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255 results for “Daucus”
Kellogg Biological Station site, station Kellogg Biological Station, study of aboveground net primary productivity of Daucus carota in units of gramsPerMeterSquaredPerYear on a yearly timescale
The EcoTrends project was established in 2004 by Dr. Debra Peters (Jornada Basin LTER, USDA-ARS Jornada Experimental Range) and Dr. Ariel Lugo (Luquillo LTER, USDA-FS Luquillo Experimental Forest) to support the collection and analysis of long-term ecological datasets. The project is a large synthesis effort focused on improving the accessibility and use of long-term data. At present, there are ~50 state and federally funded research sites that are participating and contributing to the EcoTrends project, including all 26 Long-Term Ecological Research (LTER) sites and sites funded by the USDA Agriculture Research Service (ARS), USDA Forest Service, US Department of Energy, US Geological Survey (USGS) and numerous universities. Data from the EcoTrends project are available through an exploratory web portal (http://www.ecotrends.info). This web portal enables the continuation of data compilation and accessibility by users through an interactive web application. Ongoing data compilation is updated through both manual and automatic processing as part of the LTER Provenance Aware Synthesis Tracking Architecture (PASTA). The web portal is a collaboration between the Jornada LTER and the LTER Network Office. The following dataset from Kellogg Biological Station (KBS) contains aboveground net primary productivity of Daucus carota measurements in gramsPerMeterSquaredPerYear units and were aggregated to a yearly timescale.
Mitochondrial DNA sequence phylogeny of Daucus
We explored the phylogenetic utility of mitochondrial DNA sequences in Daucus and compared the results with prior phylogenetic results using the same 36 accessions of Daucus (and two additional outgroups) with plastid DNA sequences and with other nuclear results. As in the plastid study we used Illumina HiSeq sequencer to obtain resequencing data of the same accessions of Daucus and outgroups, and analyzed the data with maximum parsimony and maximum likelihood. We obtained data from 47 of 71 total mitochondrial genes but only 17 of these 47 genes recovered major clades that were common in prior plastid and nuclear studies. Our phylogenetic trees of the concatenated data set of 47 genes were moderately resolved, with 100% bootstrap support for most of the external and many of the internal clades, except for the clade of D. carota and its most closely related species D. syrticus. There are areas of hard incongruence with phylogenies using plastid and nuclear data. In agreement with other studies, we conclude that mitochondrial sequences are generally poor phylogenetic markers, at least at the genus level, despite their utility in some other studies.
Data from: Mitochondrial gene diversity associated with the atp9 stop codon in natural populations of wild carrot (Daucus carota ssp. carota)
Mitochondrial genomes extracted from wild populations of Daucus carota have been used as a genetic resource by breeders of cultivated carrot, yet little is known concerning the extent of their diversity in nature. Of special interest is a SNP in the putative stop codon of the mitochondrial gene atp9 that has been associated previously with male-sterile and male-fertile phenotypic variants. In this study either sequence or PCR/RFLP genotypes were obtained from the mitochondrial genes atp1, atp9 and cox1 found in D. carota individuals collected from 24 populations in the eastern U.S. More than half of the 128 individuals surveyed had a CAA or AAA, rather than TAA, genotype at the position usually thought to function as an atp9 stop codon in this species. We also found no evidence for mitochondrial RNA editing (Cytosine to Uridine) of the CAA stop codon in either floral or leaf tissue. Evidence for intra-genic recombination, as opposed the more common inter-genic recombination in plant mitochondrial genomes, in our data set is presented. Indel and SNP variants elsewhere in atp9, and in the other two genes surveyed, were non-randomly associated with the three atp9 stop codon variants, though further analysis suggested that multi-locus genotypic diversity had been enhanced by recombination. Overall the mitochondrial genetic diversity was only modestly structured among populations with an Fst of 0.34.
