A Genome Sequence Assembly of the Phototactic and Optogenetic Model Fungus Blastocladiella emersonii Reveals a Diversified Nucleotide-Cyclase Repertoire

Abstract

The chytrid fungus Blastocladiella emersonii produces spores with swimming tails (zoospores); these cells can sense and swim towards light. Interest in this species stems from ongoing efforts to develop B. emersonii as a model for understanding the evolution of phototaxis and the molecular cell biology of the associated optogenetic circuits. Here we report a highly-contiguous genome assembly and gene annotation of the B. emersonii ATCC 22665 strain. We integrate a PacBio long-read library with an Illumina paired-end genomic sequence survey leading to an assembly of 21 contigs totalling 34.27 Mb. Using these data, we assess the diversity of sensory system encoding genes. These analyses identify a rich complement of G protein-coupled receptors (GPCRs), ion transporters and nucleotide-cyclases, all of which had been diversified by domain recombination and tandem duplication. In many cases these domain combinations have led to the fusion of a protein domain to a transmembrane domain, tying a putative signalling function to the cell membrane. This pattern is consistent with the diversification of the B. emersonii sensory-signalling systems, which likely plays a varied role in the complex lifecycle of this fungus.

Genomes and transcriptomes help unravel the complex life cycle of the blastoclad fungus,Coelomomyces lativittatus,an obligate parasite of mosquitoes and microcrustaceans

“…Mean completeness when run in ‘genome’ mode was only a moderate 43.1% using the fungi set, and a slightly higher 56.3% using the eukaryota set. These values were lower than the mean completeness of other blastoclads (fungi: 75.5%, eukaryota: 83.8%), including a recent long-read genome from B. emersonii (fungi: 81.8%) [81]. Additionally, fragmented BUSCOs accounted for an average 15.5% and 22.3% in the C. lativittatus draft assemblies for the fungi and eukaryota sets respectively and many of the BUSCO marker genes were not found (fungi: 41.4%, eukaryota: 21.3%).…”

Evolutionarily diverse fungal zoospores show contrasting swimming patterns specific to ultrastructure

“…Such studies would be dependent on finding element of the cell structural proteome that govern movement but for which genetic manipulation is not lethal to development of the zoospore. Genome sequences are available for many of the fungi compared here [33,[45][46][47],…”

“…Such studies would be dependent on finding element of the cell structural proteome that govern movement but for which genetic manipulation is not lethal to development of the zoospore. Genome sequences are available for many of the fungi compared here [33,45–47], however, we currently do not have any candidate gene families beyond the tubulin and actin structures identified. Genetic manipulation of such gene families, for example by gene deletion, is likely to be lethal.…”

“…We combined and curated three SSU+LSU rDNA alignments [31][32][33] adding new sequences from zoosporic fungal taxa. The new dataset of 117 sequences was aligned with MAFFT v7 [34] and trimmed with TrimAl [35] with the 'automated1' option for a total of 2578 nucleotide positions.…”

“…Zoospores for S. microbalum were obtained as described for Chytriomyces confervae CBS 675.73 in Galindo et al [31]. Zoospores were then separated from sporangia using a 20 μm pluriStrainer (pluriSelect) in 50 ml falcon We combined and curated three SSU+LSU rDNA alignments [31][32][33] adding new sequences from zoosporic fungal taxa. The new dataset of 117 sequences was aligned with MAFFT v7…”