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<p>Abstract</p> <p>Background</p> <p>The Viridiplantae (land plants and green algae) consist of two monophyletic lineages, the Chlorophyta and the Streptophyta. The Streptophyta include all embryophytes and a small but diverse group of freshwater algae traditionally known as the Charophyceae (e.g. Charales, <it>Coleochaete </it>and the Zygnematales). The only flagellate currently included in the Streptophyta is <it>Mesostigma viride </it>Lauterborn. To gain insight into the genome evolution in streptophytes, we have sequenced 10,395 ESTs from <it>Mesostigma </it>representing 3,300 independent contigs and compared the ESTs of <it>Mesostigma </it>with available plant genomes (<it>Arabidopsis, Oryza</it>, <it>Chlamydomonas</it>), with ESTs from the bryophyte <it>Physcomitrella</it>, the genome of the rhodophyte <it>Cyanidioschyzon</it>, the ESTs from the rhodophyte <it>Porphyra</it>, and the genome of the diatom <it>Thalassiosira</it>.</p> <p>Results</p> <p>The number of expressed genes shared by <it>Mesostigma </it>with the embryophytes (90.3 % of the expressed genes showing similarity to known proteins) is higher than with <it>Chlamydomonas </it>(76.1 %). In general, cytosolic metabolic pathways, and proteins involved in vesicular transport, transcription, regulation, DNA-structure and replication, cell cycle control, and RNA-metabolism are more conserved between <it>Mesostigma </it>and the embryophytes than between <it>Mesostigma </it>and <it>Chlamydomonas</it>. However, plastidic and mitochondrial metabolic pathways, cytoskeletal proteins and proteins involved in protein folding are more conserved between <it>Mesostigma </it>and <it>Chlamydomonas </it>than between <it>Mesostigma </it>and the embryophytes.</p> <p>Conclusion</p> <p>Our EST-analysis of <it>Mesostigma </it>supports the notion that this organism should be a suitable unicellular model for the last flagellate common ancestor of the streptophytes. <it>Mesostigma </it>shares more genes with the embryophytes than with the chlorophyte <it>Chlamydomonas reinhardtii</it>, although both organisms are flagellate unicells. Thus, it seems likely that several major physiological changes (e.g. in the regulation of photosynthesis and photorespiration) took place early during the evolution of streptophytes, i.e. before the transition to land.</p>