Daphne Z Hoh1,2,3, Hsin-Han Lee1, Naohisa Wada1, Wei-An Liu1, Min R Lu1, Cheng-Kuo Lai1,4, Huei-Mien Ke1, Pei-Feng Sun1,2,3, Sen-Lin Tang1,2, Wen-Hsin Chung5, Ying-Lien Chen6, Chia-Lin Chung6, Isheng Jason Tsai7,8,9. 1. Biodiversity Research Center, Academia Sinica, 115 Nangang, Taipei, Taiwan. 2. Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan. 3. Department of Life Science, National Taiwan Normal University, 116 Wenshan, Taipei, Taiwan. 4. Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan. 5. Department of Plant Pathology, National Chung Hsing University, Taichung, Taiwan. 6. Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, 10617, Taiwan. 7. Biodiversity Research Center, Academia Sinica, 115 Nangang, Taipei, Taiwan. ijtsai@gate.sinica.edu.tw. 8. Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan. ijtsai@gate.sinica.edu.tw. 9. Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan. ijtsai@gate.sinica.edu.tw.
Abstract
BACKGROUND: The Fusarium solani species complex (FSSC) comprises fungal pathogens responsible for mortality in a diverse range of animals and plants, but their genome diversity and transcriptome responses in animal pathogenicity remain to be elucidated. We sequenced, assembled and annotated six chromosome-level FSSC clade 3 genomes of aquatic animal and plant host origins. We established a pathosystem and investigated the expression data of F. falciforme and F. keratoplasticum in Chinese softshell turtle (Pelodiscus sinensis) host. RESULTS: Comparative analyses between the FSSC genomes revealed a spectrum of conservation patterns in chromosomes categorised into three compartments: core, fast-core (FC), and lineage-specific (LS). LS chromosomes contribute to variations in genomes size, with up to 42.2% of variations between F. vanettenii strains. Each chromosome compartment varied in structural architectures, with FC and LS chromosomes contain higher proportions of repetitive elements with genes enriched in functions related to pathogenicity and niche expansion. We identified differences in both selection in the coding sequences and DNA methylation levels between genome features and chromosome compartments which suggest a multi-speed evolution that can be traced back to the last common ancestor of Fusarium. We further demonstrated that F. falciforme and F. keratoplasticum are opportunistic pathogens by inoculating P. sinensis eggs and identified differentially expressed genes also associated with plant pathogenicity. These included the most upregulated genes encoding the CFEM (Common in Fungal Extracellular Membrane) domain. CONCLUSIONS: The high-quality genome assemblies provided new insights into the evolution of FSSC chromosomes, which also serve as a resource for studies of fungal genome evolution and pathogenesis. This study also establishes an animal model for fungal pathogens of trans-kingdom hosts.
BACKGROUND: The Fusarium solani species complex (FSSC) comprises fungal pathogens responsible for mortality in a diverse range of animals and plants, but their genome diversity and transcriptome responses in animal pathogenicity remain to be elucidated. We sequenced, assembled and annotated six chromosome-level FSSC clade 3 genomes of aquatic animal and plant host origins. We established a pathosystem and investigated the expression data of F. falciforme and F. keratoplasticum in Chinese softshell turtle (Pelodiscus sinensis) host. RESULTS: Comparative analyses between the FSSC genomes revealed a spectrum of conservation patterns in chromosomes categorised into three compartments: core, fast-core (FC), and lineage-specific (LS). LS chromosomes contribute to variations in genomes size, with up to 42.2% of variations between F. vanettenii strains. Each chromosome compartment varied in structural architectures, with FC and LS chromosomes contain higher proportions of repetitive elements with genes enriched in functions related to pathogenicity and niche expansion. We identified differences in both selection in the coding sequences and DNA methylation levels between genome features and chromosome compartments which suggest a multi-speed evolution that can be traced back to the last common ancestor of Fusarium. We further demonstrated that F. falciforme and F. keratoplasticum are opportunistic pathogens by inoculating P. sinensis eggs and identified differentially expressed genes also associated with plant pathogenicity. These included the most upregulated genes encoding the CFEM (Common in Fungal Extracellular Membrane) domain. CONCLUSIONS: The high-quality genome assemblies provided new insights into the evolution of FSSC chromosomes, which also serve as a resource for studies of fungal genome evolution and pathogenesis. This study also establishes an animal model for fungal pathogens of trans-kingdom hosts.
Authors: Zaira Caracuel; M Isabel G Roncero; Eduardo A Espeso; Clara I González-Verdejo; Fe I García-Maceira; Antonio Di Pietro Journal: Mol Microbiol Date: 2003-05 Impact factor: 3.501
Authors: Natalie D Fedorova; Nora Khaldi; Vinita S Joardar; Rama Maiti; Paolo Amedeo; Michael J Anderson; Jonathan Crabtree; Joana C Silva; Jonathan H Badger; Ahmed Albarraq; Sam Angiuoli; Howard Bussey; Paul Bowyer; Peter J Cotty; Paul S Dyer; Amy Egan; Kevin Galens; Claire M Fraser-Liggett; Brian J Haas; Jason M Inman; Richard Kent; Sebastien Lemieux; Iran Malavazi; Joshua Orvis; Terry Roemer; Catherine M Ronning; Jaideep P Sundaram; Granger Sutton; Geoff Turner; J Craig Venter; Owen R White; Brett R Whitty; Phil Youngman; Kenneth H Wolfe; Gustavo H Goldman; Jennifer R Wortman; Bo Jiang; David W Denning; William C Nierman Journal: PLoS Genet Date: 2008-04-11 Impact factor: 5.917
Authors: Yong Zhang; He Yang; David Turra; Shiguo Zhou; Dilay Hazal Ayhan; Gregory A DeIulio; Li Guo; Karen Broz; Nathan Wiederhold; Jeffrey J Coleman; Kerry O' Donnell; Ilan Youngster; Alexander J McAdam; Sergey Savinov; Terrance Shea; Sarah Young; Qiandong Zeng; Martijn Rep; Eric Pearlman; David C Schwartz; Antonio Di Pietro; H Corby Kistler; Li-Jun Ma Journal: Commun Biol Date: 2020-01-31
Authors: Jullie M Sarmiento-Ramírez; Elena Abella-Pérez; Andrea D Phillott; Jolene Sim; Pieter van West; María P Martín; Adolfo Marco; Javier Diéguez-Uribeondo Journal: PLoS One Date: 2014-01-21 Impact factor: 3.240