Raj at 08:41, 23 June 2016

2016-06-23T08:41:43Z

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			[[Category:Readings]][[Category:Rajkumar]]
	==summary==		==summary==
	* examining the species level variation in 20 diverse strains to understand the forces that shape the evolution		* examining the species level variation in 20 diverse strains to understand the forces that shape the evolution

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Raj at 19:19, 3 January 2010

2010-01-03T19:19:46Z

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==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
<pre>PRP: Prions (proteinaceous and infectious agents)</pre>
==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.
<pre>
Balancing selection refers to forms of natural selection which work to
maintain genetic polymorphisms (or multiple alleles) within a population.
</pre>
<pre>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.</pre>
* Presence of extensive haplotypes share is also a cause of selective sweep.

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

Common Sequence polymorphisms shaping diversity - Revision history

Raj at 08:41, 23 June 2016

Raj: 1 revision imported

Raj at 19:19, 3 January 2010