matK Gene Research Articles

DNA barcoding, pollen and seed characteristics for documentation of four monocot Mediterranean endemic plant species in Egypt

Endemic taxa are critical constituents in the flora of most parts of the world. Recently, most of these taxa have become exposed to extinction. This study aims to increase understanding of four monocot Mediterranean threatened endemic taxa in Egypt (Allium mareoticum Bornm. & Gauba, Bromus aegyptiacus Tausch, Muscari salah-eidii (Täckh. & Boulos) Hosni, Pancratium arabicum Sickenb.) by description of their pollen and seed and authentication of DNA barcoding using rbcL and matK genes. Twenty field visits were conducted from March 2017 till April 2023 including different localities through Mediterranean area for covering the presence of these species. Characterization of pollen grains and seeds were examined using a light (LM) and scanning electron microscopes (SEM). DNA barcoding was carried out for documentation of the four species. Maturase K (matK) and ribulose-bisphosphate carboxylase (rbcL) were used as primers for PCR amplification and gene sequencing. The two genes were successful in identifying Allium mareoticum, Bromus aegyptiacus, and Muscari salah-eidii at the genus level and Pancratium arabicum at both species and genus levels for rbcL marker, and the genus level for matK marker. This study is considered a leading study for new barcodes of (A) mareoticum, (B) aegyptiacus, and M. salah-eidii which were initially made available to the NCBI.

In Silico Evaluation of rbcL, matK, and psbA-trnH Regions on the Genus Spatholobus (Fabaceae)

Spatholobus is a genus that belongs to the Fabaceae that is known to contain various bioactive compounds and distributed across Asia, including Indonesia. However, exploration of Spatholobus in Indonesia is still rare. Therefore, DNA barcoding is used to support the exploration and conservation of Spatholobus in Indonesia. However, there is no universal marker that can be used across all plant species. In addition, there are still few studies related to DNA barcoding within the genus Spatholobus. The purpose of this study was to evaluate the rbcL, matK, and intergenic spacer psbA-trnH regions in silico that can be used as DNA barcodes for the genus Spatholobus. This study began with a sequence search on the NCBI database including the rbcL, matK, and intergenic spacer psbA-trnH genes in the genus Spatholobus and Phaseolus coccineus as the outgroup. Each sequence was then aligned with ClustalW. Then, a phylogenetic tree was constructed using the Maximum-Likelihood (ML) with 1000× bootstrap. As a result, the rbcL, matK, and psbA-trnH regions can be used as markers for DNA barcoding in the genus Spatholobus with different specifications. The rbcL and matK can be used to distinguish Spatholobus at the genus level, while the psbA-trnH can be used to distinguish Spatholobus at the species level.

Impact of Molecular Identification of Palm leaves on the preservation and conservation of Palm Leaves-Tala patra Manuscripts

Palm leaves manuscripts preservation is the main target of this research work. Therefore, this research study aimed at molecular identification of palm leaves by DNA Barcoding to assess the potential level on manuscript preservation. This study aims to amplify the rbcL and matK genes in palm leaves collected from different regions of Bangalore. The DNA was isolated by CTAB method and the amplification was done by PCR analysis. DNA barcoding proved to be an efficient tool for proper discrimination of the related species by generating standers that can be used universally. rbcL: A gene found in the chloroplast genome, encoding a large subunit of the enzyme ribulose-bisphosphate carboxylase. matK: Another chloroplast gene coding for maturase K, involved in splicing group II introns. The discrimination is done by accurately sequencing the standard gene region in a very short time (Hebert et al., 2003). rbcL and matK have been having most recommended and vasty studied DNA barcodes for plants, as they are proved by PWG (Pair wise group) to be potential standardized barcodes for plant DNA barcoding. These barcodes are used to properly identify and discriminate any native or foreign plant species (Maloukh et al., 2017). This work guides us the impact/role of molecular identification-DNA Barcoding of palm leaves on the preservation of Palm leaves manuscripts

