Rich Sequences Research Articles

Innovative DNA-Targeted Metallo-prodrug Strategy Combining Histone Deacetylase Inhibition with Oxidative Stress.

Cancer remains a global health challenge. There is an urgent need to develop innovative therapeutics that can overcome the shortcomings of existing cancer therapies. DNA enzymes involved in nucleic acid compaction and organization are an attractive cancer drug target for therapeutic exploitation. In this work, a family of Cu(II) prodrugs containing suberoylanilide hydroxamic acid (SAHA), a well-established histone deacetylase inhibitor (HDACi) and clinically approved cancer drug, and phenanthrene ligands as DNA intercalative components have been rationally developed. The complexes, of general formula [Cu(SAHA-1H)( N, N'-phenanthrene)]+, exhibit excellent DNA recognition with binding affinity of lead agents in the order of ∼107 M(bp)-1. Biophysical studies involving nucleic acid polymers indicate intercalative binding at both adenine-thymine (A-T) and guanine-cytosine (G-C) rich sequences but thermodynamically stable interactions are favored in G-C tracts. The complexes mediate DNA damage by producing reactive oxygen species (ROS) with spin trapping experiments showing that superoxide, the hydroxyl radical, and hydrogen peroxide play critical roles in strand scission. The agents were found to have promising antiproliferative effects against a panel of epithelial cancers, and in two representative cell lines possessing mutated p53 (SK-OV-3 and DU145), enhanced cytotoxicity was observed. Significantly, mechanistic experiments with the most promising candidates revealed HDAC inhibition activity was achieved over a shorter time frame as compared to clinical standards with DNA damage-response markers identifying upregulation of both DNA synthesis and nucleotide excision repair (NER) pathways. Finally, confocal imaging and gene expression analysis show this metallodrug class exerts cytotoxic activity predominantly through an apoptotic pathway.

Symmetry-protected topological interfaces and entanglement sequences

Gapped interfaces (and boundaries) of two-dimensional (2D) Abelian topological phases are shown to support a remarkably rich sequence of 1D symmetry-protected topological (SPT) states. We show that such interfaces can provide a physical interpretation for the corrections to the topological entanglement entropy of a 2D state with Abelian topological order found in Ref.~\onlinecite{cano-2015}. The topological entanglement entropy decomposes as $\gamma = \gamma_a + \gamma_s$, where $\gamma_a > 0$ only depends on universal topological properties of the 2D state, while a correction $\gamma_s > 0$ signals the emergence of the 1D SPT state that is produced by interactions along the entanglement cut and provides a direct measure of the stabilizing symmetry of the resulting SPT state. A correspondence is established between the possible values of $\gamma_s$ associated with a given interface - which is named Boundary Topological Entanglement Sequence - and classes of 1D SPT states. We show that symmetry-preserving domain walls along such 1D interfaces (or boundaries) generally host localized parafermion-like excitations that are stable to local symmetry-preserving perturbations.

Hydrocarbon-seep carbonates associated with Mesozoic environmental perturbations: Example from the Lower Bajocian of Morocco

In the Lower Bajocian of the Jebel Bou Kendill section (Central High Atlas Mountain), three peculiar levels of authigenic carbonates are observed within the carbonate-poor Agoudim III Member. Morphological, sedimentological and geochemical evidences indicate that the two upper levels have been deposited at a hydrocarbon seep site, whereas the lowermost level likely underlines the zone where hydrocarbon fluids were generated. The first seep carbonate level is made of mineralized burrows that have acted as fluid conduits leading to a conspicuous cap carbonate bed on top of which several chimneys and chemoherm structures are embedded. Hence, this carbonate bed is a fossilized sea-floor carbonate crust. The second seep carbonate level is made of chemoherm structures buttressed against the first carbonate beds of the Agoudim IV Member. They were probably formed within the sedimentary column, close to the sea floor.Similar seep carbonates are observed regionally within the Agoudim III Member in the highly subsiding Central High Atlas troughs. A relationship between these seep carbonates occurrence and the late Early Bajocian global environmental perturbation can be deduced, as this latter has led to the deposition of a relatively organic-matter rich sedimentary sequence in these troughs via seawater eutrophication. The decomposition by bacterial activity of this organic matter, aided by rapid burial rates, has led to the generation of alkaline-rich fluids promoting the precipitation of the seep carbonates. A similar relationship between transient environmental perturbations and seep carbonates occurrence is observed in numerous Mesozoic examples and can be explained by the fact that hydrocarbon-seeps are supply-limited systems. Transient deviation from the Mesozoic greenhouse climate norm, either toward hothouse or coldhouse climates, favours the deposition of organic-rich sediments or transient methane storage, respectively, hence increasing the likelihood for the formation of hydrocarbon seepage.

