DOI: 10.5061/dryad.9r0p6
title: Data from: Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus

description: Extensive genomic diversity within coexisting members of a microbial
 species has been revealed through selected cultured isolates and
 metagenomic assemblies. Yet, the cell-by-cell genomic composition of wild
 uncultured populations of co-occurring cells is largely unknown. In this
 work, we applied large-scale single-cell genomics to study populations of
 the globally abundant marine cyanobacterium Prochlorococcus. We show that
 they are composed of hundreds of subpopulations with distinct “genomic
 backbones,” each backbone consisting of a different set of core gene
 alleles linked to a small distinctive set of flexible genes. These
 subpopulations are estimated to have diverged at least a few million years
 ago, suggesting ancient, stable niche partitioning. Such a large set of
 coexisting subpopulations may be a general feature of free-living
 bacterial species with huge populations in highly mixed habitats.
description: Mapping between ITS and
 MDA namesThis files maps between
 the ITS sequence name and the MDA sequence name. ITS sequence names are
 described by their well in the ITS sanger sequencing plates (96-well
 plates) MDA sequence names are described by their well in the MDA
 reactions plates (384-well plates) ITS sequence name format is as follows:
 for example: &gt;B245a_520_F02_p18 means BATS cruise
 245a, MDA plate 520, ITS plate 18 well F02. To find the relavant MDA well
 use the mapping file ITS_to_MDA_mapping_final.xls In this example the MDA
 well is thus plate 520 well O2ITS_to_MDA_mapping_final.xlsxITS-rRNA multi-alignment of all single cellsAlignment of all ITS sequences used to build the trees and heatmaps in Fig. 1. The format of sequence names is as follows: ITS_all_algn.fastaITS-rRNA multi-alignment of the 96 single cellsMulti-alignment of the ITS of the 96 single cells (as well as of 5 HLII strains) used to generate the tree in Fig 2A.ITS_96_algn.fastaMapping between ITS and MDA names (96 single cells)ITS names and MDA names of the 96 single cells.ITS_to_MDA_96cells.xlsxC1 composite genomeUsed as a reference genome for the reference-guided assembly. Was built from large overlapping contigs of single-cells within the cN2-C1 clade.C1_composite_genome.gbkWhole genome alignment of the 96 single cell partial genomesMulti-alignment of the partial genomes of the 96 single cells used to generate the tree in Fig 2B.WG_96_algn.fastaWhole genome alignment of 8 clonal E. coli partial genomesMulti-alignment of the partial genomes of the 8 clonal E. coli single cells used as a control to estimate the error rate involved in single cell genomics.Ecoli_WG_8_algn.fastaClassification of genes into Clusters of Orthologous Genes (COGs).Classification of genes into Clusters of Orthologous Genes (COGs). Each entry is a gene (or partial gene sequence) in one of the 96 single cells denovo assembled genomes or in a genome of a cultured strains. The number in the beginnig of each header is the COG ID. The fatsa headers for genes in a single cell genome has the following format: &gt;COG ID|MDA name|Detailed name|contig__|Start bp|End bp|+/- Strand|Method|Description The fatsa headers for genes in a complete genome of a cultured strain has the following format: &gt;COG ID|Short name|Detailed name|Start bp|End bp|+/- Strand|Method|COGS.fasta