Genome evolution in mushrooms: insights from the assembled
chromosomes of the basidiomycete Coprinopsis cinerea (Coprinus
cinereus)
Jason E. Stajich1,2,3,4*, Sarah K. Wilke5, Dag Ahrén6, Chun H. Au7, Bruce W Birren8, Mark
Borodovsky9, Claire Burns10, Björn Canbäck6, Lorna A. Casselton11, C. K. Cheng7, Jixin Deng5,
Fred S. Dietrich4,12, David C. Fargo13, Mark Farman14, Allen C. Gathman15, Jonathan Goldberg8,
Roderic Guigo16, Patrick Hoegger17, James B. Hooker5, Ashleigh Huggins5, Timothy Y. James18,
Takashi Kamada19, Sreedhar Kilaru17 , Chinnapa Kodira8, Ursula Kues17, H. S. Kwan7, Alexandre
Lomsadze9, Weixi Li14, Walt W. Lilly15, Li-Jun Ma8, Aaron J. Mackey20 , Gerard Manning21,
Francis Martin22, Hajime Muraguchi23, Heather Palmerini10, Marilee A. Ramesh24, Cathy
Rehmeyer14, Narmada Shenoy8, Mario Stanke25, Vardges Ter-Hovhannisyan26, Anders Tunlid6,
Rajesh Velagapudi4,17, Todd J. Vision5, Qiandong Zeng8, Miriam E. Zolan10, and Patricia J.
Pukkila5*
1
Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521 USA
2
Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 USA
3
University Program in Genetics and Genomics, Duke University, Durham, NC 27710 USA
4
Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710 USA
5
Department of Biology, University of North Carolina at Chapel Hill, NC 27599 USA
6
Department of Microbial Ecology, Lund University, S-223 62, Lund, Sweden
7
Department of Biology, The Chinese University of Hong Kong, Hong Kong, China
8
Broad Institute of Harvard and MIT, Cambridge MA 02142 USA
9
Wallace H Coulter Department of Biomedical Engineering, Division of Computational Science and Engineering, Georgia
Institute of Technology, Atlanta, GA 30332 USA
10
Department of Biology, Indiana University, Bloomington, IN 47405-3700 USA
11
Department of Plant Sciences, University of Oxford, Oxford OX1 3RB UK
12
Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708 USA
13
Center for Bioinformatics, University of North Carolina at Chapel Hill, Chapel Hill NC 27599 USA
14
Department of Plant Pathology, University of Kentucky, Lexington, KY 40546 USA
15
Department of Biology, Southeast Missouri State University, Cape Girardeau, MO 63701 USA
16
Centre for Genomic Regulation, 08003 Barcelona, Spain
17
Institute of Forest Botany, Georg-August-Universität Goettingen, D-37077 Goettingen, Germany
18
Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109 USA
19
Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
20
Penn Genomics Institute, University of Pennsylvania, Philadelphia, PA 19104-6018 USA
21
Salk Institute for Biological Studies, La Jolla, CA 92037 USA
22
UMR1136, INRA-Nancy Universités, Interactions Arbres/Microorganismes, INRA-Nancy, 54280 Champenoux, France
23
Department of Biotechnology, Akita Prefectural University, Akita 010-0195 Japan
24
Department of Biology, Roanoke College, Salem, VA 24153 USA
25
Department of Bioinformatics, University of Göttingen, 37077 Göttingen, Germany
26
School of Biology, Georgia Institute of Technology, Atlanta, GA 30332 USA
Present address:
School of Bioscience, University of Exeter, Exeter EX4 4QD, United Kingdom
Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908 USA
Department of Medicine, University of Massachussets Medical School, Worcester, MA 01605 USA
* To whom correspondence should be addressed: jason.stajich@ucr.edu, pukkila@unc.edu
Abstract
The mushroom Coprinopsis cinerea (also known as Coprinus cinereus) is an important
experimental model for multicellular development in the fungi because it completes its life cycle
in two weeks, grows on defined media, and produces fruiting bodies which develop
synchronously in the laboratory. The 37-megabase genome of C. cinerea was sequenced and
assembled into 13 chromosomes. Comparison of the physical and genetic map reveals a sub-
telomeric localization of meiotic cross-overs. Although genes are uniformly distributed along
the chromosomes, paralogous multi-copy genes are over-represented in genomic regions with
high rates of meiotic recombination. The largest lineage-specific duplication involves an
unusual family of kinases with homologs only in other multicellular fungi. Several members of
this FunK1 kinase family are differentially regulated during sexual morphogenesis. The
genomes of C. cinerea and Laccaria bicolor, a symbiotic basidiomycete which colonizes conifer
and hardwood roots, share extensive regions of synteny, despite the fact that the L. bicolor
genome is nearly twice as large as the C. cinerea genome, and contains 15 times the number of
transposons and other repeated elements. The largest syntenic blocks occur in regions with low
meiotic recombination rates, no transposable elements, and tight gene spacing, where
orthologous single-copy genes are over-represented. These genomes will enable analyses of
rates of evolution and function of genes underlying complex developmental processes such as
tissue differentiation in the mushroom fruiting body, active spore discharge and stalk elongation
that are found only in the fungal kingdom, and other processes such as phototropism and
gravitropism that are also found in other multicellular organisms.
