that the convergence of structure in savanna conceals substantial differences in the relationships
between savanna woody vegetation, climate, and
fire. Just as the regional evolutionary and environmental histories underpin differences in these
relationships, these same differences will determine the contemporary vegetation response of
each region to future climates.
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Acknowledgments: C.L. conceived the project and led the
writing; C.L., T.M.A., M.S., S.I.H., W.A.H., N.H., J.F., G.D., and
S.A. compiled the data; and C.L., T.M.A., M.S., and S.I.H.
analyzed the data. All authors provided new data and
contributed to the writing and/or intellectual development of
the manuscript. M. Crisp, B. Medlyn, and R. Gallagher
provided manuscript feedback. Data used in this study are
available in the supplementary materials and at http://modis.
gsfc.nasa.gov/, http://www.worldclim.org/, and www.fao.org/nr/
Materials and Methods
Figs. S1 to S4
Tables S1 to S5
Data Sets S1 and S2
18 October 2013; accepted 18 December 2013
Effector Specialization in a Lineage of
the Irish Potato Famine Pathogen
Suomeng Dong,1 Remco Stam,1 Liliana M. Cano,1 Jing Song,2† Jan Sklenar,1
Kentaro Yoshida,1 Tolga O. Bozkurt,1 Ricardo Oliva,1‡ Zhenyu Liu,2
Miaoying Tian,2§ Joe Win,1 Mark J. Banfield,3 Alexandra M. E. Jones,1||
Renier A. L. van der Hoorn,4,5 Sophien Kamoun1¶
Accelerated gene evolution is a hallmark of pathogen adaptation following a host jump. Here,
we describe the biochemical basis of adaptation and specialization of a plant pathogen effector
after its colonization of a new host. Orthologous protease inhibitor effectors from the Irish potato
famine pathogen, Phytophthora infestans, and its sister species, Phytophthora mirabilis, which
is responsible for infection of Mirabilis jalapa, are adapted to protease targets unique to their
respective host plants. Amino acid polymorphisms in both the inhibitors and their target proteases
underpin this biochemical specialization. Our results link effector specialization to diversification
and speciation of this plant pathogen.
The potato blight pathogen, Phytophthora infestans, is a recurring threat to world ag- riculture and food security. This funguslike
oomycete traces its origins to Toluca Valley,
Mexico, where it naturally infects wild Solanum
plants (1). In central Mexico, P. infestans co-occurs with closely related species in a tight
phylogenetic clade known as clade 1c. These
species evolved through host jumps followed by
adaptive specialization on plants belonging to
different botanical families (2, 3) (fig. S1). One
species, Phytophthora mirabilis, is a pathogen
of four-o’clock (Mirabilis jalapa). It split from
P. infestans about 1300 years ago (1), and the two
species have since specialized on their Solanum
and Mirabilis hosts. Adaptive evolution after
the host jump has left marks on the genomes
of P. infestans and P. mirabilis (3). Comparative
genomics analyses revealed signatures of accel-
erated evolution, structural polymorphisms, and
positive selection in genes occurring in repeat-
rich genome compartments (3). In total, 345 genes
induced within plants show signatures of posi-
tive selection between the two sister species (3).
These include 82 disease effector genes, rapidly
evolving determinants of virulence that act on
host target molecules. We lack a molecular framework to explain how plant pathogen effectors
adapt and specialize on new hosts, even though
this process affects pathogen evolution and
To gain insight into the molecular patterns
of host adaptation after host jumps, we selected
the cystatinlike protease inhibitor EPIC1, an effector protein of P. infestans that targets extracellular (apoplastic) defense proteases of the
Solanum hosts (7, 8). The epiC1 gene and its
paralogs epiC2A and epiC2B evolved relative-
ly recently in the P. infestans lineage, most likely
as a duplication of the conserved Phytophthora
gene epiC3 (7) (Fig. 1). To reconstruct the evo-
lution of these effectors in the clade 1c species,
we aligned the epiC gene cluster sequences, per-
formed phylogenetic analyses, and calculated var-
iation in selective pressure across the phylogeny
(Fig. 1, fig. S2, and table S1) (9). We detected a
signature of positive selection in the branch of
PmepiC1, the P. mirabilis ortholog of P. infestans
epiC1 [nonsynonymous to synonymous ratio
(w) = 2.52] (Fig. 1B). This is consistent with our
hypothesis that PmEPIC1 evolved to adapt to a
M. jalapa protease after P. mirabilis diverged from
To test our hypothesis, we first determined
the inhibition spectra of the EPIC effectors using
DCG-04 protease profiling, a method based on
the use of a biotinylated, irreversible protease
inhibitor that reacts with the active site cysteine
of papainlike proteases in an activity-dependent
1The Sainsbury Laboratory, Norwich Research Park, Norwich
NR4 7UH, UK. 2Department of Plant Pathology, Ohio Agricultural Research and Development Center, The Ohio State
University, Wooster, OH 44691, USA. 3Department of Biological Chemistry, John Innes Centre, Norwich Research Park,
Norwich NR4 7UH, UK. 4The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, Oxford OX1
3RB, UK. 5Plant Chemetics Laboratory, Max Planck Institute for
Plant Breeding Research, 50829 Cologne, Germany.
*Present address: Division of Plant Sciences, University of
Dundee, Invergowrie, Dundee DD2 5DA, UK.
†Present address: Center for Proteomics and Bioinformatics,
School of Medicine, Case Western Reserve University, Cleveland,
OH 44106 USA.
‡Present address: Plant Breeding, Genetics, and Biotechnology,
International Rice Research Institute (IRRI), Los Baños, Laguna,
§Present address: Department of Plant and Environmental
Protection Sciences, University of Hawaii, Honolulu, HI 96822,
||Present address: School of Life Sciences, Gibbet Hill Campus,
The University of Warwick, Coventry, CV4 7AL, UK.
¶Corresponding author. E-mail: email@example.com