Computational protocol: The Agaricus bisporus cox1 Gene: The Longest Mitochondrial Gene and the Largest Reservoir of Mitochondrial Group I Introns

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Protocol publication

[…] The overlapping cox1 sequences were compiled and analyzed with the DNA Strider 1.2 software (Commissariat à l'énergie atomique, Gif-sur-Yvette, France). Comparisons with sequences of the GenBank and EMBL databases were performed using the BLAST search algorithm .Compilation of the complete cox1 gene sequences was performed by compiling the results (orthologous sequences) given by a BLASTx analysis using first the A. bisporus cox1 CDS as query. This analysis revealed most of the fungal cox1 sequences available in the Genbank and also numerous cox1 genes from plants. Second, all the intron heg carried by these sequences were used independently as a query for BLASTx analysis. This allowed the recovery of some additional split cox1 sequences from plants and also from other distant species such as Palythoa sp. JVK-2006 (Porifera), and species belonging to the Ichthyosporea, Choanoflagellida and Dictyosteliida phylla, which have been added to our analysis. Finally, the coral (Cnidaria) cox1 genes were added to the analysis because they contain the only introns reported to date in the Eumetazoa kingdom without homology with introns from other kingdoms. Alignments of nucleotide and protein sequences were carried out with Clustal W (1.8) software .The intron secondary structures (Supplementary information files ) were deduced from the determination of the conserved sequences P, Q, R and S of the intron cores and of the base-paired regions P1–P9 with the help of RNA-Weasel software, and by direct comparison with the standard scheme for group I introns and with the secondary structures of the database established by Damberger and Gutell.. […]

Pipeline specifications

Software tools BLASTX, Clustal W, Weasel
Application Flow cytometry
Organisms Agaricus bisporus