The mushroom Coprinus cinereus (since renamed Coprinopsis cinerea (1)) was chosen by the
Fungal Genome Initiative (2) as a key species in a cohesive genome sequencing strategy
designed to increase our understanding of the biology, evolution and biomedical implications of
the entire fungal kingdom. Studies using this convenient experimental model have provided
important insights into the regulation of multicellular development (3, 4), including the meiotic
process. Meiosis occurs with a high degree of synchrony, and meiotic mutants have been
obtained and analyzed using a variety of cytological and molecular tools. Methods for
characterization include DNA-mediated transformation (5), RNAi silencing (6), and indirect
immunofluorescence (7). Here we report the genome sequence, assembly into 13 chromosomes,
and high-resolution genetic map of C. cinerea. We have analyzed the implications of the
distinctive sub-telomeric sites of crossing-over in C. cinerea, and the non-uniform distribution
of orthologous genes, parologous genes, and transposable elements along the chromosomes.
We have also examined patterns of gene expression that underlie dikaryon formation, a central
feature of basidiomycete life history (8). Finally, we have asked if key genomic features of C.
cinerea have persisted over evolutionary time by examining the basidiomycete Laccaria bicolor,
since these species last shared a common ancestor nearly 200 Myr ago.
We have assembled 36 Mb of genomic sequence into 13 chromosomes (AACS02000000)
[supporting online material (SOM) text S1 and S2 and tables S1 and S2] consistent with
cytological (9) and genetic (10) evidence. Cytological evidence has also indicated that meiotic
exchanges are highly enriched in subtelomeric regions of the 13 chromosomes in C. cinerea (9),
suggesting that recombination rates might be non-uniform across the genome. To examine
crossover distribution, we used 133 simple sequence repeat (SSR) markers evenly distributed
across the genome and 4 additional markers to construct a genetic map (Fig. 1 and SOM text S7,
fig. S1 and table S6). The markers revealed regions of average, high, and low recombination.
The total genetic map length of the 31 Mb that could be mapped is 948 cM, indicating an
average frequency of exchange of 33 kb/cM. However, 8% of the genome, the “hot” regions,
exhibits an elevated rate of recombination (6 kb/cM) while 44% of the genome, the “cold”
regions, exhibits very little recombination (198 kb/cM).
The hot regions exhibit a strong tendency to be located in subtelomeric regions (16/18
are within the 15% of the nearest telomere, Fisher’s Exact Test p=0.0002) (SOM fig. S1). Many
organisms exhibit an elevated rate of recombination in subtelomeric regions (11-13), which may
reflect associations between the initiation of chromosome synapsis at subterminal regions and
chiasma (cross-over) formation in these species (reviewed in (14, 15)).
The extensive cold regions occupy internal chromosome locations. They contain the
presumed centromere-associated transposon clusters (SOM text S3 and tables S3a and S3b).
However, with the exception of these clusters, the cold regions were deficient in
retrotransposon-related sequences. They contain only 3 of the 44 full-length retrotransposons
(2= 23.7, p 15 anchors are indicated in dark green). Vertical scales are defined for each
bar in the bar title. Horizontal scale is Mb.
Fig. 2. Photograph and micrographs of C. cinerea. (A) Mature C. cinerea fruiting body that is
shedding spores. (B) Simple septum between two cells in a monokaryotic hypha . (C )“False
clamp” between two cells in an “Aon” hypha. (D) True clamp connection between two cells in a
dikaryotic hypha (“Aon Bon”). Magnification in B-D is the same.