matK Gene Research Articles

The study of organelle DNA variability in alloplasmic barley lines in the NGS era.

Alloplasmic lines are a suitable model for studying molecular coevolution and interrelations between genetic systems of plant cells. Whole chloroplast (cp) and mitochondrial (mt) genome sequences were obtained by the MiSeq System (Illumina). Organelle DNA samples were prepared from a set of 12 alloplasmic barley lines with different cytoplasms of Hordeum vulgare ssp. spontaneum and H. vulgare ssp. vulgare, as well as from their paternal varieties. A bioinformatic approach for analysis of NGS data obtained on an organellar DNA mix has been developed and verified. A comparative study of Hordeum organelle genomes’ variability and disposition of polymorphic loci was conducted. Eight types of chloroplast DNA and 5 types of mitochondrial DNA were distinguished for the barley sample set examined. These results were compared with the previous data of a restriction fragment length polymorphism (RFLP) study of organelle DNAs for the same material. Formerly established data about a field evaluation of alloplasmic barley lines were revised in the light of information about organelle genomes gained after NGS. Totally 17 polymorphic loci were found at exons of chloroplast genomes. Seven of the SNPs were located in the genes of the Ndh complex. The nonsynonymous changes of nucleotides were detected in the matK, rpoC1, ndhK, ndhG and infA genes. Some of the SNPs detected are very similar in codon position and in the type of amino acid substitution to the places where RNA editing can occur. Thus, these results outline new perspectives for the future study of nuclear-cytoplasmic interactions in alloplasmic lines.

Fibroblast growth factor-6 enhances CDK2 and MATK expression in microvesicles derived from human stem cells extracted from exfoliated deciduous teeth

Background: Stem cells from human exfoliated deciduous teeth (SHEDs) are considered one of the most convenient sources of adult stem cells. This study aimed to examine the effect of fibroblast growth factor 6 (FGF-6) on SHEDs and evaluate CDK2 and MATK gene expression in SHED-derived microvesicles (MVs). SHEDs were cultured from deciduous teeth pulp. Methods: SHEDs were divided into two groups: the control group and test groups, with and without FGF-6 supplementation, respectively. After the third passage, SHED proliferation was assessed by MTT assay. MVs were purified and CDK2 and MATK gene expression was assessed by real-time polymerase chain reaction. SHEDs were identified by their positivity for CD90 and CD73, and negativity for CD45 and CD34. Results: SHEDs proliferation in the test group was significantly higher than in the control group (P<0.001). mRNA from SHED-derived MVs from the test group exhibited a markedly elevated expression of CDK2 and MATK, (P<0.002 and P<0.005, respectively) in comparison with those of the control group. FGF-6 enhanced the proliferation of SHEDs. Proliferation enhancement is favorable for the production of a large number of stem cells, which will then be beneficial for cell-based therapies. Conclusions: CDK2 and MATK genes in SHED-derived MVs can be used as molecular biomarkers for SHED proliferation.

Preliminary application of DNA barcoding toward the detection of viable plant propagules at an initial, international point-of-entry in Georgia, USA

