scholarly journals Genetic Differentiation of Clariid Populations using Microsatellite Markers in Kano State Rivers

2021 ◽  
pp. 35-45
Author(s):  
I. O. Suleiman ◽  
R.O. Okeke ◽  
J. M. Madu ◽  
A. U. Umar ◽  
O.M Akinsola ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Genetic Differentiation ◽  
Dna Extraction ◽  
Genetic Characterization ◽  
Caudal Peduncle ◽  
Fta Cards ◽  
Fish Samples ◽  
Polymerase Chain ◽  
Outbred Populations

This study aimed to investigate the genetic characterization of strains of Clariid fish species in some river bodies in Kano State using microsatellite markers.One hundred and seventy seven Clariid fish samples (Clariasgariepinus and Heterobranchuslongifilis) were collected from six rivers (Thomas, Ghari, Tiga dam, Duddurun Gaya, Karaye and Bagwai) in Kano state. Blood sample was taken from each fish sample by severing the caudal peduncle and drained into FTA cards for DNA extraction, Polymerase Chain Reaction and electrophoresis to determine genetic variation between the Clariid fish populations.Genealex 6.4 software package was used to analyse the resolve bands from DNA extraction to determine their base pair and genetic variation. Results showed that the Fst values ranged from 0.00 to 0.66, Fit ranged from -0.04 to 0.12, Fis ranged from -0.35 to -0.26. It indicated a large number of gene flow (exchange) among the populations with a range of 0.46 to 0.87. There was an established magnitude of genetic divergence (91.86%) among the populations as shown by the result of the percentage polymorphism which depends on the number of alleles detected per locus and their frequencies. It can be concluded that since there was no inbreeding as shown in the study, none of the population exhibited genetic uniqueness. The populations had a high genetic differentiation between populations but moderate differentiation within populations. The populations were outbred populations; an indication that relatives avoided mating in the population.

scholarly journals GENETIC CHARACTERIZATION OF KISSING GOURAMI (Helostoma temminckii Cuvier, 1829) IN OGAN RIVER, SOUTH SUMATRA INFERRED FROM 16S rRNA AND COI MITOCHONDRIAL GENES

2019 ◽  
Vol 25 (1) ◽  
pp. 37
Author(s):  
Tuty Arisuryanti ◽  
Gregorius Altius Pratama ◽  
Lukman Hakim ◽  
Johan Putra Koentjana ◽  
Fitria Kurnia Nazira
Keyword(s):  
16S Rrna ◽  
Genetic Divergence ◽  
Nucleotide Diversity ◽  
Genetic Characterization ◽  
Haplotype Diversity ◽  
Mitochondrial Genes ◽  
Coi Gene ◽  
Fish Stock ◽  
Fish Samples

Genetic characterization data of kissing gourami are important to understand historical lineage thus enhancing sustainability of the species and to establish regulation for sustainable management of the fish stock in their habitat. However, investigation of genetic characterization of kissing gourami, one of native Indonesian freshwater fishes has poorly understood. Therefore, the aim of this study was to examine genetic characterization of the fish species collected from Ogan River, South Sumatra using partial sequences of two mitochondrial genes, 16S rRNA and COI. The results revealed that for the 621 bp determined in 16S rRNA gene of the samples, five sites were variable, of which one was parsimony informative. Concatenate data revealed three haplotypes with an overall haplotype diversity of 0.833±0.222 and nucleotide diversity of 0.003±0.001. The genetic divergence varied from 0-0.49%. Next, sequence analysis of COI gene exhibited 609 bp which can be translated into 203 amino acids. For the 609 bp sequence determined in the fish samples, three haplotypes were revealed with nine variable sites and two parsimony informatives. Haplotype diversity and nucleotide diversity of the fish samples were 0.833±0.22 and 0.00794±0.0025, respectively. The haplotype divergence between the fish samples was also supported by three nonsynonymous codons. In addition, the genetic divergence varied from 0 % to 1.16 %. The results suggest that genetic variation of the kissing gourami has to be monitored and further studies are needed to compare the same species from different location to know the historical lineage and demography.

scholarly journals Genetic differentiation of Norway spruce (Picea abies (L.) Karst.) trees with diferent crown types from the mountain Golija

Genetika ◽  
2015 ◽  
Vol 47 (3) ◽  
pp. 849-861 ◽  
Author(s):  
Vladislava Galovic ◽  
Mirjana Sijacic-Nikolic ◽  
Robert Safhauzer ◽  
Dijana Cortan ◽  
Sasa Orlovic
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Picea Abies ◽  
Genetic Differentiation ◽  
Norway Spruce ◽  
Plant Species ◽  
Genetic Characterization ◽  
Similarity Matrix ◽  
Primer Sets

