The article by Martin et al.
] uses chloroplast genomics to infer plastid phylogeny, as well as gene loss and gene transfer, for 16 sequenced plastid genomes. An important conclusion from this analysis is that two secondary endosymbiotic events involving a red alga are needed to explain the occurrence of plastids in cryptophytes (algae with phycobilin pigments in the thylakoid lumen rather than in particles on the thylakoid membrane as in cyanobacterial and red algae; an example is Guillardia
) and heterokonts (the diatom Odontella
). This contrasts with the arguments of Cavalier-Smith (recently set out in [12
]) for a single endosymbiotic event, based on evidence such as the replacement of the glyceraldehyde-3-phosphate dehydrogenase gene derived from the red algal plastid with one of host origin in both cases.
Another recent article [13
] deals with genome-based phylogenies of plastids; 19 complete chloroplast genomes are studied using a new computational method, and broadly similar conclusions are reached to those of Martin and co-workers [6
]. This work also allows novel functional assignments to a number of chloroplast open reading frames. The functional implications of chloroplast genomics, with special reference to experimental opportunities and 'directional genetics' in Arabidopsis thaliana
, have recently been reviewed by Leister [14
An important question relating to the evolution of plastid genomes in higher plants is the timing of the changes in the plastid genome in the streptophyte clade (made up of charophytes, a group of green algae or chlorophytes, plus embryophytes, or higher plants), which evolved more than 500 million years ago. From the unicellular flagellate Mesostigma
, which is either a basal chlorophyte or lies at the split between Chlorophyta and Streptophyta, to the embryophytes, of which the liverwort Marchantia
is the most basal to have been sequenced, the changes are gene losses, including transfer to the nucleus, scrambling of gene order, and intron insertion [15
An important contribution to bridging the evolutionary gap between Mesostigma
is the work of Turmel et al.
] on a member of the charophytes sensu stricto
(that is, excluding Mesostigma
) Chaetosphaeridium globosum
. Before the work of Turmel et al.
] only fragmentary data addressed the issue of gene content and organization of the eight charophytes sensu stricto
. The complete plastid genome sequence of Chaetosphaeridium globosum
] shows that most of the embryophyte characteristics were present in the charophyte alga, so that the major changes had occurred between the branch to Mesostigma
and that to Chaetosphaeridium.
The common features shared by the plastid DNA of Chaetosphaeridium
and of embryophytes include the gene content, the intron composition, and the gene order. Thus, the Chaetosphaeridium
chloroplast genome has 124 genes (compared to 136 in Mesostigma
and 110-120 in embryophytes), one Group I intron (there are none in Mesostigma
and one in embryophytes), 16 cis
-spliced Group II introns (none in Mesostigma
and 18-19 in embryophytes) and one trans
-spliced Group II intron (none in Mesostigma
, one in embryophytes). Genome size (118-155 kilobases) is relatively constant among Mesostigma, Chaetosphaeridium
and higher plant plastids. By contrast, the mitochondrial genome of Chaetosphaeridium
is closely similar to that of Mesostigma
in terms of size (57 kb and 42 kb, respectively), gene content and, perhaps, intron content. Chaetosphaeridium
has a much smaller genome size than the obese mitochondrial genomes of Marchantia
(187 kb) or Arabidopsis
(367 kb), and many more cis
-spliced Group II introns (18-25 rather than two). The apparently different tempo of evolution in mitochondria and plastids of the charophytes deserves further investigation. An important point about the functional genomics of the plastid is the determinant of which genes essential for plastid function are retained in the plastid genome. Higher plant plastid genomes have slightly fewer genes than in the plastids of the charophytes sensu lato
(that is, the charophytes sensu stricto