Molecular insights into the genetic and haplotype diversity among four populations of Catla catla from Madhya Pradesh revealed through mtDNA cyto b gene sequences

Garg, R. K.; Mishra, Vaishali

doi:10.1016/j.jgeb.2017.11.003

Cited by 19 publications

(11 citation statements)

References 22 publications

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“…This possibility is supported by Roesma et al [35] which states that if genetic mixing between species with separate locations can still occur, then genetic similarities between species are always maintained. In line with the statements of Garg and Mishra [54] which states that gene flow has the potential to reduce genetic differentiation. Zero genetic variation between Palo fish populations based on the cytochrome b gene is also predicted because these two populations come-from the same ancestor.…”

Section: Discussionsupporting

confidence: 68%

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The role of molecular taxonomy in uncovering local ornamental Palo Fish (Betta sp.: Osphronemidae) and other Betta based on Cytochrome b gene

Putri¹,

Simanjuntak²,

Febriamansyah³

et al. 2021

World J. Adv. Res. Rev.

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Cytochrome b gene mitochondrial DNA was used to study the Palo fish from Bukit Rangkak tributary, Harau Valley, West Sumatra. The study aimed to determine the taxonomy of Palo fish, which morphological suspected as the Betta group. Phylogenetic analysis was used to solve the relationship of Palo fish with other species of the Betta. The alignment of the DNA sequences was carried out with Clustal X version 2 and analysis of phylogenetic tree using MEGA 6 software program. Based on the analysis of the cytochrome b gene sequence (1047 bp), it is known that the genetic differences of Palo fish from two tributaries of Bukit Rangkak river is 0.0% and with other Betta fish ranges from 13.0-35.5%. The phylogenetic tree has shown that Palo fish has a close genetic relationship with the Betta picta (13.0%). The result showed that Palo fish is at the different species in the genus of Betta and proposed as a new species.

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Section: Discussionsupporting

confidence: 68%

“…The number of bases in Palo fish (A+T) is higher than (G+C). According to the previous researchers [51,52,53,54,55] the number of bases (A+T) in vertebrates is higher than (G+C).…”

Section: Blast Analysismentioning

confidence: 98%

The role of molecular taxonomy in uncovering local ornamental Palo Fish (Betta sp.: Osphronemidae) and other Betta based on Cytochrome b gene

Putri¹,

Simanjuntak²,

Febriamansyah³

et al. 2021

World J. Adv. Res. Rev.

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show abstract

“…The genetic variation of a species is distributed both within populations, expressed as differences between individuals and between populations, expressed as differences in the presence and frequency of alleles (Garg and Mishra, 2018). In this study, analyses of the gyrA, parC and parE sequences were found to be polymorphic with high haplotype diversity (Hd) (0.945-0.982) and low nucleotide diversity (0.01225-0.02001).…”

Section: Discussionmentioning

confidence: 70%

Phenotypic and molecular characterization of fluoroquinolone resistant Pseudomonas aeruginosa isolates in Palestine

Adwan

Omar

2022

Braz. J. Biol.

