A Colony Multiplex Quantitative PCR-Based 3S3DBC Method and Variations of It for Screening DNA Libraries

<div><p>A DNA library is a collection of DNA fragments cloned into vectors and stored individually in host cells, and is a valuable resource for molecular cloning, gene physical mapping, and genome sequencing projects. To take the best advantage of a DNA library, a good screening method is needed. After describing pooling strategies and issues that should be considered in DNA library screening, here we report an efficient colony multiplex quantitative PCR-based 3-step, 3-dimension, and binary-code (3S3DBC) method we used to screen genes from a planarian genomic DNA fosmid library. This method requires only 3 rounds of PCR reactions and only around 6 hours to distinguish one or more desired clones from a large DNA library. According to the particular situations in different research labs, this method can be further modified and simplified to suit their requirements.</p></div

A colony multiplex quantitative PCR-based 3S3DBC DNA screening method for planarian DNA library screening.

<p>A colony multiplex quantitative PCR-based 3S3DBC DNA screening method for planarian DNA library screening.</p

genome_sampling_Rscripts

Set of R scripts to randomly sample the genome using a fasta index file. See Readme file for more details

Genomic divergence is lower in sympatry than in allopatry between species.

<p>Histograms of (A) relative (<i>F</i>_ST) and (B) absolute (<i>d</i>_XY) differentiation measures for each of the species comparisons. (C) Mean genome-wide <i>F</i>_ST of the Japanese species pair compared with those of other stickleback systems taken from previously published studies [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007358#pgen.1007358.ref035" target="_blank">35</a>–<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007358#pgen.1007358.ref037" target="_blank">37</a>,<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007358#pgen.1007358.ref056" target="_blank">56</a>].</p

final_rad_lift.vcf

RAD-seq variant call format for Japan Sea, Pacific Ocean and Atlantic Ocean individuals

ms_controller_v1.7

R wrapper script to run msABC and generate simulations. Use '--help' to see available options. Requires GNU Parallel to run properly

tree_classifcation_clean

R script for classifying phylogenetic trees based on geography/species

fastsimcoal_data_and_models

Joint SFS from RAD data and models used in fastsimcoal analysis of site-frequency spectrum

abc_processor_v1.5

Rscript using abc package to postprocess output from msABC simulations. See '--help' for more information

genome_10kb_windows_data

10Kb genome window estimates of Fst, dxy, gmin, pi and tajima's D