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Phylogenomics of a new fungal phylum reveals multiple waves of reductive evolution across Holomycota

Author

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  • Luis Javier Galindo

    (AgroParisTech)

  • Purificación López-García

    (AgroParisTech)

  • Guifré Torruella

    (AgroParisTech)

  • Sergey Karpov

    (Russian Academy of Sciences
    St. Petersburg State University)

  • David Moreira

    (AgroParisTech)

Abstract

Compared to multicellular fungi and unicellular yeasts, unicellular fungi with free-living flagellated stages (zoospores) remain poorly known and their phylogenetic position is often unresolved. Recently, rRNA gene phylogenetic analyses of two atypical parasitic fungi with amoeboid zoospores and long kinetosomes, the sanchytrids Amoeboradix gromovi and Sanchytrium tribonematis, showed that they formed a monophyletic group without close affinity with known fungal clades. Here, we sequence single-cell genomes for both species to assess their phylogenetic position and evolution. Phylogenomic analyses using different protein datasets and a comprehensive taxon sampling result in an almost fully-resolved fungal tree, with Chytridiomycota as sister to all other fungi, and sanchytrids forming a well-supported, fast-evolving clade sister to Blastocladiomycota. Comparative genomic analyses across fungi and their allies (Holomycota) reveal an atypically reduced metabolic repertoire for sanchytrids. We infer three main independent flagellum losses from the distribution of over 60 flagellum-specific proteins across Holomycota. Based on sanchytrids’ phylogenetic position and unique traits, we propose the designation of a novel phylum, Sanchytriomycota. In addition, our results indicate that most of the hyphal morphogenesis gene repertoire of multicellular fungi had already evolved in early holomycotan lineages.

Suggested Citation

  • Luis Javier Galindo & Purificación López-García & Guifré Torruella & Sergey Karpov & David Moreira, 2021. "Phylogenomics of a new fungal phylum reveals multiple waves of reductive evolution across Holomycota," Nature Communications, Nature, vol. 12(1), pages 1-14, December.
  • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-25308-w
    DOI: 10.1038/s41467-021-25308-w
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    Cited by:

    1. Carlos Lax & Stephen J. Mondo & Macario Osorio-Concepción & Anna Muszewska & María Corrochano-Luque & Gabriel Gutiérrez & Robert Riley & Anna Lipzen & Jie Guo & Hope Hundley & Mojgan Amirebrahimi & Vi, 2024. "Symmetric and asymmetric DNA N6-adenine methylation regulates different biological responses in Mucorales," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
    2. Casey H. Meili & Adrienne L. Jones & Alex X. Arreola & Jeffrey Habel & Carrie J. Pratt & Radwa A. Hanafy & Yan Wang & Aymen S. Yassin & Moustafa A. TagElDein & Christina D. Moon & Peter H. Janssen & M, 2023. "Patterns and determinants of the global herbivorous mycobiome," Nature Communications, Nature, vol. 14(1), pages 1-18, December.

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