TY - JOUR ID - 1597 TI - Transcriptional Dynamics of Two Seed Compartments with Opposing Roles in Arabidopsis Seed Germination JO - Plant Physiol PY - 2013 SP - 205-215 AU - Dekkers, B.J.W. AU - Pearce, S. AU - van Bolderen-Veldkamp, R.P. AU - Marshall, A. AU - Widera, P. AU - Gilbert, J. AU - Drost, H.-G. AU - Basseli, G.W. AU - Müller, K. AU - King, J.R. AU - Wood, A.T.A. AU - Grosse, I. AU - Quint, M. AU - Krasnogor, N. AU - Leubner-Metzger, G. AU - Holdsworth, M.J. & Bentsink, L. VL - 163 UR - DO - 10.1104/pp.113.223511 AB - Seed germination is a critical stage in the plant life cycle and the first step toward successful plant establishment. Therefore, understandinggermination is of important ecological and agronomical relevance. Previous research revealed that different seed compartments (testa,endosperm, and embryo) control germination, but little is known about the underlying spatial and temporal transcriptome changes thatlead to seed germination. We analyzed genome-wide expression in germinating Arabidopsis (Arabidopsis thaliana) seedswith both temporaland spatial detail and provide Web-accessible visualizations of the data reported (vseed.nottingham.ac.uk). We show the potential of this highresolutiondata set for the construction ofmeaningful coexpression networks, which provide insight into the genetic control of germination.The data set reveals two transcriptional phases during germination that are separated by testa rupture. The first phase is marked by largetranscriptome changes as the seed switches from a dry, quiescent state to a hydrated and active state. At the end of this first transcriptionalphase, the number of differentially expressed genes between consecutive time points drops. This increases again at testa rupture, the start ofthe second transcriptional phase. Transcriptome data indicate a role for mechano-induced signaling at this stage and subsequently highlightthe fates of the endosperm and radicle: senescence and growth, respectively. Finally, using a phylotranscriptomic approach, we show thatexpression levels of evolutionarily young genes drop during the first transcriptional phase and increase during the second phase.Evolutionarily old genes show an opposite pattern, suggesting a more conserved transcriptome prior to the completion of germination. A2 - C1 - Molecular Signal Processing ER - TY - JOUR ID - 1601 TI - Optimized probe masking for comparative transcriptomics of closely related species. JO - PLOS ONE PY - 2013 SP - e78497 AU - Poeschl, Y. AU - Delker, C. AU - Trenner, J. AU - Ullrich, K. AU - Quint, M. & Grosse, I. VL - 8 UR - DO - 10.1371/journal.pone.0078497 AB - Microarrays are commonly applied to study the transcriptome of specific species. However, many available microarrays arerestricted to model organisms, and the design of custom microarrays for other species is often not feasible. Hence,transcriptomics approaches of non-model organisms as well as comparative transcriptomics studies among two or morespecies often make use of cost-intensive RNAseq studies or, alternatively, by hybridizing transcripts of a query species to amicroarray of a closely related species. When analyzing these cross-species microarray expression data, differences in thetranscriptome of the query species can cause problems, such as the following: (i) lower hybridization accuracy of probes dueto mismatches or deletions, (ii) probes binding multiple transcripts of different genes, and (iii) probes binding transcripts ofnon-orthologous genes. So far, methods for (i) exist, but these neglect (ii) and (iii). Here, we propose an approach forcomparative transcriptomics addressing problems (i) to (iii), which retains only transcript-specific probes binding transcriptsof orthologous genes. We apply this approach to an Arabidopsis lyrata expression data set measured on a microarraydesigned for Arabidopsis thaliana, and compare it to two alternative approaches, a sequence-based approach and a genomicDNA hybridization-based approach. We investigate the number of retained probe sets, and we validate the resultingexpression responses by qRT-PCR. We find that the proposed approach combines the benefit of sequence-based stringencyand accuracy while allowing the expression analysis of much more genes than the alternative sequence-based approach. Asan added benefit, the proposed approach requires probes to detect transcripts of orthologous genes only, which provides asuperior base for biological interpretation of the measured expression responses. A2 - C1 - Molecular Signal Processing ER - TY - JOUR ID - 1596 TI - Plant F-Box protein evolution is determined by lineage-specific timing of major gene family expansion waves JO - PLoS One PY - 2013 SP - e68672 AU - Navarro-Quezada, A. AU - Schumann, N. AU - Quint, M. VL - 8 UR - http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0068672 DO - 10.1371/journal.pone.0068672 AB - F-box proteins (FBPs) represent one of the largest and fastest evolving gene/protein families in the plant kingdom. The FBP superfamily can be divided in several subfamilies characterized by different C-terminal protein-protein interaction domains that recruit targets for proteasomal degradation. Hence, a clear picture of their phylogeny and molecular evolution is of special interest for the general understanding of evolutionary histories of multi-domain and/or large protein families in plants. In an effort to further understand the molecular evolution of F-box family proteins, we asked whether the largest subfamily in Arabidopsis thaliana, which carries a C-terminal F-box associated domain (FBA proteins) shares evolutionary patterns and signatures of selection with other FBPs. To address this question, we applied phylogenetic and molecular evolution analyses in combination with the evaluation of transcriptional profiles. Based on the 2219 FBA proteins we de novo identified in 34 completely sequenced plant genomes, we compared their evolutionary patterns to a previously analyzed large subfamily carrying C-terminal kelch repeats. We found that these two large FBP subfamilies generally tend to evolve by massive waves of duplication, followed by sequence conservation of the F-box domain and sequence diversification of the target recruiting domain. We conclude that the earlier in evolutionary time a major wave of expansion occurred, the more pronounced these selection signatures are. As a consequence, when performing cross species comparisons among FBP subfamilies, significant differences will be observed in the selective signatures of protein-protein interaction domains. Depending on the species, the investigated subfamilies comprise up to 45% of the complete superfamily, indicating that other subfamilies possibly follow similar modes of evolution. A2 - C1 - Molecular Signal Processing; Biochemistry of Plant Interactions ER -