Gerald L. Benny

Bio: Gerald L. Benny is an academic researcher from University of Florida. The author has contributed to research in topics: Zoopagales & Phylogenetic tree. The author has an hindex of 18, co-authored 54 publications receiving 3664 citations.

A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data

Abstract: Zygomycete fungi were classified as a single phylum, Zygomycota, based on sexual reproduction by zygospores, frequent asexual reproduction by sporangia, absence of multicellular sporocarps, and production of coenocytic hyphae, all with some exceptions. Molecular phylogenies based on one or a few genes did not support the monophyly of the phylum, however, and the phylum was subsequently abandoned. Here we present phylogenetic analyses of a genome-scale data set for 46 taxa, including 25 zygomycetes and 192 proteins, and we demonstrate that zygomycetes comprise two major clades that form a paraphyletic grade. A formal phylogenetic classification is proposed herein and includes two phyla, six subphyla, four classes and 16 orders. On the basis of these results, the phyla Mucoromycota and Zoopagomycota are circumscribed. Zoopagomycota comprises Entomophtoromycotina, Kickxellomycotina and Zoopagomycotina; it constitutes the earliest diverging lineage of zygomycetes and contains species that are primarily parasites and pathogens of small animals (e.g. amoeba, insects, etc.) and other fungi, i.e. mycoparasites. Mucoromycota comprises Glomeromycotina, Mortierellomycotina, and Mucoromycotina and is sister to Dikarya. It is the more derived clade of zygomycetes and mainly consists of mycorrhizal fungi, root endophytes, and decomposers of plant material. Evolution of trophic modes, morphology, and analysis of genome-scale data are discussed.

Evolutionary relationships among mucoralean fungi (Zygomycota) : evidence for family polyphyly on a large scale

Abstract: 32611-0680 Abstract: Mucorales (Zygomycota) are ubiquitous, morphologically simple terrestrial fungi that are unit- ed taxonomically by possession of a coenocytic my- celium upon which nonmotile mitotic spores are pro- duced asexually in uni- to multispored sporangia, and zygospores, where known, are produced follow- ing fusion of sexually compatible hyphae. Here we report the first comprehensive phylogenetic analysis of essentially all genera of Mucorales (63 species, 54 genera and 13 families) based on partial nucleotide sequence data of nuclear small subunit (18S) ribo- somal RNA and nuclear large subunit (28S) ribosom- al RNA genes, translation elongation factor-lo( gene exons, and a morphological data set consisting of 1826, 389, 1092 and 11 characters, respectively. In- dividual and combined data sets were analyzed by un- equally weighted maximum parsimony (MP) to in- vestigate evolutionary relationships among and with- in mucoralean families. A Micromucor-Umbelopsis clade, traditionally included in the Mortierellaceae, was identified as the basal sister-group to all other Mucorales. A major discovery of this study is that tra- ditional family-level classification schemes for this or- der appear to be highly artificial as evidenced by

Leveraging single-cell genomics to expand the fungal tree of life.

Abstract: Environmental DNA surveys reveal that most fungal diversity represents uncultured species. We sequenced the genomes of eight uncultured species across the fungal tree of life using a new single-cell genomics pipeline. We show that, despite a large variation in genome and gene space recovery from each single amplified genome (SAG), ≥90% can be recovered by combining multiple SAGs. SAGs provide robust placement for early-diverging lineages and infer a diploid ancestor of fungi. Early-diverging fungi share metabolic deficiencies and show unique gene expansions correlated with parasitism and unculturability. Single-cell genomics holds great promise in exploring fungal diversity, life cycles and metabolic potential.

Amoebidium parasiticum is a protozoan, not a Trichomycete.

Abstract: Classification of the Amoebidiales (Tricho- mycetes, Zygomycota) within the Fungi is problem- atical because their cell walls apparently lack chitin and they produce amoeboid cells during their life cycle. A nearly full length fragment of the nuclear small subunit (SSU) rRNA of Amoebidium parasiticum was amplified by the polymerase chain reaction (PCR) and sequenced to examine its phylogenetic relationships. Results of a BlastN search of GenBank revealed that the A. parasiticum SSU rRNA sequence was most closely related to that of Ichthyophonus hof- eri, an ichthyosporean in the Protozoa near the ani- mal-fungal divergence. Maximum parsimony analysis of ichthyosporean and fungal SSU sequences, using sequences of choanoflagellates to root the 18S rDNA gene trees, resolved A. parasiticum as a strongly sup- ported sister of I. hoferi within the Ichthyophonida clade of the protozoan class Ichthyosporea. In con- trast to other members of this class, which are mostly obligate or facultative parasites of various animals, A. parasiticum and other members of the Amoebidiales are only known to be arthropodophilous symbionts. The results also provide the first evidence that mito- chondrial cristae types exhibit homoplastic distribu- tions within the Ichthyosporea.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

Arbuscular mycorrhiza: the mother of plant root endosymbioses.

Abstract: Arbuscular mycorrhiza (AM), a symbiosis between plants and members of an ancient phylum of fungi, the Glomeromycota, improves the supply of water and nutrients, such as phosphate and nitrogen, to the host plant. In return, up to 20% of plant-fixed carbon is transferred to the fungus. Nutrient transport occurs through symbiotic structures inside plant root cells known as arbuscules. AM development is accompanied by an exchange of signalling molecules between the symbionts. A novel class of plant hormones known as strigolactones are exuded by the plant roots. On the one hand, strigolactones stimulate fungal metabolism and branching. On the other hand, they also trigger seed germination of parasitic plants. Fungi release signalling molecules, in the form of 'Myc factors' that trigger symbiotic root responses. Plant genes required for AM development have been characterized. During evolution, the genetic programme for AM has been recruited for other plant root symbioses: functional adaptation of a plant receptor kinase that is essential for AM symbiosis paved the way for nitrogen-fixing bacteria to form intracellular symbioses with plant cells.

The revised classification of eukaryotes

Abstract: This revision of the classification of eukaryotes, which updates that of Adl et al. [J. Eukaryot. Microbiol. 52 (2005) 399], retains an emphasis on the protists and incorporates changes since 2005 that have resolved nodes and branches in phylogenetic trees. Whereas the previous revision was successful in re-introducing name stability to the classification, this revision provides a classification for lineages that were then still unresolved. The supergroups have withstood phylogenetic hypothesis testing with some modifications, but despite some progress, problematic nodes at the base of the eukaryotic tree still remain to be statistically resolved. Looking forward, subsequent transformations to our understanding of the diversity of life will be from the discovery of novel lineages in previously under-sampled areas and from environmental genomic information.