matK Gene Sequences Research Articles

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.

Analysis of Genetic Variation of MatK Gene Sequences in Ammothamnus lehmannii NCBI Popset 2440747918 Using In Silico RFLP

Genetic diversity or genetic variation is variation that occurs in an organism due to differences in the sequence of nucleotide bases (adenine, thymine, guanine and cytosine) that form DNA in cells. Variation genetics can be studied in silico using available gene sequences in the NCBI genbank database. This study used the MatK (Maturase-K) gene sequence with the identity number Popset 2440747918 which was downloaded in fasta format from NCBI . Then screening of restriction enzyme candidates was carried out to determine the restriction enzymes prior to in silico RFLP. The restriction enzyme selected from the screening was the restriction enzyme HindIII which has the recognition site A'AGC_T. The results obtained from 79 samples of DNA sequences, 76 samples were cut and 3 samples were not. And found three allele variations with the percentage of the presence of fragments A1 (86.07%), A2 (10.12%) and A3 (3.79%). The percentage values and frequencies of these A1, A2 and A3 alleles indicate a low level of genetic variation.

<i>CAMELLIA SINENSIS</i> VAR. <i>MADOENSIS</i> (SECT. <i>THEA</i>, THEACEAE), A NEW TAXON FROM VIETNAM

Camellia sinensis var. madoensis is described and illustrated as a new variety of Camellia sinensis (section Thea, Theaceae) from Xuan Loc Commune, Song Cau District, Phu Yen Province. The new variety is easily distinguishable from C. sinensis var. sinensis by style free ½ to the base. The ITS sequence of this variety is also different from that of Camellia sinensis and its other varieties, while the matK gene sequences are nearly identical among Camellia taxa.

Molecular Characterization of Maturase K Gene and Protein Prediction of Vanda spathulata (L.) - An Ayurinformatics Approaches

Vanda spathulata (L.) Spreng. is an important plant of the orchid family of botanical and horticultural importance in the Ayurvedic medicinal system. The Maturase K (matK) gene of plant chloroplast is a strong marker in studying plant molecular systematics, evolution, and genetic polymorphism and is considered as the standard DNA barcode for plants. The gene has an important role in the phylogenetic reconstruction of terrestrial plants. The present study investigated the phylogenetic characterization of matK gene obtained from the plant species V. spathulata (L.) through extraction, purification, PCR amplification, and gel elution. The nucleotide BLAST search revealed similarity with 103 sequences in various closely and distantly related orchid taxa. Mega software and a real-time divergence tree discovered Apostasia odorata has the primitive species for all the sequences, including the V. spathulata which diverged about 114 million years ago. Limited gene flow was observed among the vanda and related taxa and the Tajima neutrality test was negative, indicating the purifying selection in the matK gene sequence, that evolutionary selection had played a major role rather than the neutral evolution. The species and related other species exhibited higher polymorphism at the nucleotide level. Secondary structure was predicted for the single-stranded matK gene of V. spathulata and the ancestor plant species A. odorata using the Zucker MFold web server and translated through a comparison of ORF with NCBI and BLASTN. The protein was modeled in SWISS MODELLER and compared between the two species. The sequence had high similarity with its ancestor gene sequence and the protein modeled showed a complex structure than the ancestor protein due to significant evolutionary changes.

Molecular authentication of some rare Iris (Iridaceae) species from Uzbekistan

The determination of nucleotide sequences in DNA, sequencing of chloroplast genomes techniques, based on the use of combinations a significant number genetic markers, as well as the nuclear genome are widely use for inventory of rare plant species, ecological monitoring and species diversity assessment. The results of our molecular analysis are used to examine the taxonomic identity and phylogenetic relationship of the studied Iris species collected in Uzbekistan. The genotyping of three-four functional loci of nrDNA and cpDNA was performed for efficient species identification and confident results. The nuclear ITS gene sequences and chloroplast trnL-trnF, rbcL, matK gene sequences were obtained from 10 Iris species and have proven to be useful as molecular markers for species identification. Sequences of cpDNA regions, have been used to assess interspecific relationships of Iris. Hierarchical clustering were constructed using 13 consensus matK gene sequences. In this study, we consider the possibility of successful application the DNA barcoding as a tool for assessment of wild Iris species diversity in Uzbekistan.

