maortiz

• Ortiz, Miguel Angel Naranjo; Molina, Manu; Fuentes, Diego; Mixão, Verónica & Gabaldón, Toni (2022). Karyon: a computational framework for the diagnosis of hybrids, aneuploids, and other nonstandard architectures in genome assemblies. GigaScience. doi: 10.1093/gigascience/giac088. Full text in Research Archive Show summary

  Recent technological developments have made genome sequencing and assembly highly accessible and widely used. However, the presence in sequenced organisms of certain genomic features such as high heterozygosity, polyploidy, aneuploidy, heterokaryosis, or extreme compositional biases can challenge current standard assembly procedures and result in highly fragmented assemblies. Here we present Karyon, a Python-based toolkit that uses raw sequencing data and de novo genome assembly to assess several parameters and generate informative plots to assist in the identification of nonchanonical genomic traits. Karyon includes automated de novo genome assembly and variant calling pipelines. We tested Karyon by diagnosing 35 highly fragmented publicly available assemblies from 19 different Mucorales (Fungi) species.

• Gerdol, Marco; Moreira, Rebeca; Cruz, Fernando; Gómez-Garrido, Jessica; Vlasova, Anna V & Rosani, Umberto [Show all 21 contributors for this article] (2020). Massive gene presence-absence variation shapes an open pan-genome in the Mediterranean mussel. Genome Biology. ISSN 1465-6906. 21. doi: 10.1186/s13059-020-02180-3. Full text in Research Archive Show summary

  Here, after the assembly of a 1.28-Gb reference genome and the resequencing of 14 individuals from two independent populations, we reveal a complex pan-genomic architecture in M. galloprovincialis, with a core set of 45,000 genes plus a strikingly high number of dispensable genes (20,000) subject to presence-absence variation, which may be entirely missing in several individuals. We show that dispensable genes are associated with hemizygous genomic regions affected by structural variants, which overall account for nearly 580 Mb of DNA sequence not included in the reference genome assembly. As such, this is the first study to report the widespread occurrence of gene presence-absence variation at a whole-genome scale in the animal kingdom.

• Ortiz, Miguel Angel Naranjo & Gabaldón, Toni (2020). Fungal evolution: cellular, genomic and metabolic complexity. Biological Reviews. ISSN 1464-7931. 95(5), p. 1198–1232. doi: 10.1111/brv.12605. Full text in Research Archive Show summary

  The question of how phenotypic and genomic complexity are inter-related and how they are shaped through evolution is a central question in biology that historically has been approached from the perspective of animals and plants. In recent years, however, fungi have emerged as a promising alternative system to address such questions. Key to their ecological success, fungi present a broad and diverse range of phenotypic traits. Fungal cells can adopt many different shapes, often within a single species, providing them with great adaptive potential. Fungal cellular organizations span from unicellular forms to complex, macroscopic multicellularity, with multiple transitions to higher or lower levels of cellular complexity occurring throughout the evolutionary history of fungi. Similarly, fungal genomes are very diverse in their architecture. Deep changes in genome organization can occur very quickly, and these phenomena are known to mediate rapid adaptations to environmental changes. Finally, the biochemical complexity of fungi is huge, particularly with regard to their secondary metabolites, chemical products that mediate many aspects of fungal biology, including ecological interactions. Herein, we explore how the interplay of these cellular, genomic and metabolic traits mediates the emergence of complex phenotypes, and how this complexity is shaped throughout the evolutionary history of Fungi.

• Ortiz, Miguel Angel Naranjo & Gabaldón, Toni (2019). Fungal evolution: major ecological adaptations and evolutionary transitions. Biological Reviews. ISSN 1464-7931. 94(4), p. 1443–1476. doi: 10.1111/brv.12510. Full text in Research Archive
• Baró-Montiel, Nuria; Vall-Llaura, Nuria; Usall, Josep; Teixidó, Nuria; Ortiz, Miguel Angel Naranjo & Gabaldón, Toni [Show all 7 contributors for this article] (2019). Pectin methyl esterases and rhamnogalacturonan hydrolases: weapons for successful Monilinia laxa infection in stone fruit? Plant Pathology. ISSN 0032-0862. 68(7), p. 1381–1393. doi: 10.1111/ppa.13039. Full text in Research Archive Show summary

