scholarly journals Phylogenetic Relationships of Local Durian Species based on Morphological Characteristics and PCR-RFLP Analysis of the Ribosomal Internal Transcribed Spacer (ITS) DNA

2016 ◽  
Vol 8 (3) ◽  
pp. 362
Author(s):  
Fidia Fibriana ◽  
Lutfia Nur Hadiyanti
Keyword(s):  
Phylogenetic Relationships ◽  
Internal Transcribed Spacer ◽  
Morphological Characteristics ◽  
Biology Education ◽  
Rflp Analysis ◽  
Restriction Pattern ◽  
Internal Transcribed Spacers ◽  
Central Java ◽  
Pcr Rflp ◽  
Pcr Products

<p>In this study, twenty local durian accessions obtained from Central Java in situ collection were characterized using the morphological characteristics and the restriction patterns which generated from the region spanning the internal transcribed spacers ITS LEU and ITS 4. Morphological characteristics of durian leaf, stem, tree, and fruit showed variations for the different accessions, whereas polymerase chain reaction (PCR) products of ribosomal DNA region showed a low length of variation. The size of the PCR products and the restriction analyses with the restriction endonucleases Bsp1431yielded a restriction pattern for each accessions. The results of this study can be utilized by local durian farmers as a preliminary reference for durian propagation. The data obtained need to be supported by further research using the other molecular markers to obtain more accurate data. The clear identity of durian species can help the management of propagation systems by farmers to get superior local durian.</p><p><strong>How to Cite</strong></p><p>Fibriana, F., &amp; Hadiyanti, L. N. (2016). Phylogenetic Relationships of Local Durian Species based on Morphological Characteristics and PCR-RFLP Analysis of the Ribosomal Internal Transcribed Spacer (ITS) DNA. <em>Biosaintifika: Journal of Biology &amp; Biology Education</em>, 8(3), 362-370. </p>

Genetic diversity among a complex of cereal cyst nematodes inferred from RFLP analysis of the ribosomal internal transcribed spacer region

Genome ◽  
1997 ◽  
Vol 40 (4) ◽  
pp. 479-486 ◽  
Author(s):  
S. Bekal ◽  
J. P. Gauthier ◽  
R. Rivoal
Keyword(s):  
Phylogenetic Relationships ◽  
Internal Transcribed Spacer ◽  
Rflp Analysis ◽  
Restriction Pattern ◽  
Nuclear Ribosomal Dna ◽  
Heterodera Avenae ◽  
Cyst Nematodes ◽  
Internal Transcribed Spacer Region ◽  
5.8S Rdna ◽  
Pcr Rflp

This study examined the restriction polymorphism (RFLP) of the nuclear ribosomal DNA in Heterodera avenae, H. filipjevi, H. mani, H. latipons, and the taxonomically unclear Gotland strain in order to establish a molecular characterization and phylogenetic relationships in the complex of cereal cyst nematodes (CCN). The internal transcribed spacer (ITS) and 5.8S rDNA were amplified by PCR from a single female or a cyst of 27 different geographic isolates of the CCN complex and one population of H. schachtii, used as outgroup. The amplified product was 1.2 kb long and 14 of 15 enzymes produced restriction fragments for each isolate. Relationships between populations were determined from UPGMA analysis based on distance values calculated from RFLP data. Digestions with TaqI clearly differentiated H. avenae, H. latipons, and a group composed of H. filipjevi and the Gotland strain. Six endonucleases (HaeIII, HinfI, ItaI, PstI, TaqI, and Tru9I) produced the same restriction pattern with H. filipjevi and the Gotland strain, and both were clearly separated from H. avenae with PstI. Restriction sites have revealed a mixture of the species H. latipons and H. avenae, and possible infraspecific variation in H. avenae. The inferred phylogenetic relationships of species in the CCN complex are in agreement with their morphological characterization.Key words: cereal cyst nematodes, Heterodera avenae, PCR, RFLP, ribosomal diversity.

scholarly journals Detection and Differentiation of Primate α-herpesviruses by PCR

1997 ◽  
Vol 9 (3) ◽  
pp. 225-231 ◽  
Author(s):  
Daria H. Black ◽  
R. Eberle
Keyword(s):  
Pcr Primers ◽  
Restriction Pattern ◽  
Restriction Enzyme Digestion ◽  
Gene Encoding ◽  
B Virus ◽  
Pcr Rflp ◽  
Pcr Products ◽  
Unique Restriction ◽  
Polymerase Chain ◽  
Simplex Virus

A rapid method for detection and differentiation of 5 primate αpha-herpesviruses (human herpes simplex virus types 1 and 2 [HSV1, HSV2], green monkey simian agent 8, baboon herpesvirus 2 [HVP2], and macaque B virus [BV]) was developed utilizing the polymerase chain reaction (PCR). PCR primers were located in conserved regions of the gene encoding the glycoprotein B, which flanks an intervening region that is highly divergent among the 5 viruses. Amplified PCR products from the 5 viruses were readily differentiated by their unique restriction enzyme digestion patterns. No variation in digestion patterns was noted among strains of HSV1, HSV2, or HVP2. One clinical isolate of BV exhibited variation in a single restriction site, but its overall restriction pattern remained typical of BV. This method (PCR/RFLP) allowed the presence of herpesvirus DNA in clinical swabs from primates to be readily detected and the virus unambiguously identified.

