Three reference genomes for freshwater diatom ecology and evolution

This repository contains the genome assemblies and gene models provided for "Three reference genomes for freshwater diatom ecology and evolution"

Authors:

Wade R. Roberts (email: wader [at] uark [dot] edu)

Andrew J. Alverson (email: aja [at] uark [dot] edu)

The Whole Genome Shotgun (WGS) projects are available from NCBI GenBank under accession JALLPB020000000 (C. tholiformis), JALLBG020000000 (D. pseudostelligera), and JALLAZ020000000 (P. triporus).

The following files are included:

Cyclostephanos tholiformis strain AJA228-03

    aja228-03.consensus.fasta

    aja228-03.consensus.gff3        aja228-03.consensus.proteins.fasta

    aja228-03.consensus.combined_uniprot_annotation.csv

    aja228-03.consensus.panther_annotation.csv

    aja228-03.consensus.pfam_annotation.csv

Discostella pseudostelligera strain AJA232-27

    aja232-27.consensus.fasta

    aja232-27.consensus.gff3        aja232-27.consensus.proteins.fasta

    aja232-27.consensus.combined_uniprot_annotation.csv

    aja232-27.consensus.panther_annotation.csv

    aja232-27.consensus.pfam_annotation.csv

Praestephanos triporus strain AJA276-08

    aja276-08.consensus.fasta

    aja276-08.consensus.gff3        aja276-08.consensus.proteins.fasta

    aja276-08.consensus.combined_uniprot_annotation.csv

    aja276-08.consensus.panther_annotation.csv

    aja276-08.consensus.pfam_annotation.csv

R code and phylogenetic tree to reproduce Figure 1 in the manuscript

    plot-figure-1.R

    busc.prot.concat.partition.rooted.tree