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

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.

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

Biosaintifika Journal of Biology & Biology Education ◽

10.15294/biosaintifika.v8i3.6748 ◽

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

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.How to CiteFibriana, F., & 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. Biosaintifika: Journal of Biology & Biology Education, 8(3), 362-370.

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Identification of Pneumococcal Serotypes by PCR–Restriction Fragment Length Polymorphism

Diagnostics ◽

10.3390/diagnostics9040196 ◽

2019 ◽

Vol 9 (4) ◽

pp. 196 ◽

Cited By ~ 1

Author(s):

García-Suárez ◽

González-Rodríguez ◽

Cima-Cabal ◽

Yuste ◽

Vazquez ◽

...

Keyword(s):

Restriction Fragment Length Polymorphism ◽

Restriction Fragment ◽

Length Polymorphism ◽

Dna Sequences ◽

Fragment Length ◽

Fragment Length Polymorphism ◽

Rflp Analysis ◽

Restriction Enzymes ◽

Pcr Rflp ◽

Restriction Fragment Length

Streptococcus pneumoniae shows more than 90 capsular serotypes that can be distinguished by their reactivity against antisera. The main objective of this work was the development of a molecular method for serotyping without the use of antisera. A computer program containing an algorithm was used to search in a database for potentially useful enzymes for Restriction Fragment Length Polymorphism-RFLP typing, in order to maximize the discrimination between different serotypes. DNA sequences of 90 serotypes for the region between dexB and aliA genes were compiled, and a computer screening of restriction enzymes was performed. The wzg–wzh–wzd–wze region and Sse9I restriction predicted unique PCR-RFLP patterns for 39 serotypes and eight serogroups. A second restriction enzyme resolved fragment specific patterns for 25 serotypes. The method was tested with 98 serotype-unknown clinical isolates. PCR-RFLP analysis deduced correct serotypes that were confirmed by Quellung reaction for 78.5% of the isolates.

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PCR-based genetic identification of marlin and other billfish

Marine and Freshwater Research ◽

10.1071/mf98007 ◽

1998 ◽

Vol 49 (5) ◽

pp. 383 ◽

Cited By ~ 8

Author(s):

B. H. Innes ◽

P. M. Grewe ◽

R. D. Ward

Keyword(s):

Mitochondrial Dna ◽

Genetic Test ◽

Rflp Analysis ◽

Restriction Enzymes ◽

Genetic Identification ◽

Dna Molecule ◽

Pcr Rflp ◽

D Loop ◽

Specific Variation ◽

Species Specific

A genetic test was developed for the identification of the six species of billfish found in Australian waters (black marlin, Indo–Pacific blue marlin, striped marlin, Indo–Pacific sailfish, shortbill spearfish and broadbill swordfish). The test was based on the PCR–RFLP analysis of a 1400 bp region of the mitochondrial DNA molecule, the d-loop, using four restriction enzymes (Hinf I, Rsa I and Sau3A I andTaq I). A total of 33 composite haplotypes were observed among 160 fish; all were species-specific. Three of the species—black marlin, striped marlin and broadbill swordfish—showed sufficient intra-specific variation to be useful in population structure analyses.

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PCR–RFLP analysis of mitochondrial DNA for identification of Rutilus rutilus caspicus populations on the southern coast of the Caspian Sea, Iran

Journal of the Marine Biological Association of the United Kingdom ◽

10.1017/s0025315406014524 ◽

2006 ◽

Vol 86 (6) ◽

pp. 1463-1467 ◽

Cited By ~ 1

Author(s):

Sohrab Rezvani ◽

Amin Eimanifar ◽

Reza Aghili ◽

Faramarz Laloei

Keyword(s):

Caspian Sea ◽

Rflp Analysis ◽

Restriction Enzymes ◽

Rutilus Rutilus ◽

Southern Coast ◽

The Caspian Sea ◽

Length Polymorphisms ◽

Pcr Rflp ◽

Nucleotide Divergence ◽

Genetic Pools

Genetic analysis using restriction fragment length polymorphisms (RFLPs) of cytochrome b in mtDNA was made to clarify genetic variations among two Iranian Rutilus rutilus caspicus populations of commercial importance from the southern coast of the Caspian Sea. Polymorphism was detected using six restriction enzymes and a total of six composite haplotypes were identified. Four haplotypes were rare occurring only once in two regions (west and east of the southern Caspian Sea). Nucleotide and haplotype diversities were higher in the south-west region of the Caspian Sea (π=3.43%, h=23.3).The nucleotide divergence between the two populations was low (0.064%). The test for heterogeneity of composite haplotype frequencies gave no significant outcome for all samples (χ2=0.137, P≤0.05). The results indicate that significant attention should be paid to the genetic characterization of R. rutilus caspicus populations for conservation of their genetic pools and aquaculture policies at the coastlines of the Caspian Sea.

