Computational protocol: The Nup98 Homolog APIP12 Targeted by the Effector AvrPiz-t is Involved in Rice Basal Resistance Against Magnaporthe oryzae

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Protocol publication

[…] To identify Nup98 homologues in different plant species, homolog search against the NCBI non-redundant (NR) protein database (http://blast.ncbi.nlm.nih.gov/) was performed using APIP12 as a query. Accession numbers of the homologues are as follows: LOC_Os12g06870 and LOC_ Os12g06890 (Oryza sativa, identified from rice genome database: http://rice.plantbiology.msu.edu/), NP_172510 (Arabidopsis thaliana), BAF98996 (Daucus carota), XP_010660457 (Vitis vinifera), XP_002317654 (Populus trichocarpa), XP_008673404 (Zea mays), BAK00061 (Hordeum vulgare), and XP_002446695 (Sorghum bicolor). Protein sequences were aligned using the Clustalw2 program (http://www.ebi.ac.uk/Tools/msa/clustalw2/) with the default parameters. The phylogenetic tree was viewed by using the neighbor-joining method of the MEGA 4.1 software (Tamura et al. ). A bootstrap analysis with 1000 replicates was performed to test the confidence of topology. We included Nup98 in human as an outgroup (Accession No. : AAH41136) in the phylogenetic analysis. […]

Pipeline specifications

Software tools Clustal W, MEGA
Application Phylogenetics
Organisms Magnaporthe oryzae, Oryza sativa