We used a maskless photolithography method to produce DNA oligonucleotide microarrays with unique probe sequences tiled throughout the genome of Drosophila melanogaster and across predicted splice junctions. RNA expression of protein coding and nonprotein coding sequences was determined for each major stage of the life cycle, including adult males and females. We detected transcriptional activity for 93% of annotated genes and RNA expression for 41% of the probes in intronic and intergenic sequences. Comparison to genome-wide RNA interference data and to gene annotations revealed distinguishable levels of expression for different classes of genes and higher levels of expression for genes with essential cellular functions. Differential splicing was observed in about 40% of predicted genes, and 5440 previously unknown splice forms were detected. Genes within conserved regions of synteny with D. pseudoobscura had highly correlated expression; these regions ranged in length from 10 to 900 kilobase pairs. The expressed intergenic and intronic sequences are more likely to be evolutionarily conserved than nonexpressed ones, and about 15% of them appear to be developmentally regulated. Our results provide a draft expression map for the entire nonrepetitive genome, which reveals a much more extensive and diverse set of expressed sequences than was previously predicted.

Legumes form endosymbiotic associations with nitrogenfixing bacteria and arbuscular mycorrhizal (AM) fungi which facilitate nutrient uptake. Both symbiotic interactions require a molecular signal exchange between the plant and the symbiont, and this involves a conserved symbiosis (Sym) signaling pathway. In order to identify plant genes required for intracellular accommodation of nitrogen-fixing bacteria and AM fungi, we characterized Medicago truncatula symbiotic mutants defective for rhizobial infection of nodule cells and colonization of root cells by AM hyphae. Here, we describe mutants impaired in the interacting protein of DMI3 (IPD3) gene, which has been identified earlier as an interacting partner of the calcium/ calmodulin-dependent protein, a member of the Sym pathway. The ipd3 mutants are impaired in both rhizobial and mycorrhizal colonization and we show that IPD3 is necessary for appropriate Nod-factor-induced gene expression. This indicates that IPD3 is a member of the common Sym pathway. We observed differences in the severity of ipd3 mutants that appear to be the result of the genetic background. This supports the hypothesis that IPD3 function is partially redundant and, thus, additional genetic components must exist that have analogous functions to IPD3. This explains why mutations in an essential component of the Sym pathway have defects at late stages of the symbiotic interactions.Legumes form nitrogen-fixing symbioses with soil bacteria collectively called rhizobia and, like most plant species, they also establish interactions with arbuscular mycorrhizal (AM) fungi. Both symbioses facilitate the uptake of mineral nutrients. Host plants and their symbionts form specialized structures during these interactions: rhizobia induce the development of root nodules on the host plant wherein the reduction of atmospheric nitrogen takes place, while AM fungal hyphae form a densely ramified structure in the inner cortical cells of the root where the transfer of nutrients occurs.The exchange of diffusible signaling molecules between symbionts and host plant takes place prior to physical contact. The flavonoid and isoflavonoid contents of root exudates activate rhizobia to produce nodulation (Nod) factors (NF), which induce the host plant to initiate nodulation ( Both rhizobia and mycorrhizal fungi exist as intracellular symbionts, which requires the coordinated development of both partners to allow invasion and appropriate differentiation (Jones et al. 2007;Oldroyd and Downie 2008;Parniske 2008). The best-characterized rhizobial infection strategy occurs via root hairs. Rhizobia become trapped in root hair curls and induce invaginations from these curled root hairs, forming tubular structures called infection threads (IT). The IT grows toward the newly divided cells of the developing nodule primordial, wherein the bacteria are released and colonize the host cells through endocytosis. The bacteria become enveloped with a plant-derived peribacteroid membrane, forming a cytoplasmic structure referred to as th...

BackgroundThe formation of functional symbiotic nodules is the result of a coordinated developmental program between legumes and rhizobial bacteria. Genetic analyses in legumes have been used to dissect the signaling processes required for establishing the legume-rhizobial endosymbiotic association. Compared to the early events of the symbiotic interaction, less attention has been paid to plant loci required for rhizobial colonization and the functioning of the nodule. Here we describe the identification and characterization of a number of new genetic loci in Medicago truncatula that are required for the development of effective nitrogen fixing nodules.ResultsApproximately 38,000 EMS and fast neutron mutagenized Medicago truncatula seedlings were screened for defects in symbiotic nitrogen fixation. Mutant plants impaired in nodule development and efficient nitrogen fixation were selected for further genetic and phenotypic analysis. Nine mutants completely lacking in nodule formation (Nod-) represented six complementation groups of which two novel loci have been identified. Eight mutants with ineffective nodules (Fix-) represented seven complementation groups, out of which five were new monogenic loci. The Fix- M. truncatula mutants showed symptoms of nitrogen deficiency and developed small white nodules. Microscopic analysis of Fix- nodules revealed that the mutants have defects in the release of rhizobia from infection threads, differentiation of rhizobia and maintenance of persistence of bacteria in nodule cells. Additionally, we monitored the transcriptional activity of symbiosis specific genes to define what transcriptional stage of the symbiotic process is blocked in each of the Fix- mutants. Based on the phenotypic and gene expression analysis a functional hierarchy of the FIX genes is proposed.ConclusionsThe new symbiotic loci of M. truncatula isolated in this study provide the foundation for further characterization of the mechanisms underpinning nodulation, in particular the later stages associated with bacterial release and nodule function.

A collection of 66 commercial apple (Malus ×domestica Borkh.) cultivars was screened with six previously described SSR (Simple Sequence Repeat) markers for molecular identification. In total, 55 polymorphic alleles were detected at the 6 SSR loci (average 9.2 alleles per locus) and the polymorphism information content (PIC) averaged 0.72. Successful differentiation of all apple genotypes except for somatic mutants was accomplished by using only four (CH03g07, CH04e03, CH05d11, and CH05e03) SSR markers. Sport mutants proved to be indistinguishable from each other and their progenitors. The cumulative probability of obtaining an identical SSR profile for two randomly chosen apple genotypes was 1.79 × 10–4, which confirms the high potential of simple sequence repeats (SSRs) for cultivar identification.

This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Detecting transcription with tiling arrays

A new method for designing and integrating genomic tiling array data is described and applied to Anopheles and human arrays.