[1]

Komluski J, Stukenbrock EH, Habig M. 2022. Non-Mendelian transmission of accessory chromosomes in fungi. Chromosome Research 30:241−253

doi: 10.1007/s10577-022-09691-8
[2]

Habig M, Patneedi SK, Stam R, de Fine Licht HH. 2025. Horizontal transfer of accessory chromosomes in fungi: a regulated process for exchange of genetic material? Heredity 135:590−596

doi: 10.1038/s41437-025-00746-0
[3]

Witte TE, Villeneuve N, Boddy CN, Overy DP. 2021. Accessory chromosome-acquired secondary metabolism in plant pathogenic fungi: the evolution of biotrophs into host-specific pathogens. Frontiers in Microbiology 12:664276

doi: 10.3389/fmicb.2021.664276
[4]

Zhang Y, Yang H, Turra D, Zhou S, Ayhan DH, et al. 2020. The genome of opportunistic fungal pathogen Fusarium oxysporum carries a unique set of lineage-specific chromosomes. Communications Biology 3:50

doi: 10.1038/s42003-020-0770-2
[5]

Johnson LJ, Johnson RD, Akamatsu H, Salamiah A, Otani H, et al. 2001. Spontaneous loss of a conditionally dispensable chromosome from the Alternaria alternata apple pathotype leads to loss of toxin production and pathogenicity. Current Genetics 40:65−72

doi: 10.1007/s002940100233
[6]

Coleman JJ, Rounsley SD, Rodriguez-Carres M, Kuo A, Wasmann CC, et al. 2009. The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansion. PLoS Genetics 5:e1000618

doi: 10.1371/journal.pgen.1000618
[7]

Zhang J, Tong Q, Lin F, An X, Huang H, et al. 2026. Polymorphism and evolutionary origins of accessory chromosomes in the basidiomycete Tremella fuciformis. Nature Communications 17:3275

doi: 10.1038/s41467-026-70078-y
[8]

Kohanovski I, Pontz M, Vande Zande P, Selmecki A, Dahan O, et al. 2024. Aneuploidy can be an evolutionary diversion on the path to adaptation. Molecular Biology and Evolution 41:msae052

doi: 10.1093/molbev/msae052
[9]

Fouché S, Plissonneau C, McDonald BA, Croll D. 2018. Meiosis leads to pervasive copy-number variation and distorted inheritance of accessory chromosomes of the wheat pathogen Zymoseptoria tritici. Genome Biology and Evolution 10:1416−1429

doi: 10.1093/gbe/evy100
[10]

Möller M, Habig M, Freitag M, Stukenbrock EH. 2018. Extraordinary genome instability and widespread chromosome rearrangements during vegetative growth. Genetics 210:517−529

doi: 10.1534/genetics.118.301050
[11]

Deng Y, Guo L, Lin L, Li Y, Zhang J, et al. 2023. Meiosis in an asymmetric dikaryotic genome of Tremella fuciformis Tr01 facilitates new chromosome formation. Genome Biology 24:280

doi: 10.1186/s13059-023-03093-7
[12]

Li SJ, Li B, Guo S. 2024. Chromosome-level assembly reveals a fifteen-chromosome aneuploid genome and environmental adaptation strategy of Chinese traditional medical fungus Wolfiporia hoelen. International Journal of Molecular Sciences 25:8786

doi: 10.3390/ijms25168786
[13]

Xu Y, Tian L, Tan J, Li J, O'Neil N, et al. 2025. Distribution of haploid chromosomes into separate nuclei in two pathogenic fungi. Science 388:784−788

doi: 10.1126/science.abn7811
[14]

Li SJ, Wang Q, Dong CH. 2022. Bipolar system of sexual incompatibility and heterothallic life cycle in the basidiomycetes Pachyma hoelen Fr. (Fuling). Mycologia 114:63−75

doi: 10.1080/00275514.2021.2006995
[15]

