Genome assembly and annotation using short-paired reads is challenging for eukaryotic organisms due to their large size, variable ploidy and large number of repetitive elements. However, the use of single-molecule long reads improves assembly quality (completeness and contiguity), but haplotype duplications still pose assembly challenges. To address the effect of read length on genome assembly quality, gene prediction and annotation, we compared genome assemblers and sequencing technologies with four strains of the ectomycorrhizal fungus Laccaria trichodermophora. By analysing the predicted repertoire of carbohydrate enzymes, we investigated the effects of assembly quality on functional inferences. Libraries were generated using three different sequencing platforms (Illumina Next-Seq, Mi-Seq and PacBio Sequel), and genomes were assembled using single and hybrid assemblies/libraries. Long reads or hybrid assemby resolved the collapsing of repeated regions, but the nuclear heterozygous versions remained unresolved. In dikaryotic fungi, each cell includes two nuclei and each nucleus has differences not only in allelic gene version but also in gene composition and synteny. These heterokaryotic cells produce fragmentation and size overestimation of the genome assembly of each nucleus. Hybrid assembly revealed a wider functional diversity of genomes. Here, several predicted oxidizing activities on glycosyl residues of oligosaccharides and several chitooligosaccharide acetylase activities would have passed unnoticed in short-read assemblies. Also, the size and fragmentation of the genome assembly, in combination with heterozygosity analysis, allowed us to distinguish homokaryotic and heterokaryotic strains isolated from L. trichodermophora fruit bodies.

The present study describes Hemiaustroboletus gen. nov. in the subfamily Austroboletoideae (Boletaceae). Hemiaustroboletus is supported by morphological and molecular data using LSU and RPB2 regions. Additionally, its geographic distribution and intraspecific variation were inferred using ITS sequences. The genus is characterised by pileate-stipitate basidiomata; purple, brown, reddish-brown, orange-brown to dark brown vinaceous pileus; whitish or lilac to vinaceous context and a subclavate stipe. Microscopically, it is characterised by ornamented, slightly verrucose, cracked to perforated brown basidiospores. Two species are described within the genus, Hemiaustroboletus vinaceobrunneus sp. nov. and H. vinaceus sp. nov. Hemiaustroboletus vinaceus sp. nov. is morphologically similar to Austroboletus gracilis, which suggests they may have been confused in the past. This study presents the phylogenetic placement, microscopic structures, detailed morphological descriptions and illustrations of both new species.

Antecedentes: En los genomas de hongos ectomicorrízicos, están las huellas de las interacciones biológicas que los han transformado y les confirieren sus características fisiológicas y ecológicas. Objetivos: Analizar los principales patrones relativos a la evolución y genómica funcional de los hongos ectomicorrízicos. Métodos: Se revisó la bibliografía sobre historia evolutiva, diversificación, genómica funcional y genómica comparativa de hongos ectomicorrízicos. Resultados y conclusiones: Los hongos ectomicorrízicos evolucionaron independientemente a partir de diversos ancestros saprobios con dos picos de diversificación, uno en la transición del Jurásico-Cretácico y el segundo a partir del Paleoceno. La condición ectomicorrízica generó diversificación de especies en muchos géneros que lo adoptaron. La pérdida múltiple e independiente de enzimas degradadoras de pared celular vegetal es una característica común entre estos linajes; mientras que la reinvención de la comunicación con la planta a través de nuevos genes huérfanos es característica de algunos linajes. El tamaño de ciertas familias génicas ha aumentado guiado por la actividad de transposones. Diversos estudios evidencian un mosaico evolutivo y funcional desarrollado independientemente en estos hongos. La masificación de la genómica y transcriptómica es necesaria para entender las relaciones entre las presiones ambientales o biológicas y la evolución y función de los hongos.