Studies on the interaction of a synthetic nitro-flavone derivative with DNA: A multi-spectroscopic and molecular docking approach

Interaction of a ligand with DNA is often the basis of drug action of many molecules. Flavones are important in this regard as their structural features confer them the ability to bind to DNA. 2-(4-Nitrophenyl)-4H-chromen-4-one (4NCO) is an important biologically active synthetic flavone derivative. We are therefore interested in studying its interaction with DNA. Absorption spectroscopy studies included standard and reverse titration, effect of ionic strength on titration, determination of stoichiometry of binding and thermal denaturation. Spectrofluorimetry techniques included fluorimetric titration, quenching studies and fluorescence displacement assay. Assessment of relative viscosity and estimation of thermodynamic parameters from CD spectral studies were also undertaken. Furthermore, molecular docking analyses were also done with different short DNA sequences. The fluorescent flavone 4NCO reversibly interacted with DNA through partial intercalation as well as minor-groove binding. The binding constant and the number of binding sites were of the order 104 M−1 and 1 respectively. The binding stoichiometry with DNA was found to be 1:1. The nature of the interaction of 4NCO with DNA was hydrophobic in nature and the process of binding was spontaneous, endothermic and entropy-driven. The flavone also showed a preference for binding to GC rich sequences. The study presents a profile for structural and thermodynamic parameters, for the binding of 4NCO with DNA. DNA is an important target for ligands that are effective against cell proliferative disorders. In this regard, the molecule 4NCO is important since it can exert its biological activity through its DNA binding ability and can be a potential drug candidate.

Simplifying DNA NMR spectroscopy by silencing GH8 and AH8 resonances

NMR studies of DNA oligonucleotides are limited by extensive resonance overlap and the availability of isotopically labeled samples. We have explored a nondestructive and economical method to simplify DNA NMR spectroscopy by exchanging the hydrogens of GH8 and AH8 with deuterons. Exchanging these hydrogens with deuterons results in spectral simplification and alleviates spectral overlap particularly for A and G rich sequences and is therefore uniquely suited for G-quadruplex sequences. The silencing of the GH8 and AH8 signals facilitates structural and ligand DNA binding studies.

High-resolution RNA 3'-ends mapping of bacterial Rho-dependent transcripts.

Transcription termination in bacteria can occur either via Rho-dependent or independent (intrinsic) mechanisms. Intrinsic terminators are composed of a stem-loop RNA structure followed by a uridine stretch and are known to terminate in a precise manner. In contrast, Rho-dependent terminators have more loosely defined characteristics and are thought to terminate in a diffuse manner. While transcripts ending in an intrinsic terminator are protected from 3′-5′ exonuclease digestion due to the stem-loop structure of the terminator, it remains unclear what protects Rho-dependent transcripts from being degraded. In this study, we mapped the exact steady-state RNA 3′ ends of hundreds of Escherichia coli genes terminated either by Rho-dependent or independent mechanisms. We found that transcripts generated from Rho-dependent termination have precise 3′-ends at steady state. These termini were localized immediately downstream of energetically stable stem-loop structures, which were not followed by uridine rich sequences. We provide evidence that these structures protect Rho-dependent transcripts from 3′-5′ exonucleases such as PNPase and RNase II, and present data localizing the Rho-utilization (rut) sites immediately downstream of these protective structures. This study represents the first extensive in-vivo map of exact RNA 3′-ends of Rho-dependent transcripts in E. coli.

Evaluation of simultaneous binding of Chromomycin A3 to the multiple sites of DNA by the new restriction enzyme assay

Chromomycin A3 (CMA3) is an aureolic acid-type antitumor antibiotic. CMA3 forms dimeric complexes with divalent cations, such as Mg2+, which strongly binds to the GC rich sequence of DNA to inhibit DNA replication and transcription. In this study, the binding property of CMA3 to the DNA sequence containing multiple GC-rich binding sites was investigated by measuring the protection from hydrolysis by the restriction enzymes, AccII and Fnu4HI, for the center of the CGCG site and the 5′-GC↓GGC site, respectively. In contrast to the standard DNase I footprinting method, the DNA substrates are fully hydrolyzed by the restriction enzymes, therefore, the full protection of DNA at all the cleavable sites indicates that CMA3 simultaneously binds to all the binding sites. The restriction enzyme assay has suggested that CMA3 has a high tendency to bind the successive CGCG sites and the CGG repeat.

