The KnownLeaf literature curation system captures knowledge about Arabidopsis leaf growth and development and facilitates integrated data mining
Szakonyi, D. ; Landeghem, S. van; Baerenfaller, K. ; Baeyens, L. ; Blomme, J. ; Casanova-Saéz, R. ; Bodt, S. De; Esteve-Bruna, D. ; Fiorani, F. ; Gonzalez, N. ; Grønlund, J. ; Immink, R.G.H. ; Jover-Gil, S. ; Kuwabara, A. ; Muñoz-Nortes, T. ; Dijk, A.D.J. van; Wilson-Sánchez, D. ; Buchanan-Wollaston, V. ; Angenent, G.C. ; Peer, Y. Van de; Inzé, D. ; Micol, J.L. ; Gruissem, W. ; Walsh, S. ; Hilson, P. - \ 2015
Current Plant Biology 2 (2015). - ISSN 2214-6628 - p. 1 - 11.
The information that connects genotypes and phenotypes is essentially embedded in research articles written in natural language. To facilitate access to this knowledge, we constructed a framework for the curation of the scientific literature studying the molecular mechanisms that control leaf growth and development in Arabidopsis thaliana (Arabidopsis). Standard structured statements, called relations, were designed to capture diverse data types, including phenotypes and gene expression linked to genotype description, growth conditions, genetic and molecular interactions, and details about molecular entities. Relations were then annotated from the literature, defining the relevant terms according to standard biomedical ontologies. This curation process was supported by a dedicated graphical user interface, called Leaf Knowtator. A total of 283 primary research articles were curated by a community of annotators, yielding 9947 relations monitored for consistency and over 12,500 references to Arabidopsis genes. This information was converted into a relational database (KnownLeaf) and merged with other public Arabidopsis resources relative to transcriptional networks, protein–protein interaction, gene co-expression, and additional molecular annotations. Within KnownLeaf, leaf phenotype data can be searched together with molecular data originating either from this curation initiative or from external public resources. Finally, we built a network (LeafNet) with a portion of the KnownLeaf database content to graphically represent the leaf phenotype relations in a molecular context, offering an intuitive starting point for knowledge mining. Literature curation efforts such as ours provide high quality structured information accessible to computational analysis, and thereby to a wide range of applications. DATA: The presented work was performed in the framework of the AGRON-OMICS project (Arabidopsis GRO wth Network integrating OMICS technologies) supported by European Commission 6th Framework Programme project (Grant number LSHG-CT-2006-037704). This is a data integration and data sharing portal collecting all the all the major results from the consortium. All data presented in our paper is available here. https://agronomics.ethz.ch/.
Genome-Wide Mapping of Structural Variations Reveals a Copy Number Variant That Determines Reproductive Morphology in Cucumber
Zhang, Z. ; Mao, L. ; Chen, Junshi ; Bu, F. ; Li, G. ; Sun, J. ; Li, S. ; Sun, H. ; Jiao, C. ; Blakely, R. ; Pan, J. ; Cai, R. ; Luo, R. ; Peer, Y. Van de; Jacobsen, E. ; Fei, Z. ; Huang, S. - \ 2015
The Plant Cell 27 (2015)6. - ISSN 1040-4651 - p. 1595 - 1604.
indel-associated mutation - tuberculate fruit gene - false discovery rate - arabidopsis-thaliana - population-scale - functional impact - sequencing data - synthase gene - paired-end - sativus l.
Structural variations (SVs) represent a major source of genetic diversity. However, the functional impact and formation mechanisms of SVs in plant genomes remain largely unexplored. Here, we report a nucleotide-resolution SV map of cucumber (Cucumis sativas) that comprises 26,788 SVs based on deep resequencing of 115 diverse accessions. The largest proportion of cucumber SVs was formed through nonhomologous end-joining rearrangements, and the occurrence of SVs is closely associated with regions of high nucleotide diversity. These SVs affect the coding regions of 1676 genes, some of which are associated with cucumber domestication. Based on the map, we discovered a copy number variation (CNV) involving four genes that defines the Female (F) locus and gives rise to gynoecious cucumber plants, which bear only female flowers and set fruit at almost every node. The CNV arose from a recent 30.2-kb duplication at a meiotically unstable region, likely via microhomology-mediated break-induced replication. The SV set provides a snapshot of structural variations in plants and will serve as an important resource for exploring genes underlying key traits and for facilitating practical breeding in cucumber.
