Archive for February, 2019

Divergent gene expression levels between diploid and autotetraploid Tolmiea relative to the total transcriptome, the cell, and biomass.

Tuesday, February 19th, 2019

A simplified example of how spike‐in standards can be used during read normalization to enable comparisons of expression level at different biological scales between a hypothetical diploid–polyploid pair with differing cell density. The large circles represent a unit of biomass and contain a number of cells (green squares). Beneath each circle is a depiction of how the read normalizations are calculated. Under a per transcriptome normalization, the ratio of target transcripts to the total transcriptome is compared. The per biomass normalization uses the ratio of the transcript of interest to the spike‐in transcripts. The per cell normalization also uses the ratio of the transcript of interest to spike‐in transcripts, but scales the spike‐in transcript abundance by cell density, represented here by multiplying the spike‐in abundance by the number of contributing cells. Whether the transcript of interest would be found as not differentially expressed (=) or upregulated (<) in the polyploid under each normalization is indicated (downregulated not included). DE: differential expression.

Visger, C. J., G. K.-S. Wong, Y. Zhang, P. S. Soltis, and D. E. Soltis. 2019. Divergent gene expression levels between diploid and autotetraploid Tolmiea relative to the total transcriptome, the cell, and biomass. American Journal of Botany [View on publisher’s site]

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A chromosomal-scale genome assembly of Tectona grandis reveals the importance of tandem gene duplication and enables discovery of genes in natural product biosynthetic pathways.

Wednesday, February 13th, 2019
Zhao, D., J. P. Hamilton, W. W. Bhat, S. R. Johnson, G. T. Godden, T. J. Kinser, B. Boachon, N. Dudareva, D. E. Soltis, P. S. Soltis, B. Hamberger, and C. R. Buell. 2019. A chromosomal-scale genome assembly of Tectona grandis reveals the importance of tandem gene duplication and enables discovery of genes in natural product biosynthetic pathways. Gigascience, doi: 10.1093/gigascience/giz005.

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Plastid phylogenomic insights into the evolution of Caryophyllales

Tuesday, February 12th, 2019
Graphical abstract of Gang et al 2019.Yao, G., J.-J. Jin, H.-T. Li, J.-B. Yang, V. Shiva Mandala, M. Croley, R. Mostow, N. A. Douglas, M. W. Chase, M. J. M. Christenhusz, D. E. Soltis, P. S. Soltis, S. A. Smith, S. F. Brockington, M. J. Moore, T.-S. Yi, and D.-Z. Li. 2019. Plastid phylogenomic insights into the evolution of Caryophyllales. Molecular Phylogenetics and Evolution, doi: 10.1016/j.ympev.2018.12.023.

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