Over 90% of global commercial trade occurs between seaports, which are initial points-of-entry for nonnative, potentially invasive propagules. As such, there is a need to develop means to both rapidly intercept and identify propagules as they arrive. Here, we focus on plant propagules that are assumed to be non-native, in seed form. Because standard morphological techniques alone are laborious and require taxonomic expertise, we sought to address if identification through barcoding of the plastid DNA (rbcL + matK genes) of plant seeds could improve current processes in the early detection and rapid response to prevent entry/establishment of nonnative plant species. This research conducted a preliminary foray to evaluate the utility of widely accepted plant plastid DNA barcodes to identify plant propagules (seeds, hereafter) collected from the air-intake grilles of refrigerated shipping containers of a single agricultural commodity arriving at the Port of Savannah, Georgia, USA. We ask four questions: (1) Can DNA barcoding be used to detect seeds collected from shipping containers at the port? (2) What is the genetic composition of propagules entering the port? (3) How do morphological identifications compare to those based on genetic analysis? (4) Are nonnative invasive plant species present on shipping containers entering the Port of Savannah? This research collected 11,044 seeds from 628 refrigerated shipping containers between 2015 and 2017. Seeds were then morphologically sorted into Seed Types. Barcoding of the matK and rbcL gene regions of the plastid genomes directly isolated from seeds resulted in poor amplification. This is likely due to a host of potential confounding factors. Therefore, we germinated seeds and utilized leaf-tissues for sequencing of these two gene regions. From BLASTn analyses, results returned top hits for a variety of species, with up to 22 possible nonnative plant species and one definite Federal Noxious Weed. This work investigates the interception application of DNA barcoding to improve agro- and bio-security issues posed by nonnative and invasive species. Though this study required the germination of the seeds to obtain leaf-tissue suitable for our DNA barcoding method, we effectively demonstrated seed viability. Our seed identification process was lengthy and understandably not feasible for real-time application. Therefore, we seek to improve our methods for future applications by testing other approaches that may better complement morphological identification. Next reasonable steps include improved extraction protocols, metabarcoding to generate DNA barcode sequences directly from groups of seeds harvested from shipping containers and implementing other next-generation sequencing techniques.

DNA-Barcoding of Some Medicinal Plant Species in Saudi Arabia Using rbcL and matK Genes

In the Kingdom of Saudi Arabia (KSA), thousands of plants are considered to have therapeutic value. The ambiguous use of identification mainly morphological characteristics of many plants has resulted in the adulteration and displacement of plant products which undermine their therapeutic value and weak documentation of plant resources. The aims of this study were therefore to evaluate genetic variability and explore the phylogeographic architecture for Saudi medicinal plant samples using rbcL and matK genes as barcodes for genomic identification. The matK and rbcL sequences collected for these samples were used as key markers for examining the relationship between Saudi medicinal plant species based on genetic diversity. During our study we were successful in identifying and documenting 4 different species (Foeniculum vulgare, Nitraria retusa, Dodonaea viscosa, and Rumex nervosus) located in Saudi Arabia using DNA barcoding technique. A total number of 8 sequences were obtained with a total sequence length of 6176 bp, where it ranged from 617 bp to 878 bp with an average length of 772 bp. The total number of rbcL sequences length is 2801 bp, where it ranges from 617 bp to 807 bp with an average length of 700.2 bp. Out of the 4 plant samples used, only three samples were identified correctly on the species level with an identity percentage higher than 95% using rbcL gene. Additionally, 4 matK sequences have been retrieved belong to 4 species. The total number of matK sequences length is 3375 bp, where it ranges from 819 bp to 878 bp with an average length of 843.8 bp. Out of the 4 plant samples used, only two samples were identified correctly on the species level with an identity percentage higher than 98% using matK gene. Both rbcL and matK have been able to identify most of our collected plant samples by genus, and some by species. Using only one DNA-barcoding technique was not reliable for plant identification, where matK and rbcL must be used as a dual DNA-barcoding procedure.

Systematic Approach to Establish DNA Barcode of Medicinally Important Plants in Nepal

DNA barcoding is an emerging tool for species identification that uses internationally agreed protocols and regions of DNA to create a global database of living organisms. Initiatives are taking place to generate DNA ba rcodes for all groups of living organisms make these genomic identity publically available to understand, conserve, and utilize the world 's biodiversity. Most of the terrestrial plants are characterized using two section of coding region within chloplast, part of chloroplast gene, a more conserved rbcl and more polymorphic MatK gene. In order to create high quality databases, each plants are characterized not only with the rbcl and MatK DNA sequences, an additional sequence information from internal transcribed spacer (ITS) region is more efficient. The quality of barcode depends on the various factors such as efficient primers, purity of DNA templates, as well as the quality of PCR amplicon from which the sequence data will derive. The protocol described here led to the generation of high efficient PCR amplicon which will aid in the minimization of erroneous DNA sequence infonnation from which bioinformatics procedure will generate efficient barcodes. The primers used to amplified MatK, rbcl and ITS sequence were MatK-4 13f-1 and MatK- 1227r-1, rbcl-1F and rbcl-724R, ITS1 and ITS4 showed a strong amplification successes of 80% of each in the tasted medicinal plants of Nepal. This study propose that the used sets of primers and amplification condition will help, in part, the development of DNA barcode for medicinally important plants of Nepal to conserve their identity with its nativeness.

