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Genomics

Genomics

Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...

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Population Genomics Analysis with RAD, Reprised: Stacks 2.

Angel G Rivera-Colón¹, Julian Catchen²

¹Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, Urbana, IL, USA.

Methods in Molecular Biology (Clifton, N.J.)

|June 21, 2022

Summary

This study details a Restriction site-Associated DNA (RAD) sequencing protocol using Stacks v2 for population genomics. It offers a comprehensive guide from experimental design to de novo and reference-based analyses, enhancing genetic insights in natural populations.

Keywords:

Linkage disequilibrium Population genetics Population structure RAD analysis Simulation

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Area of Science:

Population genetics
Genomics
Molecular biology

Background:

Restriction enzymes have been crucial for population genetics for 50 years.
Restriction site-Associated DNA (RAD) sequencing democratized population genomics by combining enzymes with short-read sequencing.
RAD sequencing has been widely applied across diverse taxa for over a decade.

Purpose of the Study:

To provide a detailed protocol for Restriction site-Associated DNA (RAD) analysis.
To cover experimental design, de novo analysis, parameter optimization, and reference-based analysis.
To address key challenges in molecular techniques and downstream bioinformatics.

Main Methods:

Utilizes Stacks version 2, supporting paired-end reads for assembling RAD loci up to 1000 bp.
Focuses on optimizing experimental parameters and validating analyses.
Includes both de novo and reference-based RAD sequencing approaches.

Main Results:

Presents a robust protocol for conducting RAD analyses.
Highlights Stacks v2's capability for detailed genetic analysis of natural populations.
Emphasizes validation of experimental and analytical steps.

Conclusions:

The protocol facilitates comprehensive population genomics studies.
Enables deeper understanding of genetic variation in natural populations.
Offers avenues for further advanced population genetic analyses.