DNA Extraction and PCR Optimization of Coffea arabica L. and Coffea canephora Pierre ex A. Froehner

DNA isolation is an important step for further molecular analysis. Coffee plants contain polysaccharides, polyphenols, and secondary metabolites which can contaminate the results of DNA isolation. This study was conducted to isolate DNA from arabica and robusta coffee leaves using a modified CTAB method and PCR optimization for amplification of matK and rbcL genes. DNA was isolated using buffers (CTAB 10%, PVP 1%, β-mercaptoethanol 1%, Tris-HCl 1M, NaCl 5M, and EDTA 0.5%), and eluted with TE-RNase. Genomic DNA of ten coffee plants was successfully isolated with concentrations ranging from 33-146 nm/µL with purity (A260/A280) 1.7-1.9. Based on the genomic DNA isolated, matK and rbcL genes were amplified with initial denaturation conditions of 94°C (for 1 minute of matK and 4 minutes of rbcL) followed by 35 cycles of denaturation at 94°C for 30 seconds, annealing (adjusted to each primer), and extension at 72°C for 1 minute. The optimal PCR conditions were effective to amplify matK (900 bp) and rbcL (600 bp) genes. Thus, the modified DNA isolation method and PCR optimization can be used as an efficient tool for further molecular analysis of Coffea arabica L. and Coffea canephora Pierre ex A. Froehner.

Molecular Identification Validates Morphological Identification of Javanese Cardamom from Banyumas in Central Java, Indonesia

Cardamom is one of the prominent plants with significant economic value in the Banyumas Regency, Central Java, Indonesia. Although Javanese cardamom is traditionally categorized under Amomum compactum, the morphological variations observed create ambiguity about its exact species status. DNA barcoding using the maturase K (matK) and ribulose-bisphosphate carboxylase (rbcL) genes is proven as a reliable technique to elucidate the taxonomic status of morphological variable plant cultivars. This study aimed to characterize cardamom from Banyumas Regency using morphological and molecular approaches for taxonomic status identification and genetic diversity evaluation. The matK and rbcL genes were selected as genetic markers and sequenced using a bidirectional sequencing technique. Morphological examination showed significant color variations at the cardamom stem base. All samples had high genetic identities to reference species in databases and were supported by high query cover and zero e-values. Therefore, molecular characterization, alongside geographic distribution assessment, established that this plant belongs to a single species, Amomum compactum. Additionally, the analysis conducted showed a low level of genetic diversity, as evidenced by haplotype and nucleotide diversity. Low-level genetic diversity provides additional data to convince that cardamon in Banyumas Regency belongs to a single species. These results are essential data in seed selection for further cultivation.

Timber DNA release using focused ultrasound extraction (FUSE) for genetic species identification

The use of genetic data for timber species and population assignment is a powerful tool for combating the illegal timber trade, but the challenges of extracting DNA from timber have prevented the routine use of genetics as a supply chain management tool. To overcome these challenges, we explored the feasibility of focused ultrasound extraction (FUSE) for rapid DNA release from timber. Using high-pressure ultrasound pulses, FUSE generates a cavitation bubble cloud that disintegrates samples into acellular debris, resulting in the mechanical release of DNA. In this work, FUSE was applied to white oak (Quercus alba) timber shavings to test the feasibility of using FUSE for timber DNA extraction for the first time. Results showed that FUSE processing disintegrated the tissue samples and released significant quantities of DNA. After five minutes of tissue processing DNA quantities of 0.21 ± 0.02 ng/mg, 0.99 ± 0.32 ng/mg, and 0.14 ± 0.01 ng/mg, were released from medium, coarse, and combination shaving groups, respectively. Amplification and sequencing of regions within the matK and rbcL chloroplast genes confirmed that the quality of DNA prepared with FUSE was suitable for PCR and short-read sequencing applications. Overall, these results show that FUSE can serve as a DNA sample preparation method capable of releasing high-quality DNA from timber in a fraction of the time required by conventional extraction methods. Based on the improved efficiency of DNA release with FUSE, ongoing work aims to develop this technology into portable systems that can be used to rapidly prepare timber samples for genetic species identification.