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.

Incongruence of morphological determinations and DNA barcode sequences: a case study in Cinnamomum (Lauraceae)

In the course of molecular systematic studies of Lauraceae we received a sample of a plant cultivated under the name Cinnamomum porrectum in the Botanical Garden Munchen-Nymphenburg. Preliminary determinations, both morphologically based on the Flora of China (Li & al. 2008) and by chloroplast sequences (psbA-trnH spacer, trnK intron including matK gene, trnL intron, trnL-trnF spacer and trnQ-rps16 spacer) obtained by Sanger sequencing suggested that it was C. camphora, still the plant looked different from other individuals of C. camphora cultivated in the botanical gardens of Berlin, Hamburg, Mainz, Munich and Oldenburg. Attempts to sequence the more informative nuclear internal transcribed spacer repeatedly led to mixed signals. We therefore used Illumina sequencing on a set of pre-amplified molecular markers (ITS, trnK 3′ and 5′ intron, trnL intron, and the intergenic spacers psbA-trnH, trnL-trnF, as well as parts of the trnQ-rps16 spacer), and downloaded available sequences of C. camphora and C. parthenoxylon from GenBank for comparison. Considerable differences were found among these sequences, but the haplotype groups do not coincide with the current species determinations. Particularly the internal transcribed spacer sequences are rather diverse, suggesting possible misidentifications, contaminations, and/or a common gene pool that is larger than anticipated. Concerning the plant in question, our results suggest that it may be a hybrid, with C. camphora as the maternal and another species, possibly C. parthenoxylon, as the paternal parent.Citation: Rohwer J. G., Trofimov D., Mayland-Quellhorst E. & Albach D. 2019: Incongruence of morphological determinations and DNA barcode sequences: a case study in Cinnamomum (Lauraceae). – Willdenowia 49: 383–400. doi: https://doi.org/10.3372/wi.49.49309Version of record first published online on 4 December 2019 ahead of inclusion in December 2019 issue.

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.

Genomic analysis of chloroplast matK and rbcL gene from Flacourtia inermis Roxb for plant DNA barcoding

Identification of medicinally significant plant species is helpful for their utilization as medicine. Flacourtia inermis Roxb are important medicinal plant. Aim: To Genotypic characterization of Flacourtia inermis through DNA sequence of matK and rbcL gene. Flacourtia inermis Roxb DNA was isolated using NucleoSpin® Plant II Kit (Macherey-Nagel gene extraction) Kit. Isolated DNA was amplified by using PCR (matK and rbcL gene primers). Amplified matK and rbcL gene was sequenced by ABI 3500 DNA analyzer and the sequence quality was checked using sequence scanner software v1. The results exposed basic variability of the sequences. The matK and rcbL gene phylogenic tree was constructed using MEGA 6 software. Flacourtia inermis Roxb DNA was successfully isolated using NucleoSpin® Plant II Kit (Macherey-Nagel gene extraction) Kit and confirmed by agarose gel electrophoresis. Isolated matK and rbcL genomic DNA was successfully amplified by using PCR. From the matK sequence, BLASTn analysis result Flacourtia inermis species showed 99.20% relationship with Flacourtia jangomas and rbcL BLASTn analysis result of Flacourtia inermis species showed100% relationship with Flacourtia jangomas at NCBI database. From this study, the result concluded the matK and rcbL genomes can be used for DNA identification of Flacourtia inermis. The information obtained from the study would be helpful for further research involving genotypic identification of Flacourtia sp.

