Common Sequence polymorphisms shaping diversity

summary

• examining the species level variation in 20 diverse strains to understand the forces that shape the evolution
• >1 million snps were found
• Patterns of polymorphism was found to be non-random among the gene families

Methods

• Array sequencing (on both the strands)
• SNP predictions
  • MB method: model based
  • ML method: machine learning
  • Performance of ML < MB
  • If an SNP is very close, both method fail to predict

Results

• SNP detection is shown more in coding region and intergenic regions
• SNP detection in the annotated protein coding regions shows,
  • more on NB-LRR region
  • very less on cytoplasmic ribosomal region

PRP: Prions (proteinaceous and infectious agents)

Genome wide polymorphism

• High polymorphisms near centromier
• Clusters of NB-LRR genes associated with high level of polymorphisms
• It is hard to explain these patterns
  • because no relation with base composition
  • no relation with coding and intergenic region, (they are spread all over)
  • definitely not a sequencing artifact
• One possible explanation is that balanced selection acting on these regions, which can increase the coalescence time. Therefore the polymorphisms is maintained.
• Regions with low polymorphisms is because of selective sweep or positive selection.

Balancing selection refers to forms of natural selection which work to 
maintain genetic polymorphisms (or multiple alleles) within a population.

A selective sweep is the reduction or elimination of variation among the nucleotides 
in neighboring DNA of a mutation as the result of recent and strong natural selection.

• Presence of extensive haplotypes share is also a cause of selective sweep.

Conclusion

1. Foreces affective the genetic diversity
   1. balanced selection -> due to the haplotypes adapts to certain geographic location -> shows kind of high variation and it is maintained
   2. selective sweep -> is a positive selection - again due to adaptation of certain environment.
2. The data generated (enormous SNPs) can be potential to further understand the forces shaping evolution

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