Phosphate Limitation Responses in Marine Green Algae Are Linked to Reprogramming of the tRNA Epitranscriptome and Codon Usage Bias.

"primary support was through nsf-ios0843119 doe-de-sc0004765 and gbmf 3788 to a z w data availability rna-seq data are available from the ncbi short read archive (sra) under the accession numbers srx712380 to srx712411. phylogenetic reconstructions for all trees discussed in the manuscript have been deposited to figshare repositories under the dois10 6084/m9 figshare 21164086 and 10 6084/m9 figshare 21174397 . each row corresponds to a specific modification the spheres on the left (colors corresponding to a) indicate the ribonucleotides where this modification can occur while the text on the right lists the abbreviation for the given modification (see supplementary dataset s2 supplementary material online for complete names).; all other phylogenies represented by figures in the manuscript were reconstructed using iq-tree as described above and the proteins in supplementary datasets s1 and s3 supplementary material online that were annotated via phylogenetic reconstruction were subjected to preliminary analysis using the mafft (--auto) trimal (-gt 0 8) and fasttree approach described above.; for the unannotated trna modification genes we used conventions for yeast or bacterial orthologs if available (see fig 2a ; supplementary dataset s2 supplementary material online).; for unannotated genes recovered via their codon usage bias ( supplementary dataset s3 supplementary material online) we used the names of described orthologs ( a thaliana cas; curt1a b and c; pab proteins; pgr5; stn7 and stn8; and c reinhardtii phox) or the domain name (chromo).; where multiple recent m commoda paralogs are present in a tree (the pnas family) the genes were numbered according to their transcript identifier (see supplementary dataset s3 supplementary material online). data availability rna-seq data are available from the ncbi short read archive (sra) under the accession numbers srx712380"

"Funding E.H. was supported by Gordon and Betty Moore Foundation (GBMF) 3788 and a Lumina Quaeruntur Award from the Czech Academy of Sciences (LQ200962204). E.S. was supported by Discovery Grant RGPIN-2019-04287 from the Natural Sciences and Engineering Research Council of Canada. Primary support was through NSF-IOS0843119, DOE-DE-SC0004765, and GBMF 3788 to A.Z.W."