Biology subjects

Russell, S. D.

Publications and source records attributed to Russell, S. D..

6 recordsLinked to original sources

bioRxiv2025

Revisions to the Gliophorus irrigatus complex (Agaricales, Hygrophoraceae, Gliophorus, section Unguinosae) including a new waxcap, G. alboviscidus, from the UK but detected globally via soil eDNA, two new species from eastern North America, G. fumosus and G. parafumosus, plus a new species, G. calunus, and a new combination of Hygrophorus subaromaticus in Gliophorus from western North America.

Here we report the discovery of four new agaricoid fungi in the Gliophorus irrigatus complex of the family Hygrophoraceae. Gliophorus alboviscidus sp. nov. from the UK is morphologically identical to the European G. irrigatus (which we neotypify), except that its basidiome is white or pale Buff coloured vs brownish grey. Two new species from eastern North America, Gliophorus fumosus sp. nov. (provisional name Gliophorus sp. irrigatus-IN01), and Gliophorus parafumosus sp. nov (previously labelled G. irrigatus) resemble G. irrigatus s.s. in colour and morphology but their distributions are restricted to North America. Phylogenetic reconstruction revealed that these samples form distinct clades, with >10% ITS sequence divergence from European G. irrigatus s.s. and from each other. Though G. alboviscidus sp. nov. is currently known only from two locations in the UK, searches for related sequences from eDNA (environmental DNA) sequence repositories (UNITE/GlobalFungi) suggested that this species is more widely distributed in Eurasia. G. fumosus and G. parafumosus sequences from eastern North America were divergent from both European G. irrigatus and G. alboviscidus; both were more closely related to another species with a strong odour and white/Buff basidiomes from northwestern North America, Hygrophorus subaromaticus for which we sequenced the holotype and recombine in the genus Gliophorus. We also describe a new species from northwestern North America, G. calunus sp. nov. (provisional name Gliophorus sp. irrigatus-CA01), based on vouchered specimens photographed and sequenced by an paraprofessional group, CA FUNDIS. We highlight the importance of citizen scientist groups and paraprofessionals in documenting macrofungal species and their distributions via databases such as iNaturalist, Mushroom Observer and MycoMap. Further, we discuss reasons eDNA distributions are often larger than known distributions of basidiomes, including G. alboviscidus and G. fumosus.

evolutionary biology↗

bioRxiv2025

From Field to FASTA: Onsite DNA Barcoding the Mushrooms of the 2024 NAMA Foray

Mushroom forays present unparalleled opportunities to record macrofungal biodiversity in a place and time. The 2024 NAMA annual foray at the Cispus Center near Randle, Washington was the first mass barcoding activity performed by the NAMA DNA Sequencing Committee (DNAMA). The workflows and methods utilized are presented along with planned improvements. Ultimately, 803 ITS barcodes were generated (83.7% of those attempted) for 513 unique taxa belonging to 209 Genera. Of these, 18 novel putative species-level operational taxonomic units (OTUs) were discovered as well as 28 new distribution reports at state level or above. Methods and suggestions for replicating and improving mass barcoding at forays are discussed.

genetics↗

bioRxiv2022

A CDKB/KRP/FB3 cell cycle core complex functions in rice gametes and zygotes

The cell cycle controls division and proliferation of all eukaryotic cells and is tightly regulated at multiple checkpoints by complexes of core cell cycle proteins. Due to the difficulty in accessing female gametes and zygotes of flowering plants, little is known about the molecular mechanisms underlying initiation embryogenesis despite the crucial importance of this process for seed crops. In this study, we reveal four levels of factors involved in rice zygotic cell cycle control and characterize their functions and regulation. Protein-protein interaction studies, including within zygote cells, and in vitro biochemical analyses delineate a model of the zygotic cell cycle core complex for rice. In this model, CDKB1, a major regulator of plant mitosis, is a cyclin (CYCD5)-dependent kinase; its activity is coordinately inhibited by two cell cycle inhibitors, KRP4 and KRP5; and both KRPs are regulated via F-box protein 3 (FB3)-mediated proteolysis. Supporting their critical role in controlling the rice zygotic cell cycle, mutations in KRP4, KRP5, and FB3 result in the compromised function of sperm cells and abnormal organization of female germ units, embryo and endosperm, thus significantly reducing seed-set rates. This work helps reveals regulatory mechanisms controlling the zygotic cell cycle toward seed formation in angiosperms.