Li SJ, Meng GL, Dong CH. 2022. Homokaryotic high-quality genome assembly of medicinal fungi Wolfiporia hoelen reveals auto-regulation and high-temperature adaption of probable two-speed genome. International Journal of Molecular Sciences 23:10484

doi: 10.3390/ijms231810484
[16]

Porebski S, Bailey LG, Baum BR. 1997. Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components. Plant Molecular Biology Reporter 15:8−15

doi: 10.1007/BF02772108
[17]

Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, et al. 2009. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326:289−293

doi: 10.1126/science.1181369
[18]

Wang M, Meng G, Yang Y, Wang X, Xie R, et al. 2024. Telomere-to-telomere genome assembly of Tibetan medicinal mushroom Ganoderma leucocontextum and the first Copia centromeric retrotransposon in macro-fungi genome. Journal of Fungi 10:15

doi: 10.3390/jof10010015
[19]

Chen S, Zhou Y, Chen Y, Gu J. 2018. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34:i884−i890

doi: 10.1093/bioinformatics/bty560
[20]

Cheng H, Concepcion GT, Feng X, Zhang H, Li H. 2021. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nature Methods 18:170−175

doi: 10.1038/s41592-020-01056-5
[21]

Chin CS, Peluso P, Sedlazeck FJ, Nattestad M, Concepcion GT, et al. 2016. Phased diploid genome assembly with single-molecule real-time sequencing. Nature Methods 13:1050−1054

doi: 10.1038/nmeth.4035
[22]

Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, et al. 2017. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Research 27:722−736

doi: 10.1101/gr.215087.116
[23]

Hu J, Wang Z, Sun Z, Hu B, Ayoola AO, et al. 2024. NextDenovo: an efficient error correction and accurate assembly tool for noisy long reads. Genome Biology 25:107

doi: 10.1186/s13059-024-03252-4
[24]

Servant N, Varoquaux N, Lajoie BR, Viara E, Chen CJ, et al. 2015. HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Genome Biology 16:259

doi: 10.1186/s13059-015-0831-x
[25]

Zhou ZW, Yu ZG, Huang XM, Liu J, Guo Y, et al. 2022. GenomeSyn: a bioinformatics tool for visualizing genome synteny and structural variations. Journal of Genetics and Genomics 49:1174−1176

doi: 10.1016/j.jgg.2022.03.013
[26]

Chen J, Wang Z, Tan K, Huang W, Shi J, et al. 2023. A complete telomere-to-telomere assembly of the maize genome. Nature Genetics 55:1221−1231

doi: 10.1038/s41588-023-01419-6
[27]

Chaisson MJ, Tesler G. 2012. Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory. BMC Bioinformatics 13:238

doi: 10.1186/1471-2105-13-238
[28]

Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. 2015. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31:3210−3212

doi: 10.1093/bioinformatics/btv351
[29]

Ou S, Jiang N. 2018. LTR_retriever: a highly accurate and sensitive program for identification of long terminal repeat retrotransposons. Plant Physiology 176:1410−1422

doi: 10.1104/pp.17.01310
[30]

Rhie A, Walenz BP, Koren S, Phillippy AM. 2020. Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biology 21:245

doi: 10.1186/s13059-020-02134-9
[31]

Xu Z, Wang H. 2007. LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Research 35:W265−W269

doi: 10.1093/nar/gkm286
[32]

Ellinghaus D, Kurtz S, Willhoeft U. 2008. LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons. BMC Bioinformatics 9:18

doi: 10.1186/1471-2105-9-18
[33]

Baranova MA, Logacheva MD, Penin AA, Seplyarskiy VB, Safonova YY, et al. 2015. Extraordinary genetic diversity in a wood decay mushroom. Molecular Biology and Evolution 32:2775−2783

doi: 10.1093/molbev/msv153
[34]

Flynn JM, Hubley R, Goubert C, Rosen J, Clark AG, et al. 2020. RepeatModeler2 for automated genomic discovery of transposable element families. Proceedings of the National Academy of Sciences of the United States of America 117:9451−9457

doi: 10.1073/pnas.1921046117
[35]

