Complete chloroplast genome sequences of Acanthocalyx alba and Acanthocalyx nepalensis subsp. delavayi (Caprifoliaceae)

Abstract In this study, the chloroplast genomes of Acanthocalyx alba (Hand.-Mazz., 1925) and Acanthocalyx nepalensis subsp. delavayi (Franchet, 1885) were sequenced, and their total lengths were 148,720 bp and 149,253 bp, respectively. The A. alba genome contained two inverted repeat regions (IRs) of 21,849 bp, a large single-copy region (LSC) of 89,084 bp, and a small single-copy region (SSC) of 15,938 bp, whereas A. nepalensis subsp. delavayi contained two IRs of 21,736 bp, one LSC of 89,034 bp, and one SSC of 16,747 bp. The chloroplast genomes of both A. alba and A. nepalensis subsp. delavayi contained 109 genes, including 72 mRNA, 33 tRNA, and four rRNA genes. Phylogenetic analysis suggested that A. alba is in a clade with A. nepalensis subsp. delavayi. This study provides useful data for further phylogenetic studies of A. alba and A. nepalensis subsp. delavayi.

Acanthocalyx species plants are widely distributed in southwest and northwest China. Most of them are medicinal plants commonly used in Tibetan medicine . Acanthocalyx alba (Hand.-Mazz.) M. J. Cannon (Cannon 1984) and Acanthocalyx nepalensis subsp. delavayi (Franchet) D. Y. Hong (Hong 2010) belong to the family Caprifoliaceae. They are the main sources of 'Tibetan Acanthocalyx nepalensis' in Tibetan medicines. Their aboveground parts have a good effect on symptoms such as joint pain, urinary incontinence, low back pain, vertigo, and mouth-eye deviation (Teng et al. 2002), and they are clinically used for the treatment of sore furuncle, purulent trauma, and tumors (Liu et al. 2006). As an important Chinese folk herbal medicine, A. alba has become increasingly endangered. However, most previous research has focused on its active ingredients. There are few reports about the population diversity and evolution of A. alba and A. nepalensis subsp. delavayi (Wu et al. 2014). Therefore, we sequenced their genomes and analyzed their genomic characteristics to provide a valuable reference for future studies on genetics research.
The complete genome length of A. alba (OK323963) was 148,720 bp, including two inverted repeat regions (IRs, 21,849 bp), a large single-copy region (LSC, 89,084 bp), and a small single-copy region (SSC, 15,938 bp). The GC content of the whole genome was 38.22%, which was lower than the 43.70% GC content in the IR region, but higher than the 36.46% GC content in the LSC and the 32.98% GC content in the SSC. The complete genome length of A. nepalensis subsp. delavayi (OK323964) was 149,253 bp. The whole genome contained two IRs (21,736 bp), one LSC (89,034 bp), and one SSC (16,747 bp). The GC content of the whole genome was 38.25%, which was lower than the 43.82% GC content in the IR region, but higher than the 36.47% GC content in the LSC and the 33.22% GC content in the SSC.
There were 109 genes in the chloroplast genomes of A. alba and A. nepalensis subsp. delavayi, both consisting of 72 mRNA, 33 tRNA, and four rRNA genes. The sequence coding length for amino acids in the protein (CDS) of A. alba was 50,556 bp, and that of A. nepalensis subsp. delavayi was 50,562 bp. Their sequence coding lengths for rRNA and tRNA genes were 9046 bp and 2511 bp, respectively.
A phylogenetic tree was built to infer the phylogenetic position of A. alba and A. nepalensis subsp. delavayi, with Diabelia species as an outgroup (Figure 1). The chloroplast genomes of A. alba and A. nepalensis subsp. delavayi used in this paper were derived from sequencing, and 11 other chloroplast genomes were derived from the National Center for Biotechnology Information (NCBI) website. In this study, MEGA-X version 10.2.6 software was used to construct the phylogenetic tree using the maximum-likelihood method, with 1000 bootstrap replicates (Kumar et al. 2018). Compared with previous studies based on the complete plastomes of plants (Wang et al. 2020), we mainly sequenced the complete chloroplast genomes of A. alba and A. nepalensis subsp. Delavayi to investigate their phylogenetic relationships with other Caprifoliaceae plants, and focused on the relationship between A. alba and A. nepalensis subsp. delavayi. Analyses of the plastomes and chloroplast genomes were largely consistent, and A. alba and A. nepalensis subsp. delavayi clustered together with a bootstrap value of 100%. This research provides useful data for studying the phylogenetic relationships and genetic diversity of A. alba and A. nepalensis subsp. delavayi.

Author contributions
Junjun Wang performed the data analysis and wrote the manuscript; Riza Zhao contributed to the conception of the study; and Zhifeng Zhang made critical revisions to intellectual content. All authors agreed to be accountable for all aspects of the work.

Disclosure statement
The authors declare that there are no conflicts of interest regarding the publication of this article. The authors alone are responsible for the content and writing of the paper.

Data availability statement
The genome sequence data that support the findings of this study are openly available in GenBank from NCBI at https://www.ncbi.nlm.nih.gov/ under the accession nos. OK323963 and OK323964. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA765190-PRJNA765191, SRR17933251-SRR17938363, and SAMN21547079-SAMN21547080, respectively.