Genome complexity in a lean, mean photosynthetic machine.

P hotosynthetic organisms come in all shapes and sizes. From a human perspective, the trees and plants of dry land are the most conspicuous examples, but the next time you admire a colorful tulip or marvel at the girth of a giant Sequoia, consider the following: Approximately half of the oxygen we breathe is generated by singlecelled photosynthesizers, phytoplankton, adrift in the world’s oceans, invisible to the naked eye and unfathomably large in number, quietly harnessing solar energy, fixing carbon dioxide, and producing oxygen by the bucket-load. In this issue of PNAS, Derelle et al. (1) present the complete genome sequence of the smallest of the small eukaryotic (nucleus-containing) phytoplankton, Ostreococcus tauri. This organism is best known for its diminutive cell size, about that of a typical bacterium. Its genome is equally remarkable for its small size and extreme compactness. However, the O. tauri genome is also unexpectedly complex and provides a fascinating glimpse into the genetic makeup and metabolic potential of the smallest known eukaryote at the base of the marine food chain. Oxygenic photosynthesis first evolved in the ancestors of modern-day cyanobacteria. In terms of sheer numbers, these organisms dominate the ocean (2), but from the perspective of primary productivity, eukaryotic algae are considered more significant. Marine diatoms, for example, produce up to 40% of the organic carbon generated in the ocean each year (3) and represent just one of the abundant and well studied algal lineages in the sea. Least understood of all eukaryotic phytoplankton are those with a diameter of !2–3 !m, the so-called ‘‘picoeukaryotes.’’ The first descriptions of bacterial-sized eukaryotes date back more than 40 years (e.g., ref. 4), but it is only with the application of flow cytometry (2) and molecular approaches (5) to the study of marine microbes that we have begun to grasp the extent of their abundance and diversity. O. tauri is perhaps the most famous of all picoeukaryotes and, together with its close relatives, has become the focus of concerted efforts to understand the global distribution and ecological significance of eukaryotic picoplankton (e.g., refs. 6–8). O. tauri was first discovered in 1994 in France’s Thau lagoon, a shallow offshoot of the Mediterranean Sea known for its oyster farming. Barely 1 !m in diameter and practically invisible under the light microscope, O. tauri was detected by flow cytometry and hailed as the ‘‘smallest eukaryotic organism’’ (9). It also proved to be shockingly simple in its ultrastructure: O. tauri cells lack flagella and a cell wall and contain one mitochondrion, one chloroplast, a single Golgi apparatus, and a nucleus containing a single nuclear pore (Fig. 1) (10). Molecular data (11, 12) indicate that O. tauri belongs to a group of green algae called prasinophytes, a lineage thought to be of key importance in elucidating the earliest events in the evolution of chlorophyll b-containing organisms. O. tauri appears to be ubiquitous in coastal waters and in the open ocean (e.g., refs. 6, 8, and 12), and its minimal cell structure and high growth rate have made it a promising model picoeukaryote. Preliminary molecular investigations pegged the O. tauri genome at well under 15 megabase pairs (Mbp) (11), and, like most model organisms these days, O. tauri quickly became the focus of a genome project (13). The complete genome sequence presented by Derelle et al. (1) weighs in at 12.56 Mbp, making it among the smallest, although not the smallest, nuclear genome of a freeliving eukaryote characterized thus far [that honor belongs to the 9.2-Mbp genome of the fungus Ashbya gossypii (14)]. The O. tauri genome is composed of 20 linear chromosomes between 1.07 and 0.16 Mbp (1) and, given its small size, is remarkable in the number of genes it encodes: 8,166 protein-coding genes are predicted (6,265 by similarity to known genes), far more than in the "16-Mbp genome of the red alga Cyanidioschyzon merolae (5,331 genes) (15) or in the "12-Mbp genome of the laboratory yeast Saccharomyces cerevisiae (6,563 genes) (16). With a mean intergenic distance of only 197 bp, an average intron size of 103 bp, and multiple gene fusions, the O. tauri genome appears to be the product of intense genome compaction. One wonders to what extent the complexities of transcription initiation and termination have been affected. In terms of structure, the most unusual feature of the O. tauri genome is its heterogeneity. The genome as a whole has a G#C content of "58%, but chromosome 19 and approximately half of chromosome 2 differ significantly from this average (54% and 52% G#C, respectively) and contain 77% of the 417 transposable elements encoded in the genome (1). Genes encoded in the low G#C portion of chromosome 2 also exhibit a different codon usage pattern than genes elsewhere in the genome, and they possess smaller and more compositionally biased introns. From a phylogenetic perspective, 43% of the genes on chromosome 2 are most similar to green algal homologs, which is a similar proportion to that seen for the other chromosomes (excluding chromosome 19). Therefore, despite its anomalous composition and structure, there is no evidence that the low G#C region of chromosome 2 is of exogenous origin. Derelle et al. (1) raise the possibility that it is a sex chromosome, citing the