Phylogenetic Relationship among Grasses, Wheat and Pearl Millet using matK and rbcR Genes

Fourteen genotypes of tall fescue, Brachypodium, wheat and pearl millet were used to find out phylogenetic relationships at their different ploidy level. Isolated chloroplast DNA of the 14 genotypes was sequenced using some selected matK and rbcR genetic markers. The matK and rbcR chloroplast gene sequences length were 1539bp and 1431bp, respectively. The consensus sequence length of matK gene was 1265bp in Brachypodium and wheat, 1266bp in both tall fescue Continental and Mditerranean species, 1269bp in pearl millet and for rbcR gene was only 1156bp in all studied four species. Except in Brachypodium, the variations of SNP for both matK and rbcR genes were observed in different ploidy levels of pearl millet and between the tall fescue Continental and Mediterranean species. Wheat with their different ploidy level gave the SNP variations only for matK gene. In respect of all ploidy levels, pearl millet had the highest number of SNP for both matK (247) and rbcR (130) genes. The tall fescue Continental (129) and Mediterranean (123) were in second position to show their genetic variation for matK gene. The rbcR gene had higher SNP at 5¢ regions of all four species, but matK gene only in wheat and tall fescue and 3¢ in millet and Brachypodium species. There was no in-del for rbcR gene, but the insertion of nucleotide for the matK gene was found highest in diploid wheat (11) and the deletion was in pearl millet (6). The phylogenetic analysis stated that their relationships were tall fescue Continental and tall fescue Mediterranean was much more related to wheat than pearl millet and Brachypodium. Plant Tissue Cult. & Biotech. 33(1): 57-70, 2023 (June)

Taxonomic Confirmation of Rare Fruits in West Kalimantan Using rbcL and matK Sequences

Phylogenetic analysis for plants can be very helpful in determining species identification or taxonomic status morphologically. rbcL and matK are widely used as genetic markers in constructing seed plant phylogenies. Different identification and new collection during the re-inventory from the previous study were found in two and four types of rare fruits in Sibohe Forest, West Kalimantan. The six types include pisang karok (Musa sp.) and Kandis (Garcinia sp.), as well as nubik (Artocarpus sp.), tehengan (Artocarpus sp.), smallest arok (Ficus sp.), and amok (Alpinia sp.). This study aimed to analyze the phenetic relationship of six rare fruits from Kalimantan based on rbcL and matK genes. DNA samples were obtained from dried body parts of the previous study and amplified by PCR using both forward and reverse primers for rbcL and matK genes. Amplification was observed on electrophoresis gel for rbcL gene of nubik, tehengan, smallest arok, amok, and pisang karok, while only pisang karok in matK gene. However, matK gene sequence was also obtained for amok even though the band was not seen on the gel. Phylogenetic analysis using the two genes confirmed the morphological identification reported in the previous study; however, using matK as a single gene for taxonomic confirmation must be reconsidered. The information of rbcL and matK sequences of six rare fruits from West Kalimantan could be the first information for building the DNA barcodes of the rare fruits in West Kalimantan.

Improvements in the phylogeny of Epilobium and Chamaenerion inferred from nrDNA and cpDNA data focusing on Türkiye

Epilobium and Chamaenerion included 165 and 8 species over the world, respectively. The members of the genera are distributed particularly in moist habitats from subpolar to tropical regions.This paper aims to provide improvements in the phylogeny of the genera Epilobium and Chamaenerion using Internal Transcribed Spacer (ITS) of nuclear DNA and matK gene sequence data evaluation with maximum parsimony, maximum likelihood, and Bayesian inference criterations. A total of 188 individual accessions belonging to 28 taxa were newly generated and 110 sequences imported from GenBank (NCBI) were analysed. The nrDNA and plastid DNA gene trees supported to treat Epilobium and Chamaenerion as separate genera in two well-supported clades. The matK analyses revealed a better resolution than nrDNA ITS within the Chamaenerion clade and supported the inclusion of C. angustifolium in the sect. Chamaenerion. However, most of the examined species mostly fell into the polytomy in both trees excluding E. roseum subsp. consimile which should be considered a distinct species in the Epilobium contrary to morphological treatment in many national flora books. Both phylogenetic trees also support distinguishing E. prionophyllum from E. anatolicum previously treated as a subspecies of E. anatolicum. In conclusion, these preliminary phylogenetic analyses have contributed significantly to the determination of the limits of members belonging to Epilobium and Chamaenerion distributed in Türkiye.

