The transcriptional landscape of polyploid wheat.

The coordinated expression of highly related homoeologous genes in polyploid species underlies the phenotypes of many of the world's major crops. Here we combine extensive gene expression datasets to produce a comprehensive, genome-wide analysis of homoeolog expression patterns in hexaploid bread wheat. Bias in homoeolog expression varies between tissues, with ~30% of wheat homoeologs showing nonbalanced expression. We found expression asymmetries along wheat chromosomes, with homoeologs showing the largest inter-tissue, inter-cultivar, and coding sequence variation, most often located in high-recombination distal ends of chromosomes. These transcriptionally dynamic genes potentially represent the first steps toward neo- or subfunctionalization of wheat homoeologs. Coexpression networks reveal extensive coordination of homoeologs throughout development and, alongside a detailed expression atlas, provide a framework to target candidate genes underpinning agronomic traits in wheat.

Suppressed recombination and unique candidate genes in the divergent haplotype encoding Fhb1, a major Fusarium head blight resistance locus in wheat.

KEY MESSAGE: Fine mapping and sequencing revealed 28 genes in the non-recombining haplotype containing Fhb1 . Of these, only a GDSL lipase gene shows a pathogen-dependent expression pattern. Fhb1 is a prominent Fusarium head blight resistance locus of wheat, which has been successfully introgressed in adapted breeding material, where it confers a significant increase in overall resistance to the causal pathogen Fusarium graminearum and the fungal virulence factor and mycotoxin deoxynivalenol. The Fhb1 region has been resolved for the susceptible wheat reference genotype Chinese Spring, yet the causal gene itself has not been identified in resistant cultivars. Here, we report the establishment of a 1 Mb contig embracing Fhb1 in the donor line CM-82036. Sequencing revealed that the region of Fhb1 deviates from the Chinese Spring reference in DNA size and gene content, which explains the repressed recombination at the locus in the performed fine mapping. Differences in genes expression between near-isogenic lines segregating for Fhb1 challenged with F. graminearum or treated with mock were investigated in a time-course experiment by RNA sequencing. Several candidate genes were identified, including a pathogen-responsive GDSL lipase absent in susceptible lines. The sequence of the Fhb1 region, the resulting list of candidate genes, and near-diagnostic KASP markers for Fhb1 constitute a valuable resource for breeding and further studies aiming to identify the gene(s) responsible for F. graminearum and deoxynivalenol resistance.

The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle.

The subfamily of the Lemnoideae belongs to a different order than other monocotyledonous species that have been sequenced and comprises aquatic plants that grow rapidly on the water surface. Here we select Spirodela polyrhiza for whole-genome sequencing. We show that Spirodela has a genome with no signs of recent retrotranspositions but signatures of two ancient whole-genome duplications, possibly 95 million years ago (mya), older than those in Arabidopsis and rice. Its genome has only 19,623 predicted protein-coding genes, which is 28% less than the dicotyledonous Arabidopsis thaliana and 50% less than monocotyledonous rice. We propose that at least in part, the neotenous reduction of these aquatic plants is based on readjusted copy numbers of promoters and repressors of the juvenile-to-adult transition. The Spirodela genome, along with its unique biology and physiology, will stimulate new insights into environmental adaptation, ecology, evolution and plant development, and will be instrumental for future bioenergy applications.

MIPS: analysis and annotation of genome information in 2007.

The Munich Information Center for Protein Sequences (MIPS-GSF, Neuherberg, Germany) combines automatic processing of large amounts of sequences with manual annotation of selected model genomes. Due to the massive growth of the available data, the depth of annotation varies widely between independent databases. Also, the criteria for the transfer of information from known to orthologous sequences are diverse. To cope with the task of global in-depth genome annotation has become unfeasible. Therefore, our efforts are dedicated to three levels of annotation: (i) the curation of selected genomes, in particular from fungal and plant taxa (e.g. CYGD, MNCDB, MatDB), (ii) the comprehensive, consistent, automatic annotation employing exhaustive methods for the computation of sequence similarities and sequence-related attributes as well as the classification of individual sequences (SIMAP, PEDANT and FunCat) and (iii) the compilation of manually curated databases for protein interactions based on scrutinized information from the literature to serve as an accepted set of reliable annotated interaction data (MPACT, MPPI, CORUM). All databases and tools described as well as the detailed descriptions of our projects can be accessed through the MIPS web server (http://mips.gsf.de).

MIPS: analysis and annotation of proteins from whole genomes in 2005.

The Munich Information Center for Protein Sequences (MIPS at the GSF), Neuherberg, Germany, provides resources related to genome information. Manually curated databases for several reference organisms are maintained. Several of these databases are described elsewhere in this and other recent NAR database issues. In a complementary effort, a comprehensive set of >400 genomes automatically annotated with the PEDANT system are maintained. The main goal of our current work on creating and maintaining genome databases is to extend gene centered information to information on interactions within a generic comprehensive framework. We have concentrated our efforts along three lines (i) the development of suitable comprehensive data structures and database technology, communication and query tools to include a wide range of different types of information enabling the representation of complex information such as functional modules or networks Genome Research Environment System, (ii) the development of databases covering computable information such as the basic evolutionary relations among all genes, namely SIMAP, the sequence similarity matrix and the CABiNet network analysis framework and (iii) the compilation and manual annotation of information related to interactions such as protein-protein interactions or other types of relations (e.g. MPCDB, MPPI, CYGD). All databases described and the detailed descriptions of our projects can be accessed through the MIPS WWW server (http://mips.gsf.de).