cell biology↗

bioRxiv2022

Online Forays for Macrofungi: Expediting the Rate of Documenting Biodiversity

A citizen-science oriented mushroom collecting event was organized online and held across the state of Indiana from October 23-29, 2017. Utilizing iNaturalist as the observational reporting platform, 30 members of the Hoosier Mushroom Society made over 1,300 observations of macrofungi during the week of the event. More importantly, the associated specimens were saved for more than 800 of the observations. Over 400 of the specimens were retained and received DNA barcodes, resulting in novel genotypes for 73 putative species being added to public databases. A full set of administrator and participant protocols has been compiled to aid others in conducting this style of biodiversity research for macrofungi. Methods include volunteer recruitment, participant protocols, specimen shipment, triage, and storage. Data management is also a key administrative aspect. Methodologies for integrating iNaturalist observational data with DNA sequence data and herbarium collection information are outlined for the MycoMap platform. Traditional mushroom collecting events have a number of limitations when compared to the online foray model. These advantages are discussed and key considerations for hosting online forays are examined.

ecology↗

bioRxiv2020

Resetting of 24-nt siRNA landscape is initiated in the unicellular zygote in rice

BackgroundThe zygote, a totipotent stem cell, constitutes a critical stage of the life cycle of sexually reproducing organisms. It is produced by the fusion of two differentiated cells -- the egg and sperm, which in plants have radically different siRNA transcriptomes from each other and from multicellular embryos. Due to technical challenges, the epigenetic changes that accompany the zygotic transition are poorly understood. ResultsHere, we characterized the small RNA transcriptome of rice zygotes. We found widespread redistribution of 24-nt siRNAs relative to gametes, including absence of sperm signature siRNAs, reduction at egg signature siRNA loci, and upregulation at seedling signature siRNA loci. Loci with reduced siRNAs in zygote relative to egg were gene-distal and heterochromatic, while loci with increased siRNAs relative to egg had a similar genomic distribution to canonical siRNA loci. Although both egg and zygote siRNA loci had higher mCHH level in wildtype than in drm2 embryo, zygote but not egg siRNA loci were associated with hypermethylation in mature embryo. A small fraction of siRNA loci (~1%) called siren loci accounted for 60% of all siRNAs within zygote siRNA loci, that likely arose from maternal carryover as they had similarly abundant siRNAs in egg; these siren loci were not associated with embryo hypermethylation. ConclusionsTaken together, our results indicate re-distribution of siRNAs in rice zygotes towards the canonical vegetative profile, that are consistent with the initiation of resetting of the gametic epigenome before the first embryonic division.

plant biology↗

bioRxiv2019

Reprogramming of 24nt siRNAs in rice gametes

Gametes constitute a critical stage of the plant life cycle, during which the genome undergoes reprogramming in preparation for embryogenesis. Here we characterized the small RNA transcriptomes of egg cells and sperm cells from rice to elucidate genome-wide distributions of 24nt siRNAs, which are a hallmark of RNA-directed DNA methylation (RdDM) in plants and are typically concentrated at boundaries of heterochromatin. We found that 24nt siRNAs were depleted from heterochromatin boundaries in both gametes, reminiscent of siRNA patterns in DDM1-type nucleosome remodeler mutants. In sperm, 24nt siRNAs were spread across broad heterochromatic regions, while in eggs, 24nt siRNAs were concentrated at a smaller number of heterochromatic loci throughout the genome, which were shared with vegetative tissues and sperm. In both gametes, patterns of CHH methylation, typically a strong indicator of RdDM, were similar to vegetative tissues, although lower in magnitude. These findings indicate that the small RNA transcriptome undergoes large-scale re-programming in both male and female gametes, which is not correlated with recruitment of DNA methyltransferases in gametes and suggestive of unexplored regulatory activities of gamete small RNAs in seeds after fertilization.

molecular biology↗