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Multiple sequence alignment of single-copy orthologs

Fourteen publicly available fungal genomes were used to examine the phylogenetic placement of Pseudonectria foliicola through the analysis of single copy orthologous genes. For this analysis, the predicted proteomes of Aspergillus nidulans FGSC A4 (ASM114v1), Botrytis cinerea BcDW1 (Assembly GCA000349525), Fusarium graminearum PH-1 (GCA000240135), Macrophomina phaseolina MS6 (GCA000302655), Magnaporthe oryzeae 70-15 (MG8), Neurospora crassa (GCA000786625), Penicillium oxalicum 114-2 (GCA000346795), Pyrenophora tritici-repentis (GCA000149985), Sclerotinia sclerotiorum 1980 UF-70 (ASM1469v1), Trichoderma reesei RUT C-30 (GCA000513815), Ustilago maydis 521 (UM1), Verticillium dahliae JR2 (GCA000400815) and Yarrowia lipolytica CLIB122 (GCA000002525) were downloaded from the EnsemblFungi database (https://fungi.ensembl.org/index.html). The genome of the Dactylonectria macrodidyma JAC15-245 (NCBI GenBank accession JYGD00000000 was downloaded and used to generate gene models using the program MAKER. The program OrthoMCL identified 16,356 gene clusters, from which 1,884 orthologous genes were shared across all 15 fungal species. From these shared gene clusters, 1,511 orthologous genes were found as single copy genes and used for the phylogenetic analysis. All proteomes were searched against each other using BLASTp and clustered in orthologous gene sets using OrthoMCL v1.4 in the iPLANT Discovery Environment. Single copy genes found in all 15 fungal proteomes were extracted from the orthologous dataset and amino acid alignments were performed using MUSCLE v3.8.31. Gblocks v.0.91b was used to remove ambiguously aligned regions using less stringent settings. The final aligned dataset after removal of ambiguously aligned regions consists of 388.7 Mb. The alignment is provided in PHYLIP format.

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