Molecular phylogeny of Ruppia maritima L. from Chilika Lake, Odhisa using nuclear and plastid genes

Aim: The present study aims to confirm the molecular identification of Ruppia maritima L. from Chilika Lake, Odhisa using different molecular markers and find out the evolutionary lineage of Ruppia species. Methodology: For molecular identification, R. maritima was collected from Chilika Lake and the rbcL, matK, and ITS gene sequences were investigated and analyzed using BLAST to verify the gene fragment. Phylogenetic tree was constructed using MEGA X software following Neighbor joining (NJ) and Maximum parsimony (MP) methods. Results: The nucleotide (ITS) and plastid gene (rbcL and matK) sequences of Ruppia maritima were examined. The tree topology of R. maritima rbcL and matK gene sequences revealed a paraphyletic cluster at 99 and 100% bootstrap. The conserved region was high in matK (74.8%), followed by rbcL (45.2%) and ITS (19.1%) with seagrass and freshwater species. ITS had the most significant proportion of variable sites (79.7%), followed by rbcL (52.4%) and matK (25.2%). The ITS region showed less parsimonious-informative character (66.1) than rbcL and matK region. Interpretation: The study concludes that the R. maritima was identified through molecular markers, which was a closed lineage with seagrasses than freshwater species.

Highly Resolved Papilionoid Legume Phylogeny Based on Plastid Phylogenomics.

Comprising 501 genera and around 14,000 species, Papilionoideae is not only the largest subfamily of Fabaceae (Leguminosae; legumes), but also one of the most extraordinarily diverse clades among angiosperms. Papilionoids are a major source of food and forage, are ecologically successful in all major biomes, and display dramatic variation in both floral architecture and plastid genome (plastome) structure. Plastid DNA-based phylogenetic analyses have greatly improved our understanding of relationships among the major groups of Papilionoideae, yet the backbone of the subfamily phylogeny remains unresolved. In this study, we sequenced and assembled 39 new plastomes that are covering key genera representing the morphological diversity in the subfamily. From 244 total taxa, we produced eight datasets for maximum likelihood (ML) analyses based on entire plastomes and/or concatenated sequences of 77 protein-coding sequences (CDS) and two datasets for multispecies coalescent (MSC) analyses based on individual gene trees. We additionally produced a combined nucleotide dataset comprising CDS plus matK gene sequences only, in which most papilionoid genera were sampled. A ML tree based on the entire plastome maximally supported all of the deep and most recent divergences of papilionoids (223 out of 236 nodes). The Swartzieae, ADA (Angylocalyceae, Dipterygeae, and Amburaneae), Cladrastis, Andira, and Exostyleae clades formed a grade to the remainder of the Papilionoideae, concordant with nine ML and two MSC trees. Phylogenetic relationships among the remaining five papilionoid lineages (Vataireoid, Dermatophyllum, Genistoid s.l., Dalbergioid s.l., and Baphieae + Non-Protein Amino Acid Accumulating or NPAAA clade) remained uncertain, because of insufficient support and/or conflicting relationships among trees. Our study fully resolved most of the deep nodes of Papilionoideae, however, some relationships require further exploration. More genome-scale data and rigorous analyses are needed to disentangle phylogenetic relationships among the five remaining lineages.

Phylogenetic Relationship Between the Bamboo Species of Tribe Bambuseae and Arundinarieae Based on matK Gene Sequences

Phylogenetic Relationship Between the Bamboo Species of Tribe Bambuseae and Arundinarieae Based on matK Gene Sequences

Phylogenetic analysis of six different species of Saraca L. (Fabaceae, Caesalpinioideae) based on chloroplast matK gene

