Gene Loss Rather Than Gene Gain Is Associated with a Host Jump from Monocots to Dicots in the Smut Fungus Melanopsichium pennsylvanicum.

Gene Loss Rather Than Gene Gain Is Associated with a Host Jump from Monocots to Dicots in the Smut Fungus Melanopsichium pennsylvanicum.ThinesBiodiversity and Climate Research Center (BiK-F)

SharmaBiodiversity and Climate Research Center (Bik-F)

Smut fungi are well-suited to investigate the ecology and evolution of plant pathogens, as they are strictly biotrophic, yet cultivable on media. Here we report the genome sequence of Melanopsichium pennsylvanicum, closely related to Ustilago maydis and other Poaceae-infecting smuts, but parasitic to a dicot plant. To explore the evolutionary patterns resulting from host adaptation after this huge host jump, the genome of Me. pennsylvanicum was sequenced and compared with the genomes of U. maydis, Sporisorium reilianum, and U. hordei. Although all four genomes had a similar completeness in CEGMA (Core Eukaryotic Genes Mapping Approach) analysis, gene absence was highest in Me. pennsylvanicum, and most pronounced in putative secreted proteins, which are often considered as effector candidates. In contrast, the amount of private genes was similar among the species, highlighting that gene loss rather than gene gain is the hallmark of adaptation after the host jump to the dicot host. Our analyses revealed a trend of putative effectors to be next to another putative effector, but the majority of these are not in clusters and thus the focus on pathogenicity clusters might not be appropriate for all smut genomes. Positive selection studies revealed that Me. pennsylvanicum has the highest number and proportion of genes under positive selection. In general, putative effectors showed a higher proportion of positively selected genes than noneffector candidates. The 248 putative secreted effectors found in all four smut genomes might constitute a core set needed for pathogenicity, whereas those 92 that are found in all grass-parasitic smuts but have no ortholog in Me. pennsylvanicum might constitute a set of effectors important for successful colonization of grass hosts. effector genes evolutionary biology genome assembly host jump positive selection smut fungicomparative genomicsSpeciesMelanopsichium pennsylvanicumSharmaBiodiversity and Climate Research Center (Bik-F)

ThinesBiodiversity and Climate Research Center (BiK-F)

Repeat element masked genomic sequences of Melanopsichium pennsylvanicum Mp4_V1_masked_genome.fa column #x20 ecogrid://knb/rsharma.3.1 public read ScaffoldsRepeat masked Mp4 scaffolds Text valuesMp4 gff fileMp4 gff file1727071gffhttps://dataportal.senckenberg.de/dataset/7f944577-8198-46a3-901e-1c9b345860df/resource/c990c7e2-4b50-4df3-a793-9160991a9147/download/mp4-gff-fileOtherMp4 protein sequencesMp4 protein sequences3750742aahttps://dataportal.senckenberg.de/dataset/7f944577-8198-46a3-901e-1c9b345860df/resource/c2b320a0-b00d-4fb4-af5b-25e3396b10a3/download/mp4-protein-sequencesOtherMp4_Unmasked_genome.fastaUnmasked genomic sequences of Melanopsichium pennsylvanicumMp4_Unmasked_genome.fasta19237552fastahttps://dataportal.senckenberg.de/dataset/7f944577-8198-46a3-901e-1c9b345860df/resource/99d5326b-e804-473e-a19f-7a18f790af20/download/mp4_unmasked_genome.fastaOtherMp4_CDS.fastaMelanopsichium pennsylvanicumcoding sequencesMp4_CDS.fasta11091514fahttps://dataportal.senckenberg.de/dataset/7f944577-8198-46a3-901e-1c9b345860df/resource/b6670913-5fec-468b-bddc-75b0e4b06fcd/download/mp4_cds.fastaOtherRepeat element masked genomic sequences of Melanopsichium pennsylvanicumRepeat element masked genomic sequences of Melanopsichium pennsylvanicum19621963fahttps://dataportal.senckenberg.de/dataset/7f944577-8198-46a3-901e-1c9b345860df/resource/c32dd404-ed04-40ee-9966-3e6be18c529b/download/repeat-element-masked-genomic-sequences-of-melanopsichium-pennsylvanicumOther