Computational protocol: ChLae1 and ChVel1 Regulate T toxin Production, Virulence, Oxidative Stress Response, and Development of the Maize Pathogen Cochliobolus heterostrophus

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Protocol publication

[…] The A. nidulans LaeA (accession number: AAQ95166) and VeA (accession number: AAD42946) genes were used to query the C. heterostrophus strain C5 sequence database (http://genome.jgi-psf.org/CocheC5_1/CocheC5_1.home.html) for orthologs. Alignments were created using ClustalW and phylogenetic trees built using PAUP 4.0. [...] AbLaeA: AB03558.1; Ch112516: estExt_Genewise1Plus.C_230028; Ch19119: fgenesh1_pg.C_scaffold_7000105; Ch24542: estExt_fgenesh1_kg.C_10021; Ch26577: estExt_fgenesh1_kg.C_430002; Ch28900: estExt_fgenesh1_pg.C_50334; Ch39571: gw1.10.215.1; Ch64638: e_gw1.7.1035.1; DsLaeA: e_gw1.1.991.1; HpLaeA: NODE_244_length_406169_cov_26..g3563.t1; MfLaeA: estExt_fgenesh1_kg.C_20358;MgLaeA: estExt_fgenesh1_pg.C_chr_10913; PtLaeA: PTRT_04504; RrLaeA: NODE_25109_length_74158_cov_41.g11943.t1; SmLaeA: estExt_fgenesh1_kg.C_3_t20075; SnLaeA: SNOG_11365.3; StLaeA: fgenesh1_pm.1_#_110;AbVeA: AB08060.1; DsVeA: estExt_fgenesh1_kg.C_2_t20018; HpVeA: NODE_50_length_318014_cov_25.9.g981.t1; LbVeA: gm1.12491_g; MVe1: e_gw1.2.779.1; MfVeA: Mycfi1.estExt_fgenesh1_pg.C_140014; MgVeA: e_gw1.2.779.1; PtVeA: PTRT_03646; RrVeA: NODE_929_length_97559_cov_41.6.g4671.t1; SmVeA: estExt_fgenesh1_kg.C_2_t20128; StVeA: estExt_fgenesh1_pm.C_220032; ChGsh2: estExt_Genewise1.C_7_t50456; Trx1: estExt_Genemark1.C_170072; Trx2: estExt_Genewise1Plus.C_17_t20462; Trr1: fgenesh1_pm.4_#_575. […]

Pipeline specifications

Software tools Clustal W, PAUP*, FGENESH, GeneMark
Applications Genome annotation, Phylogenetics
Organisms Zea mays, Bipolaris maydis
Diseases Machado-Joseph Disease
Chemicals Hydrogen Peroxide