Enriching barcoding markers in environmental samples utilizing a phylogenetic probe design: Insights from mock communities

AbstractHybridization capture is an emerging method making use of short oligonucleotide baits to enrich DNA libraries for genomic fragments of specific organisms thus enabling detection of their presence in environmental samples. Although it offers a primer‐independent alternative to metabarcoding, little empirical work has been dedicated to characterizing the underlying biases and coupled implications for biological interpretation. Moreover, few published bioinformatic pipelines are available for designing polynucleotide capture baits from a reference sequence collection. We designed RNA‐baits specifically targeting two chloroplast barcoding genes matK and rbcL to reveal the plant taxonomic diversity present in a given environmental sample. Our approach leverages the sensitivity of hybridization capture and the capacity of high‐throughput DNA sequencing instruments. It builds on a new and universal method based on ancestral sequence reconstruction, ultimately limiting the number of bait‐probes required and reducing experimental costs, while accessing high levels of taxonomic diversity. Our bait‐set selectively targets four main plant orders (Fagales, Pinales, Asterales, and Poales), representing ~18% of all described vascular plants. This is achieved through the use of only 4084 baits, each 80 nucleotides in length (80‐mer), capturing ~1.0–1.6 k nucleotide sequences from each taxon. Tests on mock communities revealed important factors influencing capture efficiency and relative abundance estimates, including GC‐content, the overall target length per taxa, and the bait density and mean number of mismatches to the bait sequence. Our results show that hybridization capture, like metabarcoding, requires caution when interpreting results quantitatively within (paleo)‐ecological studies. Biases detected in this work have the potential to be mitigated with bait designs that avoid extreme base compositional biases and balancing bait targets across taxa. However, we strongly recommend the use of mock communities and read simulations to quantify the accuracy of taxonomic representation when using new bait designs.

New specific primer matK and rbcL region for DNA barcode pitcher plant Nepenthes spathulata

Abstract. Utama MN, Etikawati N, Sugiyarto, Susilowati A. 2024. New specific primer matK and rbcL region for DNA barcode pitcher plant Nepenthes spathulata. Biodiversitas 25: 2515-2523. The matK and rbcL genes were proposed as the preferred plant barcoding loci by The Consortium for the Barcode of Life (CBOL). DNA barcoding efficiently identifies samples at the species level using short standard DNA sequences. The identification disclosure needs is an important basis given the confusion in systematics in Nepenthes spathulata. Therefore, this study aims to design matK and rbcL region-specific primers for DNA barcoding pitcher plants. The primary design uses Primer3Plus with a blueprint from the GenBank KDQ007081.1 for matK and MH346374.1 for rbcL. Following testing primary candidates with Oligo Analyzer and Primer-BLAST, the primers MkNs1, and RbNs4 were selected as the optimal criteria based on the values of ?G and primer specificity. Optimization of annealing temperature with PCR gradient shows that the temperature range 52-57°C produces a good band for both regions and corresponds to the matK and rbcL region with product sizes of 800-900 bp from seven samples, which could be observed from the gel electrophoresis. Sequence similarity using blast-N, the matK sequence has similarity to the N. spathulata matK gene of 99.64% and 99.63% for the rbcL gene of N. ventricosa x N. alata. This MkNs1 and RbNs4 primer can be used to discover the identity of N. spathulata and the Nepenthes genus.

Morphological and molecular characterization of two species of genus Ageratum.

