Characterization of the complete chloroplast genome of a common Chinese medicinal herb, Eriocaulon buergerianum (Eriocaulaceae: Eriocaulon)

Abstract

Eriocaulon buergerianum is a common Chinese medicinal herb and belongs to the family Eriocaulaceae genus Eriocaulon the annual herbs. In this study, the complete chloroplast genome of E. buergerianum was assembled and reported. The complete chloroplast genome of E. buergerianum is 157,016 bp in length as the circular, which harbours a large single-copy region (LSC) of 81,534 bp, a small single-copy region (SSC) of 17,114 bp, and two inverted-repeat regions (IRs) of 26,393 bp each one. The overall nucleotide content of the chloroplast genome: A of 31.8%, T of 32.4%, C of 18.2% G of 17.6%, and 35.8% GC content. The chloroplast genome of E. buergerianum contains 133 genes, which includes 88 protein-coding genes (PCGs), 37 transfer RNA (tRNAs), and 8 ribosome RNA (rRNAs). The evolutionary analysis used neighbour-joining (NJ) method and the result showed that E. buergerianum was closely related to Eriocaulon sexangulare in the family Eriocaulaceae. This study will be helpful for genome data and genomic resources of the family Eriocaulaceae for further.

Eriocaulon buergerianum is a common Chinese medicinal herb and belongs to the family Eriocaulaceae genus Eriocaulon, which also is the annual herb. Plant whole of E. buergerianum is named Gu-Jing-Cao in Chinese (Ho and Chen 2002). Thirteen genera is in the family Eriocaulaceae, which the genus Eriocaulon contains around 435 species distributed throughout the world (Ho and Chen 2002). Previous phytochemical research revealed E. buergerianum of the genus Eriocaulon led to the identification of flavonoids, naphthopyranones and γ-tocopheryl acetate (Santos et al. 2005). E. buergerianum is frequently used as anti-inflammatory and antimicrobial medicine in China. Now, we do not have knowledge about the chloroplast genome and other genome information of the E. buergerianum. So, in this study, the complete chloroplast genome of E. buergerianum was assembled, annotated, and reported, which can be valuable for genome data and genomic resources for further, also can be important for evolutionary analysis and utilization of the Eriocaulaceae family.

Plant whole of E. buergerianum was collected from Shandong University of Traditional Chinese Medicine in Jinan, Shandong, China (36.65°N, 117.05°E). The total genomic DNA of E. buergerianum was extracted from the whole plant using the modified CTAB method and stored in Shandong University of Traditional Chinese Medicine (No.SUTCM-01). The genomic DNA was purified and fragmented using the NEB Next Ultra^TM II DNA Library Prep Kit (NEB, BJ, and CN), which was sequenced. FastQC version 0.11.8 (Andrews 2015) was used to perform and remove low-quality reads and adapters for quality control. The chloroplast genome of E. buergerianum was assembled and annotated using the MitoZ (Meng et al. 2019). OrganellarGenomeDRAW version 1.3.1 (Greiner et al. 2019) was used to draw the physical map of the chloroplast genome of E. buergerianum.

The complete chloroplast genome of E. buergerianum is 151,434 base pairs (bp) in length which is the circular with the overall nucleotide content of the chloroplast genome: 31.8% A (Adenine), 32.4% T (Thymine), 18.2% C (Cytosine), 17.6% G (Guanine), and 35.8% GC content. It harbours a characteristic quadripartite structure with a large single-copy region (LSC) of 81,534 bp, a small single-copy region (SSC) of 17,114 bp, and two inverted repeat regions (IRs) of 26,393 bp. The chloroplast genome of E. buergerianum contains 133 genes, which includes 88 protein-coding genes (PCGs), 37 transfer RNA genes (tRNAs), and 8 ribosomal RNA genes (rRNAs). And 20 genes were found duplicated in IR regions at each one, which included 8 PCG genes species (rps19, rpl2, rpl23, ycf2, ndhB, rps7, rps12, and ycf1), 8 tRNA genes species (trnH-GUG, trnI-CAU, trnL-CAA, trnV-GAC, trnI-GAU, trnA-UGC, trnR-ACG, and trnN-GUU), and 4 rRNA genes species (rrn16, rrn23, rrn4.5, and rrn5). The complete chloroplast genome of E. buergerianum has submitted to the GenBank that NCBI accession No.MH9677841.

To further investigate E. buergerianum evolutionary and phylogenetic position, the neighbour-joining (NJ) tree was constructed based on the chloroplast genome sequences of 10 other species using MEGA X (Kumar et al. 2018). NJ tree analysis used NJ method and performed using 2000 bootstrap values replicate at each node. All of the nodes were inferred with strong support by the NJ methods. The final NJ evolutionary tree was edited using the iTOL version 4.0 online web (https://itol.embl.de/) (Letunic and Bork 2016). The evolutionary tree analysis result showed that E. buergerianum was closely related to Eriocaulon sexangulare (MK193813.1) in the family Eriocaulaceae (Figure 1). In a word, the complete chloroplast genome of E. buergerianum is very important for Chinese medicinal herb research value and clinical drug development for further.

Figure 1.

Phylogenetic relationships of 11 species chloroplast genome sequences based on the neighbour-joining (NJ) method analysis using 2000 bootstrap replicates. Bootstrap support is indicated for each branch.

Disclosure statement

The authors have declared that no competing interests exist.