6 Genomics of Marine Algae
183
secondary plastids, except in euglenids and most dinoflagellates, which appear
to have lost one of these membranes. The presence of these additional membranes makes transporting proteins into the plastid very complicated, and organisms
whose plastids are derived from a secondary endosymbioses possess complex transport systems that recognise proteins with bipartite target peptides (Lang et al.
1998).
As if the story of secondary endosymbiosis were not sufficiently complicated,
some dinoflagellates appear to have undergone even more complex events involving either serial secondary endosymbiosis, in which the red-alga-derived plastid
was replaced with a green-alga-derived plastid, or they have been involved in tertiary endosymbioses, capturing a secondary endosymbiotic haptophyte, cryptophyte
or heterokont alga (Keeling 2004). The chlorarachniophytes and euglenophytes
obtained their plastids in independent secondary endosymbiotic events involving
the capture of green algae (Fig. 6.1).
Horizontal (or lateral) gene transfer is a process in which genes from one organism are integrated into the genome of a second organism (which may be very
distantly related to the first) and subsequently inherited with the rest of the genetic
material of the cell (Keeling and Palmer 2008). The gene transfers associated
with endosymbiotic events are spectacular examples of horizontal gene transfer
because of the large numbers of genes that are transferred from the endosymbiont
to the host nucleus. However, they are not the only horizontal gene transfers that
occur in eukaryotes and it has become increasingly clear in recent years that many
eukaryotes, particularly protists, acquire genes from the organisms with which they
interact at a significant rate (e.g. Nosenko and Bhattacharya 2007, Bowler et al.
2008).
In the last few years genomic data has had a significant impact on our understanding of the evolution of the eukaryotes and the role that endosymbiosis has
played in this process. The availability of extensive sequence data for many key
organisms in the eukaryotic tree has allowed the selection of the most relevant gene
sequences for phylogenetic analyses and their combination in multigene sets, significantly improving the resolution of these analyses. Genome data also provides
detailed information about the process of endosymbiosis, providing information
about the partners involved in a particular endosymbiotic event and also about the
process of enslavement, particularly the transfer of endosymbiont genes to the host
nucleus. Some of the key genome projects in this domain are listed in Table 6.1 and
described below.
6.4 Algae and Marine Ecosystems
The following sections will look at how genomic approaches are being used to
explore the biology of algae, particularly with regard to their functions in a broad
range of marine ecosystems.
183
secondary plastids, except in euglenids and most dinoflagellates, which appear
to have lost one of these membranes. The presence of these additional membranes makes transporting proteins into the plastid very complicated, and organisms
whose plastids are derived from a secondary endosymbioses possess complex transport systems that recognise proteins with bipartite target peptides (Lang et al.
1998).
As if the story of secondary endosymbiosis were not sufficiently complicated,
some dinoflagellates appear to have undergone even more complex events involving either serial secondary endosymbiosis, in which the red-alga-derived plastid
was replaced with a green-alga-derived plastid, or they have been involved in tertiary endosymbioses, capturing a secondary endosymbiotic haptophyte, cryptophyte
or heterokont alga (Keeling 2004). The chlorarachniophytes and euglenophytes
obtained their plastids in independent secondary endosymbiotic events involving
the capture of green algae (Fig. 6.1).
Horizontal (or lateral) gene transfer is a process in which genes from one organism are integrated into the genome of a second organism (which may be very
distantly related to the first) and subsequently inherited with the rest of the genetic
material of the cell (Keeling and Palmer 2008). The gene transfers associated
with endosymbiotic events are spectacular examples of horizontal gene transfer
because of the large numbers of genes that are transferred from the endosymbiont
to the host nucleus. However, they are not the only horizontal gene transfers that
occur in eukaryotes and it has become increasingly clear in recent years that many
eukaryotes, particularly protists, acquire genes from the organisms with which they
interact at a significant rate (e.g. Nosenko and Bhattacharya 2007, Bowler et al.
2008).
In the last few years genomic data has had a significant impact on our understanding of the evolution of the eukaryotes and the role that endosymbiosis has
played in this process. The availability of extensive sequence data for many key
organisms in the eukaryotic tree has allowed the selection of the most relevant gene
sequences for phylogenetic analyses and their combination in multigene sets, significantly improving the resolution of these analyses. Genome data also provides
detailed information about the process of endosymbiosis, providing information
about the partners involved in a particular endosymbiotic event and also about the
process of enslavement, particularly the transfer of endosymbiont genes to the host
nucleus. Some of the key genome projects in this domain are listed in Table 6.1 and
described below.
6.4 Algae and Marine Ecosystems
The following sections will look at how genomic approaches are being used to
explore the biology of algae, particularly with regard to their functions in a broad
range of marine ecosystems.