Computational protocol: The Microbial Opsin Homolog Sop1 is involved in Sclerotinia sclerotiorum Development and Environmental Stress Response

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Protocol publication

[…] The signaling genes were identified according to the genome annotation of S. sclerotiorum (Amselem et al., ). The Phyre2 server (Kelley and Sternberg, ) was used to predict transmembrane domain regions and construct 3D structural model which was displayed by PyMOL (DeLano, ). Sequences for sop1 homologs were collected from the non-redundant protein sequence database at the NCBI website using DELTA-BLAST (Boratyn et al., ) with sop1 as the query sequence. Datasets were assembled with a cut-off E-value < 1e-6. All sequences available for sop1 homologs form Volvox carteri f. nagariensis, Dunaliella salina, Acetabularia acetabulum, Chlorella vulgaris, Guillardia theta CCMP2712, Podospora anserina S mat+, L. maculans JN3, Haloarcula argentinensis, Halobacterium salinarum, Natronomonas pharaonis, Haloarcula marismortui, Chlamydomonas reinhardtii, Cryptomonas sp. S2, Cyanophora paradoxa, N. crassa OR74A, F. fujikuroi, C. neoformans var. grubii H99, C. neoformans var. neoformans JEC21, B. cinerea B05.10 and Oryza sativa Indica Group were used to perform amino acid alignment using COBALT (Papadopoulos and Agarwala, ). These species were selected because their opsin genes were experimentally characterized or reviewed previously (Bieszke et al., ; Idnurm and Howlett, ; Brown, ; Ruiz-Gonzalez and Marin, ; Idnurm and Heitman, ; Estrada and Avalos, ; Zhang et al., ; Heller et al., ). Multiple protein sequence alignment without any truncation was viewed and edited by Jalview (Clamp et al., ). The entire protein sequence alignment was subjected to model testing with the ProtTest v.2.4, using the Aikake information criterion (AIC) and default settings (Abascal et al., ), before it was used for building a phylogenetic tree. Protein maximum likelihood (ML) tree was inferred with PhyML-mixtures (Guindon and Gascuel, ; Le et al., ), assuming the best-fit LG model (Le and Gascuel, ) according to the ProtTest and SPR tree topology search strategy (Hordijk and Gascuel, ). Gaps in alignment were systematically treated as unknown characters. The reliability of internal branches was evaluated based on aLRT SH-like branch support (Anisimova and Gascuel, ). The phylogenetic tree graphic was produced using the Interactive Tree of Life (Letunic and Bork, ). […]

Pipeline specifications

Software tools Phyre, PyMOL, DELTA-BLAST, Jalview, ProtTest, PhyML, iTOL
Applications Phylogenetics, Amino acid sequence alignment
Organisms Sclerotinia sclerotiorum