title: Phylogenomic Analyses Indicate that Early Fungi Evolved Digesting Cell Walls of Algal Ancestors of Land Plants.
abstract: 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.
authors.affiliation: Department of Botany, University of British Columbia, Vancouver, British Columbia niuerchang@gmail.com.
authors.forename: Ying
authors.initials: Y
authors.lastname: Chang
authors.affiliation: Department of Botany, University of British Columbia, Vancouver, British Columbia.
authors.forename: Sishuo
authors.initials: S
authors.lastname: Wang
authors.affiliation: Department of Botany, University of British Columbia, Vancouver, British Columbia NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, Chiba, Japan.
authors.forename: Satoshi
authors.initials: S
authors.lastname: Sekimoto
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California.
authors.forename: Andrea L
authors.initials: AL
authors.lastname: Aerts
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California.
authors.forename: Cindy
authors.initials: C
authors.lastname: Choi
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California.
authors.forename: Alicia
authors.initials: A
authors.lastname: Clum
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California.
authors.forename: Kurt M
authors.initials: KM
authors.lastname: LaButti
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California.
authors.forename: Erika A
authors.initials: EA
authors.lastname: Lindquist
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California.
authors.forename: Chew
authors.initials: C
authors.lastname: Yee Ngan
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California.
authors.forename: Robin A
authors.initials: RA
authors.lastname: Ohm
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California.
authors.forename: Asaf A
authors.initials: AA
authors.lastname: Salamov
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California.
authors.forename: Igor V
authors.initials: IV
authors.lastname: Grigoriev
authors.affiliation: Department of Botany and Plant Pathology, Oregon State University.
authors.forename: Joseph W
authors.initials: JW
authors.lastname: Spatafora
authors.affiliation: Department of Botany, University of British Columbia, Vancouver, British Columbia.
authors.forename: Mary L
authors.initials: ML
authors.lastname: Berbee
mesh_terms: D056890:Eukaryota / Q000235:genetics; D019143:Evolution, Molecular; D005658:Fungi / Q000145:classification* / Q000201:enzymology / Q000235:genetics; D016681:Genome, Fungal; D010802:Phylogeny; D010944:Plants / Q000382:microbiology; D011096:Polygalacturonase / Q000235:genetics*
chemical_list: D011096:Polygalacturonase
keywords: Gonapodya; carbohydrate active enzymes; evolution; fungal phylogeny; geological time; pectinases; streptophytes