Abstract. Sil S, De KK, Ghosh A. 2021. Phylogenetic analysis of six different species of Saraca L. (Fabaceae, Caesalpinioideae) based on chloroplast matK gene. Biodiversitas 22: 3880-3889. Saraca L. is one of the most important genera, with several horticultural and therapeutic values. Specific taxonomic and phylogenetic knowledge of Saraca through molecular data is essential for accessing its true medicinal benefits. Nineteen different Partial matK gene sequences of the chloroplast genome of six different species of Saraca, including four amplified and 15 retrieved from the NCBI gene bank, were place in a sequence alignment. The resulting data were examined to determine their phylogenetic and evolutionary interrelationships. The comparative analysis of different sequences of each of the species revealed intra-specific molecular diversity, and the comparison of the matK sequences of six different species defined their inter-specific molecular diversity. The analysis of partial matK sequences revealed the presence of 87 variable sites, 14 parsimony informative sites, 54 singleton sites, and 237 quadri-fold degenerate sites. The approximate nucleotide composition was A-31.02%, T-37.46%, C-16.06%, and G-15.46%. The value of transition/transversion bias was 0.90. About 522 codons were analyzed and the presence of 34 variable sites, 8 parsimony informative sites, and 25 singleton sites was observed within their respective amino acid sequences. The average pair-wise distance was 0.0444, and 189 segregating sites and 0.018809 nucleotide diversity were observed. The evolution of different species of Saraca and their phylogenetic interrelationships were observed by analyzing their matK sequences. The relative homogeneity of S. indica is quite low. S. dives had the earliest evolutionary trends while S. declinata had the most recent. S. asoca and S. indica are quite similar on the molecular level but can be treated as different species while the difference between S. declinata and one of its synonyms, S. palembanica, indicates the possibility of separating them into different species.

Comparative and phylogenetic analysis of the complete chloroplast genome sequences of Lactuca raddeana and Lactuca sativa

Lactuca raddeana is a biennial plant of the Lactuca genus belonging to the Asteraceae family. The classification of Lactuca is controversial, and no consistent conclusions have been reached based on the analysis of morphological characters and different molecular markers. Here, we sequenced and assembled the complete chloroplast genome of L. raddeana. This genome has a total length of 152,339 bp, a conservative quartile structure that is composed of a large single-copy (LSC) region of 83,976 bp, a small-copy (SSC) region of 18,521 bp, and a pair of inverted repeats (IRs) of 24,921 bp. The genome contains 112 unique genes, including 79 protein-coding, four rRNA, and 29 tRNA genes. Repeat analysis obtained 17 microsatellite, 16 tandem, and 17 interspersed repeats. Comparison of sequence divergence between L. raddeana and L. sativa found the intergenic spacer trnC-petN exhibited the highest degree of variation. Three phylogenetic trees based on the 72 shared protein, matK gene, and rbcL gene sequences showed that L. raddeana and L. sativa are clustered together. The acquisition and comparative analysis of the chloroplast genome provide a valuable resource for the taxonomic and phylogenetic studies of Lactuca.

Molecular characterization of endangered endemic plant Aloe pseudorubroviolacea using chloroplast matK and plastid rbcL gene

An endangered and rare species Aloe pseudorubroviolacea from the plant family Asphodelaceae which is presently recorded as endangered in Saudi Arabia collected from Al-Baha region of Saudi Arabia its GPS Latitude and Longitude coordinates 19.8345, 41.5481. The chloroplast matK and rbcL gene was considered in this study based on molecular identification the size is about 571 and 664 bp respectively. From the sequence analysis the gene matK and rbcL confirm that this species is very much closely related with A. rubroviolacea and also inter related with the species Astroloba rubriflora, Chrysopogon gryllus, Chortolirion angolense shows about 98.7% sequence homology. The partial matK and rbcL gene sequence discriminate Aloe pseudorubroviolacea from the closely related plant species, A. rubroviolacea. The gene sequence of rbcL discriminates the species from Chrysopogon gryllus and Chortolirion angolense, demonstrates the nucleotide variations in 3 different sites (623C/T; 653C/T; 700C/A). This study showed that matK and rbcL sequence region of chloroplast gene used to authenticate the samples of A. pseudorubroviolacea and which provide to help in correct identification and conservation process of this medicinally valuable endangered plant species.

