Background: Important developmental processes in both plants and animals are partly regulated by genes whose expression is modulated at the post-transcriptional level by processes such as RNA interference (RNAi). Dicers, Argonautes and RNA-dependent RNA polymerases (RDR) form the core components that facilitate gene silencing and have been implicated in the initiation and maintenance of the trigger RNA molecules, central to process of RNAi. Investigations in eukaryotes have revealed that these proteins are encoded by variable number of genes with plants showing relatively higher number in each gene family. To date, no systematic expression profiling of these genes in any of the organisms has been reported.

The complete nucleotide sequence of the chloroplast genome (150,613 bp) from the unicellular green alga Chlorella vulgaris C-27 has been determined. The genome contains no large inverted repeat and has one copy of rRNA gene cluster consisting of 16S, 23S, and 5S rRNA genes. It contains 31 tRNA genes, of which the tRNA Leu (GAG) gene has not been found in land plant chloroplast DNAs analyzed so far. Sixty-nine protein genes and eight ORFs conserved with those found in land plant chloroplasts have also been found. The most striking is the existence of two adjacent genes homologous to bacterial genes involved in cell division, minD and minE, which are arranged in the same order in Escherichia coli. This finding suggests that the mechanism of chloroplast division is similar to bacterial division. Other than minD and minE homologues, genes encoding ribosomal proteins L5, L12, L19, and S9 (rpl5, rpl12, rpl19, and rps9); a chlorophyll biosynthesis Mg chelating subunit (chlI); and elongation factor EF-Tu (tufA), which have not been reported from land plant chloroplast DNAs, are present in this genome. However, many of the new chloroplast genes recently found in red and brown algae have not been found in C. vulgaris. Furthermore, this algal species possesses two long ORFs related to ycf1 and ycf2 that are exclusively found in land plants. These observations suggest that C. vulgaris is closer to land plants than to red and brown algae.Structure and expression of the chloroplast genome have been studied in a number of plants. Gene content and the sequence of many genes in chloroplast DNA are relatively conserved among land plants and the Euglenophyta Euglena gracilis (1-3). However, recent analyses of the entire chloroplast genome from nongreen algae (4, 5) and the cyanelle genome of Cyanophora paradoxa (6) have revealed that this is not always the case. For example, the chloroplast genome of the red alga Porphyra purpurea contains over 70 new genes not found in land plant and Euglena chloroplasts (4, 7). It is generally believed that land plants evolved from green algae (8) and that during this evolution, extensive rearrangements occurred within the chloroplast genomes. To understand the process of chloroplast genome evolution, information on repeated sequences, intergenic regions, and pseudogenes in chloroplast DNA is extremely helpful. Therefore, entire nucleotide sequences of green algal chloroplast genomes have been awaited.The unicellular green alga Chlorella vulgaris C-27 is the organism for which the synchronous culture was first developed (9), and this synchronous system has long been used for studies of the cell cycle from physiological and biochemical aspects (10). In addition, the Chlorella cell contains a single large chloroplast. Thus, analysis of the Chlorella chloroplast DNA provides a unique opportunity to investigate not only the evolution but also the cell cycle-dependent expression of chloroplast genes. Though interesting, information on chloroplast DNA from the genus Chlorella was fragmentary. ...