Genomic analysis of chloroplast matK and rbcL gene from Flacourtia inermis Roxb for plant DNA barcoding

Genomic analysis of chloroplast matK and rbcL gene from Flacourtia inermis Roxb for plant DNA barcoding

Short Communication: rbcL and matK chloroplast DNA composition of green chireta (Andrographis paniculata) from Indonesia

Abstract. Arif MF, Aristya GR, Subositi D, Sai AN, Kasiamdari RS. 2019. Short Communication: rbcL and matK chloroplast DNA composition of green chireta (Andrographis paniculata) from Indonesia. Biodiversitas 20: 3575-3583. Green chireta (Andrographis paniculata (Burm.f.) Wall. ex Nees.) is often used by the traditional community as a medicinal herb in Indonesia. However, nucleotide study of green chireta from Indonesia has never been done. The objectives of this study were to analyze the rbcL and matK chloroplast gene composition of green chireta from Indonesia and to analyze the relationship with other Andrographis species. The result proved that all the DNA composition of green chireta used in this study was similar to the A. paniculata from GenBank. The rbcL composition was similar to A. paniculata KF521878, A. paniculata JQ922118, and A. paniculata JQ230990 from GenBank while the matK composition was similar to A. paniculata LC461762. Total 501 bp of rbcL and 639 bp of matK can be aligned produced 167 and 213 amino acid from translation. The amino acid translation result showed no different expression from rbcL genes but there was one sample expressed different translations from the matK gene. The phylogenetic tree was reconstructed using the Neighbor-Joining method with 1000 bootstrap values and the Kimura 2-Parameter (K2P) model in the MEGA7 software. Both rbcL and matK genes grouped the samples into the same clade as A. paniculata from GenBank. No variation was detected from the rbcL gene but two haplotypes were detected from the matK gene. This composition and sequence data serve as a database for Andrographis species from Indonesia which can be used for various studies.

Aeschynomene chicocesariana, a Striking New Unifoliolate Legume Species from the Brazilian Chapada Diamantina and its Phylogenetic Placement in the Dalbergioid Clade

Abstract—Unifoliolate leaves are relatively rare in the species-rich dalbergioid clade of papilionoid legumes (Leguminosae, Papilionoideae). For the pantropical, diverse genus Aeschynomene (ca. 180 species), the only known record of unifoliolate species described so far is the savanna-inhabiting A. simplicifolia from Chapada dos Veadeiros in Goiás, Brazil. The current work provides a description, illustrations, and a distribution map of another unifoliolate species, Aeschynomene chicocesariana, which was newly discovered in the rupestrian grasslands of Chapada Diamantina in Bahia, Brazil. Bayesian phylogenetic analyses of DNA sequence data (nuclear ribosomal ITS/5.8S and the plastid genes matK and trnL intron) have unequivocally placed A. chicocesariana with the rest of Aeschynomene species that are traditionally placed within Aeschynomene sect. Ochopodium. This result agrees with the shared morphology of A. chicocesariana and members of that section.

Oil induces chlorophyll deficient propagules in mangroves.

In Australia, some trees of the mangrove, Avicennia marina, growing in a chronic oil polluted site, produce chlorophyll deficient (albino) propagules. We tested the hypothesis that albinism was due to an oil-induced mutant allele that controls photosynthesis. We determined whether there are genetic differences between normal and chlorophyll deficient propagules. Four gene regions (nuclear 18S-26S cistron; chloroplast - trnH-psbA, rsp16 and matK) were sequenced and analysed for normal and albino propagules. Mutations occurred in both nuclear (ITS) and coding chloroplast (matK) genes of albino propagules. There were 10 mutational differences between normal and albino propagules in the matK samples. Analysis of molecular variation (AMOVA) of the matK dataset indicated highly significant genetic differentiation between normal and albino propagules. Our study suggests for the first time that PAHs from a chronic oil polluted site resulted in mutations in both nuclear and chloroplast genes, resulting in the production of albino propagules.

