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Daphnia ecotypes fed lab versus natural resources

ABSTRACT: Consumer-resource interactions are a central issue in evolutionary and community ecology because they play important roles in selection and population regulation. Most consumers encounter resource variation at multiple scales, and respond through phenotypic plasticity in the short term or evolutionary divergence in the long term. The key traits for these responses may influence resource acquisition, assimilation and/or allocation. To identify candidate genes, we experimentally assayed genome-wide gene expression in pond and lake Daphnia ecotypes exposed to alternate resource environments. One was a simple, high-quality laboratory diet, Ankistrodesmus falcatus. The other was the complex natural seston from a large lake. In temporary ponds, Daphnia generally experience high-quality, abundant resources, whereas lakes provide low-quality, seasonally shifting resources that are chronically limiting. For both ecotypes, we used replicate clones drawn from a number of separate populations.

ORGANISM(S): Daphnia pulex Daphnia pulicaria

PROVIDER: GSE31001 | GEO | 2012/01/01

SECONDARY ACCESSION(S): PRJNA146335

REPOSITORIES: GEO

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Project description:Consumer-resource interactions are a central issue in evolutionary and community ecology because they play important roles in selection and population regulation. Most consumers encounter resource variation at multiple scales, and respond through phenotypic plasticity in the short term or evolutionary divergence in the long term. The key traits for these responses may influence resource acquisition, assimilation and/or allocation. To identify candidate genes, we experimentally assayed genome-wide gene expression in pond and lake Daphnia ecotypes exposed to alternate resource environments. One was a simple, high-quality laboratory diet, Ankistrodesmus falcatus. The other was the complex natural seston from a large lake. In temporary ponds, Daphnia generally experience high-quality, abundant resources, whereas lakes provide low-quality, seasonally shifting resources that are chronically limiting. For both ecotypes, we used replicate clones drawn from a number of separate populations. We compared gene expression in whole Daphnia pulex that had been raised in the lab for 10 days, and then exposed to alternate resource environments for 24 hours. One resource environment was a 24 hour continuation of the lab resource, a satiating level of Ankistrodesmus falcatus. The alternate environment was the natural seston present in the epilimnion of Lake Murray, South Carolina. Two ecotypes were analyzed, one adapted to large lakes, and one adapted to temporary ponds. For each ecotype, eight replicate clones were used. Clones of the lake ecotype were isolated from eight independent lakes, clones of the pond ecotype were isolated from six different ponds. The total number of arrays is 16 (8 replicate clones x 2 ecotypes) x 2 resource environments). Total RNA was extracted from eight whole organisms pooled together. Pools were then converted to cDNA and labelled with a single round of amplification. For array hybridizations, samples from the two resource environments were paired for each clone, and dyes were swapped across clones.

Project description:The conservation of plant genetic resources (PGRs) is contingent on their current or potential use, so extending the knowledge about them is crucial for their valorization. The valorization and conservation of wild fruit PGRs are critical to ensure the maintenance of genetic and cultural heritage and to promote and develop of new perspectives on resource use. New strategies for characterizing PGRs are needed, and the omics approach can provide profound information that is still largely unknown. The strawberry tree (Arbutus unedo L.) is an underutilized, drought and fire-resistant species distributed in the Mediterranean area and its berries have large ethnobotanical use but were not usually consumed as fresh fruits. Although their phenolic profile and antioxidant capacity are known, they are not well characterised, particularly from a proteomic perspective. The aim of this work is the characterisation from a molecular viewpoint of two ecotypes of A. unedo (Campania and Sicily) to valorise a less known wild fruit PGR to encourage its preservation. Samples were collected from two different geographical areas to assess whether different geographical conditions could influence the characteristics of leaves and fruits at the three stages of ripening (green, veraison, red). Proteomic analysis identified 904 proteins, of which 122 showed significance along the ripening process. Some of these differentially abundant proteins, such as chalcone synthase, show a marked increase during ripening. From a proteomic perspective, there are no differences between the fruits from the two regions compared by the ripening stage. However, the pedoclimatic metabolic imprinting allowed the observation of good diversity in the metabolomic profiles between the two ecotypes, especially for anthocyanins and catechins, generally more abundant in Sicilian fruit, or the phenolic compounds more abundant in Campania fruit. Multi-omic characterisation enhanced the knowledge on a wild fruit plant species which shows specific adaptations and responses to the environment to be considered when addressing the issue of local agrobiodiversity.

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Daphnia ecotypes fed lab versus natural resources

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