The weather is grey as most days here, so let me start with some colors by talking about a column of /Nature Methods/ in 2010, written (mainly) by Bang Wong, who is now the creative director of the Broad Institute.

  • /Color coding/ and /Mapping quantitative data to color/, Nature Methods, 2010. Colors have three primary components, hue, saturation, and lightness. For categorical data, selecting a serial of different hues together with increasing saturation and lightness seems great to distinguish various categories. But it would be better to keep the number of categories not larger than six. For quantitative data, the main principle is to keep the hue but adjust the saturation. If there are two categories in data, using two hues. BTW, the whole column looks great as a starting point for data visualization, so some of them would appear again here.
  • /Heterozygous, polyploid, giant bacterium, Achromatium, possesses an identical functional inventory worldwide across drastically different ecosystems/ Molecular Biology and Evolution, 2020. Polyploids in bacterium! They are hyperpolyploids, usually with 300 chromosomes! All lineages (or strains) have more or less the same gene inventory, so it has been believed that gene expression is regulated according to their habitats, e.g., from fresh to saline water.
  • /Uncovering a novel function of the CCR4-NOT complex in phytochrome A-mediated light signaling in plants/, eLife, 2021. Phytochromes are photoreceptors for red and far-red light, while phytochrome A is mainly for far-red light. Their response to light forms a switch to sense the ratio of red:far-red light so that plants can sense sunlight from canopy shade. A gene, NOT9B, duplicated through the WGD in Brassicaceae (not sure alpha or beta), gets a new function to regulate the CCR4-NOT complex negatively. It can bind with both CCR4-NOT (the scaffold protein NOT1) and Phytochrome A, while its paralog NOT9A can only interact with NOT1 rather than Phytochrome A. When it is dark, NOT9B binds to NOT1 hence silence the activity of CCR4-NOT; when there is light, NOT9B interacts with Phytochrome A, thus relieving CCR4-NOT that triggers cascade reactions like far-red specific gene expression and isoform splicing.
  • /Synteny guided resolution of gene trees clarifies the functional impacts of whole-genome duplications/, Molecular Biology and Evolution, 2020. It is an intuitive idea to adjust gene tree topologies to obey syntenic relationships generated by WGD, followed by comparing the tree topologies with the ML trees to see if they are nearly-ML trees. One assumption behind the implementation, as far as I understand, is that orthologous syntenic pairs are more similar to paralogous syntenic pairs. Hence the method maximizes the deltaS score by threading (artificial?) syntenic regions. It then identifies orthologous and paralogous syntenic regions among species and proposes gene trees consistent with the synteny.

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