In: Biology
Next-generation sequencing technology has revolutionized nearly every biological field of study. A variety of techniques are used to create a genomic library prior to sequencing. However, cost is still a factor when deciding on which method to use for a particular research question.
(A) Briefly describe the technique of restriction-site associated DNA sequencing (RADseq). What is the difference between single-end and paired-end sequencing?
(B) Suppose you were interested in examining the population genomic structure of NYC rats throughout the five boroughs. Would it be better to use RADseq or shotgun sequencing? Explain your reasoning.
Restriction site associated sequencing is carried by using one or more restriction enzymes to digest DNA sample and the genomic library prepared and sequenced using next generation sequencing. The sequences of ends adjecent to restriction sites allow to identify flanking portion from other fragment which has the sequence continuation.
Single end sequencing means the sequencing of a start fragment at one end and look for its flipping portion from the other sequence's in the library to ensure the continuous set of sequences found in single direction.
Paired end sequencing deals with sequencing from both ends of origin and looking for its continuous sequences from both sides of it and align all possible sets and find the sequence.
B) for analysing NYC populations the Rad sequencing is better because it efforts less and still informative, it doesn't sequence the whole genome instead it sequences only sequences around restriction sites which is just a small part of whole genome sequencing as per in shotgun sequencing. It is quite helpful to generate genome-wide SNP data to address questions in population genomics, phylogenetics and speciation studies.