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Fluoroquinolones are important antimicrobial agents for the treatment of Pseudomonas infections. A total of 11 isolates of P. aeruginosa were collected from different clinical samples from different medical centers in the North West Bank-Palestine during 2017. In this study, resistance to fluoroquinolones and secretions of β-lactamases were detected by phenotypic methods, while presence of β-lactamase gene sequences and other virulence factors were detected by PCR technique. PCR product for gyrA, parC and parE genes were sequenced for further analyses. The phylogenetic analyses, population diversity indices and haplotypes determination were conducted using computer programs MEGA version 6, DnaSP 5.1001 and median-joining algorithm in the program Network 5, respectively. Results of this study showed that the MIC for ciprofloxacin and norfloxacin had a range of 32-256 µg/ml. In addition, all isolates carried either exoT or exoT and exoY genes, different β-lactamase genes and 82% of these isolates harbored class 1 integrons. Analyses of the gyrA, parC and parE sequences were found to be polymorphic, had high haplotype diversity (0.945-0.982), low nucleotide diversity (0.01225-0.02001) and number of haplotypes were 9 for each gyrA and parE genes and 10 haplotypes for parC gene. The founder haplotypes being Hap-1 (18%), Hap-2 (27.3%) and Hap-6 (9.1%) for gyrA, parC and parE genes, respectively. Two of ParE haplotypes were detected as indel haplotypes. The Median-joining- (MJ) networks constructed from haplotypes of these genes showed a star-like expansion. The neutrality tests (Tajima’s D test and Fu’s Fs test) for these genes showed negative values. Palestinian fluoroquinolone resistant P. aeruginosa strains showed high MIC level for fluoroquinolones, β-lactamase producers, carried type III secretion exotoxin-encoding genes, most of them had integrase I gene and had high level of mutations in QRDR regions in gyrA, parC and parE genes. All these factors may play an important role in the invasiveness of these strains and make them difficult to treat. Isolation of these strains from different medical centers, indicate the need for a strict application of infection control measures in Medical centers in the North West Bank-Palestine that aim to reduce expense and damage caused by P. aeruginosa infections. Molecular analyses showed that Palestinian fluoroquinolone resistant P. aeruginosa haplotypes are not genetically differentiated; however, more mutations may exist in these strains.

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“…Haplotypes reveal the genetic variation within a species based on the nucleotide sequence (Garg and Mishra 2018;Phillips et al 2019). There were four haplotypes (Hap) from both cattle (Table 2), namely haplotype_1 (Hap_1) found in Taro samples 1, 2, 3, 4, 5, 7, and 9, while in Bali cattle from Sobangan, it was found in numbers 1, 2, 3, 4, and 5.…”

Section: Discussionmentioning

confidence: 99%

Molecular analysis of Taro and Bali cattle using cytochrome oxidase subunit I (COI) in Indonesia

2020

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Abstract. Susari NNW, Suastika P, Agustina KK. 2021. Molecular analysis of Taro and Bali cattle using cytochrome oxidase subunit I (COI) in Indonesia. Biodiversitas 22: 165-172. Cytochrome oxidase subunit I (COI) is one of the molecular markers often used as a differentiator with many advantages in phylogeny analysis, and it thus rarely undergoes substitution. This research was conducted to characterize the genetics of Taro and Bali (Bos javanicus) cattle. Blood from the animals was collected from the jugularis vein and amplified by PCR. The target area was COI with a primer that was successfully amplified, namely the forward BICOIF (5'-TTC-TCAACCAACCATAAAGATATTGG-3') and the reverse BICOIR fragment (5'-TAG-ACTTCGGGGTGTCCAAAGAATCA-3'). The PCR products' sequencing was carried out by phylogeny analysis using MEGA 6 software. The amplicon value that succeeded in electrophoresis was 710bp, while six polymorphic sites were obtained at base positions of 1, 300, 379, 675, 676, and 679. The haplotypes (Hap) obtained were 4, with a genetic distance that ranged from 0.000-0.001. The nitrogenous bases of the amino acid composition from the samples showed no significant difference. The phylogenetic tree (Tamura-Nei) classified the cattle into two clades with a genetic distance of 0.0005.

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Molecular insights into the genetic and haplotype diversity among four populations of Catla catla from Madhya Pradesh revealed through mtDNA cyto b gene sequences

Cited by 19 publications

References 22 publications

The role of molecular taxonomy in uncovering local ornamental Palo Fish (Betta sp.: Osphronemidae) and other Betta based on Cytochrome b gene

The role of molecular taxonomy in uncovering local ornamental Palo Fish (Betta sp.: Osphronemidae) and other Betta based on Cytochrome b gene

Phenotypic and molecular characterization of fluoroquinolone resistant Pseudomonas aeruginosa isolates in Palestine

Molecular analysis of Taro and Bali cattle using cytochrome oxidase subunit I (COI) in Indonesia

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