Computational protocol: Evolution of Neutral and Flowering Genes along Pearl Millet (Pennisetum glaucum) Domestication

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Protocol publication

[…] Base calling, quality assessment, and sequence assembly were conducted using CodonCode Aligner (V.3.5.7). ClustalW implemented in the Bioedit software was used to perform the multiple sequences alignment of each locus. Accessions that were undetermined for their cycle length (see ) were not included in analyses conducted on early and late accessions separately. Polymorphism and molecular evolution analyses were performed using DnaSP v5.00 and Fabsim software . [...] The Arlequin software (version 3.5) was used to estimate F-statistics. The significance of each pairwise Fst value was assessed by performing 10000 permutations. The SNP data generated from the concatenated STS fragments was used to evaluate the genetic structure within the collection of accessions by using the Bayesian method implemented in the Structure software version 2.3.3 . 500,000 iterations were carried out for each run after a burn-in period of 100,000 iterations. The model allowing for admixture and correlated allele frequencies between populations was used for this analysis. Five independent replicates for each value of K (the number of a priori clusters) were performed. This procedure was repeated for K varying from 1 to 10. The optimal number of clusters (K) was identified by using the ad hoc statistics based on the second order change of the likelihood function with respect to K (ΔK) developed by Evanno et al. . […]

Pipeline specifications

Software tools CodonCode Aligner, Clustal W, BioEdit, DnaSP, FABSIM, Arlequin
Application Population genetic analysis
Organisms Cenchrus americanus