The PlaNet Consortium: a network of European plant databases connecting plant genome data in an integrated biological knowledge resource.

The completion of the Arabidopsis genome and the large collections of other plant sequences generated in recent years have sparked extensive functional genomics efforts. However, the utilization of this data is inefficient, as data sources are distributed and heterogeneous and efforts at data integration are lagging behind. PlaNet aims to overcome the limitations of individual efforts as well as the limitations of heterogeneous, independent data collections. PlaNet is a distributed effort among European bioinformatics groups and plant molecular biologists to establish a comprehensive integrated database in a collaborative network. Objectives are the implementation of infrastructure and data sources to capture plant genomic information into a comprehensive, integrated platform. This will facilitate the systematic exploration of Arabidopsis and other plants. New methods for data exchange, database integration and access are being developed to create a highly integrated, federated data resource for research. The connection between the individual resources is realized with BioMOBY. BioMOBY provides an architecture for the discovery and distribution of biological data through web services. While knowledge is centralized, data is maintained at its primary source without a need for warehousing. To standardize nomenclature and data representation, ontologies and generic data models are defined in interaction with the relevant communities.Minimal data models should make it simple to allow broad integration, while inheritance allows detail and depth to be added to more complex data objects without losing integration. To allow expert annotation and keep databases curated, local and remote annotation interfaces are provided. Easy and direct access to all data is key to the project.

The stem cell population of Arabidopsis shoot meristems in maintained by a regulatory loop between the CLAVATA and WUSCHEL genes.

The higher-plant shoot meristem is a dynamic structure whose maintenance depends on the coordination of two antagonistic processes, organ initiation and self-renewal of the stem cell population. In Arabidopsis shoot and floral meristems, the WUSCHEL (WUS) gene is required for stem cell identity, whereas the CLAVATA1, 2, and 3 (CLV) genes promote organ initiation. Our analysis of the interactions between these key regulators indicates that (1) the CLV genes repress WUS at the transcript level and that (2) WUS expression is sufficient to induce meristem cell identity and the expression of the stem cell marker CLV3. Our data suggest that the shoot meristem has properties of a self-regulatory system in which WUS/CLV interactions establish a feedback loop between the stem cells and the underlying organizing center.

Arabidopsis genome analysis as exemplified by analysis of chromosome 4.

During the last decade the small cruciferous plant Arabidopsis thaliana has become a model organism for flowering plants. Sequencing and analysis of the Arabidopsis genome is nearing completion. Beside an overview on methods and strategies for Arabidopsis genome analysis, a summary of the results from the first analysis is presented. This includes an overview on chromosomal organisation and topological features as well as a first comparison with other genomes.

Role of WUSCHEL in regulating stem cell fate in the Arabidopsis shoot meristem.

The shoot meristem gives rise to the aerial parts of higher plants by continuously initiating new organs. The basis of this activity is its ability to maintain a pool of pluripotent stem cells, which are the ultimate source of all tissues of the shoot. In Arabidopsis plants mutant for the WUSCHEL (WUS) gene, the stem cells are misspecified and appear to undergo differentiation. Here, we show that WUS encodes a novel homeodomain protein which presumably acts as a transcriptional regulator. The pattern of WUS expression suggests that stem cells in the shoot meristem are specified by an underlying cell group which is established in the 16-cell embryo and becomes localized to its prospective domain of function by asymmetric cell divisions.

Cell fate regulation in the shoot meristem.

The shoot meristem is a proliferative centre containing pluripotent stem cells that are the ultimate source of all cells and organs continuously added to the growing shoot. The progeny of the stem cells have two developmental options, either to renew the stem cell population or to leave the meristem and to differentiate, possibly according to signals from more mature tissue. The destiny of each cell depends on its position within the dynamic shoot meristem. Genetic data suggest a simple model in which graded positional information is provided by antagonistic gene functions and is interpreted by genes which regulate cell fate.

The WUSCHEL gene is required for shoot and floral meristem integrity in Arabidopsis.

Self perpetuation of the shoot meristem is essential for the repetitive initiation of shoot structures during plant development. In Arabidopsis shoot meristem maintenance is disrupted by recessive mutations in the WUSCHEL (WUS) gene. The defect is evident at all developmental stages and is restricted to shoot and floral meristems, whereas the root meristem is not affected. wus mutants fail to properly organize a shoot meristem in the embryo. Postembryonically, defective shoot meristems are initiated repetitively but terminate prematurely in aberrant flat structures. In contrast to wild-type shoot meristems, primordia initiation occurs ectopically across mutant apices, including the center, and often new shoot meristems instead of organs are initiated. The cells of wus shoot apices are larger and more vacuolated than wild-type shoot meristem cells. wus floral meristems terminate prematurely in a central stamen. Double mutant studies indicate that the number of organ primordia in the center of wus flowers is limited, irrespective of organ identity and we propose that meristem cells are allocated into floral whorl domains in a sequential manner. WUS activity also appears to be required for the formation of supernumerary organs in the center of agamous, superman or clavata1 flowers, suggesting that the WUS gene acts upstream of the corresponding genes. Our results suggest that the WUS gene is specifically required for central meristem identity of shoot and floral meristems to maintain their structural and functional integrity.