ABSTRACT
BACKGROUND: Trigonella foenum-graecum L. 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 study, we used second- and third-generation sequencing methods, which have the dual advantage of combining high accuracy and longer read length. The results showed that the mt genome of T. foenum-graecum was 345,604 bp in length and 45.28% in GC content. There were 59 genes, including: 33 protein-coding genes (PCGs), 21 tRNA genes, 4 rRNA genes and 1 pseudo gene. Among them, 11 genes contained introns. The mt genome codons of T. foenum-graecum had a significant A/T preference. A total of 202 dispersed repetitive sequences, 96 simple repetitive sequences (SSRs) and 19 tandem repetitive sequences were detected. Nucleotide diversity (Pi) analysis counted the variation in each gene, with atp6 being the most notable. Both synteny and phylogenetic analyses showed close genetic relationship among Trifolium pratense, Trifolium meduseum, Trifolium grandiflorum, Trifolium aureum, Medicago truncatula and T. foenum-graecum. Notably, in the phylogenetic tree, Medicago truncatula demonstrated the highest level of genetic relatedness to T. foenum-graecum, with a strong support value of 100%. The interspecies non-synonymous substitutions (Ka)/synonymous substitutions (Ks) results showed that 23 PCGs had Ka/Ks < 1, indicating that these genes would continue to evolve under purifying selection pressure. In addition, setting the similarity at 70%, 23 homologous sequences were found in the mt genome of T. foenum-graecum. CONCLUSIONS: This study explores the mt genome sequence information of T. foenum-graecum and complements our knowledge of the phylogenetic diversity of Leguminosae plants.
Subject(s)
Genome, Mitochondrial , Trigonella , Plant Extracts , Trigonella/genetics , Trigonella/chemistry , PhylogenyABSTRACT
Thalictrum baicalense Turcz. ex Ledeb. is a well-known herbaceous perennid that has been used as a traditional medicine to treat influenza, hepatitis, and detoxfeaction. In this study, we release and detail the complete chloroplast genome sequences of T. baicalense. The whole chloroplast genome was 155,859 bp in length and comprised 130 genes, including 84 protein-coding genes, 37 tRNA genes, eight rRNA genes. The T. baicalense chloroplast genome had a GC content of 38.39%. The phylogenetic relationships inferred that T. baicalense, T. tenue, T. minus and T. petaloideum are closely related to each other within the genus Thalictrum.
ABSTRACT
Allium mongolicum is a kind of wild vegetable with high nutritional value and even a traditional Chinese medicine. Here, we reported the complete chloroplast genome sequence of Allium mongolicum. The size of the chloroplast genome is 153,376 bp in length, including a large single copy region (LSC) of 82,912 bp, a small single copy region (SSC) of 18,054 bp, and a pair of inverted repeated regions of 26,205 bp. The Allium mongolicum chloroplast genome encodes 115 genes, including 69 protein-coding genes, 38 tRNA genes, and eight rRNA genes. Phylogenetic tree showed that Allium mongolicum is closely related to Allium przewalskianum.
ABSTRACT
Pterygocalyx volubilis Maxim. (Gentianaceae) is a traditional Chinese medicine, and its whole grass is used in the treatment of pulmonary tuberculosis and other conditions. Here, the complete chloroplast genome sequence of P. volubilis was reported based on the Illumina HiSeq Platform. The chloroplast genome genome is 154,365 bp in length, containing a pair of inverted repeated (IR) regions (25,928 bp) that are separated by a large single copy (LSC) region of 84,033 bp, and a small single copy (SSC) region of 18,476 bp. Moreover, a total of 130 functional genes were annotated, including 85 protein-coding genes, 37 tRNA genes, and eight rRNA genes. In the maximum-likelihood (ML) phylogenetic tree, Pterygocalyx clustered with the genus Swertia. This sequenced chloroplast genome of P. volubilis supports that Pterygocalyx belongs to subtribe Swertiinae.
ABSTRACT
Allium tuberosum is a popular vegetable, condiment, and even a traditional Chinese medicine. Here, the complete chloroplast genome sequence of Allium tuberosum was reported. The size of the chloroplast genome is 154,056 bp in length, including a large single copy region (LSC) of 83,068 bp, a small single copy region (SSC) of 17,958 bp, and a pair of inverted repeat (IR) regions with 26,515 bp. The Allium tuberosum chloroplast genome encodes 132 genes, including 87 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Phylogenetic tree analysis suggested that Allium tuberosum was closely related to Allium sativum.
ABSTRACT
Exacum affine Balf.f. ex Regel is a traditional medicinal plant in Yemen and also a popular potted plant. In this study, we sequenced the complete chloroplast genome of E. affine on the Illumina HiSeq Platform. The plastome sequence is 153,311 bp in length with a typical quadripartite structure, containing a pair of inverted repeated (IR) regions of 26,079 bp that are separated by a large single copy (LSC) region of 83,724 bp, and a small single copy (SSC) region of 17,509 bp. The GC content of the whole cp genome was 43.14%. A total of 132 functional genes were annotated, including 87 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The complete plastome sequence of E. affine will provide genetic and genomic information to promote its horticulture, officinal utilisation and systematics research of Gentianaceae (especially the tribe Exaceae).
ABSTRACT
Cancer prevention using natural micronutrition on epigenetic mechanisms primarily revolves around plant extracts. However, the role of macronutrition, including animal peptides, on epigenetic modification in cancer has been elusive. In traditional Chinese medicine, the soft-shelled turtle has a long-history of being a functional food that strengthens immunity through unknown mechanisms. The present study aimed to investigate the impact of soft-shelled turtle peptide on microRNA (miRNA) expression in gastric cancer (GC) cells and to analyze the potential anticancer mechanisms for GC. Affymetrix GeneChip miRNA 3.0 Array and quantitative polymerase chain reaction were used to detect the miRNA expression profile in human GC AGS cells treated with the soft-shelled turtle peptide. The results demonstrated that 101 miRNAs (49 upregulated miRNAs and 52 downregulated miRNAs) were significantly differentially expressed in the AGS cells following soft-shelled turtle peptide treatment. Several tumor suppressor miRNAs were upregulated markedly, including miRNA-375, let-7d, miRNA-429, miRNA-148a/148b and miRNA-34a. Pathway analysis indicated that soft-shelled turtle peptide may function with anticancer properties through the Hippo signaling pathway and the forkhead box O signaling pathway. Therefore, these results demonstrated that soft-shelled turtle peptide has the capacity to influence cancer-related pathways through the regulation of miRNA expression in GC cells.