The complete chloroplast genome sequence of an invasive plant, Tragopogon dubius Scopoli (asteraceae)

Abstract

Tragopogon dubius Scopoli is native to Europe and western Asia and is considered an invasive plant in China. In this study, the complete chloroplast genome of T. dubius was obtained using high-throughput next-generation sequencing technology. The whole chloroplast genome was 153,017 bp long with a GC content of 38% and comprised 130 genes (86 protein-coding genes, 36 tRNA genes, and 8 rRNA genes). Phylogenetic analysis based on the concatenated chloroplast protein-coding sequences showed that T. dubius is most closely related to Tragopogon pratensis. This study provides valuable genetic data for further phylogenetic analysis and molecular identification of species in the genus Tragopogon.

Introduction

Tragopogon dubius Scopoli 1772, is a biennial native to Europe and western Asia that grows primarily in the temperate biome (Soltis et al. 2022). T. dubius first invaded China in the 1930s (Zhang and Han 1997), where it is now considered an invasive plant (Lv et al. 2013; Wang et al. 2022). The seeds of T. dubius have large umbrella-like pappuses, which promote long distance dispersal by wind and human activities (Clements et al. 1999). So far, T. dubius has spread to multiple provinces in North and Northwest China, including Liaoning, Henan, Hebei, Shandong, and Beijing (Lin et al. 2022). This species is prone to forming a single dominant community, resulting in a reduction in species diversity within the areas it invades. Additionally, several studies have shown that hybridization often occurs between species of the Tragopogon (Cook and Soltis 1999; Li and Qiang 2012; Matthews et al. 2015). Therefore, there is a potential threat of hybridization between T. dubius with its native congeneric species T. porrifolius, T. orientalis, and T. pratensis in China and for the hybrid species to become invasive (Shan et al. 2020).

Chloroplast genomes, which contain a large amount of genetic information, have been used to trace the origins of species, including invasive plant Lepidium draba and Mikania micrantha (Gaskin et al. 2005; Daniell et al. 2016; Wang et al. 2016). The chloroplast genome of T. dubius, can thus provide us valuable information to explore its origin, evolution, and phylogenetic relationships with other species. There is also a critical need for a complete chloroplast genome to infer the invasion history of T. dubius in China, thereby providing a scientific basis for preventing new invasions. However, the complete chloroplast genome sequence of T. dubius has not yet been reported. In this study, the chloroplast genome was successfully assembled and annotated, and the relationship of T. dubius with closely related species was investigated.

Materials and methods

Fresh leaves were sampled from an individual T. dubius plant in Zhengzhou City, Henan Province, China (34°48′13″N, 113°49′42″E). The original plant was identified as T. dubius by Professor Jiamei Li (Figure 1). The voucher specimen is deposited at the Herbarium of Henan Agricultural University (Jiamei Li, jiamei_li@126.com) with specimen code 2204191 (HEAC).

Figure 1.

Photographs of T. dubius, taken by Yue Huang in Zhengzhou City, China, provide visual documentation of the plant’s characteristics. (A) Vegetative body. T. dubius is a biennial herb, typically reaching a height of 40-80(-100) cm, with an erect stem that is either simple or branched from the lower or middle third, and is glabrous. Basal and lower cauline leaves are lanceolate to linear, measuring 15-40 × 0.3-0.5 cm. (B) Root. The plant features vertical roots with a well-developed caudex. (C) Flower. The flower has 8-12(-14) phyllaries, which are longer than the florets and are equal to or longer than the achenes with pappus. The ligules are yellow. (D) Infructescence. The infructescence is terminal and solitary, with numerous scabrid bristles in the pappus, which are dirty white. (E) Seed. The seeds of the outer achenes measure 2.2-3 cm; the body of seed is pale brown, ± curviform, 1.4-1.7 mm in diam, with 5 fairly well-differentiated ribs and tuberculate. The beak of seed is whitish, slender, and measures 1.2-1.6 cm.

Total genomic DNA was extracted from fresh leaves using a modified CTAB protocol (Allen et al. 2006), and the purified DNA was sent to Novogene (Beijing, China) for genomic library construction and sequencing using the Illumina HiSeq platform (Illumina, San Diego, CA). About 6.95 Gb of sequence data were generated and used for the assembly of the chloroplast genome with GetOrganelle v1.7.7.0 (Jin et al. 2020). The complete assembled genome was annotated using Plastid Genome Annotator (PGA) (Qu et al. 2019; Guo 2021), and Geneious was used to manually correct codons and gene boundaries (Kearse et al. 2012; Yu et al. 2023). A map of the whole chloroplast genome of T. dubius was drawn using CPGView (Liu et al. 2023) (http://www.1kmpg.cn/cpgview/).

To identify the phylogenetic position of T. dubius, a maximum-likelihood (ML) phylogenetic tree was constructed based on the protein-coding sequences (CDS) of T. dubius, 17 other species within the family Asteraceae, and Arabidopsis thaliana as an outgroup (Fu et al. 2016). The ML tree was constructed using MEGA11 with 1000 bootstrap replicates (Tamura et al. 2021) and JTT + G + F model.

