Dataset Information

Genomic resources for Macadamia tetraphylla and an examination of its historic use as a crop resource in Hawaii

ABSTRACT: The goal of this project was to develop a genomic resource for macadamia agriculture in Hawai?i through constructing a transcriptome of M. tetraphylla and testing for hybridity in University of Hawai?i at M?noa breeding material.

INSTRUMENT(S): -

ORGANISM(S): Macadamia Tetraphylla

SUBMITTER: Univerisity of Hawaii at Manoa

PROVIDER: PRJEB56438 | EVA | 2022-10-06

REPOSITORIES: EVA

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Dataset's files

Source:

			Action	DRS
	SNP_variation_in_HI_879_Oahu_tetraphylla_Oahu_putative_tetraphylla_hybrid_862_merged.accessioned.vcf.gz	Vcf
	SNP_variation_in_HI_879_Oahu_tetraphylla_Oahu_putative_tetraphylla_hybrid_862_merged.accessioned.vcf.gz.csi	Vcf
	SNP_variation_in_HI_879_Oahu_tetraphylla_Oahu_putative_tetraphylla_hybrid_862_merged.vcf.csi	Other
	SNP_variation_in_HI_879_Oahu_tetraphylla_Oahu_putative_tetraphylla_hybrid_862_merged.vcf.gz	Vcf

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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.

Dataset Information

Genomic resources for Macadamia tetraphylla and an examination of its historic use as a crop resource in Hawaii

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