Species-specific genomic sequences for classification of bacteria

Paul, Babu Sena; Raj, Keerthi; Murali, Thokur Sreepathy; Satyamoorthy, Kapaettu

doi:10.1016/j.compbiomed.2020.103874

Cited by 7 publications

(4 citation statements)

References 51 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This approach also enabled the employment of versatile methods beyond Primer3 for the generation of primers and made the visualization of species-specific sequences and primers fast and convenient. The approach could be applied not only for diagnostics purposes, but also for genome analysis and taxonomic studies [30].…”

Section: Discussionmentioning

confidence: 99%

Development of qPCR Detection Assay for Potato Pathogen Pectobacterium atrosepticum Based on a Unique Target Sequence

Lukianova

Evseev

Stakheev

et al. 2021

Plants

View full text Add to dashboard Cite

The recent taxonomic diversification of bacterial genera Pectobacterium and Dickeya, which cause soft rot in plants, focuses attention on the need for improvement of existing methods for the detection and differentiation of these phytopathogens. This research presents a whole genome-based approach to the selection of marker sequences unique to particular species of Pectobacterium. The quantitative real-time PCR assay developed is selective in the context of all tested Pectobacterium atrosepticum strains and is able to detect fewer than 102 copies of target DNA per reaction. The presence of plant DNA extract did not affect the sensitivity of the assay.

show abstract

Section: Discussionmentioning

confidence: 99%

Development of qPCR Detection Assay for Potato Pathogen Pectobacterium atrosepticum Based on a Unique Target Sequence

Lukianova

Evseev

Stakheev

et al. 2021

Plants

View full text Add to dashboard Cite

show abstract

“…These techniques can identify microorganisms at low concentrations that conventional techniques can miss [21]. Furthermore, molecular and genomic techniques can be used to identify particular strains of bacteria, viruses, and fungi, which can be very helpful in infectious disease epidemics [22].…”

Section: Advantages Of Molecular and Genomic Approachesmentioning

confidence: 99%

Revolutionizing Medical Microbiology: How Molecular and Genomic Approaches Are Changing Diagnostic Techniques

Goyal,

Bankar,

Mishra

et al. 2023

Cureus

View full text Add to dashboard Cite

Molecular and genomic approaches have revolutionized medical microbiology by offering faster and more accurate diagnostic techniques for infectious diseases. Traditional methods, which include culturing microbes and biochemical testing, are time-consuming and may not detect antibiotic-resistant strains. In contrast, molecular and genomic methods, including polymerase chain reaction (PCR)-based techniques and whole-genome sequencing, provide rapid and precise detection of pathogens, early-stage diseases, and antibiotic-resistant strains. These approaches have advantages such as high sensitivity and specificity, the potential for targeted therapies, and personalized medicine. However, implementing molecular and genomic techniques faces challenges related to cost, equipment, expertise, and data analysis. Ethical and legal considerations regarding patient privacy and genetic data usage also arise. Nonetheless, the future of medical microbiology lies in the widespread adoption of molecular and genomic approaches, which can lead to improved patient outcomes and the identification of antibiotic-resistant strains. Continued advancements, education, and exploration of ethical implications are necessary to fully harness the potential of molecular and genomic techniques in medical microbiology.

show abstract

“…Furthermore, in prokaryotes, ES/ES-like segments were also reported which are not common in eukaryotic species. Even heterogeneous rRNAs with differential expression of sequences have also been observed in various eukaryotic species, e.g., Plasmodium, zebrafish, mice, and Homo sapiens [10,13].…”

Section: Introductionmentioning

confidence: 99%

Diversity of Unusual Ribosomal Genes and Ecological Origin of Rice (Oryza spp.)

Tan,

Peng,

Muhammad

et al. 2024

Agriculture

View full text Add to dashboard Cite

Tandemly organized rRNA genes are a typical example of a multigene family, where individual members evolve co-ordinately within—but independently between—species due to gene conversion and unequal crossing over. More frequently, in eukaryotic species with an interspecies hybrid origin, expression of unhomogenized rRNA genes from one progenitor is epigenetically silenced because of nucleolus dominance, and distinct rRNA genes may lose functionality and evolve faster. Interestingly, we obtained unusual ribosomal gene sequences from Oryza species that showed great diversity and did not appear in the present rice genomic sequence. The diversity of rDNA sequences indicated that the homogenization in rice is incomplete and explains the introgression of distinct rRNA gene families into ancestral rice genomes before speciation and continent separation. The divergent large subunit (LSU) ribosomal genes are expressed, some of them differentially, depending on the N fertilization of plants. Detection of differential transcripts of the rRNA genes suggested that rRNA gene families are not functionally equivalent. Phylogenetic analysis assigned Oryza species branching order to monocots, and monocot lineages probably have the same ecological origin by molecular clock calculation. Therefore, our results suggested that the geographical distances of continent-separation cause barriers to the gene flow and homogenization among Oryza species which requires further explanation.

show abstract

Species-specific genomic sequences for classification of bacteria

Cited by 7 publications

References 51 publications

Development of qPCR Detection Assay for Potato Pathogen Pectobacterium atrosepticum Based on a Unique Target Sequence

Development of qPCR Detection Assay for Potato Pathogen Pectobacterium atrosepticum Based on a Unique Target Sequence

Revolutionizing Medical Microbiology: How Molecular and Genomic Approaches Are Changing Diagnostic Techniques

Diversity of Unusual Ribosomal Genes and Ecological Origin of Rice (Oryza spp.)

Contact Info

Product

Resources

About