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. 2022 Mar 28;7(3):552–553. doi: 10.1080/23802359.2022.2054737

Complete chloroplast genome sequence of the Tibetan catnip Nepeta hemsleyana Oliver ex Prain (Lamiaceae)

Mary Ann C Bautista a,b, Xuemei Wen c, Chao Ma c, Yanli Tu c, Tao Chen a,b,✉
PMCID: PMC8967201  PMID: 35372687

Abstract

Nepeta hemsleyana Oliver ex Prain (1891) is one of the aromatic Tibetan herbs used to treat convulsions. In this study, the complete chloroplast genome of N. hemsleyana was analyzed and is presented here for the first time. The assembled genome, 152,171 bp in length, contained a large single-copy region (82,214 bp) and a small single-copy region (17,605 bp) separated by a pair of inverted repeats (25,676 bp). A total of 131 genes were identified, including 86 protein-coding genes, 37 transfer RNA genes, and eight ribosomal RNA genes. The phylogenetic analysis also confirmed the early divergence of N. hemsleyana from other species in subtribe Nepetinae.

Keywords: Chloroplast genome, Lamiaceae, Mentheae, Nepeta hemsleyana, phylogeny

Species of Nepeta L. (Lamiaceae) are herbaceous perennials known for their aromatic foliage and flowers (Li and Hedge 1994; Jamzad et al. 2003). With nearly 300 species, Nepeta is one of the largest genera in tribe Mentheae, subfamily Nepetoideae (Jamzad et al. 2003). Species of Nepeta are considered to be a rich source of compounds with numerous pharmacological effects; however, species delimitation among this group remains unclear. The morphological characters of Nepeta are highly variable, even within closely related species, and relationships with allied genera need further investigation (Jamzad et al. 2003). In line with this, we sequenced the complete chloroplast genome of Nepeta hemsleyana Oliver ex Prain, a medicinally important species of grassy slopes around Lhasa, Tibet. The information obtained from the chloroplast genome can contribute to future studies that attempt to resolve taxonomic relationships among the species of Nepeta and their close allies.

Total genomic DNA was extracted from fresh leaves of the Nepeta hemsleyana plant using the modified CTAB method (Murray and Thompson 1980). The material was collected in Chengguan, Lhasa, Tibet, China (E 91°9′50″, N 29°46′10″). A voucher specimen (2020072401) was deposited in the herbarium of the Tibet Plateau Institute of Biology (XZ, Tu Yanli, sws_wenxuemei@sti.xizang.gov.cn). Short insert-sized libraries (350 bp) were constructed using the manufacturer’s protocol for the Nextera XT DNA Library Preparation Kit. Sequencing was carried out utilizing the Illumina Novaseq 600 platform. Sequencing resulted in 150 bp paired-end reads with an average sequencing depth of 2824.9 X. After filtering the raw reads, the chloroplast genome was assembled using the de novo assembler SPAdes 3.11.0 (Vasilinetc et al. 2015). The assembled plastome was annotated using Plann software (Huang and Cronk 2015), RNAmmer 1.2 (Lagesen et al. 2007), and tRNAscan-SE (Chan and Lowe 2019) for protein-coding genes, rRNA genes, and tRNA genes, respectively.

The complete chloroplast genome of Nepeta hemsleyana (MZ618620) was 152,171 bp in length and displayed a typical quadripartite structure. It contained a large single-copy (LSC) region (82,214 bp), a small single-copy (SSC) region (17,605 bp), and a pair of inverted repeats (25,676 bp). The annotated genome had 131 genes, comprising 86 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Six protein-coding genes, seven tRNA genes, and four rRNA genes were duplicated in the IR regions. Among the identified genes, 15 genes (trnK-UUU, rps16, trnG-UCC, atpF, rpoC1, trnL-UAA, trnV-UAC, petB, petD, rpl16, rpl2, ndhB, trnI-GAU, trnA-UGC, ndhA) had a single intron, while clpP and ycf3 had two introns each; rps12 was also a trans-spliced gene. Overall, the GC content was 37.9% and highly similar to other sequences from the tribe Mentheae. Moreover, the GC content of the IR regions (43%) was higher than the LSC (35.9%) and SSC (31.9%) regions.

To determine the phylogenetic position of Nepeta hemsleyana within the tribe Mentheae and subfamily Nepetoideae, 28 chloroplast genome sequences from the same subfamily were used for phylogenetic reconstruction (Figure 1). Maximum-likelihood (ML) analysis with the GTR + I+G nucleotide substitution model was conducted in RAxML 8.2.11 (Stamatakis 2014). Brandisia swinglei was designated as the outgroup. The ML analysis revealed that N. hemsleyana belonged to the Nepetinae clade and was basal to other genera of Nepetinae, such as Glechoma, Agastache, and Dracocephalum. The tree also showed that subtribe Nepetinae had a sister-group relationship with subtribe Menthinae.

Figure 1.

Figure 1.

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Maximum-likelihood consensus tree showing phylogenetic placement of Nepeta hemsleyana within tribe Mentheae. Bootstrap support values based on 1000 iterations are indicated above the nodes; GenBank accession numbers follow the binomials.

Acknowledgements

Ethics statement: Nepeta hemsleyana plant was collected in Lhasa, Tibet, as part of the Fourth National Survey of Chinese Traditional Medicine Project. All government and institutional regulations for plant collecting in China were followed during the course of the study.

Funding Statement

This work was supported by the Fourth National Survey of Chinese Traditional Medicine Resources Project from the State Administration of Traditional Chinese Medicine [GZY-KJS-2018-004] and the Open Project from the Key Laboratory of Shenzhen South Subtropical Plant Diversity [SSTLAB-2020-03].

Authors contributions

Conception and design: T. Chen, Y. Tu; data analysis and interpretation: M. A. Bautista, C. Ma, and X. Wen; paper writing and revising: M. A. Bautista and T. Chen; final approval of the version to be published: Y. Tu, X. Wen, and T. Chen. All authors agree to be accountable for all aspects of the work.

Disclosure statement

No potential conflict of interest was reported by the authors.

Data availability statement

The complete chloroplast genome sequence of Nepeta hemsleyana was deposited in the NCBI GenBank database (https://www.ncbi.nlm.nih.gov/nuccore/MZ618620) under accession number MZ618620. Raw sequencing data are available in the SRA database (https://www.ncbi.nlm.nih.gov/sra/SRX11580391[accn]) with the BioSample number SAMN20446770, SRA number SRX11580391, and BioProject accession number PRJNA672143.

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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 complete chloroplast genome sequence of Nepeta hemsleyana was deposited in the NCBI GenBank database (https://www.ncbi.nlm.nih.gov/nuccore/MZ618620) under accession number MZ618620. Raw sequencing data are available in the SRA database (https://www.ncbi.nlm.nih.gov/sra/SRX11580391[accn]) with the BioSample number SAMN20446770, SRA number SRX11580391, and BioProject accession number PRJNA672143.

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