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Detection and characterization of Leptospira spp. isolated from aborted bovine clinical samples

Acta Veterinaria Brno ◽

10.2754/avb201281010021 ◽

2011 ◽

Vol 81 (1) ◽

pp. 21-25 ◽

Cited By ~ 1

Author(s):

Hassan Momtaz ◽

Saadat Moshkelani

Keyword(s):

Public Health Problem ◽

Rflp Analysis ◽

Restriction Enzymes ◽

Clinical Samples ◽

Dairy Herds ◽

Important Public Health Problem ◽

Pcr Rflp ◽

Beef Herds ◽

Bovine Abortion

Leptospira is recognized as an important public health problem worldwide, especially in tropical countries, and is a common cause of abortion in dairy and beef herds. The aim of the present study was to detect and characterize Leptospira as the causative agent of abortion in cattle using a PCR-RFLP in Chaharmahal va Bakhtiari and Isfahan provinces, Iran. A total of 220 bovine aborted foetuses and 120 vaginal discharges from an aborted calf were collected from 64 commercial dairy herds. After isolation of 60 Leptospira spp. from samples, RFLP analysis was carried out with HindIII and HaeIII restriction enzymes in reference strains and isolated for characterization. In a total of 340 specimens, 46 (20.9%) and 14 (11.66%) were identified positive for Leptospira spp. from aborted bovine foetuses and vaginal discharges, respectively. The present results also suggest that L. interrogans serovar hardjo has the highest prevalence in the region under study and L. hardjo is a major pathogen causing bovine abortion in Chaharmahal va Bakhtiari and Isfahan provinces of Iran.

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Increased genetic diversity in Greek populations of the genus Ligidium (Crustacea: Isopoda: Oniscidea) revealed by RFLP analysis of mtDNA segments

Contributions to Zoology ◽

10.1163/18759866-0740304003 ◽

2005 ◽

Vol 74 (3-4) ◽

pp. 255-264 ◽

Cited By ~ 4

Author(s):

Elena Klossa-Kilia ◽

George Kilias ◽

Spyros Sfenthourakis

Keyword(s):

Genetic Diversity ◽

Genetic Differentiation ◽

16S Rdna ◽

Central Europe ◽

Phylogenetic Relationships ◽

Rflp Analysis ◽

Restriction Enzymes ◽

Nominal Species ◽

Nucleotide Divergence ◽

Different Populations

We investigated mtDNA genetic differentiation and the phylogenetic relationships of 11 populations of the oniscidean genus Ligidium. We studied nine populations from Greece, assigned to three nominal species (L. euboicum, L. germanicum and L. beieri), and two from central Europe (L. germanicum and L. hypnorum), applying RFLP analysis of two mtDNA segments (12S rDNA and 16S rDNA) amplified by PCR. The analysis revealed seven monomorphic and four polymorphic populations, and 17 different haplotypes, each one present in one population only. Several restriction enzymes produced population specific patterns, enabling discrimination among the different populations. The estimated net nucleotide divergence between populations ranges from 1.06 to 16.52%, while the high NST value (0.96) indicates the existence of increased interpopulation genetic differentiation that can be attributed to the extreme isolation among Ligidium populations. The relationships between haplotypes and populations are not congruent with their geographical distribution and the established taxonomy within the genus.

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Rapid differentiation of Staphylococcus aureus isolates harbouring egc loci with pseudogenes ψent1 and ψent2 and the selu or selu v gene using PCR-RFLP

Journal of Medical Microbiology ◽

10.1099/jmm.0.46948-0 ◽

2007 ◽

Vol 56 (2) ◽

pp. 208-216 ◽

Cited By ~ 13

Author(s):

Mark M. Collery ◽

Cyril J. Smyth

Keyword(s):

Dna Sequencing ◽

Restriction Enzyme ◽

Sequence Similarity ◽

Rflp Analysis ◽

Restriction Enzymes ◽

Restriction Enzyme Digestion ◽

Pcr Rflp ◽

Intergenic Regions ◽

Unique Restriction ◽

Genomic Regions

The egc locus of Staphylococus aureus harbours two enterotoxin genes (seg and sei) and three enterotoxin-like genes (selm, seln and selo). Between the sei and seln genes are located two pseudogenes, ψent1 and ψent2, or the selu or selu v gene. While these two alternative sei–seln intergenic regions can be distinguished by PCR, to date, DNA sequencing has been the only confirmatory option because of the very high degree of sequence similarity between egc loci bearing the pseudogenes and the selu or selu v gene. In silico restriction enzyme digestion of genomic regions encompassing the egc locus from the 3′ end of the sei gene through the 5′ first quarter of the seln gene allowed pseudogene- and selu- or selu v-bearing egc loci to be distinguished by PCR-RFLP. Experimental application of these findings demonstrated that endonuclease HindIII cleaved PCR amplimers bearing pseudogenes but not those with a selu or selu v gene, while selu- or selu v-bearing amplimers were susceptible to cleavage by endonuclease HphI, but not by endonuclease HindIII. The restriction enzyme BccI cleaved selu- or selu v-harbouring amplimers at a unique restriction site created by their signature 15 bp insertion compared with pseudogene-bearing amplimers, thereby allowing distinction of these egc loci. PCR-RFLP analysis using these restriction enzymes provides a rapid, easy to interpret alternative to DNA sequencing for verification of PCR findings on the nature of an egc locus type, and can also be used for the primary identification of the intergenic sei–seln egc locus type.

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