  The secretion of cell wall-degrading enzymes is one of the mechanisms used by necrotrophic fungi to colonize host tissues. However, information about virulence factors of Monilinia spp., the causal agents of brown rot in stone fruit, is scarce. Plant cell walls have three main components that are broken down by fungal enzymes: cellulose, hemicellulose and pectin. In order to identify Monilinia laxa candidate proteins involved in pectin hydrolysis, two in vitro approaches were conducted: (i) phenotypic and ecophysiological characterization of growth of the pathogen at different pHs, in glucose- and pectin-containing solid media for 7 days' incubation; and (ii) expression analysis of genes encoding M. laxa pectin methyl esterases (MlPMEs) and rhamnogalacturonan hydrolases (MlRG-HYDs) after incubation for 0.5, 2, 6, 24 and 48 h in glucose- and pectin-containing liquid media. Phenotypic tests showed the role of carbon source on M. laxa growth rate and aggressiveness, and indicated that pectinases were greatly affected by pH. Gene expression analyses uncovered differences among members of each family of pectinases and between the two families, defining sets of genes expressed at earlier (0.5–6 h) and later (48 h) phases. Notably, the up- or down-regulation of these target genes was carbon source-dependent. Finally, an in vivo study confirmed the synergistic and complementary role that these genes play in the M. laxa–stone fruit pathosystem. Based on these results, it is hypothesized that MlPME2, MlRG-HYD1 and MlRG-HYD2 may be potential virulence factors of M. laxa in the process from infection to colonization.

• Ortiz, Miguel Angel Naranjo & Gabaldón, Toni (2019). Fungal evolution: diversity, taxonomy and phylogeny of the Fungi. Biological Reviews. ISSN 1464-7931. 94(6), p. 2101–2137. doi: 10.1111/brv.12550. Full text in Research Archive Show summary

  The fungal kingdom comprises a hyperdiverse clade of heterotrophic eukaryotes characterized by the presence of a chitinous cell wall, the loss of phagotrophic capabilities and cell organizations that range from completely unicellular monopolar organisms to highly complex syncitial filaments that may form macroscopic structures. Fungi emerged as a ‘Third Kingdom’, embracing organisms that were outside the classical dichotomy of animals versus vegetals. The taxonomy of this group has a turbulent history that is only now starting to be settled with the advent of genomics and phylogenomics. We here review the current status of the phylogeny and taxonomy of fungi, providing an overview of the main defined groups. Based on current knowledge, nine phylum-level clades can be defined: Opisthosporidia, Chytridiomycota, Neocallimastigomycota, Blastocladiomycota, Zoopagomycota, Mucoromycota, Glomeromycota, Basidiomycota and Ascomycota. For each group, we discuss their main traits and their diversity, focusing on the evolutionary relationships among the main fungal clades. We also explore the diversity and phylogeny of several groups of uncertain affinities and the main phylogenetic and taxonomical controversies and hypotheses in the field.

• Ortiz, Miguel Angel Naranjo; Rodriguez-Pires, Silva; Torres, Rosario; Cal, Antonieta de; Usall, Josep & Gabaldón, Toni (2018). Genome Sequence of the Brown Rot Fungal Pathogen Monilinia laxa. Microbiology Resource Announcements (MRA). 6(17), p. 214–218. doi: 10.1128/genomeA.00214-18. Full text in Research Archive Show summary

  Monilinia laxa (phylum Ascomycota) is a plant pathogen responsible for the brown rot blossom blight disease in stone fruit trees of the Rosaceae family, such as apricots. We report here the genome sequence of strain 8L of this species, which was assembled into 618 scaffolds, having a total size of 40.799 Mb and encoding 9,567 unique protein-coding genes.

• Aranda-Martínez, Almudena; Ortiz, Miguel Angel Naranjo; Garcia, Isabel Sofia Abihssira; Zavala-González, Ernesto & Lopez-Llorca, Luis Vicente (2017). Ethanol production from chitosan by the nematophagous fungus Pochonia chlamydosporia and the entomopathogenic fungi Metarhizium anisopliae and Beauveria bassiana. Microbiology Research. ISSN 0944-5013. 204, p. 30–39. doi: 10.1016/j.micres.2017.07.009. Full text in Research Archive Show summary

