Comparative genomics reveals the origin of fungal hyphae and multicellularity

Kiss, Enikő

doi:10.14232/phd.10657

Cited by 9 publications

(22 citation statements)

References 332 publications

(482 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Their TAI and TDI were closed to vegetative growth and sexual reproduction, and higher than spore germination (Fig. S19 and S20), suggesting that these four processes evolved, adapted and fixed against various biotic and abiotic factors much later than the spore germination (Knapp et al 2018; Kiss et al 2019; Xie et al 2020).…”

Section: Resultsmentioning

confidence: 99%

“…Genomic and transcriptomic resources of fungi and other kingdoms have massively increased in the past few years. Many comparative studies have been conducted to clarify the driven factors in fungal morphogenesis and multicellularity construction (Kiss et al 2019; Krizsán et al 2019; Varga et al 2019; Merényi et al 2020; Miyauchi et al 2020; Virágh et al 2022). Questions have been raised on the robustness of the hourglass model in fruiting body development in some fungal clades (Merényi et al 2022).…”

mentioning

confidence: 99%

mentioning

confidence: 99%

See 2 more Smart Citations

The Phylotranscriptomic Hourglass Pattern in Fungi: An Updated Model

Xie

Kwan

Chan

et al. 2022

Preprint

View full text Add to dashboard Cite

The "developmental hourglass" describes the morphological convergence to a conserved form at mid-stages of animal embryogenesis. The molecular hourglass pattern during embryogenesis was also identified across kingdoms. Previously, we reported young fruiting body as the conserved "waist" in mushroom-forming "developmental hourglass". However, its robustness is doubted because of the fungal diversity. Additionally, fungi lack embryogenesis, and develop directly from spore to hyphae with morphological similarities during the transition. Here, we updated the "developmental hourglass" model in the life cycle of fungi, namely, spore germination, vegetative growth, and sexual reproduction. Germinating spores, both sexual and asexual, showed the strongest transcriptomic conservation signals across the phyla Mucoromycota, Ascomycota and Basidiomycota. Cross kingdom comparisons revealed high expression levels of "information storage and processing" genes at the waist stages of embryonic and non-embryonic developments in animals, plants, and fungi. The "developmental hourglass" might reflect the mutual transcriptome switches on developmental transitions in eukaryotes that are additional to embryonic organogenesis.

show abstract

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

See 1 more Smart Citation

The Phylotranscriptomic Hourglass Pattern in Fungi: An Updated Model

Xie

Kwan

Chan

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“…The phylogenomic approach has also been used to investigate branching patterns within eukaryotic supergroups, including to understand species evolutionary relationships with implications for the early evolutionary events in the three best-studied eukaryotic lineages: land plants (Wickett et al, 2014), animals (King & Rokas, 2017) and fungi (Kiss et al, 2019;Y. Li et al, 2021;Strassert & Monaghan, 2021).…”

Section: Introductionmentioning

confidence: 99%

“…Over the past 15 years, the discovery of diverse novel microbial eukaryotes, coupled with methods to reconstruct phylogenies based on hundreds of protein-coding genes (known as phylogenomics (Eisen, 2003)) have led to a remarkable reshaping in our understanding of the eukaryotic tree of life, the proposal of new supergroups and the placement of enigmatic lineages in known supergroups (Brown et al, 2018; Burki et al, 2012, 2020; Gawryluk et al, 2019; Janouškovec et al, 2017; Kamikawa et al, 2014; Lax et al, 2018; Strassert et al, 2019; Tice et al, 2021; Yabuki et al, 2015). The phylogenomic approach has also been used to investigate branching patterns within eukaryotic supergroups, including to understand species evolutionary relationships with implications for the early evolutionary events in the three best-studied eukaryotic lineages: land plants (Wickett et al, 2014), animals (King & Rokas, 2017) and fungi (Kiss et al, 2019; Y. Li et al, 2021; Strassert & Monaghan, 2021).…”

Section: Introductionmentioning

confidence: 99%

EukProt: A database of genome-scale predicted proteins across the diversity of eukaryotes

Richter

Berney

Strassert

et al. 2020

Preprint

View full text Add to dashboard Cite

AbstractEukProt is a database of published and publicly available predicted protein sets and unannotated genomes selected to represent eukaryotic diversity, including 742 species from all major supergroups as well as orphan taxa. The goal of the database is to provide a single, convenient resource for studies in phylogenomics, gene family evolution, and other gene-based research across the spectrum of eukaryotic life. Each species is placed within the UniEuk taxonomic framework in order to facilitate downstream analyses, and each data set is associated with a unique, persistent identifier to facilitate comparison and replication among analyses. The database is currently in version 2, and all versions will be permanently stored and made available via FigShare. We invite the community to provide suggestions for new data sets and new annotation features to be included in subsequent versions, with the goal of building a collaborative resource that will promote research to understand eukaryotic diversity and diversification.

show abstract

Genome‐wide CRISPR‐Cas9 screen reveals a persistent null‐hyphal phenotype that maintains high carotenoid production in Yarrowia lipolytica

Lupish

Hall

Schwartz

et al. 2022

Biotech & Bioengineering

View full text Add to dashboard Cite

Yarrowia lipolytica is a metabolic engineering host of growing industrial interest due to its ability to metabolize hydrocarbons, fatty acids, glycerol, and other renewable carbon sources. This dimorphic yeast undergoes a stress-induced transition to a multicellular hyphal state, which can negatively impact biosynthetic activity, reduce oxygen and nutrient mass transfer in cell cultures, and increase culture viscosity.Identifying mutations that prevent the formation of hyphae would help alleviate the bioprocess challenges that they create. To this end, we conducted a genome-wide CRISPR screen to identify genetic knockouts that prevent the transition to hyphal morphology. The screen identified five mutants with a null-hyphal phenotype-ΔRAS2, ΔRHO5, ΔSFL1, ΔSNF2, and ΔPAXIP1. Of these hits, only ΔRAS2 suppressed hyphal formation in an engineered lycopene production strain over a multiday culture. The RAS2 knockout was also the only genetic disruption characterized that did not affect lycopene production, producing more than 5 mg L −1 OD −1 from a heterologous pathway with enhanced carbon flux through the mevalonate pathway.These data suggest that a ΔRAS2 mutant of Y. lipolytica could prove useful in engineering a metabolic engineering host of the production of carotenoids and other biochemicals.

show abstract

Comparative genomics reveals the origin of fungal hyphae and multicellularity

Cited by 9 publications

References 332 publications

The Phylotranscriptomic Hourglass Pattern in Fungi: An Updated Model

The Phylotranscriptomic Hourglass Pattern in Fungi: An Updated Model

EukProt: A database of genome-scale predicted proteins across the diversity of eukaryotes

Genome‐wide CRISPR‐Cas9 screen reveals a persistent null‐hyphal phenotype that maintains high carotenoid production in Yarrowia lipolytica

Contact Info

Product

Resources

About