The knowledge of genetic diversity degree of given species is of great importance for the successful process of breeding and genetic conservation. The aim of conducted research was to determine the genetic differentiation of Norway spruce (Picea abies (L.) Karst) genotypes with very specific narrow pyramidal and normal crown type, which grows at different altitude of the mountain Golija. For assessment of genetic similarities or differences between studied genotypes co-dominant microsatellite system had been used. This system has proven to be reliable and efficient in the genetic characterization of plant species. In total 22 primer sets have been tested, while 16 (73%) of them resulted in the successful yield of the amplified product. The analysis show that studied individuals had in total 130 alleles, in average 8.125 polymorphic alleles per each locus. The lowest polymorphism was detected in the locus EATC1D10, EATC1F03B and EATC2G09, while the highest level of polymorphism was detected in EATC2G08. Based on microsatellite date and similarity matrix, cluster analysis dendrogram indicates existence of the vertical differentiation of studied genotypes, which is consistent with results of previous Norway spruce studies.

scholarly journals Genetic diversity of Blastocystis in kindergarten children in southern Xinjiang, China

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Meng Qi ◽  
Zilin Wei ◽  
Ying Zhang ◽  
Qiyuan Zhang ◽  
Juanfeng Li ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Genetic Characterization ◽  
Intestinal Parasites ◽  
Small Subunit ◽  
Kindergarten Children ◽  
Chain Reaction ◽  
Significant Difference ◽  
Polymerase Chain ◽  
Southern Xinjiang

Abstract Background Blastocystis is one of the most common intestinal parasites in humans and various animals worldwide. Few studies are available regarding the genetic characterization of Blastocystis infections in humans in China. Methods In the present study, 609 fecal samples were collected from two- to six-year-old kindergarten children in southern Xinjiang and were examined by polymerase chain reaction (PCR). Results The infection rate of Blastocystis was 14.3% (87/609); no significant difference was observed among counties and between sexes. Blastocystis subtypes ST1 (n = 38), ST2 (n = 8), and ST3 (n = 41) were identified by sequence analysis of the small subunit ribosomal RNA gene. Genetic polymorphisms were observed at the intra-subtype level, including seven variations for ST1 (ST1A to ST1G), four for ST2 (ST2A to ST2D), and two for ST3 (ST3A and ST3B); with ST1F and ST2B being new variations. Conclusions ST1 and ST3 are the two common Blastocystis subtypes in the study area. More extensive studies in both humans and animals in different regions are needed to better characterize the transmission of Blastocystis.

Genetic characterization of Spermophagus niger (Coleoptera: Chrysomelidae: Bruchinae: Amblycerini) pest associated to seeds of Sorrel (Hibiscus sabdariffa L.) in Burkina Faso

2016 ◽  
Vol 6 (1) ◽  
pp. 07-14
Author(s):  
Jean Christophe Koussoubé ◽  
Fatimata Mbaye ◽  
Cheikh Abdou Khadre Mbacké Dia ◽  
Mbacké Sembène ◽  
Antoine Sanon
Keyword(s):  
Amino Acid ◽  
Burkina Faso ◽  
Genetic Parameters ◽  
Genetic Characterization ◽  
Mitochondrial Gene ◽  
Hibiscus Sabdariffa ◽  
Polymerase Chain ◽  
The One ◽  
First Time

In Burkina Faso, the seeds of sorrel, Hibiscus sabdariffa L. are attacked by a pest identified morphologically as Spermophagus niger which is maintained all year on seeds and causing considerable damages. In the current study, for the first time, genetic characterization for S. niger was performed to determine its genetic identity and place it in its phyletic group. Mitochondrial gene, the Cytochrome oxidase I (COI) of the pest was partially sequenced after extraction and amplification by Polymerase Chain Reaction (PCR). Then the variability of genetic parameters namely the number of polymorphic and monomorphic sites, the frequencies of the different nucleotides and amino acid composition were determined. The nucleotide sequence of S. niger ob-tained was submitted in Genbank and the accession number is KU710716. Nucleotide sequences of S. niger obtained and those of different species of Spermophagus and Z. subfasciatus available in the GenBank database, we determined the percentage of similarity on the one hand and kinship through Phylogenetics reconstructions on the other hand. The results showed the absence of polymorphic sites for 406 sites obtained with 36.5% of thymine, 17.5% of cytosine, adenine 31% and 15% of guanine. Leucine was the majority amino acid (14.50%); the lysine was minority amino acid (0.76%) and cysteine was absent. The percentage of similarity obtained and phylogenetics reconstructions showed that S. niger is very close to the different species of Spermophagus particularly S. drak and different from Z. sub-fasciatus.

scholarly journals Natural Variation in the Microcystin Synthetase Operon mcyABC and Impact on Microcystin Production in Microcystis Strains