  Chitin is the second most abundant biopolymer after cellulose and virtually unexplored as raw material for bioethanol production. In this paper, we investigate chitosan, the deacetylated form of chitin which is the main component of shellfish waste, as substrate for bioethanol production by fungi. Fungal parasites of invertebrates such as the nematophagous Pochonia chlamydosporia (Pc) or the entomopathogens Beauveria bassiana (Bb) and Metarhizium anisopliae (Ma) are biocontrol agents of plant parasitic nematodes (eg. Meloidogyne spp.) or insect pests such as the red palm weevil (Rhynchophorus ferrugineus). These fungi degrade chitin-rich barriers for host penetration. We have therefore tested the chitin/chitosanolytic capabilities of Pc, Bb and Ma for generating reducing sugars using chitosan as only nutrient. Among the microorganisms used in this study, Pc is the best chitosan degrader, even under anaerobic conditions. These fungi have alcohol dehydrogenase (ADH) and pyruvate decarboxylase (PDC) encoding genes in their genomes. We have therefore analyzed their ethanol production under anaerobic conditions using chitosan as raw material. P. chlamydosporia is the largest ethanol producer from chitosan. Our studies are a starting point to develop chitin-chitosan based biofuels.

• Gabaldón, Toni; Ortiz, Miguel Angel Naranjo & Marcet-Houben, Marina (2016). Evolutionary genomics of yeast pathogens in the Saccharomycotina. FEMS Yeast Research. ISSN 1567-1356. 16(6). doi: 10.1093/femsyr/fow064. Full text in Research Archive Show summary

  Saccharomycotina comprises a diverse group of yeasts that includes numerous species of industrial or clinical relevance. Opportunistic pathogens within this clade are often assigned to the genus Candida but belong to phylogenetically distant lineages that also comprise non-pathogenic species. This indicates that the ability to infect humans has evolved independently several times among Saccharomycotina. Although the mechanisms of infection of the main groups of Candida pathogens are starting to be unveiled, we still lack sufficient understanding of the evolutionary paths that led to a virulent phenotype in each of the pathogenic lineages.

• Escudero, Nuria; Ferreira, Sebastiao; Lopez-Moya, Federico; Ortiz, Miguel Angel Naranjo; Marín-Ortiz, Ana & Thornton, Christopher [Show all 7 contributors for this article] (2016). Chitosan enhances parasitism of Meloidogyne javanica eggs by the nematophagous fungus Pochonia chlamydosporia. Fungal Biology. ISSN 1878-6146. 120(4), p. 572–585. Full text in Research Archive
• Zavala, Ernesto; Escudero, Nuria; López-Moya, Federico; Aranda, Almudena; Exposito, Alejandro & Ricaño-Ridríguez, Jorge [Show all 9 contributors for this article] (2015). Some isolates of the nematophagous fungus Pochonia chlamydosporia promote root growth and reduce flowering time of tomato. Annals of Applied Biology. ISSN 0003-4746. 166(3), p. 472–483. Full text in Research Archive Show summary

  The fungal parasite of nematode eggs Pochonia chlamydosporia is also a root endophyte known to promote growth of some plants. In this study, we analysed the effect of nine P. chlamydosporia isolates from worldwide origin on tomato growth. Experiments were performed at different scales (Petri dish, growth chamber and greenhouse conditions) and developmental stages (seedlings, plantlets and plants). Seven P. chlamydosporia isolates significantly (P

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• Naranjo-Ortiz, Miguel Angel (2025). Hvor er alle soppene? Funga. 3. Full text in Research Archive
• Naranjo-Ortiz, Miguel Angel; Skrede, Inger; Peris, David; Krabberød, Anders Kristian; Lü, Dabao Sun & Bendiksby, Mika (2025). Expansive pangenome sin the Agaricomycetes. Full text in Research Archive Show summary

  Trichaptum abietinum (Dicks.) Ryvarden (Hymenochaetales) is a pioneer wood rot mushroom common across the Northern Hemisphere, usually growing on conifer wood. The species has emerged in recent years as a model for mushroom genomics, and extensive genomic resources are available. Here, we have analyzed patterns of gene presence-absence variation across a dataset covering T. abietinum known intraspecific geographical and genetic diversity. Our results suggest that Trichaptum abietinum has a large proportion of its genome under Presence-Absence variation, over 40% of all genes for any particular strain. This pattern seem to be common across Agaricomycetes, but not across other groups of Fungi. Core and accessory genes have distinct properties. Core genes also tend to cluster towards chromosome centers, while accessory genes are more abundant at the extremes. Core genes tend to be longer, have more introns and appear closer to other genes. Distribution of Accessory genes across the species depends on genetic distance, but this variable alone can only explain a fraction of the observed pattern. Unlike most other groups of fungi that tend to be haploid, Agaricomycetes spend most of their life cycle as a dikaryotic mycelium. Cell division in this mycelium is typically tightly regulated, which would be unnecessary were this a simple diploid. We hypothesize that extensive PAV has the potential of causing interference during mitotic recombination events, thus promoting genomic unstability. This is then prevented by keeping the two nuclei separated until meiosis. This life cycle would allow these fungi to access a much larger gene pool than it would be possible for any single haploid genet.

