Supplementary code and data for our manuscripts “Novel integrative elements and genomic plasticity in ocean ecosystems” describing Tycheposons - a new class of mobile genetic elements in Prochlorococcus and other marine bacteria that are abundant in marine vesicles and viruses.
See
element-finder/binfor the scripts to predict the mobile elements in genomic data.element-finder/datafor the profiles of signature genes.elements-profor elements in Prochlorococcus.elements-gorg-single-cellsfor elements in other marine bacteria.elements-tara-viralfor elements found in Tara Oceans viral-fraction metagenome assemblies.data-profor reference-scaffolded and annotated Prochlorococcus genomes and a phylogenetic tree.MIT0604-nanoporefor the nanopore assemblies of Prochlorococcus strain MIT0604 containing copies of a mobile element carrying a nitrate assimilation gene cluster.rnaseq-profor differential gene expression analysis of Prochlorococcus with focus on element responseYR-phylogenyfor sequences, alignment and phylogenetic tree of tyrosine recombinases.vesicles-abundancefor differential abundance analysis of element hallmark genes in vesicles