2003 ◽  
Vol 185 (9) ◽  
pp. 2774-2785 ◽  
Author(s):  
Bjørg Mikalsen ◽  
Gudrun Boison ◽  
Olav M. Skulberg ◽  
Jutta Fastner ◽  
William Davies ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Natural Variation ◽  
Gene Loss ◽  
Genetic Characterization ◽  
Adenylation Domain ◽  
Ionization Time ◽  
Microcystin Synthetase ◽  
Flight Mass Spectrometry ◽  
Microcystin Production

ABSTRACT Toxic Microcystis strains often produce several isoforms of the cyclic hepatotoxin microcystin, and more than 65 isoforms are known. This has been attributed to relaxed substrate specificity of the adenylation domain. Our results show that in addition to this, variability is also caused by genetic variation in the microcystin synthetase genes. Genetic characterization of a region of the adenylation domain in module mcyB1 resulted in identification of two groups of genetic variants in closely related Microcystis strains. Sequence analyses suggested that the genetic variation is due to recombination events between mcyB1 and the corresponding domains in mcyC. Each variant could be correlated to a particular microcystin isoform profile, as identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry. Among the Microcystis species studied, we found 11 strains containing different variants of the mcyABC gene cluster and 7 strains lacking the genes. Furthermore, there is no concordance between the phylogenies generated with mcyB1, 16S ribosomal DNA, and DNA fingerprinting. Collectively, these results suggest that recombination between imperfect repeats, gene loss, and horizontal gene transfer can explain the distribution and variation within the mcyABC operon.

Importance of flagella and enterotoxins for Aeromonas virulence in a mouse model

2007 ◽  
Vol 53 (2) ◽  
pp. 261-269 ◽  
Author(s):  
Keya Sen ◽  
Dennis Lye
Keyword(s):  
Drinking Water ◽  
Virulence Factor ◽  
Genetic Characterization ◽  
Aeromonas Veronii ◽  
Aeromonas Caviae ◽  
Polymerase Chain ◽  
Immunocompromised Mice ◽  
Immunocompromised Hosts ◽  
Virulence Factor Genes

A genetic characterization of eight virulence factor genes, elastase, lipase, polar flagella (flaA/flaB, flaG), lateral flagella (lafA), and the enterotoxins alt, act, and ast, was performed using polymerase chain reaction with 55 drinking water and nine clinical isolates. When 16 Aeromonas hydrophila strains, seven Aeromonas veronii strains, and seven Aeromonas caviae strains exhibiting different combinations of virulence factor genes were tested in immunocompromised mice by intraperitoneal injection, only those strains that had one or more of the enterotoxins flaA, flaB, and either flaG or lafA showed signs of being virulent. The correlation was seen in 97% (29/30) of the strains, which included strains from drinking water. Thus, Aeromonas water isolates have the potential to be pathogenic in immunocompromised hosts.

The Polymerase Chain Reaction (PCR) in the routine genetic characterization of retinoblastoma: A tool for the clinical laboratory

1997 ◽  
Vol 41 (4) ◽  
pp. 331-340 ◽  
Author(s):  
Domenico Mastrangelo ◽  
Nicola Squitieri ◽  
Stefano Bruni ◽  
Theodora Hadjistilianou ◽  
Renato Frezzotti
Keyword(s):  
Polymerase Chain Reaction ◽  
Genetic Characterization ◽  
Clinical Laboratory ◽  
Chain Reaction ◽  
Polymerase Chain

scholarly journals Biological and Genetic Characterization of Pod Pepper Vein Yellows Virus-Associated RNA From Capsicum frutescens in Wenshan, China

2021 ◽  
Vol 12 ◽  
Author(s):  
Jiejun Peng ◽  
Shan Bu ◽  
Yueyan Yin ◽  
Mengying Hua ◽  
Kuangjie Zhao ◽  
...  
Keyword(s):  
Yunnan Province ◽  
Genetic Characterization ◽  
Biological Properties ◽  
Capsicum Frutescens ◽  
Chain Reaction ◽  
Positive Sense ◽  
Polymerase Chain ◽  
Pepper Vein Yellows Virus ◽  
Generation Sequencing

Tombusvirus-like associated RNAs (tlaRNAs) are positive-sense single-stranded RNAs found in plants co-infected with some viruses of the genus Polerovirus. Pod pepper vein yellows virus (PoPeVYV) was recently reported as a new recombinant polerovirus causing interveinal yellowing, stunting, and leaf rolling in Capsicum frutescens plants at Wenshan city, Yunnan province, China. The complete genome sequence of its associated RNA has now been determined by next-generation sequencing and reverse transcription (RT) polymerase chain reaction (PCR). PoPeVYV-associated RNA (PoPeVYVaRNA) (GenBank Accession No. MW323470) has 2970 nucleotides and is closely related to other group II tlaRNAs, particularly tobacco bushy top disease-associated RNA (TBTDaRNA, GenBank Accession No. EF529625). In infection experiments on Nicotiana benthamiana and C. frutescens plants, synergism between PoPeVYVaRNA and PoPeVYV was demonstrated, leading to severe interveinal yellowing of leaves and stunting of plants. The results provide further information on the genetic and biological properties of the various agents associated with pepper vein yellows disease (PeVYD).

