biota). Whichever view is taken, it is important that
these groups continue to be considered anintegral part
of mycologyand not be excluded or marginalized
because of their different evolutionary origins.
Osmotrophic stramenopiles play important
roles in nutrient cycling in both marine
(Bongiorni 2012 ; Hulvey et al. 2010 ;
Raghukumar2002a,b) and freshwater (Dick
1976 , 2001a) ecosystems. Many are also
parasites, with the potential to wreak
devastation at both the species and ecosystem
levels. For example, Labyrinthulids are
responsible for coastal sea grass bed dieback
(Muehlstein and Porter 1991 ) as well as an
emerging dieback disease of overirrigated
(highly salinic) turf grasses (Olsen 2007 ).
Thraustochytrids can cause serious economic
losses to commercially reared shellfish such as
clam (Azevedo and Corral 1997 ) and abalone
(Bower 1987 ). On the positive side there is
increasing interest in exploiting marine
thraustochytrids as an alternative to fish as a
source of polyunsaturated fatty acids such as
docasahexaenoic acid, which are important die-
tary supplements for both animals (Miller et al.
2007 ) and humans (Domergue et al. 2005 ;
Kobayashi et al. 2011 ; Raghukumar 2008 ).
Oomycetes are responsible for a number of
potentially species-threatening diseases in
freshwater ecosystems, such as the crayfish
plague caused by Aphanomyces astaci
(Cerenius et al. 1988 ) and the salmon disease
(ulcerative dermal necrosis) caused bySapro-
legnia parasitica(Phillips et al. 2008 ; van West
2006 ). In addition to being one of the earliest
documented diseases of cultivated plants,
potato blightcaused byPhytophthora infestans
remains a major threat to potato production
worldwide today (Haas et al. 2009 ).
Phytophthora cinnamomihas been responsible
for the widespreaddiebackof native forest in
Australia and New Zealand (Hardham 2005 ;
Newhook and Podger 1972 ), and over the past
decade there have been a number of new and
emerging Phytophthora diseases caused by
species such asPh. ramorumandPh. kernoviae,
which threaten both native and exotic tree
species in North America (Davidson et al.
2003 ; Martin and Tooley 2008 ) and Europe
(Brasier and Weber 2010 ).
The downy mildew Hyaloperonospora
arabidopsidis and white blister rust Albugo
laibachiiboth infect the model plantArabidop-
sis and have provided excellent systems in
which to explorehost–pathogen interactions
at the molecular level (Kemen and Jones
2012 ; Thines et al. 2009a). Much recent
effort has been directed at unravelling
themolecular basis of pathogenicityin eco-
nomically important plant pathogenic oomyce-
tes [see reviews by Jiang and Tyler ( 2012 )
and Thines and Kamoun ( 2010 )].
However, compared with true Fungi, genetic
manipulation of stramenopiles has generally
proven difficult and frustrating. With a few
exceptions, such as Phytophthora capsici,it
has been difficult to develop routine, stable
transformation systems for oomycetes—or,
for that matter, any other stramenopile
(Judelson and Ah-Fong 2009 ). In general, gene-
silencing techniques often have been the only
tool available to explore gene functions (Whis-
son et al. 2009 ). Representatives of the phyto-
pathogenic generaAlbugo(Kemen et al. 2011 ;
Links et al. 2011 ), Hyaloperonospora (Baxter
et al. 2010 ), severalPhytophthora species(e.g.
Haas et al. 2009 ; Tyler et al. 2006 ),Pseudopero-
nospora(Tian et al. 2011 )andPythium ultimum
(Le ́vesque et al. 2010 ), and the fish pathogen
Saprolegnia parasitica(Jiang et al. 2013 )have
had their full or partial genome sequences
released. These add to genome sequences
from other stramenopiles, including the human
gut parasiteBlastocystis(Denoeud et al. 2011 ),
the ochrophytesAureococcus(Gobler et al. 2011 )
and Ectocarpus (Cock et al. 2010 ), and the
diatoms Pheodactylum (Bowler et al. 2008 )
andThallassiosira(Armbrust et al. 2004 )that
have been published to date. Preliminary
genome sequences for several members of the
Labyrinthulomycota also have recently been
released (Collier 2012 ). Comparative genomics
promises to unlock many interesting secrets
about these organisms (Lamour et al. 2007 ;
Martens et al. 2008 ; Seidl et al. 2012 ). One
surprising discovery seems to be the extent to
which the genomes of oomycetes contain
genes derived from other prokaryotes and
eukaryotes, providing evidence of horizontal
gene transfer from bacteria, true fungi, and red40 G.W. Beakes et al.