Horizontal Gene Transfer as an Indispensable Driver for Evolution of Neocallimastigomycota into a Distinct Gut-Dwelling Fungal Lineage

Abstract

Survival and growth of the anaerobic gut fungi (AGF; Neocallimastigomycota) in the herbivorous gut necessitate the possession of multiple abilities absent in other fungal lineages. We hypothesized that horizontal gene transfer (HGT) was instrumental in forging the evolution of AGF into a phylogenetically distinct gut-dwelling fungal lineage. The patterns of HGT were evaluated in the transcriptomes of 27 AGF strains, 22 of which were isolated and sequenced in this study, and 4 AGF genomes broadly covering the breadth of AGF diversity. We identified 277 distinct incidents of HGT in AGF transcriptomes, with subsequent gene duplication resulting in an HGT frequency of 2 to 3.5% in AGF genomes. The majority of HGT events were AGF specific (91.7%) and wide (70.8%), indicating their occurrence at early stages of AGF evolution. The acquired genes allowed AGF to expand their substrate utilization range, provided new venues for electron disposal, augmented their biosynthetic capabilities, and facilitated their adaptation to anaerobiosis. The majority of donors were anaerobic fermentative bacteria prevalent in the herbivorous gut. This study strongly indicates that HGT indispensably forged the evolution of AGF as a distinct fungal phylum and provides a unique example of the role of HGT in shaping the evolution of a high-rank taxonomic eukaryotic lineage. IMPORTANCE The anaerobic gut fungi (AGF) represent a distinct basal phylum lineage (Neocallimastigomycota) commonly encountered in the rumen and alimentary tracts of herbivores. Survival and growth of anaerobic gut fungi in these anaerobic, eutrophic, and prokaryote-dominated habitats necessitates the acquisition of several traits absent in other fungal lineages. We assess here the role of horizontal gene transfer as a relatively fast mechanism for trait acquisition by the Neocallimastigomycota postsequestration in the herbivorous gut. Analysis of 27 transcriptomes that represent the broad diversity of Neocallimastigomycota identified 277 distinct HGT events, with subsequent gene duplication resulting in an HGT frequency of 2 to 3.5% in AGF genomes. These HGT events have allowed AGF to survive in the herbivorous gut by expanding their substrate utilization range, augmenting their biosynthetic pathway, providing new routes for electron disposal by expanding fermentative capacities, and facilitating their adaptation to anaerobiosis. HGT in the AGF is also shown to be mainly a cross-kingdom affair, with the majority of donors belonging to the bacteria. This study represents a unique example of the role of HGT in shaping the evolution of a high-rank taxonomic eukaryotic lineage.

Fungal evolution: cellular, genomic and metabolic complexity

“…Once it became possible to search for HGT in a wide taxonomic range of Fungi, it was revealed that these evolutionary phenomena affect Pezizomycotina preferentially (Marcet‐Houben & Gabaldón, ; Wisecaver et al ., ; Gluck‐Thaler et al ., ), at least compared with Saccharomycotina and Basidiomycota. Furthermore, in some cases, HGT has been shown to have been key in the appearance of important adaptations, as shown in Neocallimastigomycotina and its outstanding carbohydrate‐degrading enzymatic pool (Garcia‐Vallvé, Romeu & Palau, ; Rosewich & Kistler, ; Murphy et al ., ).…”

Fungal evolution: diversity, taxonomy and phylogeny of the Fungi

“…Neocallimastigomycota present large genomes (101 Mb in Orpinomyces ) with high content of repetitive elements and a very low GC content (as low as 17% in Orpinomyces ) (Billon‐Grand et al ., ; Youssef et al ., ). These genomes harbour a very wide and rich repertoire of carbohydrate‐degrading enzymes (Youssef et al ., ; Gruninger et al ., ), shaped by gene expansions and horizontal gene‐transfer events (Garcia‐Vallvé, Romeu, & Palau, ; Murphy et al ., ; Wang et al ., ). Members of this phylum have been isolated or detected almost exclusively in the gut of herbivorous mammals and iguanas, where they decompose plant organic matter.…”

Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere

“…5a). While the GH 9 endoglucanase family has not previously been defined as a horizontally acquired gene, a number of carbohydrate-active enzymes have been observed as horizontally transferred genes between anaerobic gut fungi and bacteria [50].…”