The DNA barcode of red fruit pandan (Pandanaceae) cultivar from Wamena, Papua Province, Indonesia based on matK gene

Abstract. Zebua LI, Gunaedi T, Budi IM, Lunga N. 2019. The DNA barcode of red fruit pandan (Pandanaceae) cultivar from Wamena, Papua Province, Indonesia based on matK gene. Biodiversitas 20: 3405-3412. The red fruit pandan has been used by the people of Wamena in central highlands of Papua as medicinal plants, food ingredients, and religious ceremonies. Based on morphological characters, there are 39 cultivars of red fruit pandan in New Guinea. A standard method for plant species identification through DNA barcodes has been recommended to use matK gene. The research aimed to determine similarities in DNA barcode sequences of six red fruit pandan cultivars with its close relative that listed in NCBI system and to recommend the reliable DNA barcode for identification of this cultivar. Polymerase Chain Reaction was employed DNA to amplify matK gene fragments using an available forward primer (5’CGA TCT ATT CAT TCA ATA TTT C 3’) and reverse primer (5’TCT AGC ACA CGA AAGTCG AAG T 3’). The software BLAST, Bioedit, and ClustalX were used to analyze the data. Barcode DNA of red fruit pandan showed 1474 bp nucleotides sequence based on matK gene. An indication of six red fruit pandan cultivars showed that high similarity 99% with Pandanus conoideus Lam. It can be concluded that matK gene can be used to determine the species level in Pandanus.

Integrating DNA Barcoding and Traditional Taxonomy for the Identification of Dipterocarps in Remnant Lowland Forests of Sumatra.

DNA barcoding has been used as a universal tool for phylogenetic inferences and diversity assessments, especially in poorly studied species and regions. The aim of this study was to contrast morphological taxonomy and DNA barcoding, using the three frequently used markers matK, rbcL, and trnL-F, to assess the efficiency of DNA barcoding in the identification of dipterocarps in Sumatra, Indonesia. The chloroplast gene matK was the most polymorphic among these three markers with an average interspecific genetic distance of 0.020. The results of the molecular data were mostly in agreement with the morphological identification for the clades of Anthoshorea, Hopea, Richetia, Parashorea, and Anisoptera, nonetheless these markers were inefficient to resolve the relationships within the Rubroshorea group. The maximum likelihood and Bayesian inference phylogenies identified Shorea as a paraphyletic genus, Anthoshorea appeared as sister to Hopea, and Richetia was sister to Parashorea. A better discriminatory power among dipterocarp species provided by matK and observed in our study suggests that this marker has a higher evolutionary rate than the other two markers tested. However, a combination of several different barcoding markers is essential for reliable identification of the species at a lower taxonomic level.

Barcoding assessment of the Citrus species cultivated in the eastern Afghanistan

The establishment of a modern fruit culture in developing countries requests an accurate evaluation of the preexisting germplasm and its health status. This to prevent the possibility to introduce new germplasm which can be easily prey of the endemic diseases carried by asymptomathic host plants. Therefore, after the identification of cases of citrus plants affected by Tristeza virus, a survey of the germplasm cultivated in the Nangarhar valley and some nearby regions was run. The survey was focussed on the identification of the main Citrus species widely cultivated using barcoding analysis of conserved sequences located in the plastid DNA. The sequences of matK and rbcl genes did not show any discriminatory ability while the analysis of the the non-coding psbA-trnH intergenic spacer (psbA-trnH) showed a robust single nucleotide polymorphism (sNP) discriminating C. aurantium from C. sinensis in all analysed samples. These non-coding regions have no known function; thus, much of the variation may result from the spread of mutations unconstrained by selection. Because nucleotide variation in the psbA-trnH spacer region is high, mutational hot spots may be useful to detect species-level variations. According to our study, the afghan citrus germplasm belong to the C. aurantium species which is commonly used in citrus culture as a rootstock. In Afghanistan it is widely cultivated for fresh consumption, without topworking with selected varieties and this may be the reason why symptoms are often mild and cultivation can be anyhow carried on.

