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479 results on '"Aanen, Duur K."'

1. Comparative genomics unravels a rich set of biosynthetic gene clusters with distinct evolutionary trajectories across fungal species (Termitomyces) farmed by termites

Author

Schmidt, Suzanne, Murphy, Robert, Vizueta, Joel, Schierbech, Signe Kjærsgaard, Conlon, Benjamin H., Kreuzenbeck, Nina B., Vreeburg, Sabine M. E., van de Peppel, Lennart J. J., Aanen, Duur K., Silué, Kolotchèlèma S., Kone, N’Golo A., Beemelmanns, Christine, Weber, Tilmann, and Poulsen, Michael

Published
2024
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2. Genomic data provide insights into the classification of extant termites

Author

Hellemans, Simon, Rocha, Mauricio M., Wang, Menglin, Romero Arias, Johanna, Aanen, Duur K., Bagnères, Anne-Geneviève, Buček, Aleš, Carrijo, Tiago F., Chouvenc, Thomas, Cuezzo, Carolina, Constantini, Joice P., Constantino, Reginaldo, Dedeine, Franck, Deligne, Jean, Eggleton, Paul, Evans, Theodore A., Hanus, Robert, Harrison, Mark C., Harry, Myriam, Josens, Guy, Jouault, Corentin, Kalleshwaraswamy, Chicknayakanahalli M., Kaymak, Esra, Korb, Judith, Lee, Chow-Yang, Legendre, Frédéric, Li, Hou-Feng, Lo, Nathan, Lu, Tomer, Matsuura, Kenji, Maekawa, Kiyoto, McMahon, Dino P., Mizumoto, Nobuaki, Oliveira, Danilo E., Poulsen, Michael, Sillam-Dussès, David, Su, Nan-Yao, Tokuda, Gaku, Vargo, Edward L., Ware, Jessica L., Šobotník, Jan, Scheffrahn, Rudolf H., Cancello, Eliana, Roisin, Yves, Engel, Michael S., and Bourguignon, Thomas

Published
2024
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3. Evolution content in school textbooks: data from eight European countries

Author

Panayides, Andreas, Sá-Pinto, Xana, Mavrikaki, Evangelia, Aanen, Duur K., Aboim, Sara, Cavadas, Bento, Dvorakova, Radka Marta, Eens, Marcel, Filova, Eliska, Gregorčič, Tanja, Kapsala, Nausica, Nieuwenhuis, Mathijs, Ometto, Lino, Papadopoulou, Penelope, Pinxten, Rianne, Realdon, Giulia, Ribeiro, Nuno, Coelho da Silva, José Luis, Sousa, Bruno, Torkar, Gregor, and Korfiatis, Konstantinos

Published
2024
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10. The obligate alkalophilic soda‐lake fungus Sodiomyces alkalinus has shifted to a protein diet

Author

Grum‐Grzhimaylo, Alexey A, Falkoski, Daniel L, van den Heuvel, Joost, Valero‐Jiménez, Claudio A, Min, Byoungnam, Choi, In‐Geol, Lipzen, Anna, Daum, Chris G, Aanen, Duur K, Tsang, Adrian, Henrissat, Bernard, Bilanenko, Elena N, de Vries, Ronald P, van Kan, Jan AL, Grigoriev, Igor V, and Debets, Alfons JM

Subjects
Microbiology, Biological Sciences, Nutrition, Alkalies, Ascomycota, Gene Transfer, Horizontal, Genome, Fungal, Hydrogen-Ion Concentration, Lakes, Phylogeny, Plants, alkalophilic fungus, brine shrimps, enzymes, HGT, prokaryotes, Sodiomyces alkalinus, Evolutionary Biology, Biological sciences
Abstract

Sodiomyces alkalinus is one of the very few alkalophilic fungi, adapted to grow optimally at high pH. It is widely distributed at the plant-deprived edges of extremely alkaline lakes and locally abundant. We sequenced the genome of S. alkalinus and reconstructed evolution of catabolic enzymes, using a phylogenomic comparison. We found that the genome of S. alkalinus is larger, but its predicted proteome is smaller and heavily depleted of both plant-degrading enzymes and proteinases, when compared to its closest plant-pathogenic relatives. Interestingly, despite overall losses, S. alkalinus has retained many proteinases families and acquired bacterial cell wall-degrading enzymes, some of them via horizontal gene transfer from bacteria. This fungus has very potent proteolytic activity at high pH values, but slowly induced low activity of cellulases and hemicellulases. Our experimental and in silico data suggest that plant biomass, a common food source for most fungi, is not a preferred substrate for S. alkalinus in its natural environment. We conclude that the fungus has abandoned the ancestral plant-based diet and has become specialized in a more protein-rich food, abundantly available in soda lakes in the form of prokaryotes and small crustaceans.