The species of genus Ageratum (family Asteraceae) are distributed in various parts of the world. Ageratum conyzoides and A. houstonianum are the most commonly occurring species in India. These species are quite similar in their morphology thus creating a challenge in identification during the field survey and taxonomic validation. The accurate identification of the species is highly significant especially when those are of medicinal interest. To overcome the barriers in morphological based identification, DNA barcoding has been employed during the present investigation. Morphological and DNA barcodes matK and ITS genes, were employed to differentiate between Ageratum conyzoides and A. houstonianum. The obtained matK and ITS gene sequences were submitted to GenBank and BOLD system to obtain accession numbers. The DNA sequences were aligned with database sequences using BLAST and phylogenetic trees were constructed through neighbor-joining algorithm in MEGA 11 software. The distinguish features of A. conyzoides include ovate to elliptic-oblong leaves with a cuneate base and inflorescence heads forming domed to flat-topped clusters. However, A. houstonianum has triangular to ovate leaves with a cordate to truncate base, cymose clusters in the inflorescence and stipulate glandular involucre bracts. The matK gene has shown the highest identity percentages (100%) for A. houstonianum and 99.87% for A. conyzoides. The phylogenetic tree analysis has demonstrated a close association of A. conyzoides and A. houstonianum with their respective species, supported by bootstrap values in the matK and ITS trees. This study revealed that morphological and molecular data can be successfully utilized in the identification of A. conyzoides and A. houstonianum. The matK and ITS barcodes provide promising results in the identification of Ageratum species, with their phylogeny supporting classification within the family asteraceae.

Molecular Identification of Morus ssp. in Duhok Using Nuclear ITS Region and Chloroplast Matk Gene

Since Mulberries (Morus)is a tree species with a considerable plant variety. Molecular techniques are methods used to distinguish between species accurately, easily and quickly. This study examines a Molecular method for distinguishing different Morus species in the Duhok - Kurdistan region/ Iraq. The method is based on the use of four techniques: matK gene, the ITS region, PCR-RFLP, and SRAP markers. Twelve Morus species have been selected for this study from different region of Duhok. The ITS region's PCR result was 700 bp, but the matK gene's PCR produce was 900 bp. The same restriction site was found for all utilized cultivars when the 700bp of ITS fragment was used for PCR-RFLP with two restriction enzymes, RsaI GT/AC and HaeIII GG/CC. This study also used six combinations of SRAP markers to aid in grouping and identifying genetic similarities. The results of PCR-RFLP demonstrated an insufficient link between Morus physical appearance and genetic traits, but differences across studied cultivars could be identified using SRAP markers. Furthermore, this study demonstrated the possibility of DNA barcoding Morus cultivars, as well as additional sequence analysis and the identification of probable SNP between cultivars.

The Effect of The Insecticide Hulk on Some Genetic Characteristics of The Whitefly and The Cucumber Plant That Parasitizes It

Background: Whitefly, Bemisia tabaci is one of the major injurious sucking pests in tropical and subtropical regions. The effect of the insecticide Hulk, which is used to kill the whitefly, was revealed, and its effect on some of its genes and the genes of the cucumber plant that parasitizes it, was revealed. Materials and Methods: The current study was conducted in Kirkuk Governorate. DNA was extracted from whiteflies treated with Hulk pesticides and not treated with pesticides as a control, and DNA was also extracted from cucumber leaves treated with the Hulk pesticide and not treated with the pesticide as a control in order to compare them. detecting the specific primer of gene 28s in the whitefly Bemisia tabaci and Matk gene in the plant Cucumis sativus. Three treatments of each pesticide at three concentrations (25% a quarter lethal, 50% half lethal, 100% lethal). Results: The research found that 25% of the pesticide Halk killed 20% of the insects, 50% killed 40%, and 100% killed 70% within 24 hours. Pesticide Hulk found that cucumber plant mutations in the Matk gene and gene 28s had the best insecticidal effects against whitefly Bemisa tabaci. Conclusions: Overall, results suggest that ethanolic DNA extracts pesticide Hulk is the occurrence of mutations in the Matk gene in the plant Cucumis sativus and gene 28s in the whitefly Bemisia tabaci showed the highest insecticidal effects on whitefly Bemisa tabaci.