Serine Rich Splicing Factor 2 (SRSF2) Flips for RNA Binding

Mistakes in alternative splicing of RNA cause diseases such as acute myeloid leukemia. Serine Rich Splicing Factor 2 (SRSF2) is a splicing factor that controls alternative splicing by promoting exon inclusion, so it is not surprising that mutations to SRFS2 are linked to cancers. SR proteins harbor an RNA recognition motif (RRM) at the N‐terminus that binds to mRNA. SRSF2 has the unusual ability to bind to both pyrimidine and purine rich RNA sequences by flipping two C or G nucleotides in the mRNA into anti or syn orientations. The RRM specifically recognizes only C2, C3, and G5. Arg61 forms a hydrogen bond to C3, Phe59 hydrogen bonds to C2, and Lys17 is involved in flipping C2 or G2 into syn or anti conformations. Tyr92 binds with C2 and forms a hydrogen bond with C3. The mutation Pro95His binds better to UCCAGU and has been linked to cancer. The Hartford Union High School SMART (Students Modeling A Research Topic) Team modeled SRSF2 using 3D printing technology to highlight structural characteristics involved in RNA binding. Additional research on SRSF2 mutations and sequence binding has the potential to find both causes of and treatments for diseases like cancer.Support or Funding InformationThe MSOE Center for BioMolecular Modeling would like to acknowledge and thank the National Institutes of Health Science Education Partnership Award (NIH‐SEPA 1R25OD010505‐01) and the National Institutes of Health Clinical and Translational Science Award (NIH‐CTSA UL1RR031973) for their support in funding the 2017‐2018 SMART Team Team program.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Metacaspases of the Fungus S. commune Are Activated by Calcium and Specific for Arginine

Metacaspases belong to a class of cysteine peptidase protein enzymes and are known to be involved in several programmed cell death (PCD) mechanisms in plants and lower eukaryotes. Similar to caspases, metacaspases contain a cysteine‐histidine catalytic dyad and can undergo autoprocessing for increased activity. However, these proteases cleave after arginine or lysine residues, while caspases are aspartate specific. Previous studies have shown that Ca2+ plays a critical role in metacaspase activity. The metacaspase structures of MCA2 (Trypanosoma brucei) and YCA1 (Saccharomyces cerevisiae) have been found to contain calcium‐binding site(s) necessary for complete enzyme activity. A subset of metacaspases possesses an N‐terminal prodomain containing a proline rich sequence. We have identified five metacaspase genes in this subset from the split‐gilled fungus Schizophyllum commune (ScMC1‐5). All genes for ScMC1‐5 have been cloned with and without the prodomain (Δpro) into a SUMO vector construct, expressed, purified and tested for enzymatic activity.The goal of this project was to characterize ScMC1‐5Δpro by determining substrate specificity, optimal Ca2+ concentrations, and optimal pH levels for each enzyme using a metacaspase fluorogenic activity assay. Results show that all ScMC1‐5Δpro showed arginine and lysine specificity, with higher efficiency for arginine. All enzymes performed best within a pH range of 7 and 8. Optimal calcium concentrations ranged from 5 mM to 50 mM Ca2+. Only ScMC1Δpro is completely inactive at 0 mM calcium. ScMC1&5Δpro have a much higher optimal concentration (50 mM), compared to ScMC2, 3 and 4Δpro, suggesting that calcium may have different binding affinities and play different roles in each enzyme. These data agree with current literature for other similarly characterized metacaspases. Increasing our understanding of metacaspase enzymes could provide vital information for the development of future anti‐fungal and antibacterial treatments.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

NOTCH1 mutation and its prognostic significance in Chinese chronic lymphocytic leukemia: a retrospective study of 317 cases.

