You are conducting population genetic research on dung beetles and you would lik

Question

You are conducting population genetic research on dung beetles and you would like to use RADseq. Based on this answer the questions below a. Give three reasons that RADseq is a great method for analyzing genetic variation for the cost, and contrast this method of obtaining genomic variation data with sequencing whole genomes, and amplicon approaches. b. Assume the genome is 3Mbp. If you cut the genome with two enzymes, a 7bp cutter and a 4bp cutter, and followed the normal protocol for ddRADseq, how many fragments of the genome would you generate in your Radseq library? c. Why might a reference genome be helpful for conducting RADseq analysis - what situations might you avoid, particularly in most eukaryotes (think about genome structure in eukaryotes)? How important do you think it would be to have a very well assembled genome with very large scaffolds, versus a relatively fragmentary genome assembly (keep in mind that you only want to interpret genome variation at unique single-copy loci)?

Explanation / Answer

Answer:

1)Restriction site Associated DNA Sequencing (RAD-Seq) is a fractional genome sequencing strategy,by digesting the genome with a restriction nuclease and attaching a series of adapters to the resulting DNA fragments, large numbers of genetic variations such as SNPs can be readily identified from analysis of next generation DNA sequence data.
2) To identify Population structure, RAD sequencing is a popular method.
3) To identify Linkage and quantitative trait locus mapping, RAD sequencing is useful

RAD-Seq works by first fragmenting the target genome using a restriction enzyme. After digestion, a series of molecular processing steps transform the DNA into a fragment library suitable for sequencing on a NGS platform.

Depending on the end goal, either single end or paired end sequencing can be used to generate the appropriate amount of information.

Sequence data is then analyzed to identify and score genetic variations in the samples or population of interest. SO no need to analysing the whole genome, so it is cost effective.
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1 Mbp=1,000,000 bp
3 Mbp= 3000000 bp
7 cutter= 428572 fragments
4 bp cutter= 857144 fragments
total fragments=857144 fragments

To identify short genetic variations it is better to have a reference genome. In eukaryotes there are more SNPs to identify these reference genome is used.

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