Phylogeny of Tacca (Taccaceae) and traits in reproductive structures, with description of a new Bornean species

Abstract. Wong SY, Chua KS. 2019. Phylogeny of Tacca (Taccaceae) and traits in reproductive structures, with description of a new Bornean species. Biodiversitas 20: 3096-3118. A phylogenetic study of 16 of the c. 20 Tacca species is presented using nuclear ITS and plastid matK gene regions. Tacca leontopetaloides and T. maculata are a sister clade to the rest of the Tacca species. Tacca palmata and T. palmatifida are strongly supported together in a clade with this clade sister to T. bibracteata and T. plantaginea. All endemic Bornean taxa except T. bibracteata formed a derived clade together with non-Bornean T. cristata and T. sumatrana. The Bornean taxa are separated into three clades with T. borneensis sister to the other two clades. Twelve morphological characteristics are coded and mapped onto the Maximum Parsimony tree to elucidate potential evolutionary patterns. Results indicated shifts from a geophytic (irregularly-) seasonally dormant to an evergreen mesophytic habit, a decompound to a simple leaf blade, a long to a short peduncle, green to dark-colored inflorescences, numerous to few inner bracts, bracteoles, and flowers, and a low to an increased number of ovules. Within the Bornean taxa, there is a reversal from showy bracts and elaborate inflorescences to less showy bracts and simplified inflorescences. Tacca cristata Jack is resurrected from within T. integrifolia Ker Gawl. sensu Drenth. A new species, Tacca havilandii S.Y.Wong & K.S.Chua from Borneo is described.

Phylogenetic study of living fossil Psilotum nudum L. from Himalayan range of Pakistan using DNA barcodes

The genus Psilotum belongs to Psilotaceae family, with about 133 to 189 species having outstanding social, economic and medically important relict plants. However, being living fossil plant, many hurdles come in way while trying to discern its phylogenetics reconstruction. The partial conserve nucleotide sequences of rbcLa, trnA, trnV, matK, ITS, ycF3 and rpoB genes were used to select the best suitable barcodes in Psilotum nudum L. The amplified fragments were subjected to Sanger sequencing and then Maximum likelihood, Maximum Parsimony and Neighbor Joining trees were generated using bioinformatics software. i.e., MUSCLE, BioEdit and Mega-7. Current population showed the best match between P. complanatum (KY099851.1), population reported from New Zealand and P. nudum (F384430.1) with identity value 100 and 99% having E-value 0.0 and 0.0 by rbcLa and trnA barcode region, respectively. The findings showed that P. nudum L. sequences are ever first reported from the Himalaya regions of Pakistan and could be utilized for further comparison among different populations of this relict plant species across the globe.

Nuevos iniciadores matK para código de barras de la vida en especies del género Dasylirion


 Las especies de Dasylirion se encuentran dentro de las más importantes del desierto chihuahuense en términos ecológicos y económicos. Su uso principal es la elaboración de una bebida alcohólica tradicional llamada sotol. El género comprende 22 especies, no todas aptas para este fin y su identificación es difícil. Herramientas moleculares como el código de barras de la vida facilitan su identificación y generan información genética. Hay iniciadores universales para el gen matK, cuya secuencia es apropiada para código de barras de la vida, que no funcionan para algunas especies de este género. La diferencia de un solo nucleótido puede generar problemas en la amplificación. El objetivo de este trabajo fue diseñar y probar nuevas secuencias iniciadoras del gen matK, que permitan amplificación en las plantas del género Dasylirion. Para el diseño se utilizaron los programas Primer3 Plus, FastPCR y la secuencia completa del gen matK de D. wheeleri. Los nuevos oligonucleótidos fueron probados con las especies D. texanum, D. leiophyllum, D. occidentalis y D. palaciosii, con amplificación limpia del gen matK (fragmento aproximado 1 000 pb) en cada una de ellas. Estos resultados contrastaron con los obtenidos a partir de los iniciadores universales matK 390F y matK 1 326R, que generaron bandas secundarias o fallaron en la amplificación. Ya que los nuevos iniciadores amplificaron exitosamente el gen matK en las especies estudiadas de Dasylirion, se consideran de valor para como herramientas para la obtención de código de barras de la vida en sotol. Investigación realizada durante los años 2016 a 2018.