Schmidt, S.*, Murphy, R.1*, Vizueta, J., Schierbech, S.K., Conlon, B.H., Kreuzenbeck, N.B., Vreeburg, S.M.E., van de Peppel, L.J.J., Aanen, D.K., Kolotchèlèma Silue, S., Koné, N.A., Beemelmanns, C., Weber, T., and Poulsen, M. (2024). Comparative genomics unravels a rich set of biosynthetic gene clusters with distinct evolutionary trajectories across fungal species farmed by termites. Communications Biology, in press

Data: XXX

*Murphy, R., *Sinotte, V.M., Cuesta-Maté, A., Renelies-Hamilton, J., Lenz-Strube, M., and Poulsen, M. (2024). Shaping the tripartite symbiosis: are termite microbiome functions directed by the environmentally acquired fungal cultivar? BMC Animal Microbiome 6, 44. https://doi.org/10.1186/s42523-024-00332-5

Data:

• Amplicon sequences, raw metagenome reads, and assembled metagenomes are available in GenBank via accessions SRR27833599, SRR27833600, SRR27833601, SRR27833602, SRR27833603, SRR27833604, SRR27833605, SRR27833606 ,SRR27833607, SRR27833608, SRR27833609, SRR27833610, SRR27833611, SRR27833612, SRR27833613, SRR27833614, SRR27833615, SRR27833616, SRR27833617, SRR27833618, SRR27833619, SRR27833620, SRR27833621, SRR27833622, and SRR27833623.
• Raw data for AZCL assays and ddPCR are included as Table S9 and S10 respectively.
• Metadata used for 16 S rRNA amplicon sequencing can be found in Table S11. All code used for analyses is available on GitHub: https://github.com/Rob-murphys/pre-post_fungus

Murphy, R., Lenz-Strube, M., Schmidt, S., Silué, K.S., Koné, N.A., Rosendahl, S., and Poulsen, M. (2024). Non-Ribosomal Peptide Synthase profiles remain structurally similar despite minimally shared features across fungus-farming termite microbiomes. ISME Communications 4, ycae094 https://doi.org/10.1093/ismeco/ycae094

Data

• Amplicon sequences are available in the SRA archive in GenBank (BioProject PRJNA1082695)
• Barcodes for termite species verification are available from available from GenBank accessions PP986973-PP986994.
• Scripts generated for analysis available from https://github.com/Rob-murphys/NRPS_composition.

This excel document is a continuously updated database of chemical compounds that have been identified or discovered from organisms involved in the fungus-farming termite symbiosis: the termites, Termitomyces, bacteria, complex communities and Pseudoxylaria. The natural products have been identified by an extensive screening of literature and is the first in-depth investigation into all natural products associated with this termite symbiosis. The table includes molecular formula, mass, compound name, natural product class, termite host (when known), producing organism, country the source material was found in, method of identification and the articles that have discovered the compound from sources related to the fungus-growing termites symbiosis. Subsequently, hundreds of articles were screened for antimicrobial activities linked to each individual natural product, or lack thereof. If possible, the presumed mode of action(s) and reported synergies are indicated as are other known bioactivities. The references associated to bioactivities, mode of action and synergies are reported in the "Reference" column indicated by (no.). An asterisk (*) Indicates that the compound was found from multiple symbiosis sources.

v1. of this database is available from our review in Natural Product Reports in 2022; https://pubs.rsc.org/en/content/articlehtml/2022/np/d1np00022e and subsequent versions will be available from this link: https://sid.erda.dk/sharelink/HzAES0VItX

Li, G., Leal-Dutra, C.A., Cuesta-Maté, A., Conlon, B.H., Peereboom, N., Beemelmanns, C., Aanen, D.K., Rosendahl, S., de Beer, Z.W. and Poulsen, M. (2023). Resolution of eleven reported and five novel Podaxis species based on ITS phylogeny, phylogenomics, morphology, ecology, and geographic distribution. Persoonia: Molecular Phylogeny and Evolution of Fungi 51, 257-279https://doi.org/10.3767/persoonia.2023.51.07

Data:

• ITS sequences are available from GenBank with accessions OP739101– OP739205.
• Low-coverage genome sequences available from GenBank with BioProject ID: PRJNA896504.

