EST sequencing and time course microarray hybridizations identify more than 700 Medicago truncatula genes with developmental expression regulation in flowers and pods

Firnhaber C, Pühler A, Küster H. EST sequencing and time course microarray hybridizations identify more than 700 Medicago truncatula genes with developmental expression regulation in flowers and pods. Planta. 2005;222(2):269-283.To evaluate the molecular mechanisms during pod and seed formation in legumes, starting with the development of reproductive organs, we constructed two cDNA libraries from developing flowers (MtFLOW) and pods including seeds (MtPOSE) of the model plant Medicago truncatula Gaertner. A total of 2,516 expressed sequence tags (ESTs) clustered into 1,776 non-redundant sequences (2k-set), which were annotated and assigned to functional classes. While about 30% of the ESTs encoded proteins of yet unknown function, typical annotations pointed to seed storage proteins, LTPs and lipoxygenases. The 2k-set was used to upgrade Mt6k-RIT microarrays (Kuster et al. in J Biotechnol 108: 95, 2004) to Mt8k versions representing approximately 6,300 nonredundant M. truncatula genes. These were used to perform time course expression profiling studies based on hybridizations of samples that covered eight different developmental stages from flower buds to almost mature pods versus leaves as a common reference. About 180 up- and 70 downregulated genes were typically found for each stage and in total, 782 genes were either twofold up- or downregulated in at least one of the eight stages investigated. Based on this set, a combination of self-organizing map and hierarchical clustering revealed genes displaying expression regulation during characteristic stages of M. truncatula flower and pod development. Amongst those, several genes encoded proteins related to seed metabolism and development including novel regulators and proteins involved in signaling

A Gondwanan Imprint on the Global Diversity and Domestication of the Wine and Cider Yeast Saccharomyces uvarum

In addition to Saccharomyces cerevisiae, the cryotolerant yeast species S. uvarum is also used for wine and cider fermentation but nothing is known about its natural history. Here we use a population genomics approach to investigate its global phylogeography and domestication fingerprints using a collection of isolates obtained from fermented beverages and from natural environments on five continents. South American isolates contain more genetic diversity than that found in the Northern Hemisphere. Moreover, coalescence analyses suggest that a Patagonian sub-population gave rise to the Holarctic population through a recent bottleneck. Holarctic strains display multiple introgressions from other Saccharomyces species, those from S. eubayanus being prevalent in European strains associated with humandriven fermentations. These introgressions are absent in the large majority of wild strains and gene ontology analyses indicate that several gene categories relevant for wine fermentation are overrepresented. Such findings constitute a first indication of domestication in S. uvarum.Fil: Almeida, Pedro. Universidade Nova de Lisboa; PortugalFil: Goncalves, Carla. Universidade Nova de Lisboa; PortugalFil: Teixeira, Sara. Universidade Nova de Lisboa; PortugalFil: Libkind Frati, Diego. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Patagonia Norte. Instituto de Investigación en Biodiversidad y Medioambiente; Argentina. Universidad Nacional del Comahue; ArgentinaFil: Bontrager, Martín. University Of Wisconsin; Estados UnidosFil: Masneuf Pomarede, Isabelle. Bordeaux Sciences agro; FranciaFil: Albertin, Warren. Universite de Bordeaux; FranciaFil: Durrens, Pascal. Universite de Bordeaux; FranciaFil: Sherman, David James. Universite de Bordeaux; FranciaFil: Marullo, Philippe. Universite de Bordeaux; Francia. BIOLAFFORT; FranciaFil: Hittinger, Chris Todd. University Of Wisconsin; Estados UnidosFil: Gonçalves, Paula. Universidade Nova de Lisboa; PortugalFil: Sampaio, José Paulo. Universidade Nova de Lisboa; Portuga