Daucus carota (Apiaceae) - inflorescence - closeup of flower interior
Image of Daucus carota (Apiaceae) - inflorescence - closeup of flower interior
Daucus carota (Apiaceae) - inflorescence - closeup of flower interior
Image of Daucus carota (Apiaceae) - inflorescence - closeup of flower interior
Daucus carota (Apiaceae) - inflorescence - whole - unspecified
Image of Daucus carota (Apiaceae) - inflorescence - whole - unspecified
Daucus carota (Apiaceae) - leaf - on upper stem
Image of Daucus carota (Apiaceae) - leaf - on upper stem
Daucus carota (Apiaceae) - inflorescence - frontal view of flower
Image of Daucus carota (Apiaceae) - inflorescence - frontal view of flower
Daucus carota (Apiaceae) - inflorescence - lateral view of flower
Image of Daucus carota (Apiaceae) - inflorescence - lateral view of flower
Daucus carota (Apiaceae) - inflorescence - ventral view of flower + perianth
Image of Daucus carota (Apiaceae) - inflorescence - ventral view of flower + perianth
Daucus carota (Apiaceae) - stem - showing leaf bases
Image of Daucus carota (Apiaceae) - stem - showing leaf bases
Daucus carota (Apiaceae) - leaf - basal or on lower stem
Image of Daucus carota (Apiaceae) - leaf - basal or on lower stem
Daucus carota (Apiaceae) - whole plant - in flower - general view
Image of Daucus carota (Apiaceae) - whole plant - in flower - general view
Fig. 2 in Polyoxygenated germacranes from Daucus carota and their antimalarial transmission blocking activity
Fig. 2. Left: COSY (red) and HMBC (arrows) correlations of 4; right: ROESY correlations of 4. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
Fig. 3 in Polyoxygenated germacranes from Daucus carota and their antimalarial transmission blocking activity
Fig. 3. In vitro P. berghei ookinete development assays with metabolites from D. carota assessed at concentrations of 0.001, 0.01, 0.1, 1 and 50 mM. Values were calculated with respect to negative control (DMSO). * = significant inhibition (p value <0.05 paired t-test). Error bars indicate SEM within biological triplicates.
Data from: Mitochondrial gene diversity associated with the atp9 stop codon in natural populations of wild carrot (Daucus carota ssp. carota)
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Subspecies variation of Daucus carota coastal (“gummifer”) morphotypes (Apiaceae) using genotyping-by-sequencing
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Data from: Identification of transcription factor genes involved in anthocyanin biosynthesis in carrot (Daucus carota L.) using RNA-Seq
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Mitochondrial DNA sequence phylogeny of Daucus
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Data from: Genotyping-by-sequencing provides the discriminating power to investigate the subspecies of Daucus carota (Apiaceae)
Background: The majority of the subspecies of Daucus carota have not yet been discriminated clearly by various molecular or morphological methods and hence their phylogeny and classification remains unresolved. Recent studies using 94 nuclear orthologs and morphological characters, and studies employing other molecular approaches were unable to distinguish clearly many of the subspecies. Fertile intercrosses among traditionally recognized subspecies are well documented. We here explore the utility of single nucleotide polymorphisms (SNPs) generated by genotyping-by-sequencing (GBS) to serve as an effective molecular method to discriminate the subspecies of the D. carota complex. Results: We used GBS to obtain SNPs covering all nine Daucus carota chromosomes from 162 accessions of Daucus and two related genera. To study Daucus phylogeny, we scored a total of 10,814 or 38,920 SNPs with a maximum of 10 or 30 % missing data, respectively. To investigate the subspecies of D. carota, we employed two data sets including 150 accessions: (i) rate of missing data 10 % with a total of 18,565 SNPs, and (ii) rate of missing data 30 %, totaling 43,713 SNPs. Consistent with prior results, the topology of both data sets separated species with 2n = 18 chromosome from all other species. Our results place all cultivated carrots (D. carota subsp. sativus) in a single clade. The wild members of D. carota from central Asia were on a clade with eastern members of subsp. sativus. The other subspecies of D. carota were in four clades associated with geographic groups: (1) the Balkan Peninsula and the Middle East, (2) North America and Europe, (3) North Africa exclusive of Morocco, and (4) the Iberian Peninsula and Morocco. Daucus carota subsp. maximus was discriminated, but neither it, nor subsp. gummifer (defined in a broad sense) are monophyletic. Conclusions: Our study suggests that (1) the morphotypes identified as D. carota subspecies gummifer (as currently broadly circumscribed), all confined to areas near the Atlantic Ocean and the western Mediterranean Sea, have separate origins from sympatric members of other subspecies of D. carota, (2) D. carota subsp. maximus, on two clades with some accessions of subsp. carota, can be distinguished from each other but only with poor morphological support, (3) D. carota subsp. capillifolius, well distinguished morphologically, is an apospecies relative to North African populations of D. carota subsp. carota, (4) the eastern cultivated carrots have origins closer to wild carrots from central Asia than to western cultivated carrots, and (5) large SNP data sets are suitable for species-level phylogenetic studies in Daucus.
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