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98 results for “Data Cloning”

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dryad28/100

Data from: Genome sequence of M6, a diploid inbred clone of the high glycoalkaloid-producing tuber-bearing potato species Solanum chacoense, reveals residual heterozygosity

Cultivated potato (Solanum tuberosum L.) is a highly heterozygous autotetraploid that presents challenges in genome analyses and breeding. Wild potato species serve as a resource for the introgression of important agronomic traits into cultivated potato. One key species is Solanum chacoense and the diploid, inbred clone M6, which is self-compatible and has desirable tuber market quality and disease resistance traits. Sequencing and assembly of the genome of the M6 clone of S. chacoense generated an assembly of 825,767,562 bp in 8,260 scaffolds with an N50 scaffold size of 713,602 bp. Pseudomolecule construction anchored 508 Mb of the genome assembly into 12 chromosomes. Genome annotation yielded 49,124 high confidence gene models representing 37,740 genes. Comparative analyses of the M6 genome with six other Solanaceae species revealed a core set of 158,367 Solanaceae genes and 1,897 genes unique to three potato species. Analysis of single nucleotide polymorphisms across the M6 genome revealed enhanced residual heterozygosity on chromosomes 4, 8 and 9 relative to the other chromosomes. Access to the M6 genome provides a resource for identification of key genes for important agronomic traits and aids in genome-enabled development of inbred diploid potatoes with the potential to accelerate potato breeding.

opencc-zeroDec 2017View details →

dryad28/100

Data from: Host species of a sexual-parasite do not differentiate between clones of Amazon mollies

A major mechanism of pre-zygotic isolation is the ability for individuals to recognize conspecifics. In gynogenetic species complexes, the sexual host species occur in syntopy with the unisexual species that relies on the sexuals' sperm for reproduction, which provide an excellent opportunity for the evolution of fine-tuned species recognition capabilities. Here, we examined if males and females from both parental species (sailfin molly, Poecilia latipinna, and Atlantic molly, P. mexicana) can distinguish between different clonal lineages of the hybrid, all-female Amazon molly (P. formosa). Both males and females were presented with the choice of two different pairings of Amazon mollies: 1) a sympatric female and an allopatric female; and 2) two sympatric females. We found that neither males nor females of sailfin or Atlantic mollies show a preference for a clone type. These results suggest that either the parental species do not have the ability to recognize different Amazon molly clones or they recognize but do not have a preference for a specific Amazon molly clone.

opencc-zeroDec 2016View details →

dryad28/100

Data from: How clonal are clones? A quest for loss of heterozygosity during asexual reproduction in Daphnia magna

Due to the lack of recombination, asexual organisms are predicted to accumulate mutations and show high levels of within-individual allelic divergence (heterozygosity) however, empirical evidence for this prediction is largely missing. Instead, evidence of genome homogenization during asexual reproduction is accumulating. Ameiotic crossover recombination is a mechanism that could lead to long genomic stretches of loss of heterozygosity (LOH) and unmasking of mutations that have little or no effect in heterozygous state. Therefore, LOH might be an important force for inducing variation among asexual offspring and may contribute to the limited longevity of asexual lineages. To investigate the genetic consequences of asexuality, here we used high-throughput sequencing of Daphnia magna for assessing the rate of LOH over a single generation of asexual reproduction. Comparing parthenogenetic daughters with their mothers at several thousand genetic markers generated by Restriction site Associated DNA (RAD) sequencing resulted in high LOH rate estimation that largely overlapped with our estimates for the error rate. To distinguish these two, we Sanger re-sequenced the top 18 candidate RAD-loci for LOH, and all of them proved to be false positives. Hence, even though we cannot exclude the possibility that short stretches of LOH occur in genomic regions not covered by our markers, we conclude that LOH does not occur frequently during asexual reproduction in D. magna and ameiotic crossovers are very rare or absent. This finding suggests that clonal lineages of D. magna will remain genetically homogeneous at least over time periods typically relevant for experimental work.

opencc-zeroDec 2018View details →

dryad28/100

Data from: Assessing parameter identifiability in phylogenetic models using Data Cloning