BARKOD DNA PADA TANAMAN GAMBIR (Uncaria gambir(Hunter) Roxb.) BERDASARKAN GEN matK DAN rbcL

Gambir ( Uncaria gambir (Hunter) Roxb.) is a superior commodity of West Sumatra that has many benefits and has been used as a drug. Plant identification carried out morphologically has many weaknesses, with the development of electronic and genetic technology now a new method of species identification has been developed. plants and animals, namely DNA barcoding technology that uses standard short pieces of DNA Species identification methods have been agreed to using standard DNA barcodes are rbcL genes and matK genes. The purpose of this study is to find out DNA Barkoding candidates between matK and rbcL which can identify gambier ( Uncaria gambir (Hunter) Roxb.) Which is good. Polymerase Chain Reaction (PCR) technique is used to amplify rbcL and matK gene sequences through universal primers. The DNA sequences of the MATC sequence in the GR sample (Riau Gambir) produced a similarity rate of 98.79% with Nauclea diderrichii , for the rbcL sequence GC (Cubadak Gambir) samples produced a similarity rate of 99.81% with Uncaria macrophylla , and GR (Gambir Riau) samples produced the similarity rate was 96.84% with Uncaria macrophylla based on analysis with BOLD Systems. This similarity indicates the low variation in intraspecific genetics for the identification or confirmation of gambir species

A Molecular Phylogeny of Panax L. Genus (Araliaceae) Based on ITS-rDNA and matK Support for Identification of Panax Species in Vietnam

Panax L. is a small genus in the Araliaceae family. In Vietnam, this genus is distributed in the high mountains in the North and in some high mountains in the Central Highlands. In traditional medicine, roots and rhizomes of all Panax species are of high utility. Recently, the finding of new distributions of some Panax species in Vietnam has caused much controversy and confusion. This study investigates 27 fresh specimens of 6 taxa of Panax genus that have been collected from 6 provinces of Vietnam. Based on the combined ITS-rDNA and matK dataset, a well-resolved phylogeny of Panax species/varieties distributed in Vietnam was constructed. Thereby, the study suggests identifying Tam that la xe as Panax stipuleanatus H.T.Tsai et K.M.Feng and Sam puxailaileng as Panax vietnamensis var. fuscidiscus K.Komatsu, S.Zhu & S.Q.Cai, which contributes a new distribution point of this variety in Vietnam. The study also shows that ITS-rDNA and matK genes are highly potential in identifying and distinguishing the taxa of Panax genus.
 Keywords
 Panax, ginseng, molecular phylogeny, taxonomy, ITS-rDNA, matK.
 References
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Applicability of inter-simple sequence repeat (ISSR), start codon targeted (SCoT) markers and ITS2 gene sequencing for genetic diversity assessment in Moringa oleifera Lam

Moringa oliefera Lam. is the most widely cultivated species among the members of Moringa genus in tropics for its nutritional and medicinal values. Almost all plant parts have been used in human's nutrition and therapy. The molecular characterizations are required for effective improvement for better utilization. In the present study, genetic variation in ten individual Moringa oleifera plants were investigated using ten primers of each inter-simple sequence repeat (ISSR) and start codon targeted (SCoT) markers. In current study, SCoT is used for the first time to assess the genetic diversity in moringa. The results of ISSR and SCoT analysis for the ten local M. oleifera revealed approximately 91 and 108 different banding patterns, 73 and 87 of them consider as monomorphic bands and other 18 and 21 fragments consider as polymorphic bands with a percentage about 19.7 and 19.4%, respectively. Low levels of polymorphism were observed between ISSR and SCoT which means that they are useful tools for genetic similarity detection in M. oleifera species. Sequence identity of M. oleifera plants in relation to NCBI data base were 96, 100, 99 and 99 with ITS2, matK, psbA and rbcL genes, respectively, with lower E value (≤1e). Moreover, the phylogenetic Neighbor-joining (NJ) tree was constructed using rbcL, matK, psbA and ITS gene sequences. M. oleifera clustered into two clades with 99% similarity. The results suggest that the neighbor-joining phylogeny tree could effectively identify M. oleifera from its adulterants, including its closely related species. M. oleifera showed a sister relationship to M. oleifera MG548808.1 and M. oleifera KT737756.1. The results confirmed the usefulness of molecular techniques such ISSR, SCoT and ITS barcoding markers to assess the genetic diversity among the selected M. oleifera types for genetic conservation and plant improvement.

