Flow cytometry reveals that the rust fungus, Uromyces bidentis (Pucciniales), possesses the largest fungal genome reported—2489 Mbp

Abstract

Among the Eukaryotes, Fungi have relatively small genomes (average of 44.2 Mbp across 1850 species). The order Pucciniales (Basidiomycota) has the largest average genome size among fungi (305 Mbp), and includes the two largest fungal genomes reported so far (Puccinia chrysanthemi and Gymnosporangium confusum, with 806.5 and 893.2 Mbp, respectively). In this work, flow cytometry was employed to determine the genome size of the Bidens pilosa rust pathogen, Uromyces bidentis. The results obtained revealed that U. bidentis presents a surprisingly large haploid genome size of 2489 Mbp. This value is almost three times larger than the previous largest fungal genome reported and over 50 times larger than the average fungal genome size. Microscopic examination of U. bidentis nuclei also showed that they are not as different in size from the B. pilosa nuclei when compared with the differences between other rusts and their host plants. This result further reinforces the position of the Pucciniales as the fungal group with the largest genomes, prompting studies addressing the role of repetitive elements and polyploidy in the evolution, pathological specialization and diversity of fungal species.

The coffee leaf rust pathogen Hemileia vastatrix: one and a half centuries around the tropics

“…Nevertheless, the c . 800‐Mbp genome of H. vastatrix (Carvalho et al ., ; Tavares et al ., ) stands out as one of the largest among rusts (Ramos et al ., ; Tavares et al ., ) and the largest genome of fungal pathogens of economic relevance. The genome of H. vastatrix appears to also vary in size: in a preliminary study including 11 isolates representing distinct races, the genome size ranged from 765 to 839 Mbp, with a general average (± standard deviation) of 797 ± 27 Mbp (CIFC team, unpublished data).…”

Peer Review #1 of "Invasions of gladiolus rust in North America are caused by a widely-distributed clone of Uromycestransversalis (v0.1)"

“…However, the main focus of this study was not the whole genome sequencing and assembly, but to use these data to develop markers. Although useful for marker development, the three draft genomes were highly fragmented (4.3 -7.4 million assembled reads or contigs compared to 6.0 -9.9 million unassembled), which could be the result of repetitive DNA and a large genome, which are common among rust fungi (Ramos et al, 2015;Tavares et al, 2014). Manuscript to be reviewed Although we were unable to detect genetic diversity among isolates of U. transversalis across a wide geographic range, the genome sequences will serve as a resource for further studies on this destructive fungal pathogen of Gladiolus.…”

Invasions of gladiolus rust in North America are caused by a widely-distributed clone ofUromycestransversalis

“…However, the main focus of this study was not the whole genome sequencing and assembly, but to use these data to develop markers. Although useful for marker development, the three draft genomes were highly fragmented (4.3–7.4 million assembled reads or contigs compared to 6.0–9.9 million unassembled), which could be the result of repetitive DNA and a large genome, which are common among rust fungi (Ramos et al, 2015; Tavares et al, 2014).…”