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Pipeline publication

[…] of the ratio of (Lduplicate×Lsingle-copy) over Lcombined, to a chi-square distribution with 2 degrees of freedom (): (1)D=2lnLduplicateL sin gle-copyLcombined∼χ2(2)., We performed the same analysis with the triplicated genes and single-copy genes from the comparison of B. rapa and B. oleracea., To quantify the actions of selection at the population level, we estimated the number of circulating synonymous and nonsynonymous polymorphisms using SNP data. For A. thaliana, we obtained polymorphism data in variant call format (VCF) from 1,135 natural inbred lines curated by the 1001 Genomes Project (). SNPs in protein-coding genes were annotated as synonymous or nonsynonymous polymorphisms using SnpEff ()., The B. rapa SNPs were called from the transcriptomes of 126 accessions (), and also annotated with SnpEff. Low quality SNPs were removed with vcffilter (https://github.com/vcflib/vcflib; last accessed March 21, 2018) and VCFtools (): only SNPs identified in regions with read depth >10 and root mean square mapping quality >30 were used for subsequent analyses., To normalize the number of observed SNPs per gene, we counted the number of nonsynonymous positions in each protein-coding gene showing polymorphism and divided that number by the total number of nonsynonymous changes possible in the gene. We denote this ratio as pN. Similarly, pS is the number of polymorphic synonymous positions divided by the number of possible synonymous sites (). We then calculated the ratio of pN/pS for all possible protein-coding genes in A. thaliana and B. rapa. We removed genes with pS = 0 and pN ≤ 1; for those with pS =  […]

Pipeline specifications

Software tools SnpEff, vcflib, VCFtools
Organisms Arabidopsis thaliana
Diseases Chromosome Aberrations