Plant Genomics

Research Interests

Our group is interested in the mechanisms underlying sexual reproduction and early embryogenesis with a particular focus on the role of the male gametes. Contrary to previous assumptions recent studies have shown that male gametes both in the plant and animal kingdom carry complex sets of RNA molecules, including not only mRNAs but also small RNAs. We are particularly interested in the role of these two RNA classes before, during and after double fertilization as it occurs in higher plants. Using Arabidopsis thaliana as our primary experimental model we are addressing specific questions like: (1) What are the functions of small RNA and DNA methylation pathways in sperm cells? (2) Do sperm cell derived RNAs play a role after fertilization? (3) Do conserved core sets of genetic modules underlie common characteristics of male gametes across kingdoms?
In a second research line we are analyzing the symbiotic transcriptome of the model legume Medicago truncatula, both for nodule and mycorrhizal symbiosis, leading to the creation of a gene expression database that will allow the in-depth analysis of the symbiontic genetic programme.

Group Members

Research Project

The symbiotic genetic programme of the model legume Medicago truncatula

Legumes (Leguminosae) are among the most important agricultural taxons on earth. Their unique feature is the ability to enter a nitrogen-fixing root nodule symbiosis with prokaryotes, resulting in the conversion of atmospheric nitrogen to ammonia that is subsequently supplied to the plant for incorporation into amino acids. As most of higher plants, legumes can also establish an arbuscular mycorrhiza (AM) symbiosis with fungi. In return for the supply with carbohydrates the fungus transfers minerals, and in particular phosphorus, from the soil to the plant. This project aims to provide a large-scale analysis of the symbiotic transcriptome of the model legume Medicago truncatula. Selected stages of nodule and mycorrhizal symbioses are being analyzed on Affymetrix Medicago truncatula GeneChip arrays and data will be made freely accessible in the Truncatulix database. The in depth analysis of the datasets obtained within this project is expected to foster the development of novel, testable hypotheses for diverse aspects of the genetic basis underlying the symbiotic programme of leguminous plants.

Funding

Fundação para a Ciência e a Tecnologia
Expression profiling studies to specify the symbiotic genetic programme of the model legume Medicago truncatula.

Collaborators

Instituto de Biologia Molecular e Celular, Porto, Portugal
Helena Carvalho

Institute for Plant Genetics, Unit IV - Plant Genomics, Leibniz University Hanover, Germany
Helge Küster

Instituto Superior Técnico, Lisbon, Portugal
Leonilde Moreira

Publications

(Selected) Update April (2009).

Slotkin RK, Vaughn M, Borges F, Tanurdžić M, Becker, JD, Feijó JA, Martienssen R. (2009). Epigenetic reprogramming and small RNA silencing of transposable elements in pollen Cell 136 :461–472

Borges F, Gomes G, Gardner R, Moreno N, McCormick S, Feijó JA, Becker, JD (2008). Comparative transcriptomics of Arabidopsis thaliana sperm cells Plant Physiology 148 :1168-1181

Johnston AJ , Meier P, Gheyselinck J, Federer M, Wuest AEJ, Schlagenhauf E, Becker, JD, Grossniklaus U. (2007). Genetic subtraction profiling identifies genes essential for Arabidopsis reproduction and reveals interaction between the female gametophyte and the maternal sporophyte Genome Biology 8 :R204

Becker, JD, Feijó JA. (2007). How many genes are needed to make a pollen tube? Lessons from transcriptomics Annals of Botany 100 :1117-1123

Marsch-Martinez N, Greco F, Becker, JD, Dixit S, Karaba A, Bergervoet J, de Folter S, Pereira A. (2006). BOLITA, an Arabidopsis AP2/ERF-like transcription factor that affects cell expansion and proliferation/differentiation pathways Plant Molecular Biology 62 :825-843

Sessa G, Carabelli M, Sassi M, Ciolfi A, Possenti M, Mittempergher F, Becker, JD, Morelli G, Ruberti I. (2005). A dynamic balance between gene activation and repression regulates the shade avoidance response in Arabidopsis Genes & Development 19 :2811-2815

Pina C, Pinto F, Feijó JA, Becker, JD. (2005). Gene family analysis of the Arabidopsis pollen transcriptome reveals biological implications for cell growth, division control and gene expression regulation Plant Physiology 138 :744-756

Feijó JA, Costa SS, Prado AM, Becker, JD, Certal AC. (2004). Signalling by tips Current Opinion in Plant Biology 7 :589-598

Becker, JD, Boavida LC, Carneiro J, Haury M, Feijó JA (2003). Transcriptional profiling of Arabidopsis tissues reveals the unique characteristics of the pollen transcriptome Plant Physiology 133 :713-725

Becker, J.D, Moreira LM, Kapp D, Frosch SC, Pühler A, Perlick AM (2001). The nodulin VfENOD18 is an ATP-binding protein in infected cells of Vicia faba L. nodules Plant Molecular Biology 47 :749-759