PHYLOGENOMICS AND SECONDARY PLASTIDS:ALOOKBACKANDALOOKAHEAD
Edward L. Braun
Department of Zoology, University of Florida, Gainesville, Florida 32611, USA
and Naomi Phillips
Biology Department, Arcadia University, 450 S. Easton Rd., Glenside, Pennsylvania 19038, USA
Despite their importance to evolution, ecology,
and cell biology, eukaryotes that acquired plastids
through secondary endosymbiosis remain poorly
studied from a genomic standpoint. Chromalveolata,
a eukaryotic supergroup proposed to have des-
acquired a red algal plastid by secondary endosymbi-
osis, includes four major lineages (alveolates, cryp-
cellular organization, and the available data suggest
that they exhibit equal diversity in their genome
organization. One of the most obvious differences
in cellular organization is the retention of a highly
reduced red algal nucleus in cryptophytes (also
known as cryptomonads), but there are other major
differences among chromalveolate lineages, includ-
ing the loss of photosynthesis in multiple lineages.
Although the hypothesis of chromalveolate mono-
phyly is appealing, there is limited support for the
hypothesis from nuclear genes, and questions have
even been raised about the monophyly of chromal-
veolate plastids. Evidence for the chromalveolate
hypothesis from large-scale nuclear data sets is
reviewed, and alternative hypotheses are described.
The potential for integrating information from
chromalveolate genomics into functional genomics
is described, emphasizing both the methodological
challenges and the opportunities for future phyloge-
nomic analyses of these groups.
Key index words:
alveolates; chromists; crypto-
phytes; haptophytes; heterokonts; phylogenomics
EST, expressed sequence tag
Chromalveolata is a proposed eukaryote super-
group that has emerged in recent large-scale molec-
ular phylogenies (e.g., Delsuc et al. 2005). Although
Chromalveolata has been included in only one for-
mal taxonomy (see Parfrey et al. 2006), the group
was proposed to provide a very plausible and parsi-
monious explanation for the presence of plastids in
both chromists and alveolates (Cavalier-Smith 1999).
Thus, the de±nition of the chromists and alveolates
and the origin of plastids in these groups are closely
linked to the de±nition of the supergroup.
Chromalveolate plastids are proposed to have an
origin that is distinct from the plastids in the Plan-
tae (also called Archaeplastida, see Parfrey et al.
2006). Plastids in the Plantae arose directly from a
cyanobacterial ancestor by endosymbiosis (primary),
while the plastids in chromalveolates arose by a sec-
ondary endosymbiotic event of a red algal ancestor.
Chromalveolate plastids have the same cyanobacteri-