The assembly and reassembly of the genomes of several cotton varieties is reported in Nature Genetics this week, offering insights into the crop plant's evolution and potential avenues for its improvement. A team led by scientists from Wuhan University assembled the genome of the allotetraploid Upland cotton Gossypium herbaceum, which dominates the world's cotton commerce, and improved existing Gossypium arboretum and Gossypium hirsutum genome assemblies. The investigators uncover evidence that all three species may have all originated from a common ancestor that was more phylogenetically related to G. herbaceum than G. arboretum, and discover that allotetraploid formation preceded the speciation of these two cotton types. Other findings include abundant species-specific structural variations in genic regions that changed the expression of many important genes, which may have led to fiber cell improvement in G. hirsutum.
An atlas of the thermal stability of 48,000 proteins across 13 species, ranging from archaea to humans and covering melting temperatures of 30 to 90 degrees Celsius, is published in Nature Methods this week by a Technical University of Munich-led team. Compiled using a mass spectrometry-based proteomic approach, the Meltome atlas represents a resource that can be used to study the relationships between protein stability, protein sequence, protein function, and protein-protein interactions. By mining the data in the atlas, the researchers show, among other things, that "protein thermal stability not only correlates with the optimal growth temperatures at which different species thrive, but also reflects particular physiological and pathological molecular contexts."
A University of Washington team, in collaboration with Illumina, has developed a new method for measuring the dynamics of gene expression in large numbers of single cells and at the level of the whole transcriptome. Called Sci-fate, the technique uses combinatorial cell indexing and 4-thiouridine labeling of newly synthesized mRNA to concurrently profile the whole and newly synthesized transcriptome in each of many single cells. The researchers use Sci-fate to study the cortisol response in more than 6,000 single cultured cells, quantifying the dynamics of the cell cycle and glucocorticoid receptor activation, and exploring their intersection. They also developed software to infer and analyze cell-state transitions.