established whether these are the result of sexual
reproduction (Karling 1981 ; Porter 1990 ).
Labyrinthulomycete thalli have a cell coat
made up ofscales(Fig.3.3b), composed either
offucoseorgalactosederivates (Honda et al.
1999 ; Moss 1985 , 1986 ), that, when compacted,
form a wall around the thallus body but not the
tracks or rhizoids (Fig.3.3a–c). Scales also coat
thraustochytrid, but not labyrinthulid, zoos-
pores (Porter 1990 ).
The first molecular systematic studies of
labyrinthulids were based on SSU rRNA gene-
sequence comparisons (Honda et al. 1999 ;
Leander and Porter 2001 ; Leander et al. 2004 ).
The former reported that their isolates fell into
two major clades, which they described as the
thraustochytrid phylogenetic group(TPG) and
thelabyrinthulid phylogenetic group (LPG).
The TPG clade contained genera such as
Schizochytrium,Ulkenia, and manyThrausto-
chytriumspp. (Honda et al. 1999 ). The labyr-
inthulids were part of a more diverse
monophyletic assemblage and included a
number of species traditionally placed in the
Thraustochytriaceae. The LPG clade included
Labyrinthula and Aplanochytrium (Labyr-
inthuloides) in one subclade andSchizochy-
trium minutum and Thraustochytrium
multirudientale in another (Honda et al.
1999 ). Genera in theLPG cladegenerally had
fucosederivates as their major cell wall consti-
tuents, whilst those in the TPG clade had
galactosederivates (Honda et al. 1999 ). In a
concurrent study, Leander and Porter ( 2001 )
recognized three major labyrinthulomycete
clades (Fig.3.2). One clade included two spe-
cies,Labyrinthuloides yorkensisandL. minuta,
which were subsequently transferred to genus
Aplanochytrium, which was subsequently given
family-level status, the Aplanochytriacaeae
(Leander et al. 2004 ) as sister to the Labyrinthu-
laceae (Table3.1). Most of the thraustochytrids
clustered in a third clade (the thraustochytrid
clade), together with the enigmatic,
bothrosome-lacking, planktonic protist
Diplophrys marina [recently transferred by
Anderson and Cavalier-Smith ( 2012 )toAmphi-
fila] (Fig.3.1b, Table3.1) and two isolates of the
Mercenaria(quahog clam) pathogen (QPX iso-
lates).
Many thraustochytrid genera, such as
Schizochytrium, Thraustochytrium, and
Ulkenia, turned out to be paraphyletic (Honda
et al. 1999 ; Leander and Porter 2001 ; Leander
et al. 2004 ), which showed that traditional
morphological characters (Fig. 3.2) are not
good indicators of phylogenetic relatedness.
Subsequent studies led to a radical revision
in thraustochytrid nomenclature, with the
introduction of many new genera (Aurantio-
chytrium, Botryochytrium, Oblongichytrium,
Parietichytrium, Sicyoidochytrium) based on
combined molecular and biochemical charac-
teristics (Table 3.1) (Yokoyama and Honda
2007 ; Yokoyama et al. 2007 ). An example of a
recent phylogenetic tree of labyrinthulomycetes
based on SSU rRNA gene sequences is shown in
Fig.3.2[adapted from Yokoyama and Honda
( 2007 ) and Yokoyama et al. ( 2007 )]. The inclu-
sion of environmental sequences for unknown
picoeukaryote marine stramenopiles in phylo-
genetic SSU rRNA analyses has revealed a novel
clade that is a sister clade to all sequenced
labyrinthulomycote species (Fig.3.1b) (Moreira
and Lo ́pez-Garcia 2002 ; Yubuki et al. 2010 ).
Environmental sequencing from diverse
marine ecosystems has revealed a hitherto
unsuspected biodiversity amongst these organ-
isms (Anderson and Cavalier-Smith 2012 ;
Richards et al. 2012 ; Worden and Not 2008 ).
Recently, Anderson and Cavalier-Smith
( 2012 ) proposed a revised classification of the
group, summarized in Table3.1, although we
have given both the generally accepted
mycological and protistological forms of their
nomenclature. This scheme gives order-level
status to theThraustochytridialesandLabyr-
inthulales(Table3.1). The former order con-
tains six families, encompassing more than ten
genera, whilst the latter comprises just two
monotypic families, theLabyrinthulaceaeand
Aplanochytridiaceae(Table3.1).C. Systematics of HyphochytriomycotaTheHyphochytriomycota(Fig.3.4, Table3.2)
are characterized by their anteriorly flagellate,
mastigonate zoospores (Figs.3.4h, rand3.16d)
(Karling 1977 ; Fuller 1990 , 2001 ). Morphologi-46 G.W. Beakes et al.