1,720,972 research outputs found
Identification of three large full-sib families of Quercus rubra for genetic mapping in an isolated planting outside the species’ range in Germany
No full textAbstract Forest tree breeding faces challenges due to long generation times and high costs. To address these issues, the concept of “breeding without breeding” (BwB) offers the opportunity to accelerate breeding cycles by using naturally generated half- sib and full-sib families. An isolated population of trees may provide an ideal environment to identify full-sib families for genetic mapping without the need for controlled pollination. In this study, paternity analysis based on genotyping of 16 SSR markers in 1232 seedlings identified three large full-sib families of Quercus rubra (Qr_N - Qr_W with 576 siblings, Qr_N - Qr_S with 175 siblings and 124 siblings in the family Qr_P - Qr_11). Paternity assignments were effectively corroborated by segregation analysis, resulting in large F 1 full-sib families for further experiments such as Quantitative Trait Locus (QTL) mapping
De novo assembly and annotation of a transcriptome during xilogenesis in Pinus canariensis Sm. ex. D.C
No full textTranscriptomic analysis of Pinus canariensis during the resprouting process in response to mechanical wounding
No full textDe novo assembly and annotation of a transcriptome during xilogenesis in Pinus canariensis Sm. ex. D.C
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Transcriptome analysis of developing xylem of Pinus canariensis during the growing season
No full textHardware Performance Evaluation of De novo Transcriptome Assembly Software in Amazon Elastic Compute Cloud
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Background:
Bioinformatics software for RNA-seq analysis has a high computational
requirement in terms of the number of CPUs, RAM size, and processor characteristics.
Specifically, de novo transcriptome assembly demands large computational infrastructure due to
the massive data size, and complexity of the algorithms employed. Comparative studies on the
quality of the transcriptome yielded by de novo assemblers have been previously published,
lacking, however, a hardware efficiency-oriented approach to help select the assembly hardware
platform in a cost-efficient way.
Objective:
We tested the performance of two popular de novo transcriptome assemblers, Trinity
and SOAPdenovo-Trans (SDNT), in terms of cost-efficiency and quality to assess limitations, and
provided troubleshooting and guidelines to run transcriptome assemblies efficiently.
Methods:
We built virtual machines with different hardware characteristics (CPU number, RAM
size) in the Amazon Elastic Compute Cloud of the Amazon Web Services. Using simulated and
real data sets, we measured the elapsed time, cost, CPU percentage and output size of small and
large data set assemblies.
Results:
For small data sets, SDNT outperformed Trinity by an order the magnitude, significantly
reducing the time duration and costs of the assembly. For large data sets, Trinity performed better
than SDNT. Both the assemblers provide good quality transcriptomes.
Conclusion:
The selection of the optimal transcriptome assembler and provision of computational
resources depend on the combined effect of size and complexity of RNA-seq experiments.
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Transcriptomic analysis of wound xylem formation in Pinus canariensis
No full textWoody plants, especially trees, usually must face several injuries caused by different agents during their lives. Healing of injuries in stem and branches, affecting the vascular cambium and xylem can take several years. In conifers, healing takes place mainly from the remaining vascular cambium in the margin of the wound. The woundwood formed in conifers during healing usually presents malformed and disordered tracheids as well as abundant traumatic resin ducts. These characteristics affect its functionality as water conductor and its technological properties
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