The chloroplast genome of Cuphea hookeriana Walp. (Lythraceae), a Mexico ornamental plant

Abstract

Cuphea hookeriana Walp. is an ornamental plant belonging to the Lythraceae. In this study, we reported the complete chloroplast (cp) genome sequence here and analyzed the phylogenetic relationship among Lythraceae plants. The length of the cp genome was 158,999 bp, including a large single-copy (LSC, 89,311 bp) region and a small single-copy (SSC, 18,436 bp) region separated by a pair of inverted repeats (IRs, 25,626 bp). There were 72 unique protein-coding genes (PCGs), 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes in the cp genome of C. hookeriana. A total of 223 simple sequence repeats (SSRs) and 34 long repeat sequences were identified. Phylogenetic analyses using maximum-likelihood (ML) revealed that C. hookeriana was close to C. hyssopifolia. In addition, the two Cuphea species were the sister group of Woodfordia fruticosa.

Keywords:

• Chloroplast genome
• phylogeny
• Cuphea hookeriana

Introduction

Cuphea hookeriana Walp. 1897 is a member of the Lythraceae family (Figure 1) and originated in Mexico and distributed in tropical and south subtropical areas (Duss 1897). C. hookeriana is a small shrub with purple flowers that bloom all year. It is a popular ornamental plant that can be found in gardens, parks, and roadside green spaces and is now cultivated in Beijing, Tianjin, and Shaanxi, among other places in China. Besides, C. hookeriana is also identified as having economic value as an industrial oil plant, and the research about it is mainly focused on fatty acid synthases (Dehesh et al. 2001; Feng et al. 2018). Herein, in order to provide the basic genomic information for researching the evolution of Lythraceae, we described the entire chloroplast (cp) genome of C. hookeriana for the first time and carried out a phylogenetic analysis to resolve the relationship with close relatives.

Figure 1. Plant materials of C. hookeriana. It is a shrub with little purple flowers which can bloom for 10–12 months a year. C. hookeriana in the photo was planted in Zhejiang A&F University and the photo itself was shooted by Sidan Hong.

Materials and methods

Fresh leaves samples of C. hookeriana were collected from the greenhouse of the College of Landscape and Architecture in Hangzhou (Hangzhou, China; 30°3′ N; 120°21′ E). The leaf of C. hookeriana was stored subsequently as a specimen at the Herbarium of Zhejiang A&F University under the accession code ZAFU20220106 (Cuihua Gu, [email protected]). The total DNA was extracted following the method of previous reports (Wang et al. 2021). Subsequently, the pair-end raw reads were produced based on the Illumina HiSeq platform at Beijing Genomics Institute (Shenzhen, China). After being purified by removing the adapter and low-quality reads, 3 Gb clean reads of C. hookeriana were used to perform the de novo assembly process. To obtain the complete cp genome of C. hookeriana, first, the reads of C. hookeriana were filtered by SeqKit (Shen et al. 2016). Subsequently, the resulting reads were assembled by SPAdes (Bankevich et al. 2012) using the cp genome of C. hyssopifolia (NC046574) as a reference. To know the accuracy of the assembly, we mapped the clean reads to assemble cp genome by Geneious Prime version 11.1.5 (Figure S1) (Deng et al. 2020). Subsequently, the assembled sequence was annotated and visualized by GeSeq (Tillich et al. 2017) after Bandage (Wick et al. 2015) made the necessary adjustments. In addition, the CPGVIEW (www.1kmpg.cn/cpgview/) (Liu et al. 2023) was applied to structures to visualize the intron-containing genes. The completed annotation was uploaded to GenBank and assigned the accession number OM949050. MISA (Beier et al. 2017) was used to search for simple sequence repeats (SSRs) of one to six nucleotide units (mono-, bi-, tri-, tetra-, penta-, and hexa-) across the cp genome. The minimal threshold of the unit size for searching was set as: 8, 5, 4, 3, 3, and 3. To find the long repeat sequences throughout the cp genome, REPuter (Kurtz et al. 2001) (https://bibiserv.cebitec.uni-bielefeld.de/reputer) was performed. The parameters are as follows: minimum size = 30, hamming distance = 3, and maximum computed repeats = 5000.