Yan H, Bombarely A, Li S. 2020. DeepTE: a computational method for de novo classification of transposons with convolutional neural network. Bioinformatics 36:4269−4275

doi: 10.1093/bioinformatics/btaa519
[36]

Bedell JA, Korf I, Gish W. 2000. MaskerAid: a performance enhancement to RepeatMasker. Bioinformatics 16:1040−1041

doi: 10.1093/bioinformatics/16.11.1040
[37]

Blin K, Shaw S, Augustijn HE, Reitz ZL, Biermann F, et al. 2023. antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation. Nucleic Acids Research 51:W46−W50

doi: 10.1093/nar/gkad344
[38]

Chen C, Wu Y, Li J, Wang X, Zeng Z, Xu J, Liu Y, Feng J, Chen H, He Y, Xia R. 2023. TBtools-II: a "one for all, all for one" bioinformatics platform for biological big-data mining. Molecular Plant 16:1733−1742

doi: 10.1016/j.molp.2023.09.010
[39]

Kanehisa M, Goto S. 2000. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Research 28:27−30

doi: 10.1093/nar/28.1.27
[40]

Gene Ontology Consortium, Aleksander SA, Balhoff J, Carbon S, Cherry JM, et al. 2023. The Gene Ontology knowledgebase in 2023. Genetics 224 http://doi.org/10.1093/genetics/iyad031
[41]

Zhang Q, Chen X, Xu C, Zhao H, Zhang X, et al. 2019. Horizontal gene transfer allowed the emergence of broad host range entomopathogens. Proceedings of the National Academy of Sciences of the United States of America 116:7982−7989

doi: 10.1073/pnas.1816430116
[42]

Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25

doi: 10.1186/gb-2009-10-3-r25
[43]

Tarasov A, Vilella AJ, Cuppen E, Nijman IJ, Prins P. 2015. Sambamba: fast processing of NGS alignment formats. Bioinformatics 31:2032−2034

doi: 10.1093/bioinformatics/btv098
[44]

McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, et al. 2010. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research 20:1297−1303

doi: 10.1101/gr.107524.110
[45]

Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, et al. 2021. Twelve years of SAMtools and BCFtools. GigaScience 10:giab008

doi: 10.1093/gigascience/giab008
[46]

Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, et al. 2012. Primer3: new capabilities and interfaces. Nucleic Acids Research 40:e115

doi: 10.1093/nar/gks596
[47]

Emms DM, Kelly S. 2015. OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biology 16:157

doi: 10.1186/s13059-015-0721-2
[48]

Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32:1792−1797

doi: 10.1093/nar/gkh340
[49]

Castresana J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molecular Biology and Evolution 17:540−552

doi: 10.1093/oxfordjournals.molbev.a026334
[50]

Shen W, Le S, Li Y, Hu F. 2016. SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation. PLoS ONE 11:e0163962

doi: 10.1371/journal.pone.0163962
[51]

Darriba D, Taboada GL, Doallo R, Posada D. 2011. ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics 27:1164−1165

doi: 10.93/bioinformatics/btr088
[52]

Kozlov AM, Darriba D, Flouri T, Morel B, Stamatakis A. 2019. RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics 35:4453−4455

doi: 10.1093/bioinformatics/btz305
[53]

Houben A. 2017. B chromosomes: a matter of chromosome drive. Frontiers in Plant Science 8:210

doi: 10.3389/fpls.2017.00210
[54]

Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. 2019. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nature Biotechnology 37:907−915

doi: 10.1038/s41587-019-0201-4
[55]

Liao Y, Smyth GK, Shi W. 2014. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30:923−930

doi: 10.1093/bioinformatics/btt656
[56]

Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C. 2017. Salmon provides fast and bias-aware quantification of transcript expression. Nature Methods 14:417−419

doi: 10.1038/nmeth.4197
[57]