A simple molecular method for rapid identification of commercially used Amblyseius and Neoseiulus species (Acari: Phytoseiidae)

Zootaxa ◽  
2018 ◽  
Vol 4394 (2) ◽  
pp. 270
Author(s):  
M.Y. SYROMYATNIKOV ◽  
A.V. KOKINA ◽  
N.A. BELYAKOVA ◽  
E.G. KOZLOVA ◽  
V.N. POPOV
Keyword(s):  
Molecular Genetic ◽  
Mite Species ◽  
Rapid Identification ◽  
Internal Transcribed Spacers ◽  
Dna Fragments ◽  
Neoseiulus Cucumeris ◽  
Accurate Identification ◽  
Pcr Rflp ◽  
Pcr Products ◽  
Its1 And Its2

Predatory mites from the Amblyseius (Neoseiulus) genus (Family Phytoseiidae, Order Parasitiformes) are widely used for protecting plants against pests, especially thrips. The differentiation of Amblyseius and Neoseiulus species by their morphological features is problematic despite the fact that they are taxonomically different genera. The Phytoseiidae family includes a lot of species that are extremely difficult to distinguish from each other. The discovery of new molecular genetic markers might considerably facilitate the express identification of commercial mite species. Despite their high morphological similarity, the three common commercial Amblyseius and Neoseiulus mite species (Neoseiulus cucumeris, Amblyseius swirskii, and Neoseiulus barkeri) differed significantly in the nucleotide sequences of DNA fragments containing the ITS1 and ITS2 internal transcribed spacers. We found that when PCR products of the amplified DNA fragments from A. swirskii, N. cucumeris, and N. barkeri were treated with a combination of AccB1I, AspLEI, and SspI endonucleases and the resulting products were separated by electrophoresis in agarose gel, the obtained picture was sufficiently specific to provide accurate identification of the analyzed mite species. The lengths of the digestion products were different enough to allow their resolution in agarose gels. The PCR-RFLP method developed by us allows the rapid and accurate identification of commercially used Amblyseius and Neoseiulus species without DNA sequencing. The combination of the three endonucleases (AccB1I, AspLEI, and SspI) and FaeI can be used for the differentiation of all other but less frequently commercially used Phytoseiidae mites. 

scholarly journals PHYLOGENETIC RELATIONSHIPS AMONGST 10 Durio SPECIES BASED ON PCR-RFLP ANALYSIS OF TWO CHLOROPLAST GENES

2013 ◽  
Vol 6 (1) ◽  
pp. 20 ◽  
Author(s):  
Panca J. Santoso ◽  
Ghizan B. Saleh ◽  
Norihan M. Saleh ◽  
Suhaimi Napis
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Rflp Analysis ◽  
Restriction Enzymes ◽  
Rbcl Gene ◽  
Research Station ◽  
Taxonomic Level ◽  
Pcr Rflp ◽  
Young Leaves ◽  
Reliable Marker

Twenty seven species of Durio have been identified in Sabah and Sarawak, Malaysia, but their relationships have not been studied. This study was conducted to analyse phylogenetic relationships amongst 10 Durio species in Malaysia using PCR-RFLP on two chloroplast DNA genes, i.e. ndhC-trnV and rbcL. DNAs were extracted from young leaves of 11 accessions from 10 Durio species collected from the Tenom Agriculture Research Station, Sabah, and University Agriculture Park, Universiti Putra Malaysia. Two pairs of oligonucleotide primers, N1-N2 and rbcL1-rbcL2, were used to flank the target regions ndhC-trnV and rbcL. Eight restriction enzymes, HindIII, BsuRI, PstI, TaqI, MspI, SmaI, BshNI, and EcoR130I, were used to digest the amplicons. Based on the results of PCR-RFLP on ndhC-trnV gene, the 10 Durio species were grouped into five distinct clusters, and the accessions generally showed high variations. However, based on the results of PCR-RFLP on the rbcL gene, the species were grouped into three distinct clusters, and generally showed low variations. This means that ndhC-trnV gene is more reliable for phylogenetic analysis in lower taxonomic level of Durio species or for diversity analysis, while rbcL gene is reliable marker for phylogenetic analysis at higher taxonomic level. PCR-RFLP on the ndhC-trnV and rbcL genes could therefore be considered as useful markers to phylogenetic analysis amongst Durio species. These finding might be used for further molecular marker assisted in Durio breeding program.