The proto‐oncogene NOTCH1 is frequently mutated in around 10% of patients with chronic lymphocytic leukemia (CLL). This study analyzed NOTCH1 mutation status of 317 Chinese patients with CLL by Sanger sequencing. The frequencies of NOTCH1 mutation in the PEST (proline (P), glutamic acid (E), serine (S), threonine (T)‐rich protein sequence) domain and the 3′ untranslated regions (UTR) were 8.2% and 0.9%, with the most frequent mutation being c.7541_7542delCT and c.*371A>G, respectively. Clinical and biological associations were determined including NOTCH1 mutations with advanced stage (Binet stage, P = 0.010), unmutated immunoglobulin heavy‐chain variable region (IGHV) gene (P < 0.001) and trisomy 12 (+12) (P = 0.014). NOTCH1‐mutated patients had lower CD20 expression intensity than NOTCH1‐unmutated patients (P = 0.029). In addition, NOTCH1‐mutated patients had shorter overall survival (OS) (P = 0.002) and treatment‐free survival (TFS) (P = 0.002) than NOTCH1‐unmutated patients, especially for patients with NOTCH1 c.7541_7542delCT and/or c.*371A>G mutations. Patients with both mutated NOTCH1 and unmutated IGHV had shorter OS (P < 0.001) and TFS (P < 0.001) than those with unmutated NOTCH1 or mutated IGHV. These data provide a comprehensive view of the clinical relevance and prognostic impact of NOTCH1 mutations on Chinese patients with CLL.

Detection of biotin-streptavidin interactions based on poly(thymine)-templated copper nanoparticles coupled with Exo III-aided DNA recycling amplification

The recognition and analysis of small molecule–protein interactions plays an important role in chemical genetics, clinical diagnostics, and drug development. However, various established highly sensitive fluorescence strategies still involve the use of expensive fluorescence dye-labelled nucleic acids. Herein, we constructed a highly sensitive and label-free fluorescent assay for small molecule–protein interactions on the basis of exonuclease III (Exo III)-assisted signal amplification and poly(thymine)-templated fluorescent copper nanoparticles (CuNPs) as signal probes. Biotin–streptavidin system was taken as a model. It was designed that biotinylated double-strand DNA served as the binding probe. Biotin was labelled at the 3′-end of the trigger strand. One kind of stem-loop DNA, which consisted of the thymine rich sequence and the trigger DNA recognition domain, was also designed. Once streptavidin bind to the binding probe, with the help of Exo III digestion, the trigger strand was able to reach the cycle for multiple poly(thymine) sequences generation. The produced poly(thymine) sequences can be used as a template for the formation of CuNPs. Comparing with no Exo III-aided DNA recycling amplification, significantly improved signals for the quantitative determination of streptavidin were obtained.

Statistical analysis of Bacteria GeneChips for possible effects caused by Hoogesteen hydrogen bonding between Guanines

According to Watson-Crick base pairing, Guanine binds to Cytosine and Adenine binds to Thymine to form a double helix DNA molecule; however, it is observed that guanine can also bind with another guanine through hoogesteen hydrogen bonding at about 90 degrees. Thus a tetrad is formed if four guanines are attached with each other. These tetrads are the cause of the formation of unusual structures called G-quadruplex structures. These structures not only formed by a single guanine rich nucleic acid sequence but their formation is also possible by two or four parallel sequences collectively. These structures (or guanine rich sequences through which they are formed) affect a well known technology named Affymetrix GeneChip which is popular for gene expression measurement effectively and cheaply. Since the nucleic acid sequences are placed very closely on GeneChip, they are able to interact with each other and then form G-quadruplex structures. In this case, they are not ready to hybridize with their target sequences. It is found that raw or hybridization level data of human, mouse and rat (mammalian in general) are affected by guanine rich sequences. This paper exhibits that GeneChips of two Bacterias are also affected by guanine-guanine interaction and hence measurement of gene expressions using these chips could be misleading.

Electrochemical Monitoring of the Reversible Folding of Surface-Immobilized DNA i-Motifs.

Two cytosine (C) rich DNA sequences folding in i-motif upon protonation of C at low pH have been immobilized at gold electrodes to study the impact of the electrode|electrolyte interface on the stability of the noncanonical DNA secondary structure. The effects of the molecular composition and environment on the melting and folding of the structures immobilized at the gold surface have been compared to the properties of the DNA strands in solution. The DNA folding into i-motif upon protonation, both at the surface and in solution, results in a significant variation of the charge density which is monitored electrochemically through the electrostatic interactions between the DNA strand and the electroactive hexaammineruthenium(III). This method is shown to be sufficiently sensitive to distinguish hemiprotonated folded state and single strand unfolded state of i-motif. The pH of melting has been determined for both sequences in the bulk and at the gold|electrolyte interface. The results evidence a stabilizing effect of the interface on i-motif structure, whereby the pH of melting is higher for the sequences immobilized at the surface. The reversibility and precision of the electrochemical model described here allows a clear and simple characterization of DNA structures and does not require any labeling of the sequence.

