Computational protocol: Molecular Characterization of Sec2 Loci in Wheat—Secale africanum Derivatives Demonstrates Genomic Divergence of Secale Species

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Protocol publication

[…] The controlled wheat gliadin used as comparison controls was obtained from the NCBI website [] The Sec2 gene sequences from the wheat—S. africanum 6Rafr substitution line, CSDA2R and S. sylvestre sequences cloned here were analyzed by the ORF finder program at the NCBI network service []. Sequences were aligned using BioEdit software. The sequences HQ266670–HQ266677 of S. cereale Sec2 genes published by Wang et al. [] were also included in our study. All DNA sequences were aligned using ClustalW Version 1.8 []. Multiple alignment parameters were scored up to 12 for the gap opening penalty and 0.1 for the gap extension penalty. Alignments were confirmed manually using sequential pairwise comparisons. MEGA4 was used for calculating pairwise sequence divergences and nucleotide compositions and for performing neighbor-joining (NJ) analyses []. The phylogenetic tree was linearized assuming equal evolutionary rates in all lineages and was drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. A consensus tree was generated using 1000 bootstrap replicates. DnaSP Version 5.0 [] was used to compare the nucleotide diversity [] of the Sec2 DNA polymorphism among Secale species. […]

Pipeline specifications

Software tools Open Reading Frame Finder, BioEdit, Clustal W, MEGA, DnaSP
Application Phylogenetics
Organisms Triticum aestivum, Secale cereale