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. 2022 Apr 13;7(4):658–660. doi: 10.1080/23802359.2022.2062265

The complete chloroplast genome of Laportea bulbifera (Sieb. et Zucc.) Wedd. and its phylogenetic analysis

Kaifen Sun 1, Qingwen Sun 1, Wenfen Xu 1,✉, Chunling Chen 1,✉, Bo Wang 1, Yueyun Wang 1
PMCID: PMC9009949  PMID: 35434362

Abstract

The circle complete chloroplast genome of Laportea bulbifera (Sieb. et Zucc.) Wedd. was sequenced for the first time. The genome length of L. bulbifera is 150,042 bp with 36.80% of GC content. The genome consists of a large single copy (LSC) region of 82,414 bp, a small single copy (SSC) region of 17,714 bp, and two inverted repeat (IRa and IRb) regions of 24,957 bp each. A total of 129 genes were annotated, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis was conducted by 29 species from the Rosales, the results presented a closed relationship between the species Laportea bulbifera and Poikilospermum lanceolatum.

Keywords: Laportea bulbifera, Urticaceae, chloroplast genome, medicinal plant

Laportea bulbifera (Sieb. et Zucc.) Wedd. 1856 first mentioned. is a perennial herb of genus Laportea Gaudich in the Urticaceae family, it is mainly distributed in Guizhou, Yunnan, Hunan and Heilongjiang province of China and also in Japan, Russia, India, Sri Lanka, and other countries (ECFC 1995). As a traditional Chinese medicine, L. bulbifera mainly contains flavonoids, coumarins, volatile oils with a wide range of pharmacological effects (Zhu et al. 2011; Lin et al. 2018; Zhang et al. 2019), and has long been utilized in TCM for the treatment of RA and some other autoimmune diseases (Xiang et al. 2009; Hou et al. 2010; Luo et al. 2011; Wang et al. 2013). Despite its high medicinal value, the complete chloroplast genome of L. bulbifera has not been reported yet. On the other hand, because of rare plant resources of L. bulbifera, the protection, development, and utilization of it were severely restricted. Therefore, the chloroplast genome of L. bulbifera was sequenced and the phylogenetic analysis was performed without species of Ficus auriculata, in order to enrich gene information and promote sustainable medicinal plant resources use of L. bulbifera.

Fresh leaves of L. bulbifera were collected from Longli county, Guizhou province, China (E 106°54′52″, N 26°23′14″). The voucher specimen (voucher No. LB20210703) and total DNA samples were deposited in the Center of Herbarium, Guizhou University of Traditional Chinese Medicine (http://www.gzy.edu.cn/, Qingwen Sun, sunqingwen445@gzy.edu.cn). Total DNA was extracted from L. bulbifera fresh leaves using the EZNA Plant DNA extraction kit according to the manufacturer’s instruction (Yingfei Biotech Co., Ltd., Shanghai, China). The genome sequence was performed on the Illumina NovaSeq Sequencing System to generate paired-end 2*150bp reads. A total of 6.43 Gb raw data was filtered by Trimmomatic (Bolger et al. 2014), then 6.41 Gb clean data was obtained. GetOrganelle (Jin et al. 2020) and CpGAVAS2 (Shi et al. 2019) were used to assemble and annotate the chloroplast genome, respectively, with the Poikilospermum lanceolatum chloroplast genome sequences (NC_056983.1) as reference. The annotated genome sequence was submitted to the GenBank (Accession number: OL334513).

The chloroplast genome of L. bulbifera is a double-stranded DNA molecule with a length of 150,042bp, it presents a typical quadripartite structure, including a large single copy (LSC) region, a small single copy (SSC) region, and two inverted repeat (IRa and IRb) regions. The LSC and SSC regions are 82,414 and 17,714bp, respectively, which are alternated by a pair of IR regions of 24,957bp each. The overall GC content of L. bulbifera is 36.8% (LSC, 34.4%; SSC, 30.5%; IRs, 42.9%). A total of 129 genes were annotated, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Among these genes, 6 protein coding genes (rps12, rps7, rpl23, rpl2, ndhB, and ycf2), 7 tRNA genes (trnA-UGC, trnI-CAU, trnI-GAU, trnL-CAA, trnN-GUU, trnR-ACG, and trnV-GAC), and 4 rRNA genes (rrn16, rrn23, rrn4.5, and rrn5) contain two repeating units. Furthermore, 19 genes equip with one intron, including 11 protein-coding genes (atpF, ndhA, ndhB × 2, petB, petD, rpl16, rpl2 × 2, rpoC1, and rps16) and 8 tRNA genes (trnA-UGC × 2, trnG-UCC, trnI-GAU × 2, trnK-UUU, trnL-UAA, and trnV-UAC). A total of four genes contain two introns (rps12 × 2, clpP, and ycf3). In addition, two genes (ycf1 and rps19) were annotated as pseudogenes.

The whole chloroplast genomes of 28 species in one family of Urticaceae were used for phylogenetic analysis with Ficus auriculata from Moraceae family as an out species (Figure 1). After sequence alignment by MAFFT (Katoh and Standley 2013), MEGA X (Kumar et al. 2018) was used to perform maximum likelihood (ML) tree with the Tamura Nei model. The results indicated that different species from different genera make difference, the significant factor attributes to different inner chloroplast genome construction. Previous studies showed that the genera of Boehmeria and Debregeasia species were each closely clustered into one group (Wu et al. 2018; Fu and Zhang 2021), which was consistent with our study results of phylogenetic analysis. However, the phylogenetic analysis of Laportea genus has not been reportedyet, its the first time to make phylogenetic analysis for L. bulbifera species. Present study showed that the species L. bulbifera from Laportea genus and P. lanceolatum from Poikilospermum genus of Urticaceae family showed closed relationship. These newly characterized phylogenetic analysis fruits can be used to develop markers for further study on the phylogeny and evolution of the genus Laportea.

Figure 1.

Figure 1.

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Phylogenetic relationships of 29 Rosales species constructed from the complete chloroplast genome sequences using maximum likelihood (ML).

Ethical approval

Research and collection of plant material was conducted according to the guidelines provided by GZY (Guizhou University of Traditional Chinese Medicine). Permission was granted by the National Natural Science Foundation of China.

Author contributions

Wenfen Xu and Chunling Chen planned and designed the study; Qingwen Sun and Yueyun Wang collected the plant materials; Kaifen Sun and Bo Wang: analysis of data; Kaifen Sun: drafting of the manuscript. All the authors agreed to be accountable for all aspects of the work.

Funding Statement

This work was supported by the Excellent Young Scientific and Technological Talents Project of Guizhou Province [[2019]5658], the National Natural Science Foundation of China [81260687], Guizhou Governor Fundation Project [QSZHZ[2011]61H].

Disclosure statement

No potential 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] (https://www.ncbi.nlm.nih.gov/) under the accession no. OL334513. The associated BioProject, SRA, and BioSample numbers are PRJNA778584, SRR16853987, and SAMN22965352 respectively.

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

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] (https://www.ncbi.nlm.nih.gov/) under the accession no. OL334513. The associated BioProject, SRA, and BioSample numbers are PRJNA778584, SRR16853987, and SAMN22965352 respectively.

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