Published
2018

32. Resolution of eleven reported and five novel Podaxis species based on ITS phylogeny, phylogenomics, morphology, ecology, and geographic distribution

Author

Li, G.S., Leal-Dutra, C.A., Cuesta-Maté, A., Conlon, B.H., Peereboom, N., Beemelmanns, C., Aanen, (Duur K.), Rosendahl, S., Debeer, Z.W., Poulsen, M., Li, G.S., Leal-Dutra, C.A., Cuesta-Maté, A., Conlon, B.H., Peereboom, N., Beemelmanns, C., Aanen, (Duur K.), Rosendahl, S., Debeer, Z.W., and Poulsen, M.

Abstract

The genus Podaxis was first described from India by Linnaeus in 1771, but several revisions of the genus have left the taxonomy unclear. Forty-four Podaxis species names and nine intraspecific varieties are currently accepted, but most fungarium specimens are labelled Podaxis pistillaris. Recent molecular analyses based on barcoding genes suggest that the genus comprises several species, but their status is largely unresolved. Here we obtained basidiospores and photographs from 166 fungarium specimens from around the world and generated a phylogeny based on rDNA internal transcribed spacer ITS1, 5.8S and ITS2 (ITS), and a phylogenomic analysis of 3839 BUSCO genes from low-coverage genomes for a subset of the specimens. Combining phylogenetics, phylogenomics, morphology, ecology, and geographical distribution, spanning 250 years of collections, we propose that the genus includes at least 16 unambiguous species. Based on 10 type specimens (holotype, paratype, and syntype), four recorded species were confirmed, P. carcinomalis, P. deflersii, P. emerici, and P. farlowii. Comparing phylogenetic analysis with described species, including morphology, ecology, and distribution, we resurrected P. termitophilus and designated neotypes, epitypes, or lectotypes for five previously described species, P. aegyptiacus, P. africana, P. beringamensis, P. calyptratus, and P. perraldieri. Lastly, based on phylogenies and morphology of type material, we synonymized three reported species, P. algericus, P. arabicus, and P. rugospora with P. pistillaris, and described five new species that we named P. desolatus, P. inyoensis, P. mareebaensis, P. namaquensis, and P. namibensis.

Published
2023
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34. A genetic linkage map and improved genome assembly of the termite symbiont Termitomyces cryptogamus

Author

Vreeburg, Sabine M.E., Auxier, Ben, Jacobs, Bas, Bourke, Peter M., van den Heuvel, Joost, Zwaan, Bas J., Aanen, Duur K., Vreeburg, Sabine M.E., Auxier, Ben, Jacobs, Bas, Bourke, Peter M., van den Heuvel, Joost, Zwaan, Bas J., and Aanen, Duur K.

Abstract

The termite-fungus symbiosis is an ancient stable mutualism of two partners that reproduce and disperse independently. With the founding of each termite colony the symbiotic association must be re-established with a new fungus partner. Complementarity in the ability to break down plant substrate may help to stabilize this symbiosis despite horizontal symbiont transmission. An alternative, non-exclusive, hypothesis is that a reduced rate of evolution may contribute to stabilize the symbiosis, the so-called Red King Effect. Methods: To explore this concept, we produced the first linkage map of a species of Termitomyces, using genotyping by sequencing (GBS) of 88 homokaryotic offspring. We constructed a highly contiguous genome assembly using PacBio data and a de-novo evidence-based annotation. This improved genome assembly and linkage map allowed for examination of the recombination landscape and its potential effect on the mutualistic lifestyle. Results: Our linkage map resulted in a genome-wide recombination rate of 22 cM/Mb, lower than that of other related fungi. However, the total map length of 1370 cM was similar to that of other related fungi. Conclusions: The apparently decreased rate of recombination is primarily due to genome expansion of islands of gene-poor repetitive sequences. This study highlights the importance of inclusion of genomic context in cross-species comparisons of recombination rate.