• Winden, Veerle Van; Bendiksby, Mika; Naranjo-Ortiz, Miguel Angel & Bjorå, Charlotte Sletten (2025). PhyloFun - Spatial Phylogenetics of Fungi in Norway for Biodiversity Management. Full text in Research Archive Show summary

  Fungi are among the most understudied branches of life, despite their great diversity and crucial ecological roles. The PhyloFun project explores patterns of fungal diversity from an evolutionary perspective using Norway as a model. PhyloFun integrates occurrence records with phylogenetic information to carry out a spatial phylogenetic assessment. Occurrence data are harvested from various online data repositories, including both observational as well as specimens-based records. In addition, PhyloFun uses DNA sequence data systematically produced within the NorBol barcoding project combined with sequences harvested from GenBank. To reduce imbalance in taxon and marker sampling, PhyloFun also produces new DNA sequence data from both fungarium specimens and freshly collected materials. An existing, systematically organised framework, Nature in Norway (NiN), provides an important and innovative data source, with which to compare the distribution patterns of clades at all levels. With its extensive fungal occurrence data, its diverse habitat, and the NiN system Norway represents an ideal location to undertake this research. Focusing on Norway as a model system, the PhyloFun project hopes to assess how evolutionary relationships shape fungal community composition across spatial scales.

• Winden, Veerle Van; Bendiksby, Mika; Naranjo-Ortiz, Miguel Angel & Bjorå, Charlotte Sletten (2024). PhyloFun: spatial phylogenetics of fungi in Norway. doi: https:/www.forbio.uio.no/events/meeting/2024/biosystematikk_program.pdf. Full text in Research Archive Show summary

  The PhyloFun project aims to map the spatial distribution of fungal phylogenetic diversity and endemism across various Norwegian ecosystems by integrating molecular phylogenetic data with species occurrence records. The project pioneers the first spatial phylogenetic study of fungi, using Norway as a model system to explore the evolutionary and ecological diversity of these crucial organisms. Occurrence data will be combined with phylogenetic techniques to uncover patterns of phylogenetic diversity, identify environmental variables influencing these patterns, and assess spatial phylogenetic diversity across Norway's ecosystems. For this, we will supplement existing barcode data with newly generated sequences derived from Norway’s natural history collections. Besides the aim to fill a critical knowledge gap in fungal biodiversity, we also aim to enhance biodiversity management practices through phylogenetically informed conservation strategies. By integrating the Nature in Norway (NiN) framework with spatial phylogenetic methods, PhyloFun will provide novel insights into the distribution and ecological significance of fungi in Norway. The outcomes will set the stage for future parallel studies in other regions, such as California, and contribute to a broader understanding of global fungal diversity. PhyloFun will advance the field of biodiversity research, promoting a deeper understanding of the intrinsic and extrinsic factors which determine the diversity of fungi, as well as their evolutionary and ecological roles in maintaining healthy ecosystems.

• Ortiz, Miguel Angel Naranjo; Skrede, Inger; Bendiksby, Mika; Lü, Dabao Sun; Navarro, David Peris & Krabberød, Anders Kristian (2024). Pangenome analyses of the mushroom Trichaptum abietinum (Hymenochaetales) reveals extensive presence-absence variation. Full text in Research Archive
• Ortiz, Miguel Angel Naranjo (2024). Fungateria: Bringing life to the materials of tomorrow. Funga. Full text in Research Archive
• Ortiz, Miguel Angel Naranjo (2024). Mushroom hunting through time and space: The MUSHEUM project. Funga. Full text in Research Archive
• Ortiz, Miguel Angel Naranjo; Israel, Araoz; Hellem, Mellado & Vinker, Gabriel (2024). Picantísimas. [Radio]. Radio Latinamerica. Full text in Research Archive
• Ortiz, Miguel Angel Naranjo; Reyes, Valentín & Puentes, Jose Luis (2023). El nórdico no es solo una manta #2x12: Una de setas. [Internet]. Spotify. Full text in Research Archive
• Ortiz, Miguel Angel Naranjo (2023). In the Shoes of a Mushroom: On Genomics and the Fungal Point of view. Full text in Research Archive

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