Botanical Biometrics: Exploring Morphological, Palynological, and DNA Barcoding Variations in White Kwao Krua (Pueraria candollei Grah. ex Benth. and P. mirifica Airy Shaw & Suvat.)

White Kwao Krua, a crucial Thai medicinal plant, contains various phytoestrogen substances used to alleviate menopausal symptoms in estrogen-deficient women. It originates from two species, namely Pueraria candollei Wall. ex Benth. and P. mirifica Airy Shaw & Suvat. However, there exists morphological variation, and the taxonomic status between both species is ambiguous, making discrimination challenging. In this study, we aim to clarify and differentiate the morphological characteristics, palynology, and DNA barcoding of both species. The morphological results showed the stipule size is a phenotypic marker for the differentiation of both species during the vegetative stage. The palynological results, however, exhibited similarity. Through an examination of nucleotide sequences and neighbor-joining tree analysis, it was determined that the DNA barcoding of the matK region has the capability to distinguish between P. candollei and P. mirifica at nucleotide position 702. Specifically, P. candollei manifested a G base, contrasting with the C base observed in P. mirifica. This study concludes that stipule size and the matK gene in DNA barcoding serve as a distinctive characteristic for distinguishing between P. candollei and P. mirifica. These methodologies prove valuable for ensuring the accurate identification of white Kwao Krua for horticulturists.

Plastome comparison reveals hotspots of nucleotide diversity and positive selection pressure on accD, matK, psaA and rbcL genes in Smilacaceae

Plastome comparison reveals hotspots of nucleotide diversity and positive selection pressure on accD, matK, psaA and rbcL genes in Smilacaceae

Morpho-anatomical characterization and DNA barcoding of Artemesia vulgaris L.

Artemisia vulgaris L. belongs to Asteraceae, is a herbal plant that has various benefits in the medical field, so that its use in the medical field can be explored optimally, the plant must be thoroughly identified. This study aims to identify A. vulgaris both in terms of descriptive morpho-anatomy and DNA barcoding using BLAST and phylogenetic tree reconstruction. The morpho-anatomical character was observed on root, stem, and leaf. DNA barcoding analysis was carried out through amplification and alignment of the rbcL and matK genes. All studies were conducted on three samples from Taman Husada (Medicinal Plant Garden) Graha Famili Surabaya, Indonesia. The anatomical slide was prepared by the paraffin method. Morphological studies revealed that the leaves of A. vulgaris both on the lower-middle part and on the upper part of the stem have differences, especially in the character of the stipules, petioles, and incisions they have. Meanwhile, from the study of anatomy, A. vulgaris has an anomocytic type of stomata and its distribution is mostly on the ventral part of the leaves. Through the BLAST process and phylogenetic tree reconstruction, the plant sequences being studied are closely related to several species of the genus Artemisia as indicated by a percentage identity above 98% and branch proximity between taxa in the reconstructed phylogenetic tree.

DNA barcoding-based molecular profiling of Bougainvillea, Dianthus, and Plumeria using matK locus

DNA barcoding, a robust tool for species identification, holds significant promise for enhancing authenticity and quality control in herbal and Ayurvedic medicines. The traditional methods, often time-consuming and impractical for industrial-scale applications, are complemented by DNA barcoding, which offers efficient and reliable plant species identification. However, the identification of the subspecies or variants within species is a difficult task and has challenges due to higher sequence similarity for marker genes and correct identification of variants. This research presents a comprehensive methodology for DNA barcoding in three variants of common medicinal plants, namely, Bougainvillea, Dianthus, and Plumeria, using the maturase K (matK) as a molecular marker. The sequenced matK regions with 500–700 bp size have a variability of approximately 1% to 2.7% among inter and intra-species variants, facilitating the easy identification of the species through high-quality barcodes. The sequence and phylogenetic analysis revealed that our sequences were clustered with the matK genes of closely related species. The two-dimensional barcodes generated for the nine inter and intra-species variants can be scanned easily. Our findings underscore the potential of DNA barcoding as a powerful tool for the identification and authentication of inter and intra-species variants over conventional means.

