Computational protocol: Independent mitochondrial and nuclear exchanges arising in Rhizophagus irregularis crossed-isolates support the presence of a mitochondrial segregation mechanism

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Protocol publication

[…] Each amino acid sequences of the Saccharomyces cerevisiae MSA and/or protein involved in nucleoid formation (i.e. MMM1, MDM10, MDM12, MMM2, MDM31, MDM32, ABF2, ACO1 and ILV5) were searched across the R. irregularis DAOM-197198 genome assembly [] and transcriptome [], using TBLASTN. Orthologous candidates in R. irregularis genome were identified using the best-reciprocal BLAST hit to these proteins. Seven putative orthologous sequences were retrieved in R. irregularis; Uniprot accession numbers U9U1X0, U9UEK3, U9UFF5, U9TTI3, U9UF16, U9UI83 and U9UJR1, respectively. Furthermore, clusters of orthologous genes (COGs), gathering sequences from numerous organisms, were determined using STRING version 9.05 [] for each protein candidate. The resulting COGs were aligned using COBALT version 2.01 []. Phylogenetic analyses and finding the best evolutionary model was done using the integrative software TOPALI version 2.5 []. For each protein candidate, maximum likelihood phylogenetic analyses were done with the closest orthologs found in fungi. Phylogenies were performed accordingly to its predicted model: the MMM1 protein phylogeny was done using the JTT + I + G model, MMM2 with JTT + I + G, MDM12 with JTT + G, MDM10 with WAG + I + G, ACO1 with WAG + I + G, ABF2 with WAG + I + G, and finally the ILV5 phylogeny was performed using the WAG + G model. The robustness of internal branches was evaluated based on 1000 bootstrap replicates (<60 % cut-off). Tree figures were completed using TreeGraph version 2.0.47 []. […]

Pipeline specifications

Software tools TBLASTN, TOPALi, TreeGraph
Applications Phylogenetics, Amino acid sequence alignment
Organisms Rhizophagus irregularis, Saccharomyces cerevisiae