Results

The complete chloroplast genome sequence of T. dubius (GenBank accession number: OR840963) was 153,017 bp with a GC content of 38% (Figure 2). The minimal and average read mapping depths for assembled genomes were 20× and 1654× (Figure S1), respectively. Similar to the chloroplast genomes of most angiosperms, the T. dubius chloroplast genome had a typical quadripartite structure (Zhao et al. 2020), with a large single copy (LSC) region (84,239 bp in length), a small single copy (SSC) region (18,408 bp in length), and two inverted repeat (IR) regions (each 25,185 bp in length). The chloroplast genome harbors 130 genes including 86 protein-coding genes, 36 tRNA genes, and 4 ribosomal genes. Additionally, 11 cis-splicing genes including rps16, rpoC1, atpF, ycf3, clpP, petB, petD, rpl16, rpl2, ndhB, and ndhA (Figure S2), and one trans-splicing gene rps12 (Figure S3) were detected. Phylogenetic analysis showed that T. dubius and T. pratensis are most closely related to each other among species in the family Asteraceae (Figure 3).

Figure 2.

Map of the chloroplast genome of T. dubius. The map contains six tracks. From the center outward, the first track shows the dispersed repeats, consisting of direct and palindromic repeats, connected with red and green arcs. Second track: long tandem repeats (short blue bars). Third track: short tandem repeats or microsatellite sequences (short bars) with different colors representing the type of repeat. Black: complex repeat; green: repeat unit size 1; yellow: repeat unit size 2; purple: repeat unit size 3; blue: repeat unit size 4; orange: repeat unit size 5; red: repeat unit size 6. Fourth track: small single-copy (SSC), inverted repeat (IRa and IRb), and large single-copy (LSC) regions. Fifth track: GC content. Sixth track: annotated genes color-coded by functional classification (bottom left corner). Codon usage bias is displayed in parentheses after the gene name. The transcription directions for the inner and outer genes are clockwise and anticlockwise, respectively.

Figure 3.

Phylogenetic tree based on the CDS sequences of T. dubius, 17 species in the asteraceae family, and one outgroup species in the brassicaceae family. The tree was generated using the ML method in MEGA11 with 1000 bootstrap replicates. Numbers on the nodes indicate bootstrap values. The following sequences were used: Taraxacum mongolicum (KU736961, Kim et al. 2016), lactuca raddeana (MN-402448, Jiang et al. 2021), crepis rigescens (OM320794, Li et al. 2022), sonchus canariensis (NC042381, Kim et al. 2019), sonchus asper (MK371015, Abdalla et al. 2020), sonchus oleraceus (MH908962, Cho et al. 2019), cichorium intybus (MK569377, Yang et al. 2019), tragopogon pratensis (OR499755.1, direct submission), pertya multiflora (MW148616, Liu et al. 2021), centaurea cyanus (OP161554.1, direct submission), eclipta prostrata (KU361242, Park et al. 2016), tagetes erecta (MN462588, direct submission), glebionis coronaria (MW874476, Li et al. 2021), artemisia annua (MF623173, Shen et al. 2017), artemisia fukudo (MK569048, Min et al. 2019), artemisia argyi (NC-030785, Chen et al. 2019), artemisia scoparia (MT830857, Li et al. 2020), and Arabidopsis thaliana (NC-000932, Sato et al. 1999).

Discussion and conclusions

Sequencing of the complete chloroplast genome of T. dubius revealed that its size (153,017 bp) and gene content are not significantly different from those of most chloroplast genomes or plastomes in the genus Tragopogon. Although there are approximately 150 species in this genus, the chloroplast genome data in NCBI are relatively limited. Therefore, additional complete chloroplast genome sequences for Tragopogon species are required to further study the evolutionary history of this genus. Our research results provide valuable genetic data for further study of the phylogeny and molecular identification of species in the genus Tragopogon.

The identification of the dispersal source is often a challenge when studying the diffusion process of invasive plants. Chloroplast molecular markers can be used trace the dispersal source through analysis of the haplotype composition within and between populations. The acquisition of the chloroplast genome of T. dubius serves as a prerequisite for the development of chloroplast molecular markers, providing a possibility for tracing the dispersal origin.

Funding Statement

This research was supported by grants from the National Key R&D Program of China (2021YFC2600400, 2022YFC2601000), the National Nature Science Foundation of China (32272569, 31471827) and Xinyang Academy of Ecological Research Open Foundation (2023XYMS05).

Ethical approval

The authors declare no ethical or legal violations when obtaining the study materials and performing the research.

Authors’ contributions

Rui Wang, Jiamei Li, Mengxin Zhao, Jianying Guo, and Yue Huang collectively conceived and designed this study. Jiamei Li, Yue Huang, and Rui Wang collected plant samples. Yue Huang, Jingjing Cao, Jiamei Li, Mengxin Zhao, and Jianying Guo collaborated to assemble and annotate the chloroplast genome. Yue Huang, Jingjing Cao, Rui Wang, and Jiamei Li drafted the initial manuscript. All authors contributed to revising and approving the final manuscript.

Disclosure statement

No potential conflict of interest was reported by the authors.

Data availability statement

The genome sequence data of this study are available in the NCBI GenBank database at https://www.ncbi.nlm.nih.gov/ under accession no. OR840963. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA1050040, SRR27154907, SAMN38725175, respectively.