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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
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Diploid organisms inherit genetic material through chromosomes from both parents. Copies of the same gene are known as alleles. In most cases, both alleles are simultaneously expressed and allow various cellular processes to function optimally. If one of the alleles is missing or mutated, the expression of the other allele can compensate; however, this is not true for all genes.
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PlasFlow: predicting plasmid sequences in metagenomic data using genome signatures.

Pawel S Krawczyk1,2, Leszek Lipinski1, Andrzej Dziembowski1,2

  • 1Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.

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Summary

PlasFlow is a new bioinformatics tool that identifies bacterial plasmid DNA in environmental samples using genomic signatures and neural networks. This method accurately recovers plasmid sequences, aiding in understanding microbial adaptation to environmental conditions.

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Area of Science:

  • Microbiology
  • Bioinformatics
  • Environmental Science

Background:

  • Plasmids are mobile genetic elements crucial for microbial environmental adaptation.
  • Current methods for analyzing plasmid pools (plasmidomes) in environmental samples are limited, especially in diverse environments or for large plasmids.

Purpose of the Study:

  • To develop a novel computational tool, PlasFlow, for accurate identification of bacterial plasmid sequences in environmental samples.
  • To overcome limitations of existing methods in terms of environmental diversity and plasmid size recovery.

Main Methods:

  • PlasFlow utilizes genomic signatures and a neural network approach to identify plasmid sequences.
  • The tool analyzes assembled metagenomes without requiring prior knowledge of sample composition.
  • It can differentiate between circular and linear plasmids and perform initial taxonomic classification.

Main Results:

  • PlasFlow achieves up to 96% accuracy in identifying plasmid sequences from environmental samples.
  • It outperforms existing tools in performance on test datasets.
  • Analysis of contaminated microbial mats showed plasmids constitute a significant portion of metagenomes and carry heavy-metal resistance genes.

Conclusions:

  • PlasFlow is an effective tool for analyzing plasmidomes in diverse environmental samples.
  • Plasmids play a critical role in microbial adaptation to environmental challenges, such as heavy metal contamination.