Benjamin H. Conlon, Suzanne Schmidt, Michael Poulsen, Jonathan Z. Shik,
STAR Protocols,
Volume 3, Issue 1, 2022, 101126, https://doi.org/10.1016/j.xpro.2022.101126.
Summary
There are few protocols available for DNA extraction from fungi. Here we present four complementary protocols for extraction of genomic DNA from fungi. We quantify the efficacy of extractions and compare eight species from five filamentous fungal genera, including both basidiomycetes and ascomycetes. These protocols should be useful for extraction of DNA from a variety of filamentous fungi. 

Data

Conlon, B.H., Gostinčar, C., Fricke, J., Kreuzenbeck, N., Daniel, J.-M., Schlosser, M.S.L., Peereboom, N. Aanen, D.K., De Beer, Z.W., Beemelmanns, C., Gunde-Cimerman, N., Poulsen, M. (2021). Genome reduction and relaxed selection is associated with the transition to symbiosis in the basidiomycete genus Podaxis. iScience 24, 102680
ITS sequence data, NCBI – GenBank: MW430027-MW430047
Whole-genome sequence data NCBI – BioProject: PRJNA681736

Um, S., Rischer, M., Murphy, R., Benndorf, R., Braga, D., Poulsen, M. Lackner, G., and Beemelmanns, C. (2021). ACS Chemical Biology, https://doi.org/10.1021/acschembio.1c00357

Genomes accession numbers RB110−1: JAEKDS000000000.1 and RB110−2: JAEKDR000000000.1.

Schalk, F., Gostinčar, C., Kreuzenbeck, N., Conlon, B.H., Sommerwerk, E., Rabe, P., Burkhardt, I., Krüger, T., Kniemeyer, O., Brakhage, A.A., Gunde-Cimerman, N., de Beer, Z.W., Dickschat, J., Poulsen, M. and Beemelmanns, C. (2021). mBio 12, e03551-20. https://doi.org/10.1128/mBio.03551-20  
Redox, CAZy and proteomics analyses available from zenodo via https://zenodo.org/record/4781753#.YRYhCO2xXdc 

Murphy, R. Benndorf, R., de Beer, Z.W., Vollmers, J., Beemelmanns, C., and Poulsen, M. (2021). mSphere 6, e01233-20. https://doi.org/10.1128/mSphere.01233-20 
RB22, RB24, RB33, and RB110 assemblies and annotated GenBank files were deposited to Zenodo (https://doi.org/10.5281/zenodo.4302144).

Schwitalla, J.W., Benndorf, R., Martin, K., Vollmers, J., Kaster, A.-K., de Beer, Z.W., Poulsen, M. and Beemelmanns, C. International Journal of Systematic and Evolutionary Microbiology https://doi.org/10.1099/ijsem.0.004478 
The GenBank/EMBL accession number for the partial 16S rRNA gene sequence of strain RB5T is KY558696.2. This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession WEGJ00000000. The version described in this paper is WEGJ01000000.1.

Benndorf, R., Schwitalla, J.W., Martin, K., de Beer, Z.W., Vollmers, J., Kaster, A.-K., Poulsen, M., and Beemelmanns, C. International Journal of Systematic and Evolutionary Microbiology https://doi.org/10.1099/ijsem.0.004398 
The GenBank/EMBL accession numbers for the partial 16S rRNA gene sequences of strains RB20T and RB56T are KY558706.2 and KY558730.2, respectively. This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accessions WEGK00000000.1 and WEGI00000000.1, respectively. The versions described in this paper are version WEGK01000000.1 and WEGI01000000.1, respectively

Bodawatta, K. H., Koane, B., Maiah, G., Sam, K. Poulsen, M and Jønsson, K. A. (2021). Proceedings of the Royal Society B 288: 20210446, https://doi.org/10.1098/rspb.2021.0446.
Microbiome data is available from the GenBank SRA archive (PRJNA673614, PRJNA673602, PRJNA673580, PRJNA673591).

