The complete chloroplast genome of Lonicera acuminata Wall. and its phylogenetic analysis

Abstract Lonicera acuminata Wall. is a medicinal and edible homologous plant in folk medicine that displays excellent pharmacological activities. However, the phylogenetic relationship between L. acuminata and other related family members remains unclear. In this study, we assembled the chloroplast genome of L. acuminata. The circular chloroplast genome was 154,282 bp in size, including a large single-copy region of 88,373 bp and a small single-copy region of 18,455 bp, which were separated by two inverted repeat regions (23,727 bp each). A total of 128 genes were predicted, including 8 ribosomal RNAs, 37 transfer RNAs and 83 protein-coding genes. The phylogenetic analysis revealed that L. acuminata was clustered together with L. pampaninii, L. macranthoides and L. hypoglauca.

Lonicera acuminata Wall. 1824 belongs to the family Caprifoliaceae, which is mainly distributed in Sichuan, Guizhou, Yunnan, Taiwan and other places in China (Gou and Wan 2005). In addition, L. acuminata is mainly used for carbuncles and treating sores, erysipelas, wind-heat, cold and fever because of its clearing heat and detoxifying, antibacterial and antiviral effects (Wei et al. 2010;Yang et al. 2010;Zheng et al. 2012;Liu et al. 2020;Qiu et al. 2020). In the new edition of Flora of China, L. acuminata and L. pampaninii have been merged into a single species because there is little difference in plant morphology (Chinese Academy of Science Flora of China Editorial Board 2013). However, due to the lack of molecular evidence, this study intends to provide a reference for the taxonomic merging of the two species at the molecular level.
Young  (FEIYANG, Guangzhou, China) and stored at À80 C in the laboratory (room number: 1403) of the School of Life Sciences, Guizhou Normal University. A total amount of 1000 ng DNA per sample was used as input material for the DNA sample preparations. The DNA library was constructed using the TruseqTM RNA Sample Prep Kit. Total DNA was used to generate libraries with an average insert size of 400 bp. The library preparations were sequenced on an Illumina platform, and approximately 3 GB of 150-bp pairedend reads were obtained and saved in fastq format. The quality of the raw data obtained was checked using FastQC for single base quality, base content distribution, GC content distribution, and sequence base quality. After the removal of adapter sequences, the filtered reads were assembled using the program GetOrganelle (Jin et al. 2020) with Lonicera japonica (GenBank accession number: MH028738) as the initial reference genome, and the assembled chloroplast genome was annotated using the online software GeSeq (Tillich et al. 2017). Finally, the accurate, annotated, complete chloroplast genome was submitted to GenBank with accession number MZ901373.
To further understand the phylogenetic position of L. acuminata, 21 chloroplast genome sequences of the family Caprifoliaceae and one outgroup (Sinadoxa corydalifolia) were downloaded from GenBank to construct phylogenetic trees with L. acuminata through maximum-likelihood (ML) method. The ML tree based on the GTR þ G þ I model was constructed using IQ-tree 2.04 with 1000 bootstrap replicates (Nguyen et al. 2015). The phylogenetic analysis revealed that L. acuminata was clustered together with L. pampaninii, L. macranthoides and L. hypoglauca (Figure 1).
In the new edition of Flora of China, the scientific name of L. pampaninii has been changed to L. acuminata, but in our phylogenetic tree they are treated as two separate clades, so here we suggest that L. pampaninii and L. acuminata should still be treated as two independent valid species.

Disclosure statement
No potential conflict of interest was reported by the author(s).

Funding
This study was supported by the National Natural Science Foundation of China [Grant No. U1812401, 32060068].

Data availability statement
The genome sequence data that support the findings of this study are openly available in GenBank of NCBI at https://www.ncbi.nlm.nih.gov under the accession number MZ901373. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA756814, SRR15561335, and SAMN20926716 respectively.