Whole-genome sequencing reveals principles of brain retrotransposition in neurodevelopmental disorders.

Neural progenitor cells undergo somatic retrotransposition events, mainly involving L1 elements, which can be potentially deleterious. Here, we analyze the whole genomes of 20 brain samples and 80 non-brain samples, and characterized the retrotransposition landscape of patients affected by a variety of neurodevelopmental disorders including Rett syndrome, tuberous sclerosis, ataxia-telangiectasia and autism. We report that the number of retrotranspositions in brain tissues is higher than that observed in non-brain samples and even higher in pathologic vs normal brains. The majority of somatic brain retrotransposons integrate into pre-existing repetitive elements, preferentially A/T rich L1 sequences, resulting in nested insertions. Our findings document the fingerprints of encoded endonuclease independent mechanisms in the majority of L1 brain insertion events. The insertions are "non-classical" in that they are truncated at both ends, integrate in the same orientation as the host element, and their target sequences are enriched with a CCATT motif in contrast to the classical endonuclease motif of most other retrotranspositions. We show that L1Hs elements integrate preferentially into genes associated with neural functions and diseases. We propose that pre-existing retrotransposons act as "lightning rods" for novel insertions, which may give fine modulation of gene expression while safeguarding from deleterious events. Overwhelmingly uncontrolled retrotransposition may breach this safeguard mechanism and increase the risk of harmful mutagenesis in neurodevelopmental disorders.

Microanalysis of Multimodal Communication in Therapy: A Case of Relational Trauma in Parent-Infant Psychoanalytic Psychotherapy

ABSTRACTThis article explains the role of multimodal, microanalytic examinations of the therapeutic process in parent-infant psychotherapy. The work described involves the adaptation of the microanalytic approach that has been applied to exploring the dyad and the rich interactional sequences of behaviors that constitute the parent-infant relationship. The approach in this article widens the focus to include the therapist’s interactions with parent and infant in considering how parent-infant psychotherapy works. Using a clinical case study, several perspectives of the therapeutic processes, including transcripts from videoed sessions, microanalysis of a brief five-second event; clinical session notes, and the therapist’s own narrative, are drawn upon to follow the therapeutic encounter and to consider how the micro-interventions on the part of the therapist, often in the form of subtle embodied communications, interact with the evolving interactional behaviors of the dyad to bring about change in the parent-infant relationship.

DNA-Templated Silver Nanoclusters for DNA Methylation Detection.

DNA methylation entails the covalent addition of a methyl group to C-5 position of cytosine by a family of DNA methyltransferase enzymes and has a significant role in gene regulation. Epigenetic changes such as DNA methylation of CpG islands located in the promoter region of some tumor suppressor genes are very common in human diseases such as cancer. Detection of aberrant methylation pattern could serve as an excellent diagnostic approach. It is key to develop methods for the direct and simple detection of methylated DNA or of methyltransferase activity without using antibodies, chemical modification, labeling and enzymatic treatments. In this study, we employ DNA-templated silver nanoclusters for detection of DNA methylation. This method entails use of cytosine rich DNA sequence as an effective template. By monitoring changes in fluorescence intensity, DNA methylation and DNA methyltransferase activity is detected. Upon DNA methylation, the fluorescence intensity of DNA templated Ag/NCs is decreased in a linear range when the concentration of methylated DNA is increased.

Ganodermanontriol inhibits expression of special AT rich sequence binding protein 1 gene in human hepatocellular carcinoma.

The metastasis of liver cancer is a major cause of clinical treatment failure, restrain, and control the cancer metastasis is the major strategy of the treatment and prevention of the disease. Special AT-rich sequence-binding protein 1 (SATB1) gene was overexpressed in many malignant tumors and considered as a potential target of anticancer drug. This study investigated the mechanism how ganodermanontriol effect the expression of SATB1 and thus inhibits the growth and metastasis in hepatocellular carcinoma (HCC). This study explored mainly on the mechanism how ganodermanontriol affects the expression of SATB1 and inhibits proliferation of tumor on human hepatoma cell line HepG2. The cancer cells were treated with ganodermanontriol. The status of the cells was detected by different methods. The mechanism was checked by various methods. In HepG2 cancer cells treated with various concentrations of ganodermanontriol, the cell proliferation of was detected by MTT assay, cell apoptosis was analyzed by flow cytometry; the mRNA of SATB1, Bcl-2, Bax were detected by reverse transcription-polymerase chain reaction (RT-PCR) and the protein level of SATB1, Bcl-2, Bax, and caspase 3 were analyzed by Western blot. Data are presented as the mean ± standard deviation. The data were analyzed using SPSS 18.0 software (SPSS, Inc., Chicago, IL, USA) and GraphPad Prism software (GraphPad Software, Inc., La Jolla, CA, USA). A one-way analysis of variance test was used to compare the differences among groups. This study showed that ganodermanontriol could significantly reduce the expression level of SATB1. Therefore, downregulate the cascade effect caused by the expression level of Bcl-2 in HCC HepG2 cells.

