title: Genome size analyses of Pucciniales reveal the largest fungal genomes.
abstract: Rust fungi (Basidiomycota, Pucciniales) are biotrophic plant pathogens which exhibit diverse complexities in their life cycles and host ranges. The completion of genome sequencing of a few rust fungi has revealed the occurrence of large genomes. Sequencing efforts for other rust fungi have been hampered by uncertainty concerning their genome sizes. Flow cytometry was recently applied to estimate the genome size of a few rust fungi, and confirmed the occurrence of large genomes in this order (averaging 225.3 Mbp, while the average for Basidiomycota was 49.9 Mbp and was 37.7 Mbp for all fungi). In this work, we have used an innovative and simple approach to simultaneously isolate nuclei from the rust and its host plant in order to estimate the genome size of 30 rust species by flow cytometry. Genome sizes varied over 10-fold, from 70 to 893 Mbp, with an average genome size value of 380.2 Mbp. Compared to the genome sizes of over 1800 fungi, Gymnosporangium confusum possesses the largest fungal genome ever reported (893.2 Mbp). Moreover, even the smallest rust genome determined in this study is larger than the vast majority of fungal genomes (94%). The average genome size of the Pucciniales is now of 305.5 Mbp, while the average Basidiomycota genome size has shifted to 70.4 Mbp and the average for all fungi reached 44.2 Mbp. Despite the fact that no correlation could be drawn between the genome sizes, the phylogenomics or the life cycle of rust fungi, it is interesting to note that rusts with Fabaceae hosts present genomes clearly larger than those with Poaceae hosts. Although this study comprises only a small fraction of the more than 7000 rust species described, it seems already evident that the Pucciniales represent a group where genome size expansion could be a common characteristic. This is in sharp contrast to sister taxa, placing this order in a relevant position in fungal genomics research.
authors.affiliation: Centro de Investigação das Ferrugens do Cafeeiro, BioTrop, Instituto de Investigação Científica Tropical Oeiras, Portugal ; Plant Cell Biology Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal.
authors.forename: Sílvia
authors.initials: S
authors.lastname: Tavares
authors.affiliation: CEER-Biosystems Engeneering, Instituto Superior de Agronomia, Universidade de Lisboa Lisbon, Portugal.
authors.forename: Ana Paula
authors.initials: AP
authors.lastname: Ramos
authors.affiliation: Centro de Investigação das Ferrugens do Cafeeiro, BioTrop, Instituto de Investigação Científica Tropical Oeiras, Portugal ; Plant Cell Biology Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal.
authors.forename: Ana Sofia
authors.initials: AS
authors.lastname: Pires
authors.affiliation: Centro de Investigação das Ferrugens do Cafeeiro, BioTrop, Instituto de Investigação Científica Tropical Oeiras, Portugal ; CEER-Biosystems Engeneering, Instituto Superior de Agronomia, Universidade de Lisboa Lisbon, Portugal.
authors.forename: Helena G
authors.initials: HG
authors.lastname: Azinheira
authors.affiliation: Department of Life Sciences, Centre for Functional Ecology, University of Coimbra Coimbra, Portugal.
authors.forename: Patrícia
authors.initials: P
authors.lastname: Caldeirinha
authors.affiliation: Institut für Phytomedizin, Universität Hohenheim Stuttgart, Germany.
authors.forename: Tobias
authors.initials: T
authors.lastname: Link
authors.affiliation: Plant Cell Biology Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal.
authors.forename: Rita
authors.initials: R
authors.lastname: Abranches
authors.affiliation: Centro de Investigação das Ferrugens do Cafeeiro, BioTrop, Instituto de Investigação Científica Tropical Oeiras, Portugal ; CEER-Biosystems Engeneering, Instituto Superior de Agronomia, Universidade de Lisboa Lisbon, Portugal.
authors.forename: Maria do Céu
authors.initials: Mdo C
authors.lastname: Silva
authors.affiliation: Institut für Phytomedizin, Universität Hohenheim Stuttgart, Germany.
authors.forename: Ralf T
authors.initials: RT
authors.lastname: Voegele
authors.affiliation: Department of Life Sciences, Centre for Functional Ecology, University of Coimbra Coimbra, Portugal.
authors.forename: João
authors.initials: J
authors.lastname: Loureiro
authors.affiliation: Centro de Investigação das Ferrugens do Cafeeiro, BioTrop, Instituto de Investigação Científica Tropical Oeiras, Portugal ; Plant Cell Biology Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal ; CEER-Biosystems Engeneering, Instituto Superior de Agronomia, Universidade de Lisboa Lisbon, Portugal.
authors.forename: Pedro
authors.initials: P
authors.lastname: Talhinhas
keywords: Gymnosporangium confusum; flow cytometry; mycological cytogenomics; nuclear DNA content; rust fungi