Computational protocol: Comparative analysis of NBS-LRR genes and their response to Aspergillus flavus in Arachis

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Protocol publication

[…] The genome sequences of A. duranensis and A. ipaënsis have been released (http://peanutbase.org) []. The hidden Markov model (HMM) profile of the NB–APAF-1, R proteins, and CED-4 (ARC) domain (PF00931) was downloaded from the Pfam database (http://pfam.janelia.org). NBS–LRR proteins from two wild peanut were extracted using HMMER [] and in-house Perl script. TIR, NBS, and LRR domains were confirmed in the Pfam database. The CC domain was surveyed using Paircoil2 (http://groups.csail.mit.edu/cb/paircoil2/). The P-score cutoff was 0.03. [...] Multiple sequence alignment of CNL and TNL full-length proteins from A. duranensis and A. ipaënsis was performed using MAFFT 7.0 []. A phylogenetic tree was constructed by MEGA 6.0 [] using maximum likelihood (ML) with the Jones-Taylor-Thornton model and neighbor-joining (NJ) based on 1,000 replicates. If two genes from different species were clustered in pairs in the phylogenetic tree, these genes were considered as orthologous genes; if two genes from one species were clustered in pairs in the phylogenetic tree, these genes were considered as paralogous genes [,].Protein sequences were converted into the corresponding nucleotide sequences by PAL2NAL []. PAML 4.0 [] was used to calculate the Ka/Ks (nonsynonymous/synonymous) ratio. Generally, Ka/Ks = 1, >1, and <1 indicate neutral, positive, and purifying selection, respectively. [...] The chromosomal location of NBS–LRR genes in A. duranensis and A. ipaënsis was obtained from peanutbase (http://peanutbase.org/). The map was generated by Circos v0.69 []. […]

Pipeline specifications

Software tools MAFFT, MEGA, PAL2NAL, PAML, Circos
Databases PeanutBase
Applications Phylogenetics, Nucleotide sequence alignment, Genome data visualization
Diseases Infection