"Transposon signatures of allopolyploid genome evolution" -works outside of natural selection Article review


Background to article:

Transposable elements (TEs) are DNA sequences that can move from one location to another within a genome. They are a major component of all eukaryotic genomes, and they can have a significant impact on the evolution of organisms.

Neo-Darwinism is a theory of evolution that states that evolution occurs through natural selection, which is the process by which heritable traits that are beneficial to an organism in its environment are more likely to be passed on to offspring.

TEs defeat neo-Darwinism because they can introduce new genetic material into a genome, which can lead to the evolution of new traits. For example, TEs can insert themselves into genes, which can change the function of the gene. TEs can also create new genes, which can give organisms new capabilities.

Points to consider:

  • TEs can move around the genome, which can disrupt genes and cause mutations. This can lead to the evolution of new traits without natural selection even if the TE itself does not code for any new genes.

  • TEs can copy themselves faster than neodarwins random point mutations and can lead to the rapid spread of new genetic material through a population. This can make it difficult for natural selection to keep up, and it can lead to the rapid evolution of new traits.

  • TEs can interact with each other, which can create new combinations of genetic material outside natural selection . This can also lead to the evolution of new traits without Darwin.

TEs are a powerful force that can drive evolution. They can introduce new genetic material into genomes, they can disrupt genes, and they can copy themselves. This makes them a major challenge to neo-Darwinism, which relies on natural selection to drive evolution. 

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Summary:

Allopolyploidy is a type of polyploidy that occurs when two or more diploid species hybridize and their genomes are doubled. The resulting polyploid has two or more subgenomes, each of which is derived from one of the diploid progenitors.

Transposons are mobile genetic elements that can insert themselves into the genome at random. They can be used to track the evolutionary history of a genome, as they tend to accumulate mutations over time.

A new study published in Nature Communications has found that transposons can be used to identify the subgenomes of allopolyploid genomes. The study's authors developed a statistical method for identifying transposon signatures that are specific to each subgenome. They applied this method to several allopolyploid genomes, including tobacco, cotton, and strawberry.

The results of the study showed that the transposon signatures were consistent with the known evolutionary histories of the polyploids. This suggests that transposons can be a valuable tool for studying the evolution of allopolyploid genomes.

The study's findings could have implications for a number of fields, including plant breeding, evolutionary biology, and conservation biology. For example, plant breeders could use transposon signatures to identify genes that are important for traits such as yield or resistance to pests. Evolutionary biologists could use transposon signatures to track the evolution of allopolyploids over time. And conservation biologists could use transposon signatures to identify populations of allopolyploids that are at risk of extinction.

Here are some of the key findings of the study:

  • Transposons can be used to identify the subgenomes of allopolyploid genomes.

  • The transposon signatures are consistent with the known evolutionary histories of the polyploids.

  • Transposons could be a valuable tool for studying the evolution of allopolyploid genomes.

The study's findings have the potential to make a significant contribution to our understanding of allopolyploidy and its impact on evolution.

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Article snippets

Transposon signatures of allopolyploid genome evolution

Hybridization brings together chromosome sets from two or more distinct progenitor species. Genome duplication associated with hybridization, or allopolyploidy, allows these chromosome sets to persist as distinct subgenomes during subsequent meioses

This subgenome-enriched transposable element signal is intrinsic to the polyploid, allowing broader applicability than other approaches that depend on the availability of sequenced diploid relatives

These analyses provide insight into the origins of these polyploids

In autopolyploids, each chromosome can choose among multiple meiotic partners allowing recombination among equivalent homologous chromosomes and producing polysomic inheritance (more than two alleles per locus); diploidy and disomic inheritance may be restored by the subsequent evolution of pairing preferences

In allopolyploids, however, genome doubling associated with interspecific hybridization ensures that all chromosomes have defined homologous meiotic partners derived from their respective progenitors

In contrast, in homoploid hybrids (i.e., interspecific hybridization without genome doubling) recombination between homoeologous chromosomes shuffles the genetic contributions of the progenitor species, and subgenomes generally cannot persist as stable entities except in rare cases of asexual reproduction10 or fixed translocation heterozygosity preventing the production of viable recombinants1

Thus, we can define homoeologs as chromosomes that have diverged by evolution in different species but are ultimately derived from the same ancestral chromosome

discussion

Our approach to recognizing the chromosomes belonging to an evolutionarily coherent subgenome based on the distribution of repetitive elements was inspired by inference of authorship for unsigned essays in The Federalist Papers

By combining these individually weak word-by-word signals, Mosteller and Wallace robustly identified the author of anonymously published essays.

By analogy, in the case of polyploid genomes each subgenome is also written by a different author (i.e., progenitor), and distinctive DNA word usage between subgenomes is due to past transposon activity

we may not have a training set of chromosomes of known diploid provenance.

We show below how to bootstrap the identification of discriminatory DNA words from chromosome comparisons even in the absence of a training set.

By analogy with the authorship problem, we seek short DNA words of a defined length k (k-mers) that serve as markers for subgenome-enriched families of repetitive elements

These repetitive words are intrinsic features of the polyploid genome sequence, and our method does not depend on information from lower ploidy relatives, although such information can also be integrated

The use of repetitive sequences to identify subgenomes in polyploids is an increasingly used methodology

our approach enables statistical testing of alternate subgenome hypotheses based on asymmetric distribution of repetitive elements

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