Enzyme-free and label-free miRNA detection based on target-triggered catalytic hairpin assembly and fluorescence enhancement of DNA-silver nanoclusters

We herein describe a simple, enzyme-free, and label-free strategy for the detection of miRNA based on target-triggered catalytic hairpin assembly (CHA) and fluorescence enhancement of DNA-silver nanoclusters (DNA-AgNCs). This strategy employs two hairpin probes that are rationally designed to contain AgNCs and guanine (G)-rich DNA sequence, respectively. In principle, the two hairpin probes, which exist independently, form a hybridized complex in the presence of target miRNA through CHA reaction, thereby inducing strong fluorescence signal of AgNCs by the presence of G-rich sequence placed in close proximity. Importantly, target miRNA is released after the first CHA reaction, which promotes another CHA reaction, consequently leading to the significantly enhanced fluorescence signal of AgNCs. Based on this one-step, homogeneous, and isothermal amplification method, we successfully detected the target miRNA with high selectivity and sensitivity. In addition, the practical applicability of this strategy was also demonstrated by analyzing the target miRNA in human serum.

Syntheses of Zn(II) and Cu(II) Schiff base complexes using N,O donor Schiff base ligand: Crystal structure, DNA binding, DNA cleavage, docking and DFT study

Two mononuclear Schiff base complexes, [Zn(L)2] (1) and [Cu(L)2] (2) are synthesized involving bidentate N,O-donor ligand viz. 2-((E)-(3-methoxypropylimino)methyl)-6-methoxyphenol. Different spectroscopic tools like FTIR, UV–Vis, 1H NMR, 13C NMR etc. have been deployed to characterize complexes 1 and 2. Complex 1 has been analyzed using single crystal X-ray diffraction analysis method. Complexes 1 and 2 show affinity towards A-T rich sequence of DNA which is further supported by molecular docking analysis. Interestingly, only complex 2 exhibits oxidative DNA cleavage activity in presence of H2O2 which is investigated by gel electrophoresis method. Complex 1 is found to be nontoxic whereas complex 2 is cytotoxic.

Comparative Analysis of the Complete Chloroplast Genome of Four Known Ziziphus Species.

Ziziphus Mill. (Rhamnaceae) is comprised of about 170 species that are mainly distributed in tropical to subtropical regions, with few in the temperate zone. Several Ziziphus fruit tree species are important energy, nutrient, and medicinal resources for human populations, particularly for those living in rural regions. To date, limited genomic information is available for this genus. Here, we assembled the complete chloroplast genomes of four best known Ziziphus species, i.e., Ziziphus jujuba, Ziziphus acidojujuba, Ziziphus mauritiana, and Ziziphus spina-christi, based on the Illumina Paired-end sequencing method. The chloroplast genomes of the four Ziziphus species are all very similar to one another, and exhibit structural, gene content, and order characteristics that are similar to other flowering plants. The entire chloroplast genome encodes 113 predicted unique genes (85 protein-coding genes, 8 rRNA, and 37 tRNA), 17 of which are duplicated in the inverted repeat regions. Rich single sequence repeats loci (217) were detected in Z. jujuba and 106 SSR loci, composed of A/T, displayed polymorphism across the four species by comparative genomic analysis. We found only four genes under positive selection between Z. jujuba and Z. acidojujuba, and two genes for Z. mauritiana vs. Z. spina-christi, respectively, while half of the 78 protein-coding genes experienced positive selection between the two groups. Phylogenetic analyses revealed that Ziziphus (Rhamnaceae) was sister to Elaeagnaceae, and the four species of Ziziphus were clustered into two groups (Z. jujuba and Z. acidojujuba, Z. mauritiana and Z. spina-christi). Our results provide genomic resources for intrageneric classifications of Ziziphus, and valuable genetic markers for investigating the population genetics and biogeography of closely related Ziziphus species.