Hypericum monogynum L. is a representative species belonging to the genus Hypericum that includes 500 species approximately [1] [2]. Widely distributed in the tropical and subtropical areas of China, H. monogynum has gained a highly reputation for its neuroprotective [3] and anti-oxidant [2] effects, besides it has been applied to treat mild-to-moderate depressions in European countries [4]. Not only does H. monogynum play a vital role in modern medical health cause but also it has obvious ornamental values as a shrub. It is reported that extracts and isolated compounds from various genus Hypericum exhibit extensive bioactivities in modern pharmacology, such as anti-oxidation, anti-bacteria and anti-virus [5] [6]. Based on these, there is no denying that replenishing information about genomes of species in the Hypericum family is urgent, which can help protect and make most of the resources. Although a few studies related to transcriptome sequencing and small RNA sequencing of H. monogynum has been reported [7], the chloroplast genome sequence of it has not been available till now, even no any chloroplast genome of the genus Hypericum. Here, we perform the partial chloroplast genome sequence of H. monogynum to provide a genomic resource and to clarify the phylogenetic relationship of this plant with other species in the Guttiferae family and other common plants.
Total genomic DNA was extracted from the fresh and healthy leaves of a single individual of H. monogynum, which was sampled from Anhui University of Traditional Chinese Medicine Anhui, China. DNA was obtained by CTAB method, then operated by Genewiz Biotechnology Co. Ltd. (Suzhou, China). DNA libraries with different indices were multiplexed and loaded on an Illumina HiSeq instrument according to manufacturer’s instructions (Illumina, San Diego, CA, USA). Sequencing was carried out using a 2 × 150 paired-end configuration, image analysis and base calling were conducted by the HiSeq control software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument. The reads with controlled quality assembled using Velvet (version 1.2.10) [8], and gaps filled with SSPACE (version 3.0) [9] and GapFiller (version 1-10) [10]. Based on the clean data, the coding gene, tRNA, rRNA and other ncRNAs were predicted by software Prodigal (version 2.6.3) [11], and then Rfam database (version 12.0) [12] was used to align genome sequence to Rfam library. The chloroplast genome of H. monogynum was assembled de novo.
The partial chloroplast genome of H. monogynum was obtained which has a total length of 120,005 bp in this study. The overall GC content is 36.96%. There are 70 protein coding genes, 33 tRNA genes, and 7 rRNA genes typical for the chloroplast genome of H. monogynum. By phylogenetic analysis with 15 complete chloroplast genomes of related plants, though H. monogynum is a representative
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Note: Numbers on the nodes are bootstrap values from 1000 replicates.
Figure 1. Phylogenetic tree of H. monogynum with 15 previously reported species was constructed by partial chloroplast genome sequences.
species belonging to the Guttiferae family. However, according to Figure 1, it does not group with any other species in the Guttiferae family analyzed, it could well function as an external group.
Data Availability Statement
The data that support the findings of this study are openly available in GenBank of NCBI at https://www.ncbi.nlm.nih.gov, reference number BankIt2434712.
Funding
This work was supported by the NSF of Anhui Province (Grant No. 1908085MH268), Key Natural Science Research Projects in Anhui Universities (Grant No. KJ2019A0453).