TAXONOMIC STUDY OF SOME EUPHORBIA L. SPECIES BY LEAF ANATOMICAL AND MOLECULAR CHARACTERISTICS USING RBCL AND MATK GENES

A current study assessed the leaf anatomical and molecular characteristics of eight species of the genus Euphorbia (Euphorbiaceae), i.e., E. craspedia Boiss, E. denticulate Lam., E. falcate L., E. hirta L., E. helioscopia L., E. peplus L., E. kansuensis L., and E. macroclada Boiss ,collected from several districts of the Middle and Northern Iraq. The anatomical result refers to a uniseriate epidermis (single layer), except for the species E. kansuensis and E. peplus, wherein the upper epidermis recorded a variable thickness among the species. The highest epidermis thickness (28 μm) was visible in the species E. falcata, while the mean decreased to 17 μm in the species E. helioscopia. Based on the anatomical attributes, further species groupings resulted in two. In the first group, the leaf’s crosssection was unifacial, with the palisade tissues on both sides of the blade. This group included E. hirta, E. peplus, E. macroclada?, and E. denticulata. Contrastingly, the second group has a bifacial leaf, with the mesophyll distinguished as palisade and spongy. The said group comprised the E. craspedia and E. helioscopia species. In the genus Euphorbia species, the study of the genetic relationship continued according to the sequencing method of rbcl and matk genes. The results revealed that most species samples showed light bands, characterized by their intensity ranging from 800 to 1000 bp. The highest recorded genetic affinity through the rbcl gene emerged in E. denticulata and E. kansuensis, whereas the lowest was in E. macroclada and E. hirta. Based on matk gene results, the highest genetic affinity observed resulted in the species E. kansuensis and E. denticulata with an average value of 0.0160, with the lowest recorded in the species E. helioscopia and E. peplus with a value of 0.1307.

Molecular Phylogenetics and Molecular Dating of Arecaceae In Bangladesh Inferred from Matk and Rbcl Genes

A molecular phylogenetic investigation was undertaken for 30 species belonging to 15 genera of the palm family Arecaceae in Bangladesh to infer evolutionary relationships and molecular dating utilizing plastid-based matK and rbcL genes through multifaceted-algorithm driven approaches with Neighbor-Joining, Maximum-Likelihood, and Bayesian Inference methods. The study revealed that matK has better species discrimination efficiency than rbcL gene due to its highly variable nature. Transition/transversion bias test corroborated this finding as matK showed higher bias (2.632) than rbcL (2.235). Nucleotide substitution patterns were visualized via HYPERMUT program, which unveiled higher variability in matK and lower variability in rbcL alignment. Phylogenetic trees constructed with matK revealed monophyletic nature of origin for all the three subfamilies, viz. Arecoideae, Coryphoideae and Calamoideae, while rbcL trees exhibited polyphyly for Coryphoideae and monophyly for Arecoideae and Calamoideae. All the nine tribes belonging to three subfamilies demonstrated monophyletic nature in matK trees. Bootstrap support and Bayesian posterior probability were found to be higher in matK topologies than that of rbcL. The molecular clock test unraveled an equal evolutionary rate for matK and unequal rate for rbcL sequences. Molecular dating approach unveiled Calamoideae to be the most ancient subfamily (65.75 MYA) among the three subfamilies that originated during the Late Cretaceous period in the Mesozoic era, whereas Coryphoideae and Arecoideae were found to have originated in the Cenozoic era. Bangladesh J. Plant Taxon. 30(2): 213-232, 2023 (December)

