The genus Oryza comprises approximately 23 species natively found tropical or subtropical habitats. One species, the Asian rice Oryza sativa, is a major food crop and source of calories for more than half of the world's population. Besides Asian rice, only one additional member of the genus, O. glaberrima, has agricultural importance, mainly in West-African countries. In contrast to its Asian relatives, O. glaberrima tolerates more severe climatic conditions including drought stress and less fertile soils. To overcome the substantially lower yields of African rice compared to Asian rice varieties, O. sativa and O. glaberrima were recently crossed to generate the NERICA (New Rice for Africa) rice lines. In this session, we introduce the O. glaberrima genome project and we will present current analysis and characteristics of this genome sequenced by next-generation sequencing technologies. Comparative studies and analysis of variants between this and other rice species, including two subspecies of O. sativa and a more distant relative, Oryza brachyantha, hold great promise to decipher and delineate accurately functional elements, gene families and selective forces in these genomes of prime importance for human nutrition.

Using publicly available gene expression data comparing different tissue types in Populus we identified genes that are informative in the discrimination of leaf and non-leaf tissues. Topological Overlap Matrix analysis was used to identify transcriptional modules within this set of genes within a set of microarray data collected from leaves sampled under a diverse range of developmental stages, biotic, abiotic and transgenic experiments. Expression of the transcriptional modules was examined in more detail within a subset of the dataset to select genes that were particularly active during the early stages of leaf development. We then examined the co-location of these genes to published Quantitative Trait Loci for leaf phenotypic traits and examined the conservation of expression of genes within the modules.

To extend the approach, we developed a systems biology model of the regulatory network within the same dataset. The network was reverse-engineered from promoter information and expression profiles with the model incorporating interactions between regulators by evaluating increasingly more complex regulatory mechanisms allowing identification of new regulators of leaf development not found by traditional genomics methods based on pair-wise expression similarity. The approach explained available gene function information and to provided robust prediction of expression levels in new data. The predictive capability of the model was also tested to identify condition-specific regulation as well as conserved regulation between Populus and Arabidopsis.

Colinearity of genes in plant genomes generally decreases with increasing evolutionary distance while the actual number of genes remains more or less constant. This results in the observation of genes “moving” to non-orthologous positions. Such observations were made in many genomes, both from different dicot and monocot plant families. This erosion of colinearity does not seem to depend on genome size as loss of colinearity is observed similarly in small and large plant genomes. To characterise the molecular mechanisms of this "gene movement", we identified non-colinear genes by three-way comparison of the three “small” grass genomes of Brachypodium, rice and sorghum. We found that genomic fragments of up to 50 kb containing the non-colinear genes are duplicated to acceptor sites elsewhere in the genome. Apparent movement of genes may usually be the result of subsequent deletions of genes in the donor region. Often, the duplicated fragments are precisely bordered by transposable elements (TEs) at the acceptor site. Highly diagnostic sequence motifs at these borders strongly suggest that these gene movements were the result of double-strand break (DSB) repair through synthesis-dependent strand annealing. In these cases, a copy of the foreign DNA fragment is used as filler DNA to repair the DSB linked with the transposition of TEs. Interestingly, most TEs we found associated with gene movement have a very low copy number in the genome and for several we did not find autonomous copies. This suggests that some of these elements spontaneously arose from unspecific interaction with TE proteins that are encoded by autonomous elements. Additionally, we found evidence that gene movements can also be caused when DSBs are repaired after template slippage or unequal crossing-over events. The observed frequency of gene movements can explain the erosion of gene colinearity between plant genomes during evolution.

Genome-wide classification of transcription-associated proteins (TAPs, comprising transcription factors and transcriptional regulators) can be achieved using a comprehensive set of rules employing PFAM domains, and is the basis for phylogenetic comparative (PC) analyses of plant and algal TAP evolution. Based on this, we are able to demonstrate that evolutionary retention of duplicated genes encoding TAPs is positively correlated with increasing morphological complexity and paleopolyploidizations, especially within the plant kingdom. The timeline of loss, gain, and expansion of TAPs among Viridiplantae reveals two major bursts of gain/expansion, coinciding with the water-to-land transition and the radiation of flowering plants. Analyses of the genomes of uni- and multicellular algae with regard to their TAP complement allows insights into the shaping of gene regulatory networks underlying the evolution of organism complexity.

Plant cell walls are complex structures mainly composed of high molecular weight polysaccharides, which present key precursors for industrial applications. Cellulose, a hydrogen-bonded b-1,4-linked glucan microfibril, is a key cell wall component and is synthesized by large multi-meric complexes at the cell surface. Very little is, however, known about regulatory modes of the complex, and the functional context of cellulose synthesis. We have shown that many genes that are transcriptionally coordinated with the genes encoding the cellulose synthases are associated with cellulose production. To assess the function of these genes vis-à-vis cellulose synthesis we are using genetic and various molecular techniques, including high-definition microscopy. To extend the co-expressed relationships we have constructed genome level co-expression networks for nine plant species. Through comparative analyses of co-expressed network vicinities we show conservation and diversification of the cellulose synthesizing machinery. We propose that this approach may readily be used to transfer knowledge from model organisms to species with more societal impact.

In an attempt to unravel the structure and evolution of the plantl ancestor genome we have re-assed the synteny and duplications of eudicot and monocot genomes to to identify and characterize shared duplications. We combined the data on the intra-genomic duplications with those on the colinear blocks and found duplicated segments that have been conserved at orthologous positions since the divergence of plants. By conducting detailed analysis of the length, composition, and divergence time of the conserved duplications we identified common and lineage-specific patterns of conservation between the different genomes that allowed us to propose a model in which the plant genomes have evolved from a common ancestor with a basic number of five/seven chromosomes (90 MYA) through whole genome duplications (tetraploidization) and translocations followed by lineage specific segmental duplications, chromosome fusions and translocations (Abrouk et al. 2010; Murat et al. 2010).

Based on these data an ‘inner circle’ comprising 5/7 ancestral chromosomes with 10000 protogenes was defined providing a new reference for the plant chromosomes and new insights into their ancestral relationships that have led to arrange their chromosomes into concentric ‘crop circles’ of synteny blocks (Abrouk et al. 2010). The established plant ancestor genome structure in term of chromosome structure and gene content offered the opportunity to study the impact of evolutionary shuffling events such as polyploidizations on (i) genome structure (witch mechanism drives the diploidization process); (ii) gene expression (role of epigenetics on neo/sub-functionalisation); (iii) agronomical trait genesis (role of whole or segmental genome duplications on QTL epistatic interactions), that will be discussed in details (Quraishi et al 2010ab).

Our long-term goal is to investigate the mechanisms by which plants control gene expression and to elucidate the structure and dynamics of the underlying gene regulatory networks (GRNs) with the objective of manipulating plant form and metabolism. My laboratory has used a number of cellular processes as “windows” to explore the architecture of plant GRNs in monocots (e.g., maize) and dicots (e.g., Arabidopsis). The control of flavonoid biosynthesis has provided an exceptional system to understand combinatorial gene regulation, and how transcription factors with similar DNA-binding domains control specific sets of target genes. The application of systems approaches to the differentiation of Arabidopsis epidermal cells is providing a first picture of the architecture and dynamic behavior of a developmental GRN. Combined with the construction of two public databases, AGRIS (http://arabidopsis.med.ohio-state.edu/) for Arabidopsis and GRASSIUS (www.grassius.org) for maize and other grasses, information on transcription factors, promoters and their interactions is integrated, facilitating the identification and visualization of GRNs.