Karakterisasi Genetik Fragmen Gen Penyandi RNA Polimerase Infectious Myonecrosis Virus (IMNV) yang Menginfeksi Udang Vannamei (Litopenaeus vannamei Boone.) dari Lampung, Gresik dan Pontianak

2014 ◽  
Vol 16 (1) ◽  
pp. 18
Author(s):  
Yason Lukman Sudjito ◽  
Christina Retna Handayani ◽  
Hermin Pancasakti Kusumaningrum ◽  
Anto Budiharjo
Keyword(s):  
Genetic Variation ◽  
Amino Acid ◽  
Rna Polymerase ◽  
Litopenaeus Vannamei ◽  
Genetic Characterization ◽  
Rdrp Gene ◽  
Rt Pcr ◽  
Infectious Myonecrosis Virus

A massive death of vannamei shrimp (Litopenaeus vannamei Boone.) due to Infectious Myonecrosis Virus (IMNV) infection has occurred in Indonesia recently and still cannot be eradicated efficiently. The fast reproduction of IMNV depends on the RdRp gene that encodes for RNA polymerase. Genetic characterization of IMNV RdRp gene from Indonesia is important in order to compare with other IMNV to find out genetic variation as a base for combating this virus. IMNV-infected vannamei were taken from major aquaculture region in Indonesia (Lampung, Gresik and Pontianak). RNA polymerase coding genes (12 and 13 region) from infected vannamei were amplified using RT-PCR with appropriate primer. Amplification products were sequenced and the results were analyzed using BioEdit 7.1.3.0, ClustalW2, CLC free workbench 6.6.2. and ClustalX programs. Results showed that homology value of IMNV RdRp gene  from Lampung and Gresik were 98,04-9958% compared with IMNV from Brazil (Acc. No. AY570982). Amino acid analysis revealed homology value of IMNV RdRp gene  from Lampung  and Gresik were 100% and 99.04% compared with IMNV from Brasil. IMNV RdRp gene  from Pontianak cannot be analysed due to low quality of RNA.   Key words: vannamei, IMNV, RdRp, genetic characterization

scholarly journals Epidemiology, Haematology and Molecular Characterization of Haemoprotozoon and Rickettsial Organisms Causing Infection in Cattle of Jammu Region, North India

2020 ◽  
Author(s):  
Rabjot Kaur ◽  
Anish Yadav ◽  
Shafiya Imtiaz Rafiqi ◽  
Rajesh Godara ◽  
Vikrant Sudan ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Genetic Characterization ◽  
Disease Mapping ◽  
Genomic Diversity ◽  
North India ◽  
Prevalence Studies ◽  
Red Blood Cell Count ◽  
Polymerase Chain ◽  
Blue Print

Abstract Background: The present study was aimed to establish the prevalence, epidemiology and molecular characterization of major haemoprotozoons (Babesia and Theileria) and rickettsia (Anaplasma) of cattle in Jammu region (North India) using microscopy and Polymerase chain reaction (PCR). Hematology, Microscopy and PCR based prevalence studies were undertaken with 278 blood samples from cattle. Molecular prevalence studies were followed by genetic characterization of the isolates of Babesia, Anaplasma and Theileria spp. based on 18S rRNA, 16S rRNA and Tams1 gene, respectively. The data related to metrology and epidemiological variables like temperature, rainfall, season, age and type of livestock rearing was analyzed and correlated with disease by statistical methods. Results: The study revealed prevalence of Babesia spp., Anaplasma spp. and Theileria spp. to be 14.02%, 23.74% and 1.079% respectively. The metrological and epidemiological variables made inroads for the propagation of vector ticks and occurrence of infection. Haematological alterations predominantly related to haemoglobin, red blood cell count and packed cell volume were evident in diseased animals and collaterally affected the productivity. Further the genetic characterization of Babesia spp. (MN566925.1, MN567603, MN566924.1), Anaplasma spp. (MH733242.1, MN567602.1) and Theileria spp. (MT113479) provided a representative data of the isolates circulating in the region and their proximity with available sequences across the world.Conclusions: Despite holding much significance to the animal sector, comprehensive disease mapping has yet not been undertaken in several parts of India. The present study provides a blue print of disease mapping, epidemiological correlations and genomic diversity of Babesia spp., Anaplasma spp. and Theileria spp circulating in the region.

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