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Evolutionary relationships of the three genes were studied using a MEGA 5 software tool.
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MEGA 5.2 [ 54] tool was used to estimate the position-by-position (ML) relative evolutionary rate under JTT + G + I amino acid substitution model.
In case of ML, evolutionary model was inferred by MEGA 6.0 model selection tool, based on Sample-corrected Akaike information criterion (AICc).
Sequence similarity was analyzed against the EzTaxon-e Database (http://eztaxon-e.ezbiocloud.net/) [ 67] and aligned using CLUSTAL W tool in MEGA version 5.05 [ 68].
The high-quality sequences generated for each gene were aligned among 96 chickpea genotypes (Supplementary Table S1) using the CLUSTALW multiple sequence alignment tool in MEGA 4.0 and mined the single nucleotide polymorphism (SNP) loci.
The SNP loci validated in the stress-responsive gene sequences across 91 diverse rice genotypes were aligned using CLUSTALW multiple sequence alignment tool in MEGA [ 79] 4.0 and results exported in meg format.
All nucleotide sequences were aligned by using the ClustalW tool in MEGA 5 and trimmed to equal lengths, but at least 90% of the coding region as follows: HA, 1630 nt; NA, 1350 nt; polymerase basic protein 1 (PB1), 2213 nt; polymerase basic protein 2 PB2), 2214 nt; polymerase acidic (PA), 2069 nt; nucleoprotein (NP), 1416 nt; Matrix (M), 744 nt; and non-structural (NS), 693 nt.