Published
2023

36. Termitomyces cryptogamus sp. nov. associated with Macrotermes natalensis in Africa

Author

Van de Peppel, Lennart J.J., de Beer, Z.W., Aanen, Duur K., and Auxier, Ben

Subjects
Laboratory of Genetics, Plant Science, PE&RC, Agaricales, Lyophyllaceae, phylogeny, Laboratorium voor Erfelijkheidsleer, Ecology, Evolution, Behavior and Systematics
Abstract

A new species of Termitomyces symbiotic with the termite Macrotermes natalensis is described from Africa. As there are no records of field collected basidiocarps within this lineage, traditional basidiocarp-based morphological taxonomy is not practical. While basidiocarps may be obtained rarely from incubation of fungal comb fragments, their practical use for taxonomical purposes is limited. Therefore, the species is described based on an ITS nucleotide sequence, with comparisons to an asexual culture. Based on samples with similar ITS sequences, this species is likely associated with multiple termite hosts across a large part of Africa.

Published
2022
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39. Additional file 4 of A genetic linkage map and improved genome assembly of the termite symbiont Termitomyces cryptogamus

Author

Vreeburg, Sabine M. E., Auxier, Ben, Jacobs, Bas, Bourke, Peter M., van den Heuvel, Joost, Zwaan, Bas J., and Aanen, Duur K.

Abstract

Additional file 4: Supplementary Figure 3. DotPlotly visualisation of the alignment between the T. cryptogamus assembly v2.0 and the T. cryptogamus v1.0 assembly. On the x-axis the contigs of the v2.0 assembly, on the y-axis the scaffolds of the v1.0 assembly. Vertical and horizontal lines indicate edges of scaffolds or contigs. Dots indicate regions of similar sequence.

Published
2023
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40. Additional file 1 of A genetic linkage map and improved genome assembly of the termite symbiont Termitomyces cryptogamus

Author

Vreeburg, Sabine M. E., Auxier, Ben, Jacobs, Bas, Bourke, Peter M., van den Heuvel, Joost, Zwaan, Bas J., and Aanen, Duur K.

Abstract

Additional file 1: Supplementary Table 1. Crossing table between 30 individuals from the mapping population against 6 siblings from the mapping population with legend. A “+” indicates a successful heterokaryon, “-“ no heterokaryon, “U” indicates unclear, and “NC” indicates cross not performed. Supplementary Table 2. An overview of the number of markers per contig present in each linkage group in the strictly filtered linkage map. Supplementary Table 3. Linkage group assignment and genetic position for each marker in the strictly filtered dataset. Supplementary Table 4. An overview of the number of markers per contig present in each linkage group in the Forced order linkage map. Supplementary Table 5. Linkage group assignment and genetic position for each marker in the Forced Order Linkage map. Supplementary Table 6. Intervals between markers and between grouped markers with less or more recombination than expected. Supplementary Table 7. Markers with a skewed minor allele frequency (cumulative p-value < 0.05 under binomial distribution).

Published
2023
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41. Additional file 5 of A genetic linkage map and improved genome assembly of the termite symbiont Termitomyces cryptogamus

Author

Vreeburg, Sabine M. E., Auxier, Ben, Jacobs, Bas, Bourke, Peter M., van den Heuvel, Joost, Zwaan, Bas J., and Aanen, Duur K.

Abstract

Additional file 5: Supplementary Figure 4. DotPlotly visualisation of the alignment between the contigs of the new reference assembly that form LG12 in the forced order linkage map and the assembly of mt50a. On the x-axis the contigs of the new reference genome, on the y-axis the scaffolds of the mt50a assembly.

Published
2023
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47. Complementary symbiont contributions to plant decomposition in a fungus-farming termite

Author

Poulsen, Michael, Hu, Haofu, Li, Cai, Chen, Zhensheng, Xu, Luohao, Otani, Saria, Nygaard, Sanne, Nobre, Tania, Klaubauf, Sylvia, Schindler, Philipp M., Hauser, Frank, Pan, Hailin, Yang, Zhikai, Sonnenberg, Anton S. M., de Beer, Z. Wilhelm, Zhang, Yong, Wingfield, Michael J., Grimmelikhuijzen, Cornelis J. P., de Vries, Ronald P., Korb, Judith, Aanen, Duur K., Wang, Jun, Boomsma, Jacobus J., and Zhang, Guojie

Published
2014

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