Dataset Information

The first complete chloroplast genome of Tetradium daniellii (Benn.) T. G. Hartley.

ABSTRACT: Tetradium daniellii (Benn.) T. G. Hartley is an important medicinal, ornamental, and timber tree species and belongs to genus Tetradium in family of Rutaceae. It is widely distributed in warm temperate deciduous broad-leaved forest areas in northern China, Korean Peninsula and Japan. In this study, we sequenced its sample and determined complete chloroplast genome. The CP genome of T. daniellii has a circle structure with the length 158,446 bp, includes a small single copy region (17, 972 bp), a large single copy (86, 478 bp) and two inverted repeats (26,998 bp). There were 131 genes, which included 86 protein-coding genes, 8 rRNA and 37 tRNA, and overall GC content covered by 38.3%. The gene trnK-UUU, rps16, trnG-UCC, atpF, rpoC1, trnL-UAA, trnV-UAC, petB, petD, rpl16, rpl2, ndhB, trnI-GAU, trnA-UGC and ndhA contained an intron; gene clpP, ycf3 contained 2 introns. The phylogenetic result showed that T. daniellii had the closest relationship with Tetradium ruticarpum (NC_052830).

SUBMITTER: Yu M

PROVIDER: S-EPMC8788364 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Similar Datasets

Project description:Bignoniaceae is a Pantropical plant family that is especially abundant in the Neotropics. Members of the Bignoniaceae are diverse in many ecosystems and represent key components of the Tropical flora. Despite the ecological importance of the Bignoniaceae and all the efforts to reconstruct the phylogeny of this group, whole chloroplast genome information has not yet been reported for any members of the family. Here, we report the complete chloroplast genome sequence of Tanaecium tetragonolobum (Jacq.) L.G. Lohmann, which was reconstructed using de novo and referenced-based assembly of single-end reads generated by shotgun sequencing of total genomic DNA in an Illumina platform. The gene order and organization of the chloroplast genome of T. tetragonolobum exhibits the general structure of flowering plants, and is similar to other Lamiales chloroplast genomes. The chloroplast genome of T. tetragonolobum is a circular molecule of 153,776 base pairs (bp) with a quadripartite structure containing two single copy regions, a large single copy region (LSC, 84,612 bp) and a small single copy region (SSC, 17,586 bp) separated by inverted repeat regions (IRs, 25,789 bp). In addition, the chloroplast genome of T. tetragonolobum has 38.3% GC content and includes 121 genes, of which 86 are protein-coding, 31 are transfer RNA, and four are ribosomal RNA. The chloroplast genome of T. tetragonolobum presents a total of 47 tandem repeats and 347 simple sequence repeats (SSRs) with mononucleotides being the most common and di-, tri-, tetra-, and hexanucleotides occurring with less frequency. The results obtained here were compared to other chloroplast genomes of Lamiales available to date, providing new insight into the evolution of chloroplast genomes within Lamiales. Overall, the evolutionary rates of genes in Lamiales are lineage-, locus-, and region-specific, indicating that the evolutionary pattern of nucleotide substitution in chloroplast genomes of flowering plants is complex. The discovery of tandem repeats within T. tetragonolobum and the presence of divergent regions between chloroplast genomes of Lamiales provides the basis for the development of markers at various taxonomic levels. The newly developed markers have the potential to greatly improve the resolution of molecular phylogenies.

Dataset Information

The first complete chloroplast genome of Tetradium daniellii (Benn.) T. G. Hartley.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets