Phylogenomic Analyses Indicate that Early Fungi Evolved Digesting Cell Walls of Algal Ancestors of Land Plants

Chang, Ying; Wang, Sishuo; Sekimoto, Satoshi; Aerts, Andrea L.; Choi, Cindy; Clum, Alicia; LaButti, Kurt M.; Lindquist, Erika A.; Yee Ngan, Chew; Ohm, Robin A.; Salamov, Asaf A.; Grigoriev, Igor V.; Spatafora, Joseph W.; Berbee, Mary L.

doi:10.1093/gbe/evv090

Phylogenomic Analyses Indicate that Early Fungi Evolved Digesting Cell Walls of Algal Ancestors of Land Plants

Journal Article · Wed May 13 00:00:00 EDT 2015 · Genome Biology and Evolution

DOI:https://doi.org/10.1093/gbe/evv090· OSTI ID:1625338

Chang, Ying ^[1]; Wang, Sishuo ^[2]; Sekimoto, Satoshi ^[3]; Aerts, Andrea L. ^[4]; Choi, Cindy ^[5]; Clum, Alicia ^[5]; LaButti, Kurt M. ^[5]; Lindquist, Erika A. ^[5]; Yee Ngan, Chew ^[5]; Ohm, Robin A. ^[5]; Salamov, Asaf A. ^[5]; Grigoriev, Igor V. ^[5]; Spatafora, Joseph W. ^[6]; Berbee, Mary L. ^[2]

University of British Columbia, Vancouver, (British Columbia). Department of Botany; DOE/OSTI
University of British Columbia, Vancouver, (British Columbia). Department of Botany
University of British Columbia, Vancouver, (British Columbia). Department of Botany; National Institute of Technology and Evaluation, Chiba (Japan). NITE Biological Resource Center (NBRC)
DOE Joint Genome Institute, Walnut Creek, California (United States).
DOE Joint Genome Institute, Walnut Creek, California (United States).
Oregon State University (United States). Department of Botany and Plant Pathology

As decomposers, fungi are key players in recycling plant material in global carbon cycles. We hypothesized that genomes of early diverging fungi may have inherited pectinases from an ancestral species that had been able to extract nutrients from pectin-containing land plants and their algal allies (Streptophytes). We aimed to infer, based on pectinase gene expansions and on the organismal phylogeny, the geological timing of the plant–fungus association. We analyzed 40 fungal genomes, three of which, including Gonapodya prolifera, were sequenced for this study. In the organismal phylogeny from 136 housekeeping loci, Rozella diverged first from all other fungi. Gonapodya prolifera was included among the flagellated, predominantly aquatic fungal species in Chytridiomycota. Sister to Chytridiomycota were the predominantly terrestrial fungi including zygomycota I and zygomycota II, along with the ascomycetes and basidiomycetes that comprise Dikarya. The Gonapodya genome has 27 genes representing five of the seven classes of pectin-specific enzymes known from fungi. Most of these share a common ancestry with pectinases from Dikarya. Indicating functional and sequence similarity, Gonapodya, like many Dikarya, can use pectin as a carbon source for growth in pure culture. Shared pectinases of Dikarya and Gonapodya provide evidence that even ancient aquatic fungi had adapted to extract nutrients from the plants in the green lineage. This implies that 750 million years, the estimated maximum age of origin of the pectin-containing streptophytes represents a maximum age for the divergence of Chytridiomycota from the lineage including Dikarya.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1625338

Journal Information:: Genome Biology and Evolution, Journal Name: Genome Biology and Evolution Journal Issue: 6 Vol. 7; ISSN 1759-6653

Publisher:: Society for Molecular Biology and EvolutionCopyright Statement

Country of Publication:: United States

Language:: English

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Early Diverging Insect-Pathogenic Fungi of the Order Entomophthorales Possess Diverse and Unique Subtilisin-Like Serine Proteases Arnesen, Jonathan A.; Małagocka, Joanna; Gryganskyi, Andrii G3: Genes\|Genomes\|Genetics, Vol. 8, Issue 10 https://doi.org/10.1534/g3.118.200656	journal	August 2018
Pectin Digestion in Herbivorous Beetles: Impact of Pseudoenzymes Exceeds That of Their Active Counterparts Kirsch, Roy; Kunert, Grit; Vogel, Heiko Frontiers in Physiology, Vol. 10 https://doi.org/10.3389/fphys.2019.00685	journal	May 2019
A Glimpse of Nucleo-Cytoplasmic Large DNA Virus Biodiversity through the Eukaryotic Genomics Window Gallot-Lavallée, Lucie; Blanc, Guillaume Viruses, Vol. 9, Issue 1 https://doi.org/10.3390/v9010017	journal	January 2017
A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data Spatafora, Joseph W.; Chang, Ying; Benny, Gerald L. Mycologia, Vol. 108, Issue 5 https://doi.org/10.3852/16-042	journal	September 2016