Assembly and comparative analysis of the complete mitochondrial genome of Trigonella foenum-graecum L.

Abstract

Abstract Background Trigonella foenum-graecum L. (T. foenum-graecum) is a Leguminosae plant, and the stems, leaves, and seeds of this plant are rich in chemical components that are of high research value. The chloroplast (cp) genome of T. foenum-graecum has been reported, but the mitochondrial (mt) genome remains unexplored. Results In this paper, we use second- and third-generation sequencing methods, which have the dual advantage of combining high accuracy and longer read length. The T. foenum-graecum mitochondrial genome was assembled and other analyses such as annotation of the assembled sequences were performed. The results showed that the mitochondrial genome of T. foenum-graecum was 345,604 bp in length and 45.28% in GC content. There are 59 genes, including: 33 protein-coding genes (PCGs), 21 tRNA genes, 4 rRNA genes and 1 pseudo gene. Among them, 11 genes contained introns. Significant AT preferences for codons in the mitochondrial genome of T. foenum-graecum A total of 202 dispersed repetitive sequences, 96 simple repetitive sequences (SSRs) and 19 tandem repetitive sequences were detected. Nucleotide polymorphism analysis counted the variation in each gene, with atp6 being the most notable. Both synteny and phylogenetic analyses showed that T. foenum-graecum was similar to Trifolium pratense, Trifolium meduseum, Trifolium grandiflorum, Trifolium aureum, Medicago truncatula, which are five species of Leguminosae with high similarity. Among them, the highest similarity with Medicago truncatula was 100%. The interspecies non-synonymous substitutions (Ka)/synonymous substitutions (Ks) results showed that 23 Protein-coding genes had Ka/Ks < 1, indicating that these genes would continue to evolve under purifying selection pressure. In addition, 23 homologous sequences were detected in the mitochondrial genome of T. foenum-graecum, and tRNAs were more conserved than PCGs during gene migration. Conclusions This paper explores the mitochondrial genome sequence information of T. foenum-graecum and advances the phylogenetic diversity of Leguminosae plants.