Novak JE, Ross-Macdonald PB, Roeder GS. 2001. The budding yeast Msh4 protein functions in chromosome synapsis and the regulation of crossover distribution. Genetics 158:1013−1025

doi: 10.1093/genetics/158.3.1013
[58]

Uehara DT, Mitsubuchi H, Inazawa J. 2021. A missense variant in NUF2, a component of the kinetochore NDC80 complex, causes impaired chromosome segregation and aneuploidy associated with microcephaly and short stature. Human Genetics 140:1047−1060

doi: 10.1007/s00439-021-02273-4
[59]

Gonzalo A, Lucas MO, Charpentier C, Sandmann G, Lloyd A, et al. 2019. Reducing MSH4 copy number prevents meiotic crossovers between non-homologous chromosomes in Brassica napus. Nature Communications 10:2354

doi: 10.1038/s41467-019-10010-9
[60]

Zhang T, Zhou Y, Qi ST, Wang ZB, Qian WP, et al. 2015. Nuf2 is required for chromosome segregation during mouse oocyte meiotic maturation. Cell Cycle 14:2701−2710

doi: 10.1080/15384101.2015.1058677
[61]

Dong S, Raffaele S, Kamoun S. 2015. The two-speed genomes of filamentous pathogens: waltz with plants. Current Opinion in Genetics & Development 35:57−65

doi: 10.1016/j.gde.2015.09.001
[62]

Castanera R, López-Varas L, Borgognone A, LaButti K, Lapidus A, et al. 2016. Transposable elements versus the fungal genome: impact on whole-genome architecture and transcriptional profiles. PLoS Genetics 12:e1006108

doi: 10.1371/journal.pgen.1006108
[63]

Faino L, Seidl MF, Shi-Kunne X, Pauper M, van den Berg GCM, et al. 2016. Transposons passively and actively contribute to evolution of the two-speed genome of a fungal pathogen. Genome Research 26:1091−1100

doi: 10.1101/gr.204974.116
[64]

Badet T, Tralamazza SM, Feurtey A, Croll D. 2024. Recent reactivation of a pathogenicity-associated transposable element is associated with major chromosomal rearrangements in a fungal wheat pathogen. Nucleic Acids Research 52:1226−1242

doi: 10.1093/nar/gkad1214
[65]

Gao C, Liu X, Zhao B, Feng H, Huang L. 2026. High-quality genome assembly of Diplocarpon coronariae unveils LTR retrotransposon-driven structural dynamics in fungi evolution. Molecular Ecology Resources 26:e70070

doi: 10.1111/1755-0998.70070
[66]

van Westerhoven AC, Aguilera-Galvez C, Nakasato-Tagami G, Shi-Kunne X, Martinez de la Parte E, et al. 2024. Segmental duplications drive the evolution of accessory regions in a major crop pathogen. New Phytologist 242:610−625

doi: 10.1111/nph.19604
[67]

Sauters TJC, Rokas A. 2025. Patterns and mechanisms of fungal genome plasticity. Current Biology 35:R527−R544

doi: 10.1016/j.cub.2025.04.003
[68]

Machín F, Torres-Rosell J, Jarmuz A, Aragón L. 2006. Transcription of ribosomal genes can cause nondisjunction. Journal of Cell Biology 173:893−903

doi: 10.1083/jcb.200511129
[69]

Ross-Macdonald P, Roeder GS. 1994. Mutation of a meiosis-specific MutS homolog decreases crossing over but not mismatch correction. Cell 79:1069−1080

doi: 10.1016/0092-8674(94)90037-x
[70]

Nabetani A, Koujin T, Tsutsumi C, Haraguchi T, Hiraoka Y. 2001. A conserved protein, Nuf2, is implicated in connecting the centromere to the spindle during chromosome segregation: a link between the kinetochore function and the spindle checkpoint. Chromosoma 110:322−334

doi: 10.1007/s004120100153