scholarly journals Molecular Identification and VOMs Characterization of Saccharomyces cerevisiae Strains Isolated from Madeira Region Winery Environments

Processes ◽  
2020 ◽  
Vol 8 (9) ◽  
pp. 1058 ◽  
Author(s):  
Mariangie Castillo ◽  
Emanuel da Silva ◽  
José S. Câmara ◽  
Mahnaz Khadem
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Solid Phase ◽  
Rflp Analysis ◽  
Selective Adaptation ◽  
Internal Transcribed Spacers ◽  
Gas Chromatography Mass Spectrometry ◽  
Pcr Rflp ◽  
Volatile Organic ◽  
Major Chemical

The quality and typical characteristic of wines depends, among other factors, on the volatile organic metabolites (VOMs) that are biosynthesized by yeasts, mainly Saccharomyces cerevisiae species. The yeast strain influences the diversity and proportions of the VOMs produced during the fermentation process, as the genetic predisposition of the strains is a by-product of selective adaptation to the ecosystem. The present work reports the characterization of S. cerevisiae strains isolated from grape must, used in the Demarcated Region of Madeira (DRM) for winemaking. Yeast species were identified by amplification and by restriction fragment length polymorphism (RFLP) analysis of the region 5.8S-internal transcribed spacers (PCR-RFLP of 5.8S-ITS) of ribosomal DNA (rDNA). The strains identification was performed by analyzing the RFLP pattern of mitochondrial DNA (RFLP-mtDNA). The representative strains were selected for the characterization of the volatile profile through headspace solid-phase microextraction (HS-SPME) followed by gas chromatography-mass spectrometry (GC-MS) analysis. A total of 77 VOMs were identified. Higher alcohols, esters, and fatty acids were the major chemical families representing 63%, 16%, and 9%, respectively, in strain A and 54%, 23%, and 15% in strain B. The results indicate the influence of the strain metabolism in the production of VOMs, many of which probably participate in the aroma of the corresponding wines.

Association of polymorphism at intron 2 of FABP3 Gene with milk production traits in Sahiwal and Karan Fries cattle

2018 ◽  
Author(s):  
Alok Kumar Yadav ◽  
Anupama Mukherjee ◽  
Suchit Kumar
Keyword(s):  
Milk Production ◽  
Rflp Analysis ◽  
Production Traits ◽  
Milk Production Traits ◽  
Pcr Rflp ◽  
Sahiwal Cattle ◽  
Pcr Products ◽  
The Mean ◽  
Intron 2 ◽  
Karan Fries

PCR-RFLP analysis of PCR products were carried out using Aci I / SSi I for 100 Sahiwal and 115 Karan Fries cattle. In Sahiwal cattle and Karan Fries cattle, 438bp has three genotypes AA (438), AB (438+299+139 bp) and BB (299+139 bp). In Sahiwal cattle these genotypes are highly significant for FL305DPY but in Karan Fries cattle these genotypes are highly significant for FL305DMY, FLTMY, FL305DFY and FL305DPY. In Sahiwal cattle, mean ± SE of AA genotype for FL305DMY, FLTMY, FL305DFY, FL305DSNFY, FL305DPY were 1809.90 ± 15.7 kg, 2029.4 ± 15.6 kg, 99.90 ± 0.66 kg, 154.87 ± 0.17 kg and 44.81 ± 0.06 kg, respectively and for AB genotype were 1800.76 ± 9.48 kg, 1993.99 ± 9.42 kg, 100.54 ± 0.39 kg, 154.79 ± 0.10 kg, 43.99 ± 0.04 kg, respectively and for BB genotype were 1830.0 ± 14.10 kg, 2032.80 ± 14.0 kg, 100.24 ± 0.59 kg, 155.11 ± 0.15 kg, 42.98 ± 0.05 kg, respectively. Heterozygous AB genotype was found to be superior for, FL305DFY trait. AA genotype was significantly superior for FL305DPY traits whereas BB genotype was found to be superior for FL305DMY, FLTMY, FL305DSNFY. In Karan Fries cattle, the mean ± SE of AA genotype for FL305DMY, FLTMY, FL305DFY, FL305DSNFY, FL305DPY were 3442.17 ± 8.39 kg, 4461.93 ± 8.39 kg, 124.96 ± 7.20 kg, 277.35 ± 0.08 kg and 112.51 ± 0.08 kg, respectively and for AB genotype were 3572.69 ± 5.93 kg, 4592.45 ± 5.93 kg, 140.17 ± 5.09 kg, 278.60 ± 0.06 kg, 113.91 ± 0.05 kg, respectively and for BB genotypes were 3502.41 ± 9.19 kg, 4522.17 ± 9.19 kg, 136.91 ± 7.89 kg, 277.93 ± 0.09 kg, 113.19 ± 0.08 kg, respectively.

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