DNA barcoding of an endangered plant species, salvadora oleoides

Salvadora oleoides Decne is an endangered plant species. This species is important as the plant is used for multiple purposes. Natives use the plants for their medicinal needs in treating rheumatic pains and coughs, and many others. This species is threatened by over-exploitation and deforestation or illegal logging, as well as its very slow growth rate, so the accurate identification of this species is important. Knowledge about threats or even distribution is limited, making identifying species more difficult. Therefore, this research aimed at DNA barcoding of endangered species Salvadora oleoides to assess their potential at the meaningful taxonomic level. This study aims to amplify the rbcL and matK genes in Salvadora oleoides collected from the different regions of Pakistan. The plant DNA isolation was carried out by the CTAB method. PCR analysis was performed, which showed amplification of both rbcL and matK regions. The amplified products were purified and sent for sequencing. The results revealed a 100% sequencing rate for rbcL; however, the matK amplified product was not sequenced due to the high heterozygosity in this region, which might result in polymerase slippage during the Sanger sequencing method. The rbcL sequence was checked for homology by BLASTn and then submitted to NCBI for GenBank accession. The accession number assigned to Salvadora oleoides was OP046316 for rbcL. Keywords: DNA Barcoding, Medicinal Plants, matk, rbcl, BLAST, Species Identification.

Phylogenetic Determination of Chenopodium quinoaBased on the Chloroplast Genes rbcL and matK

Chenopodium quinoa is an Andean species of great interest because of its excellent nutritional quality and great adaptability to different environmental conditions. In addition, the high phenotypic diversity has caused difficulties in the correct taxonomic identification, and there are few studies on the phylogenetic relationships of quinoa in Colombia. Therefore, the objective of this research was to determine the phylogenetic relationships of quinoa with the matK and rcbL chloroplastid genes to characterize the genetic diversity in Colombian quinoa. Evolutionary analyses were performed using nucleotide substitution rates, pattern, base composition, and phylogeny construction. The rbcL gene presented approximately 1344 bp, and matK had 646 bp, which were translated into 434 and 215 amino acids, respectively. The nucleotide composition of the genes showed high percentages of similarity and identity with the Chenopodium quinoa sequences registered in GenBank and BOLD. Similar phylogenetic trees were obtained with the rbcL and matK genes, and both concatenated sequences grouped the accessions into clades. The results showed that Colombian quinoa has low rates of genetic differentiation that may be due to the domestication processes of the species, the lack of certified seeds, and the constant exchange of seeds between farmers in the principal producing areas of the Andean region.

Complete chloroplast genome sequences of the ornamental plant Prunus cistena and comparative and phylogenetic analyses with its closely related species

BackgroundPrunus cistena is an excellent color leaf configuration tree for urban landscaping in the world, which has purplish red leaves, light pink flowers, plant shape and high ornamental value. Genomic resources for P. cistena are scarce, and a clear phylogenetic and evolutionary history for this species has yet to be elucidated. Here, we sequenced and analyzed the complete chloroplast genome of P. cistena and compared it with related species of the genus Prunus based on the chloroplast genome.ResultsThe complete chloroplast genome of P. cistena is a 157,935 bp long typical tetrad structure, with an overall GC content of 36.72% and higher GC content in the in the inverted repeats (IR) regions than in the large single-copy (LSC) and small single-copy (SSC) regions. It contains 130 genes, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The ycf3 and clpP genes have two introns, with the longest intron in the trnK-UUU gene in the LSC region. Moreover, the genome has a total of 253SSRs, with the mononucleotide SSRs being the most abundant. The chloroplast sequences and gene arrangements of P. cistena are highly conserved, with the overall structure and gene order similar to other Prunus species. The atpE, ccsA, petA, rps8, and matK genes have undergone significant positive selection in Prunus species. P. cistena has a close evolutionary relationship with P. jamasakura. The coding and IR regions are more conserved than the noncoding regions, and the chloroplast DNA sequences are highly conserved throughout the genus Prunus.ConclusionsThe current genomic datasets provide valuable information for further species identification, evolution, and phylogenetic research of the genus Prunus.