"Global transmission of broad-host-range plasmids" aka Junk DNA doesn't prove common ancestry anymore


"Global transmission of broad-host-range plasmids" a recent study published in the journal Nucleic Acids Research has found evidence of global transmission of broad-host-range (BHR) plasmids derived from the human gut microbiome. BHR plasmids are a type of extrachromosomal DNA that can be transferred between different bacterial species. They can carry genes that confer antibiotic resistance, virulence factors, and other traits that can be beneficial to the host bacterium.

The study, conducted by researchers at the Shenzhen Institutes of Advanced Technology in China, analyzed the genomes of gut bacterial isolates from Chinese and American donors. They identified 5372 plasmid-like clusters (PLCs), of which 820 were estimated to be complete and 155 were classified to known replicon types. Haplotype analyses of two widespread PLCs demonstrated their spreading and evolutionary trajectory, suggesting frequent and recent exchanges of the BHR plasmids in environments.The findings of this study suggest that BHR plasmids can be transmitted globally.

Broad-host-range (BHR) plasmids are extrachromosomal DNA elements that can replicate and maintain themselves in a wide range of different bacterial species. They are important for horizontal gene transfer (HGT), the process by which genes are transferred between unrelated organisms. BHR plasmids can carry genes for antibiotic resistance, virulence factors, and other traits that can be beneficial to the host bacterium.

BHR plasmids are typically large, ranging in size from 10 to 200 kilobases. They often contain genes for replication, mobilization, and incompatibility. Replication genes are responsible for the duplication of the plasmid DNA. Mobilization genes allow the plasmid to be transferred between bacteria. Incompatibility genes prevent two plasmids with the same incompatibility group from coexisting in the same cell.

BHR plasmids are found in a wide variety of bacteria, including Gram-positive and Gram-negative bacteria, archaea, and eukaryotes. They are particularly common in bacteria that live in harsh environments, such as the soil and the human gut.

BHR plasmids are thought to have evolved apart from natural selection and slow random mutations. Bacteria that harbor BHR plasmids have a competitive advantage over those that do not, because they can acquire new genes that allow them to adapt to new environments. As a result, BHR plasmids have become widespread in the bacterial world.

Here are some additional facts about BHR plasmids:

  • They can be transferred between bacteria by conjugation, transformation, or transduction.

  • They can carry genes for a variety of traits, including antibiotic resistance, virulence factors, and metabolic pathways.

  • They are thought to have evolved without natural selection.

Site-specific integration of plasmids is a process by which plasmids can be inserted into a specific location in the genome of a host cell. This is done using a recombinase enzyme, which is a protein that catalyzes the recombination of two DNA molecules.

The recombinase enzyme recognizes a specific DNA sequence, called a target sequence, on both the plasmid and the host cell genome. Once the recombinase enzyme binds to the target sequences, it catalyzes the cutting and rejoining of the DNA molecules, resulting in the insertion of the plasmid into the host cell genome.

Site-specific integration of plasmids is an accurate way of transferring DNA. These transfers give the appearance of common design whereas different species can be infected by the same plasmid and it is put in the same location of each species.

As well site-specific integration of TEs may give the impression of common ancestry. This is because TEs can move from one genome to another, and they can do so in a precise manner. This means that two organisms that are not closely related may share the same TEs, simply because the TEs have moved from one genome to the other.

This can be a problem when using TEs to infer evolutionary relationships. For example, if two organisms share a particular TE, it is not necessarily because they share a common ancestor. It is also possible that the TE has moved from one genome to the other, giving the impression of common ancestry.

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