EphyBase

FResources

Genome assembly, gene models and sequences

• Genome assembly (gzipped .fa)
  Assembly of Ephydatia muelleri genome
• Gene models (gff)
  Gene models in gff format, giving co-ordinates and content
  
• Gene sequences (aa, cds, mRNA, exons)
  Assorted sequence files representing genome contents
  
• Masked version of genome (hard masked)
  Repetitive sequence within genome masked as ‘N’
  
• jBROWSE website
  Browsable version of the E. muelleri genome
• BLAST server
  Blastable version of the E. muelleri genome and protein set
• RNAseq data: Differential gene expression: Transcript and Gene 
• Raw RNAseq reads (associated with the above Transcript/Gene data from Kenny et al 2020)

Paper and supplementary files

• Genome paper: Nature Communications
  Main text of paper describing the genome of E. muelleri
• Supplementary Information File (contains Supplementary Notes 1-11)
• Supplementary Data 1: Flavobacterium sp. sequence, predicted proteins and cds sequences 
• Supplementary Data 2: BLAST/functional annotation results, Ephydatia muelleri gene annotations
• Supplementary Data 3: Comparative genome statistics and scripts used in generating figures 
• Supplementary Data 4: Synteny analysis, additional plots and data
• Supplementary Data 5: Full lists of genes, gain/loss analyses
• Supplementary Data 6: Full results and orthogroups, positive selection analyses (and more)
• Supplementary Data 7: Clustering analyses, lists of genes in each cluster (and with original fasta here)
• Supplementary Data 8: SNARE data, full gene sequences and annotation
• Supplementary Data 9: Amplicon sequencing data, raw and intermediate results
• High quality versions of all figures are available here
• In case of issues with the above links, a mirror of the data is available here

Additional resources

• Behind the paper – Nature Ecology & Evolution Community Blog
• ‘Sneezing’ Ephydatia muelleri
  Inflation-contraction responses in response to stimuli
  
• Useful papers: a community resource
  A variety of papers from the Leys lab
  And freshwater sponges in particular
• Other sponge data & videos
  • Other Sponge transcriptomes
  • Ephydatia muelleri Algal symbiosis transcriptomes

Mirror download site