Bodawatta, K. H., Freiberga, I., Puzejova, K., Sam, K., Poulsen, M., and Jønsson, K. A. (2021). BMC Animal Microbiome 3:20, https://doi.org/10.1186/s42523-021-00076-6.
Microbiome data is available from the GenBank SRA database (PRJNA548757).

Bodawatta, K. H., Schierbech, S. K., Petersen, N. R., Bos, N., Jønsson, K.A. and Poulsen, M. (2020). Frontiers in Microbiology 11: 1735, https://doi.org/10.3389/fmicb.2020.01735.
Microbiome data is available from the GenBank SRA database (SAMN14479100–SAMN14479109) and bacterial Sanger sequences are available in GenBank (MT276619–MT276666).

Bodawatta, K. H., Synek, P., Bos, N., Garcia-del-Rey, E., Koane, B., Marki, P. Z., Albrecht, T., Lifjeld, J., Poulsen, M., Munclinger, P., Sam, K., and Jønsson, K. A. (2020). Molecular Ecology 19: 2431 – 2448, https://doi.org/10.1111/mec.15486. 
Haemosporidian sequences are available on GenBank under accessions MK061561–MK061743.

Bodawatta, K. H., Puzejova, K. Sam, K., Poulsen, M., and Jønsson, K. A. (2020). BMC Animal Microbiome 2: 9, https://doi.org/10.1186/s42523-020-00026-8.
Microbiome data is available from the GenBank SRA database (PRJNA591550, SAMN13383021 – SAMN13383134, SRR9295628, SRR9295605, SRR9295561,SRR9295668, SRR9295635, SRR9295590, SRR9295610, SRR9295576, SRR9295676, SRR9295651, SRR9295639, SRR9295585).

Justinn Renelies-Hamilton, Kristjan Germer, David Sillam-Dussès, Kasun H. Bodawatta, Michael Poulsen. mSphere Jan 2021, 6 (1) e01023-20; https://doi.org/10.1128/mSphere.01023-20

SRA data: BioProject PRJNA642018

Other supplementary data: https://zenodo.org/record/4074900 with DOI 10.5281/zenodo.4074900

Bos, N., Guimaraes, L., Palenzuela, R. et al. BMC Evol Biol 20, 163 (2020). https://doi.org/10.1186/s12862-020-01727-z

Data

• MiSeq amplicon sequences, BioProject
• DNA sequences: GenBank accessions MT887350—MT887596.

Otani, S., Challinor, V.L., Kreuzenbeck, N.B. et al. Sci Rep 9, 8819 (2019). https://doi.org/10.1038/s41598-019-45364-z

• 454 and MiSeq data have been submitted to NCBI (SRR6856127-SRR6856172)
• ITS sequences are available in GenBank (accession no. KJ817309-KJ817331)
• LCMS data in mzXML format are available through the Dryad data repository

Hu H, da Costa RR, Pilgaard B, Schiøtt M, Lange L, Poulsen M. mSphere. 2019 May 15;4(3):e00165-19. DOI: 10.1128/mSphere.00165-19

• Clean reads and metagenome assembly have been submitted to the SRA and GenBank under BioProject accession numbers PRJNA476694 and PRJNA193472.

Poulsen, M., Hu, H., Li, C., Chen, Z., Xu, L., Otani, S., … Zhang, G. (2014). Proceedings of the National Academy of Sciences, 111(40), 14500–14505. doi:10.1073/pnas.1319718111

Datasets: http://gigadb.org/dataset/100055

• Draft genome of M. natalensis (dataset 100057)
• Draft genome of Termitomyces sp. J132 (dataset 100056)
• Gut metagenomes from workers, soldiers and a queen (dataset 100058).

Otani, S., Zhukova, M., Koné, N.A., da Costa, R.R., Mikaelyan, A., Sapountzis, P. and Poulsen, M. (2019), Environmental Microbiology Reports, 11: 196-205. https://doi.org/10.1111/1758-2229.12728

• Clean reads are submitted to GenBank, where sample sequences with their accession numbers are under a single SRA submission with the accession SRP144287