most closely related to Prunella vulgaris in the Lamiaceae family. Our findings offer important genetic insights for further research on this Lamiaceae species. To the best of our knowledge, this study is the first description of the entire mitogenome of T. mongolicus.