The (r)evolution of gene regulatory networks controlling Arabidopsis plant reproduction; a two decades history
Pajoro, A. ; Biewers, S. ; Dougali, E. ; Valentim, F.L. ; Mendes, M.A. ; Porri, A. ; Coupland, G. ; Peer, Y. Van de; Dijk, A.D.J. van; Colombo, L. ; Davies, B. ; Angenent, G.C. - \ 2014
Journal of Experimental Botany 65 (2014)17. - ISSN 0022-0957 - p. 4731 - 4745.
floral organ identity - flowering-locus-t - mads-box genes - chromatin immunoprecipitation chip - domain transcription factors - cell-fate determination - short-vegetative-phase - homeotic gene - circadian clock - target genes
Successful plant reproduction relies on the perfect orchestration of singular processes that culminate in the product of reproduction: the seed. The floral transition, floral organ development, and fertilization are well-studied processes and the genetic regulation of the various steps is being increasingly unveiled. Initially, based predominantly on genetic studies, the regulatory pathways were considered to be linear, but recent genome-wide analyses, using high-throughput technologies, have begun to reveal a different scenario. Complex gene regulatory networks underlie these processes, including transcription factors, microRNAs, movable factors, hormones, and chromatin-modifying proteins. Here we review recent progress in understanding the networks that control the major steps in plant reproduction, showing how new advances in experimental and computational technologies have been instrumental. As these recent discoveries were obtained using the model species Arabidopsis thaliana, we will restrict this review to regulatory networks in this important model species. However, more fragmentary information obtained from other species reveals that both the developmental processes and the underlying regulatory networks are largely conserved, making this review also of interest to those studying other plant species.
The heterothallic sugarbeet pathogen Cercospora beticola contains exon fragments of both MAT genes that are homogenized by concerted evolution
Bolton, M.D. ; Jonge, R. de; Inderbitzin, P. ; Liu, Z. ; Birla, K. ; Peer, Y. Van de; Subbarao, K. ; Thomma, B.P.H.J. ; Secor, G. - \ 2014
Fungal Genetics and Biology 62 (2014). - ISSN 1087-1845 - p. 43 - 54.
de-novo identification - sexual reproduction - neurospora-tetrasperma - molecular-organization - fungal pathogens - loci - systems - recombination - resistance - tool
Dothideomycetes is one of the most ecologically diverse and economically important classes of fungi. Sexual reproduction in this group is governed by mating type (MAT) genes at the MAT1 locus. Self-sterile (heterothallic) species contain one of two genes at MAT1 (MAT1-1-1 or MAT1-2-1) and only isolates of opposite mating type are sexually compatible. In contrast, self-fertile (homothallic) species contain both MAT genes at MAT1. Knowledge of the reproductive capacities of plant pathogens are of particular interest because recombining populations tend to be more difficult to manage in agricultural settings. In this study, we sequenced MAT1 in the heterothallic Dothideomycete fungus Cercospora beticola to gain insight into the reproductive capabilities of this important plant pathogen. In addition to the expected MAT gene at MAT1, each isolate contained fragments of both MAT1-1-1 and MAT1-2-1 at ostensibly random loci across the genome. When MAT fragments from each locus were manually assembled, they reconstituted MAT1-1-1 and MAT1-2-1 exons with high identity, suggesting a retroposition event occurred in a homothallic ancestor in which both MAT genes were fused. The genome sequences of related taxa revealed that MAT gene fragment pattern of Cercospora zeae-maydis was analogous to C. beticola. In contrast, the genome of more distantly related Mycosphaerella graminicola did not contain MAT fragments. Although fragments occurred in syntenic regions of the C. beticola and C. zeae-maydis genomes, each MAT fragment was more closely related to the intact MAT gene of the same species. Taken together, these data suggest MAT genes fragmented after divergence of M. graminicola from the remaining taxa, and concerted evolution functioned to homogenize MAT fragments and MAT genes in each species.