After aligning and trimming the cp genome by mafft v 7 (Katoh et al. 2019) and Gblocks 0.91b (Talavera and Castresana 2007), respectively, the IQtree v 1.6 (Nguyen et al. 2015) was used for generating a maximum-likelihood tree based on sequence from 14 Lythraceae species, three sequences from Onagraceae species were selected as an outgroup. The bootstrap was set to 1000 replicates, and the best-fit substitution model for the data (GTR + F + R2) was chosen by ModelFinder v 1.6.8 (Kalyaanamoorthy et al. 2017). The following sequences were used: NC037023 (Xue et al. 2017), MZ617461 (Fan et al. 2022), NC054309 (Lin et al. 2021), MN833212 (Wang et al. 2020), MK881637 (Gu et al. 2019), MK881626 (Gu et al. 2019), NC042891 (Gu et al. 2019), NC046574 (Ma et al. 2020), NC010358 (Gu et al. 2019), NC010361 (Chapman et al. 1999), NC029211 (Chapman et al. 1999), MK881638 (Gu et al. 2019), MG921615 (Gu et al. 2018), NC042897 (Xu et al. 2017), NC042896 (Xu et al. 2017), KF572028 (Wang et al. 2023), NC042890 (Wang et al. 2023), MH727532 (Jian and Ren 2019), and MK881631 (Gu et al. 2019).

Results

From the cp genome map of C. hookeriana (Figure 2), the total length of the cp genome of C. hookeriana was 158,999 bp. A pair of inverted repeats (IRs, 25,626 bp) separated the large single-copy (LSC, 89,311 bp) region and small single-copy (SSC, 18,436 bp) region. LSC, SSC, and IRs contained the GC content of 36.97%, 31.05%, and 42.72%, respectively. A total of 106 unigenes were identified totally (44 of which were duplicated in the IRs) including 72 unique protein-coding genes (PCGs), 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. In addition, ycf 3, clpP, and ndhB had two introns (Figure S2). There 223 SSRs were found (Supple 1), including 196 mono-nucleotide, nine bi-nucleotide, seven tri-nucleotide, nine tetra-nucleotide, and four penta-nucleotide. With the threshold of e-value <1e–5, 34 long repeat sequences (Supple 2) were identified, consisting of 15 forward matches, 18 palindromic matches, and one reverse repeat.

Figure 2. Complete and regional genome map of C. hookeriana. The different colored legend below presents the different types of unigenes.

As shown in the phylogenetic tree (Figure 3), the relationship of C. hookeriana in Lythraceae was presented. The C. hookeriana was mostly related to C. hyssopifolia with high bootstrap support, and as the sister group to Woodfordia fruticosa with C. hyssopifolia together.

Figure 3. The maximum-likelihood tree indicates the position of C. hookeriana with other chloroplast sequences from 14 Lythraceae species and Onagraceae species as an outgroup. Number of the node represents the bootstrap value of ML methods.

Discussion and conclusions

C. hookeriana belongs to the Cuphea genus, and is a member of Lythraceae. Up to now, the research on phylogenetic analysis of the Lythraceae family has attracted much attention. The cp genome has been performed from many species of Lagerstroemia (Gu et al. 2016; Gu, Tembrock, Wu 2017; Gu, Tembrock, Zhang, et al. 2017), Heimia (Gu et al. 2018), Punica (Wang et al. 2020), and Trapa (Gu et al. 2019; Lin et al. 2021). In addition, the phylogenetic information of C. hyssopifolia has been published (Ma et al. 2020). However, the lack of cp genome sequence information from the tribe Cuphea makes it difficult to resolve the phylogenetic relationships of Cuphea species among the Lythraceae family. Herein, the cp genome of C. hookeriana was first sequenced and assembled to solve its relationship with other species in Lythraceae. As the result, C. hookeriana and C. hyssopifolia are most closely related, and they are the closest sister group to W. fruticosa.

Ethical approval

This research was carried out following the guidelines provided by the College of Landscape and Architecture, Zhejiang A&F University.

Author contributions

Sidan Hong, Yu Zhao, and Weili Shao were involved in the conception and design, Cuihua Gu, Yacheng Ye, and Guozhe Zhang participated in the analysis and drafting of the paper, as well as revised it critically for intellectual content; Mengxin Yu, Mingzhu Bai, and Qingqing Ma were involved in the interpretation of the data; and that all authors agree to be accountable for all aspects of the work.

Disclosure statement

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

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 OM949050. The numbers of BioProject, Biosample, and SRA number are PRJNA814813, SAMN26567440, and SRR18298639, respectively.

Additional information

Funding

This work was supported by grants from the Zhejiang Science and Technology Major Program on Agricultural New Variety Breeding [Grant No. 2021C02071-4] and Zhejiang Provincial Natural Science Foundation of China [Grant No. LY21C160001].