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Science Papers Describe Influence of Nutrient Availability on Marine Genomes, Single-Cell Seasquirt Study

The selective pressure of nutrient availability can influence the protein-coding genome of marine microbes, suggesting a role for the environment in the evolution of the genetic code, according to a study in Science this week. Nitrogen and carbon are major limiting factors in a variety of ecosystems and their availability is believed to be a strong selective force among microbes, which have evolved to optimize nutrient use. Still, little is known about the impact of so-called "resource-driven selection" on the structure of the microbial genetic code. To investigate, scientists from Rockefeller University analyzed sets of metagenomic and single-cell genome data of marine microbes, along with environmental measurements, and find that a significant portion of the selection exerted on microbes is explained by the environment and is associated with nitrogen availability. Notably, nitrogen conservation optimization is encoded in the structure of the standard genetic code, the study's authors write, "providing robustness against mutations that increase carbon and nitrogen incorporation into protein sequences."

A single-cell RNA sequencing analysis of lineage specification in early chordate embryogenesis, using the seasquirt (Ciona savigny) as a model, is published in Science Advances this week. A team led by scientists from the Sloan Kettering Institute reconstructed a developmental landscape of 47 cell types over eight cell cycles in the wild-type seasquirt embryo and identified eight fate transformations upon fibroblast growth factor inhibition. For most of the asymmetric cell divisions, they find that the bipotent mother cell predominantly shows the gene signature of one daughter. The investigators also expanded the notochord gene regulatory network with 18 genes that may function in parallel to the master regulator Brachyury. When the findings were compared to a mouse dataset on early embryogenesis, they found only a small number of transcription factors are conserved between homologous tissues.