The Complete Chloroplast Genome of Tamarix Ramosissima and Comparative Analysis of Tamaricaceae Species 

Abstract

Background: Tamarix ramosissima is a deciduous shrub resided in arid and semi-arid regions. Although of ecological and medicinal values, some Tamarix species are considered invasive as they have dominated the riparian zones of dryland in some parts of the world. Chloroplast (cp) DNA is highly conserved in structure and gene arrangement, making cp genomic data valuable resources for species delimitation and phylogenetics. The cp genome of T. ramosissima was de novo assembled with the aim of providing reference and data resource for further cp-derived marker development and species delimitation of Tamarix.

Results: Here, the complete chloroplast (CP) genome of T. ramosissima was sequenced and analyzed, showing a size of 156150 bp and a GC content of 36.5%. The plastome displayed a typical quadripartite structure, consisting of a pair of inverted repeat (IR) regions of 26554 bp, separated by a large single copy (LSC) region of 84795 bp, and a small single copy (SSC) region of 18247 bp. The cp genome encoded 130 genes, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. A total of 32 repeat sequences and 64 simple sequence repeats (SSR) were identified in the plastome, and an obvious A/T bias was observed in the majority of the SSRs detected. By comparing the T. ramosissima cp genome with those of four other Tamaricaceae species, a number of divergence hotspots were identified among these plastomes. Together with the SSRs and long repeats identified, these divergence hotspots could be developed as potential molecular markers facilitating species discrimination and evolutionary studies. Using plastome sequences, we re-investigated the phylogenetic relationship among 19 species, and T. ramosissima was found to be a sister of Tamarix chinensis.

Conclusions: Taken together, our study provides valuable genomic resources to deepen the understanding of the plant photosynthetic mechanism and phylogenomics.

Background

Tamarix plants belong to the Tamaricaceae family and are ancient species native to Mediterranean region (Zhang et al. 2006). The Tamaricaceae family is composed of about 120 species distributed into 3–5 genera, among which Tamarix is the largest genus encompassing over 90 species (Gaskin et al. 2004). Although several Tamarix species are considered invasive in the United States, the supplementing of Tamarix plants in traditional medicine reveals their value in medical applications (Bahramsoltani et al. 2020). For instance, the leaves of Tamarix species are reported to have pharmacological effects such as detoxification, expelling rheumatism, and diuresis promotion in traditional Chinese medicine. While in Middle Eastern countries, an extract of Tamarix leaves has been used as an antiseptic agent (KalamUrfi et al. 2016). In addition, the bark of Tamarix aphylla, which differs in chemical constitution from the leaf, has been used as a herbal remedy for alleviating eczema capitis (Yu and Al 2011).

Chloroplasts (CPs) are photosynthetic organelles converting light energy from the sun into chemical energy stored in carbohydrates. Therefore, the cp proteome is abundant with enzymatic machineries catalyzing photosynthesis, and proteins responsible for starch synthesis, amino acid synthesis, fatty acid synthesis, phytohormone synthesis, and DNA and RNA synthesis (Yu et al. 2019). The multifaceted roles cp played in plant metabolism make it a key organelle for plant productivity and survival. Metabolic processes in the cp are, however, regulated by both the nucleus and the cp genome itself (Barajas-López et al. 2013). The cp genome, which is also known as cpDNA, is inherited maternally in most plants. Double-stranded cpDNAs usually exhibit a circular structure, with genome sizes ranging from 107 to 218 kB (Turmel et al. 2015). Further alignment of published cp genomes reveals their conserveness in gene arrangement. In angiosperms, most plastomes share a quadripartite structure, consisting of two inverted repeat regions (IRa and IRb) separated by a small single copy (SSC) region and a large single copy (LSC) region (Bogorad and Vasil 1990). Sequences of LSC and SSC are consistently conserved across most plant species. In Gymnospermae, however, the inverted repeats could vary substantially between species, and the changes in inverted repeat regions often lead to massive adjustment in DNA arrangement (Yang et al. 2020). For example, when lacking a large inverted repeat, extensive rearrangements of chloroplast DNA are observed in two conifer plants (Strauss et al. 1988).

The moderate evolutionary rate of cp genomes makes them potentially valuable resources in phylogenetic studies (Duan et al. 2020). In comparison with nuclear genomes, cpDNAs are smaller in size, and contain more conserved sequences. With an increasing number of cp genomes being sequenced, plastome-based phylogenomics could provide novel solutions for resolving phylogenetic ambiguities in plants.

In the present study, we report the first complete cp genome of Tamarix ramosissima and compare it with those of family Tamaricaceae. Through comparison, we elicidate the differences among the cp genomes of five Tamaricaceae species. Data in this study would facilitate the development of cp-derived molecular markers and the elucidation of phylogenetic relationship among Tamaricaceae species.

Materials And Methods

Phylogenetic Analysis

To investigate the phylogenetic relationships among Tamaricaceae species, a total of 18 plastome sequences were retrieved from GenBank and used for phylogeny construction. All sequences were first aligned with the MAFFT program. The nucleotide alignment was then subjected to phylogenetic analysis using the MEGA X program (Kumar et al. 2018). The phylogenetic relationship was inferred using both the neighbor-jointing (NJ) and the maximum likelihood (ML) methods.

