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Living apart together : crosstalk between the core and supernumerary genomes in a fungal plant pathogen

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Abstract
Background: Eukaryotes display remarkable genome plasticity, which can include supernumerary chromosomes that differ markedly from the core chromosomes. Despite the widespread occurrence of supernumerary chromosomes in fungi, their origin, relation to the core genome and the reason for their divergent characteristics are still largely unknown. The complexity of genome assembly due to the presence of repetitive DNA partially accounts for this. Results: Here we use single-molecule real-time (SMRT) sequencing to assemble the genome of a prominent fungal wheat pathogen, Fusarium poae, including at least one supernumerary chromosome. The core genome contains limited transposable elements (TEs) and no gene duplications, while the supernumerary genome holds up to 25 % TEs and multiple gene duplications. The core genome shows all hallmarks of repeat-induced point mutation (RIP), a defense mechanism against TEs, specific for fungi. The absence of RIP on the supernumerary genome accounts for the differences between the two (sub) genomes, and results in a functional crosstalk between them. The supernumerary genome is a reservoir for TEs that migrate to the core genome, and even large blocks of supernumerary sequence (> 200 kb) have recently translocated to the core. Vice versa, the supernumerary genome acts as a refuge for genes that are duplicated from the core genome. Conclusions: For the first time, a mechanism was determined that explains the differences that exist between the core and supernumerary genome in fungi. Different biology rather than origin was shown to be responsible. A "living apart together" crosstalk exists between the core and supernumerary genome, accelerating chromosomal and organismal evolution.
Keywords
Single-molecule real-time sequencing, Supernumerary chromosomes, Fusarium, Repeat-induced point mutation, Translocation, Gene duplications, Transposable elements, CONDITIONALLY DISPENSABLE CHROMOSOME, INDUCED POINT MUTATIONS, FUSARIUM-GRAMINEARUM, B-CHROMOSOMES, HORIZONTAL GENE, SEQUENCE, REVEALS, EVOLUTION, POPULATIONS, GENERATION

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Chicago
Vanheule, Adriaan, Kris Audenaert, Sven Warris, Henri van de Geest, Elio Schijlen, Monica Höfte, Sarah De Saeger, Geert Haesaert, Cees Waalwijk, and Theo van der Lee. 2016. “Living Apart Together : Crosstalk Between the Core and Supernumerary Genomes in a Fungal Plant Pathogen.” Bmc Genomics 17.
APA
Vanheule, A., Audenaert, K., Warris, S., van de Geest, H., Schijlen, E., Höfte, M., De Saeger, S., et al. (2016). Living apart together : crosstalk between the core and supernumerary genomes in a fungal plant pathogen. BMC GENOMICS, 17.
Vancouver
1.
Vanheule A, Audenaert K, Warris S, van de Geest H, Schijlen E, Höfte M, et al. Living apart together : crosstalk between the core and supernumerary genomes in a fungal plant pathogen. BMC GENOMICS. 2016;17.
MLA
Vanheule, Adriaan, Kris Audenaert, Sven Warris, et al. “Living Apart Together : Crosstalk Between the Core and Supernumerary Genomes in a Fungal Plant Pathogen.” BMC GENOMICS 17 (2016): n. pag. Print.
@article{8164218,
  abstract     = {Background: Eukaryotes display remarkable genome plasticity, which can include supernumerary chromosomes that differ markedly from the core chromosomes. Despite the widespread occurrence of supernumerary chromosomes in fungi, their origin, relation to the core genome and the reason for their divergent characteristics are still largely unknown. The complexity of genome assembly due to the presence of repetitive DNA partially accounts for this. 
Results: Here we use single-molecule real-time (SMRT) sequencing to assemble the genome of a prominent fungal wheat pathogen, Fusarium poae, including at least one supernumerary chromosome. The core genome contains limited transposable elements (TEs) and no gene duplications, while the supernumerary genome holds up to 25 \% TEs and multiple gene duplications. The core genome shows all hallmarks of repeat-induced point mutation (RIP), a defense mechanism against TEs, specific for fungi. The absence of RIP on the supernumerary genome accounts for the differences between the two (sub) genomes, and results in a functional crosstalk between them. The supernumerary genome is a reservoir for TEs that migrate to the core genome, and even large blocks of supernumerary sequence ({\textrangle} 200 kb) have recently translocated to the core. Vice versa, the supernumerary genome acts as a refuge for genes that are duplicated from the core genome. 
Conclusions: For the first time, a mechanism was determined that explains the differences that exist between the core and supernumerary genome in fungi. Different biology rather than origin was shown to be responsible. A {\textacutedbl}living apart together{\textacutedbl} crosstalk exists between the core and supernumerary genome, accelerating chromosomal and organismal evolution.},
  articleno    = {670},
  author       = {Vanheule, Adriaan and Audenaert, Kris and Warris, Sven and van de Geest, Henri and Schijlen, Elio and H{\"o}fte, Monica and De Saeger, Sarah and Haesaert, Geert and Waalwijk, Cees and van der Lee, Theo},
  issn         = {1471-2164},
  journal      = {BMC GENOMICS},
  keyword      = {Single-molecule real-time sequencing,Supernumerary chromosomes,Fusarium,Repeat-induced point mutation,Translocation,Gene duplications,Transposable elements,CONDITIONALLY DISPENSABLE CHROMOSOME,INDUCED POINT MUTATIONS,FUSARIUM-GRAMINEARUM,B-CHROMOSOMES,HORIZONTAL GENE,SEQUENCE,REVEALS,EVOLUTION,POPULATIONS,GENERATION},
  language     = {eng},
  pages        = {18},
  title        = {Living apart together : crosstalk between the core and supernumerary genomes in a fungal plant pathogen},
  url          = {http://dx.doi.org/10.1186/s12864-016-2941-6},
  volume       = {17},
  year         = {2016},
}

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