Mountain View
biomedical and healthCAre Data Discovery Index Ecosystem
help Advanced Search
Repositories
  • ArrayExpress (9)
  • BioProject (43)
  • ClinicalTrials.gov (1)
  • Dataverse (22)
  • Dryad (5)
  • Figshare (21)
  • ICPSR (2)
  • NURSA (1)
  • NeuroVault:Cols (1)
  • OmicsDI (7)
  • PDB (24)
  • ProteomeXchange (2)
  • SimTK (1)
  • UniProt:Swiss-Prot (12)
  • Zenodo (1)

Feedback?

If you are having problems using our tools, or if you would just like to send us some feedback, please post your questions on GitHub.

Displaying 5 of 5 results for "CALCOCO1"
i
Switch View:
Sorted By:
Title Date Issued Date Released Description
Cocoa all primers riju et al., 2009.xls
08-20-2009 10-29-2015
n/a
Data from: Can intercropping with the world’s three major beverage plants help improve the water use of rubber trees?
06-25-2016 03-07-2017
The dramatic expansion of rubber plantations in mainland South-East Asia and south-west China has caused many eco-environmental problems, especially negative hydrological consequences. These problems have gradually worsened and pose formidable threats to rubber agriculture, especially in the light of increasingly frequent extreme weather events. Although rubber-based agroforestry systems are regarded as the best solution for improving the sustainability of rubber agriculture and environmental conservation, plant water use and related interactions have rarely been examined in such systems. We primarily used stable isotope (δD, δ18O and δ13C) methods to test whether intercropping could improve the water use and extreme weather tolerance (extreme cold and drought in our study) of rubber trees in three types of promising agroforestry systems (i.e. rubber with tea, coffee and cocoa) in Xishuangbanna, China. We found that the rubber tree is a drought-avoidance plant with strong plasticity with respect to water uptake. This characteristic is reflected by its ability to cope with serious seasonal drought, allowing it to avoid interspecific competition for water. The rubber trees showed wasteful water behaviour unless they were intercropped with tea or coffee. However, these intercropped species exhibited drought-tolerance strategies and maintained lower water use efficiencies to strengthen their competitive capacity for surface soil water. The stable δ13C values of the intercrop leaves indicated that all the agroforestry systems have stable internal microclimatic environments or higher resistance. Synthesis and applications. This study suggests that interspecific competition for water can enhance the water use efficiency of drought-avoidance plants (i.e. rubber trees) and lead to complementarity between the root distributions of plants in rubber agroforestry systems (i.e. rubber with tea, coffee and cocoa). All agroforestry systems have higher resistance, but tea was the most suitable intercrop in terms of water use because the interspecific competition for water was moderate and the agroforestry system retained much more soil water and improved the water use efficiency of the rubber tree. Considering the root characteristics of the tea trees, we suggest that the crops selected for intercropping with rubber trees should have a relatively fixed water use pattern, short lateral roots and a moderate amount of fine roots that overlap with the roots of the rubber trees in the shallow soil layer.
Saenko_data archive
11-22-2011 10-20-2015
This file contains phenotypes and genotypes of Bicyclus anynana individuals used in the analysis of linkage between melanine and Ba_black, and Chocolate and Ba_CSAD loci.
Data from: Genetic basis of stage-specific melanism: a putative role for a cysteine sulfinic acid decarboxylase in insect pigmentation
01-11-2012 10-20-2015
Melanism, the overall darkening of the body, is a widespread form of animal adaptation to particular environments, and includes bookcase examples of evolution by natural selection, such as industrial melanism in the peppered moth. The major components of the melanin biosynthesis pathway have been characterized in model insects, but little is known about the genetic basis of life-stage specific melanism such as cases described in some lepidopteran species. Here, we investigate two melanic mutations of Bicyclus anynana butterflies, called Chocolate and melanine, that exclusively affect pigmentation of the larval and adult stages, respectively. Our analysis of Mendelian segregation patterns reveals that the larval and adult melanic phenotypes are due to alleles at different, independently segregating loci. Our linkage mapping analysis excludes the pigmentation candidate gene black as the melanine locus, and implicates the gene encoding a putative PLP-dependant cysteine sulfinic acid decarboxylase as the Chocolate locus. We show variation in coding sequence and in expression levels for this candidate larval melanism locus. This is the first study that suggests a biological function for this gene in insects. Our findings open up exciting opportunities to study the role of this locus in the evolution of adaptive variation in pigmentation, and the uncoupling of regulation of pigment biosynthesis across developmental stages with different ecologies and pressures on body coloration.
Data from: Genotyping-by-sequencing provides the first well-resolved phylogeny for coffee (Coffea) and insights into the evolution of caffeine content in its species: GBS coffee phylogeny and the evolution of caffeine content
02-16-2017 02-24-2017
A comprehensive and meaningful phylogenetic hypothesis for the commercially important coffee genus (Coffea) has long been a key objective for coffee researchers. For molecular studies, progress has been limited by low levels of sequence divergence, leading to insufficient topological resolution and statistical support in phylogenetic trees, particularly for the major lineages and for the numerous species occurring in Madagascar. We report here the first almost fully resolved, broadly sampled phylogenetic hypothesis for coffee, the result of combining genotyping-by-sequencing (GBS) technology with a newly developed, lab-based workflow to integrate short read next-generation sequencing for low numbers of additional samples. Biogeographic patterns indicate either Africa or Asia (or possibly the Arabian Peninsula) as the most likely ancestral locality for the origin of the coffee genus, with independent radiations across Africa, Asia, and the Western Indian Ocean Islands (including Madagascar and Mauritius). The evolution of caffeine, an important trait for commerce and society, was evaluated in light of our phylogeny. High and consistent caffeine content is found only in species from the equatorial, fully humid environments of West and Central Africa, possibly as an adaptive response to increased levels of pest predation. Moderate caffeine production, however, evolved at least one additional time recently (between 2 and 4 Mya) in a Madagascan lineage, which suggests that either the biosynthetic pathway was already in place during the early evolutionary history of coffee, or that caffeine synthesis within the genus is subject to convergent evolution, as is also the case for caffeine synthesis in coffee versus tea and chocolate.