Results

General features of the T. ramosissima chloroplast genome

The complete cp genome of T. ramosissima was 156,150 bp in length, displayed a typical quadripartite structure, in which a small-copy region (SSC, 18247 bp) and a large single-copy region (LSC, 84795 bp) were separated by two identical inverted repeats (IR, 26554 bp) (Fig. 1). After comparing the size and structure of cp genomes from Tamaricaceae species, we found that the lengths of the five plastomes varied from 154533 bp to 156167 bp; T. chinensis had the largest, while R. trigyna had the smallest (Table 1). The overall GC content of the T. ramosissima plastome was 36.5%, which was similar to those of the other four Tamaricaceae species. As shown in Table 1, the T. ramosissima cp genome encoded 130 genes, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The sequence of the newly assembled T. ramosissima plastome has been submitted to GenBank, and deposited under the accession number MN726883.

All the genes annotated in the T. ramosissima cp genome are listed in Table 2. Of the 130 genes annotated, a total of 16 genes contained introns. Among these intron-containing genes, 14 genes contained one intron, including 8 tRNA genes (trna-UUU, trna-CGA, trna-UUC, trna-UAA, trna-ACA, trna-UGC) and 6 protein-coding genes (ndhA, ndhB, atpF, rpoC1, rpl2, rps12). Two genes contained two introns (clpP, ycf3). rps12 was the only trans-spliced gene in the T. ramosissima plastome.

Discussion

In the present study, we obtained the complete chloroplast genome of T. ramosissima by Illumina sequencing and compared it with those of other four Tamaricaceae species. As shown in Table 1, the plastome size ranged from 154533 bp to 156167 bp with GC content varying slightly from 36.3–37.0%. Each of the five Tamaricaceae cp genomes encoded 130 genes, including 85 protein coding genes, 37 tRNA genes, and 8 rRNA genes. The five cp genomes were highly conserved in genome size and structure, especially for T. ramosissima and T. chinensis. However, boundary regions between SSC/IRs and LSC/IRs exhibited slight variations, which might be exerted by the expansion or contraction of IRs. Among the five Tamaricaceae species, plastome size was positively correlated with the length of IR, which was consistent with previous observations that changes in the IRs and their adjacent border regions were the main driving force for genome size variation and evolution (Fu et al. 2017; Xue et al. 2019).

SSRs or microsatellites are short tandem repeats that can be developed into molecular markers (Li et al. 2002). Chloroplast SSRs have been extensively used to study genetic diversity and phylogenetics in plants (Bi et al. 2018; Huang et al. 2015). Among the 64 SSRs identified in the T. ramosissima plastome, 40 (62.5%) were A/T mononucleotide repeats, and 12 (18.75%) were AT/AT di-nucleotide repeats. The high abundance of A and T in chloroplast SSRs were also observed in plastomes of the other four Tamaricaceae species. The findings in our study are consistent with those described previously in other species, including Xanthium sibiricum (Somaratne et al. 2019), Populus species (Gao et al. 2019), and Lilium plants (Du et al. 2017). The SSRs identified in T. ramosissima plastome, as well as those in other four Tamaricaceae species, could be developed as potential molecular markers facilitating future phylogenetic research.

Long repeats in plastid contribute to genome rearrangement and variation through unconventional combination at the repeat regions (Zhang et al. 2016), which might promote genetic diversity of the plastome (Timme et al. 2007). In the present study, we identified 32–49 repeats in the five Tamaricaceae cp genomes, the majority of which were localized in the LSC region. These repeat sequences, varying in types and sizes, may promote evolution of the plastids of Tamaricaceae species by generating new variation.

Due to the scarcity of cp genomic data, phylogenetic study at plastomic level was previously difficult to accomplish (Reginato et al. 2016). With the rapid development of high-throughput sequencing, plastome-based phylogenomics is emerging as a new tool for phylogenetics and evolutionary study in plants (McKain et al. 2018). We re-investigated the phylogenetic relationship in Tamaricaceae using the complete cp genome sequences available in the public database. Our analysis revealed that two Tamarix species, T. ramosissima and T. chinensis, were clustered together. Tamarix plants were more closely related to M. paniculate, a species that shows resemblance in appearance to plants in the genus Tamarix. As a genus erected from Tamarix (Liu 2009), the close relationship between Tamarix and Myricaria has also been confirmed in previous research (Naz et al. 2018; Yao et al. 2019). The complete cp genome sequence of T. ramosissima reported in our study will provide useful data resources for marker development and phylogenetics of Tamaricaceae species.

Conclusions

In the present study, the complete cp genome of T. ramosissima was first obtained by Illumina sequencing, and comprehensively compared with those from other four Tamaricaceae species. The newly sequenced T. ramosissima plastome is 156150 bp in length, encoding 130 genes. The deciphered cp genome exhibits a typical quadripartite structure, consisting a large single copy, a small single copy, and two inverted repeats. Thirty-two repeat sequences and 64 SSRs are identified in the plastome, which could be used as potential molecular markers for species discrimination and evolutionary studies. Phylogenetic relationship among Tamaricaceae species were re-investigated using the complete cp genome sequences. T. ramosissima has a close relationship with T. chinensis, which is strongly supported by high bootstrap values. In summary, the complete T. ramosissima cp genome assembled provides additional information for further studies, which will benefit future phylogenetic and evolutionary research.

Abbreviations

Declarations

Author contributions

LW analyzed the data, and drafted the manuscript. LW provided advices on our analysis. ZHG provided the samples and supervised the work.

Funding

This research was supported by Science and Technology Project of Qinghai Province (2019-ZJ-962Q; 2016-ZJ-Y01), The Open Project of State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University (2019-ZZ-05), and The Youth Foundation of Qinghai University (2019-QNY-2).

Availability of data and materials

The complete cp genome sequence of T. ramosissima has been submitted to GenBank and deposited under the accession number MN726883.

Ethics approval and consent to participate

Not applicable.

Consent for publication

Not applicable.

Competing interests

The authors declare that they have no competing interests.

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