The success of model-based methods in phylogenetics has motivated much research aimed at generating new, biologically informative models. This new computer-intensive approaches to phylogenetics demands validation studies and sound measures of performance. To date such work has consisted only of simulation studies, estimation of known phylogenies and difficult mathematical analyses assessing the estimability of parameters. Little practical guidance has been available to practitioners and theoreticians alike as to when and why the parameters in a particular model can be identified reliably. Here, we illustrate how Data Cloning (DC), a recently developed methodology to compute the Maximum Likelihood estimates along with their asymptotic variance, can be used to diagnose structural parameter non-identifiability (NI) and distinguish it from other parameter estimability problems including the case where parameters are structurally identifiable, but are not estimable in given data set (INE), and the case where parameters are identifiable, and estimable, but only weakly so (WE). The application of the DC theorem uses well-known and widely used Bayesian computational techniques. With the DC approach, practitioners can use any Bayesian phylogenetics software to be able to diagnose non-identifiability. Theoreticians and practitioners alike now have a powerful tool to detect non-identifiability while investigating complex modeling scenarios, where getting closed-form expressions in a probabilistic study is complicated. Furthermore, here we also show how DC can be used as a tool to examine and eliminate the influence of the priors, in particular if the process of prior elicitation is not straightforward. Finally, when applied to phylogenetic inference, DC can be used to study at least two important statistical questions: assessing identifiability of discrete parameters, like the tree topology, and developing efficient sampling methods for computationally expensive posterior densities.

opencc-zeroDec 2011View details →

dryad28/100

Data from: Species level phylogeny and polyploid relationships in Hordeum (Poaceae) inferred by next-generation sequencing and in-silico cloning of multiple nuclear loci

Polyploidization is an important speciation mechanism in the barley genus Hordeum. To analyze evolutionary changes after allopolyploidization, knowledge of parental relationships is essential. One chloroplast and 12 nuclear single-copy loci were amplified by polymerase chain reaction (PCR) in all Hordeum plus six out-group species. Amplicons from each of 96 individuals were pooled, sheared, labeled with individual-specific barcodes and sequenced in a single run on a 454 platform. Reference sequences were obtained by cloning and Sanger sequencing of all loci for nine supplementary individuals. The 454 reads were assembled into contigs representing the 13 loci and, for polyploids, also homoeologues. Phylogenetic analyses were conducted for all loci separately and for a concatenated data matrix of all loci. For diploid taxa, a Bayesian concordance analysis and a coalescent-based dated species tree was inferred from all gene trees. Chloroplast matK was used to determine the maternal parent in allopolyploid taxa. The relative performance of different multilocus analyses in the presence of incomplete lineage sorting and hybridization was also assessed. The resulting multilocus phylogeny reveals for the first time species phylogeny and progenitor-derivative relationships of all di- and polyploid Hordeum taxa within a single analysis. Our study proves that it is possible to obtain a multilocus species-level phylogeny for di- and polyploid taxa by combining PCR with next-generation sequencing, without cloning and without creating a heavy load of sequence data.

opencc-zeroDec 2014View details →

zenodo28/100

Lipid data for clone BL21.pLS12.pLS29

Lipid data describing the composition of clone BL21.pLS12.pLS29 in triplicate

opencc-by-4.0Jul 2024View details →

dryad28/100

Primary data used to calculate predator-induced morphological changes in two Daphnia species-associated clones

The expression of inducible defences in reaction to an inconsistent predation pressure is especially well investigated in the freshwater keystone filter-feeder Daphnia. Out of their many inducible defences, which increase their fitness, the highest diversity of induced traits is found within their morphology. In recent time the focus of studies on these has switched, from the previously thoroughly covered large-scale defences, e.g., elongated/enlarged tail-spines, helmets and crests, to rather small-scale predator-induced changes. Inconspicuous spinules that cover the dorsal and ventral carapace margins have only rarely been featured in studies. We, therefore, tested two well-studied Daphnia species (D. magna and D. longicephala) for predator-induced changes concerning the spinules, i.e., their area of distribution relative to the body length (relative dorsal/ventral spinules-bearing area, relSBA) and their change in length (mean spinule length of the five central spinules along the dorsal/ventral carapace margin, mean SL). As invertebrate and vertebrate predators display differently built catching structures, those of invertebrate predators being more delicate, the defensive structures against these predator groups might vary accordingly. To test this, we exposed the daphnids to the vertebrate Leucaspius delineatus and a well co-studied predator of the respective Daphnia species, i.e., Triops cancriformis or Notontecta maculata. Our study discovered induced changes of the spinules' lengths and an area they cover. These changes of inconspicuous traits appear not only to be predator-dependent, but also Daphnia-specific. The inconspicuous morphological changes of Daphnia, in combination with the large scale defences, here measured pointers for the expression of inducible defences were the tail spines (relative tail spine length, relTSL) in both species and the crest in D. longicephala, and some ultrastructural defences are suspected to be rather specifically customised collective defences.

opencc-zeroNov 2022View details →

dryad28/100