Genetic diversity of sago palm (Metroxylon sagu) accessions based on plastid cpDNA matK gene as DNA barcoding

Abstract. Abbas B, Tjolli I, Munarti. 2020. Genetic diversity of sago palm (Metroxylon sagu) accessions based on plastid cpDNA matK gene as DNA barcoding. Biodiversitas 21: 219-225. Metroxylon sagu Rottb is one of the plant species including in the Palmae family that deposits starch in the trunk. Sago palm was reported has high capability to produce a large amount of starch and large variation starch qualities which were mostly influenced by genetic factors. The objectives of this study are revealed sequence chloroplast DNA (cpDNA) associated with matK genes for the genetic diversity identification of sago palm accessions. Plant materials used in the studies were derived from Sago Research Center (SRC) collection. DNA extraction has adopted the procedure of Plant Genomic DNA Mini Kit. Polymerase chain reaction (PCR) was performed by using primer sets of MatK-1RKIM-f and MatK-3FKIM-r. DNA PCR product was sequenced by the 1st Base Asia, Singapore. Results of the study showed that the cpDNA sequence associated with matK genes in the genome of sago palm showed differences among accessions. Molecular diversities of sago palm accessions based on matK gene showed sago palm accessions separated into two genotypes. Genotype-1 incorporated of ten individuals of 15 accessions and genotype-2 incorporated five individuals of 15 accessions. A mutation site and deletion site occurred in the sequences of matK gene of the Genotype-2. Ten of the 15 sequences of the matK gene (belong to Genotype-1) were registered in the GenBank, NCBI as DNA barcoding and authenticity of sago palm germplasm from Papua islands, Indonesia territorials.

The effects of water pollution on the phylogenetic community structure of aquatic plants in the East Tiaoxi River, China

Abstract Water pollution is one of the most serious aquatic environmental problems worldwide. In China, recent agricultural and industrial development has resulted in rapid changes in aquatic ecosystems. Here, we reveal the effects of water pollution on the phylogenetic community structure of aquatic macrophytes in the Tiaoxi River, China. We placed a rectangular plot at 47 sites within the Tiaoxi River from the mouth of the river to 88.5 km upstream, in which we recorded species abundance and measured 22 physico‐chemical variables. Bayesian phylogeny using the rbcL and matK gene sequences was employed to quantify phylogenetic α‐ and β‐diversity, and test the phylogenetic signal in four growth forms: emergent, floating‐leaved, free‐floating, and submerged. Within communities, water contamination and phytoplankton abundance decreased species richness and phylogenetic diversity, which resulted in phylogenetic clustering; species within communities were more closely related to each other than expected. Between communities, differences in geographical distance and phytoplankton abundance resulted in phylogenetic dissimilarity among plots. Aquatic macrophytes showed phylogenetic signals in which related species responded more similarly to disturbance. Thus, the observed patterns could be explained by environmental filtering and suggested that water pollution by human activity has added more filters to the existing environmental filters that drive the species assembly of macrophyte communities.

DNA barcoding of different Triticum species

BackgroundThe genus Triticum L. includes diploid, tetraploid, and hexaploid species. DNA barcoding is a new method to identify plant taxa by using short sequences of DNA and within a short time. In this investigation, we determined a phylogenetic analysis of 20 different Triticum species by partial chloroplast Maturase encoding gene (matK).Materials and methodsTwenty accessions of different Triticum species diploid, tetraploid, and hexaploid were obtained from different countries. Genomic DNA was isolated from young leaves of studied samples and then used as a template for PCR reaction. PCR products were checked by electrophoresis, purified, sequenced, and submitted in the GenBank nucleotide sequence database, the nucleotide sequence was translated into an amino acid sequence. The nucleotide and amino acid sequences were aligned with Clustal W multiple sequence alignment programs to obtain the phylogenetic tree depending on two statistical data analysis such as bootstrapping and pairwise distance from both nucleotide and amino acid sequences.ResultsThe phylogenetic tree obtained from both nucleotide and amino acid sequences divided the 20 Triticum species into two groups, A and B. Group A represented the diploid Triticum species. Group B was divided into two subgroup, I and II. Subgroup I represented the hexaploid Triticum species and subgroup II represented the tetraploid species.ConclusionThe matK gene sequence has a critical role in discriminating the closely related Triticum species. So these sequences could be used as a DNA barcode for detecting the evolutionary history of Triticum species.