Supporting data for "Binning Enables Efficient Host Genome Reconstruction in Cnidarian Holobionts"

Dataset type: Genomic, Transcriptomic, Metagenomic
Data released on June 25, 2018

Celis JS; Wibberg D; Ramírez-Portilla C; Rupp O; Sczyrba A; Winkler A; Kalinowski J; Wilke T (2018): Supporting data for "Binning Enables Efficient Host Genome Reconstruction in Cnidarian Holobionts" GigaScience Database. http://dx.doi.org/10.5524/100462

DOI10.5524/100462

Many cnidarians, including stony corals, engage in complex symbiotic associations, comprising the eukaryotic host, photosynthetic algae, and highly diverse microbial communities – together referred to as holobiont. This taxonomic complexity makes sequencing and assembling coral host genomes extremely challenging. Therefore, previous cnidarian genomic projects were based on symbiont-free tissue samples. However, this approach may not be applicable to the majority of cnidarian species for ecological reasons. We therefore evaluated the performance of an alternative method based on sequence binning for reconstructing the genome of the stony coral Porites rus from a hologenomic sample, and compared it to traditional approaches.
Our results demonstrate that binning performs well for hologenomic data, producing sufficient reads for assembling the draft genome of P. rus. An assembly evaluation based on operational criteria showed comparable results to symbiont-free approaches in terms of completeness and usefulness, despite a high degree of fragmentation in our assembly. In addition, we found that binning provides sufficient data for exploratory k-mer estimation of genomic features, such as genome size and heterozygosity.
Binning constitutes a powerful approach for disentangling taxonomically complex coral hologenomes. Considering the recent decline of coral reefs on the one hand and previous limitations to coral genome sequencing on the other hand, binning may facilitate rapid and reliable genome assembly. This study also provides an important milestone in advancing binning from the metagenomic to the hologenomic and from the prokaryotic to the eukaryotic level.

Additional details

Read the peer-reviewed publication(s):

Celis, J. S., Wibberg, D., Ramírez-Portilla, C., Rupp, O., Sczyrba, A., Winkler, A., … Wilke, T. (2018). Binning enables efficient host genome reconstruction in cnidarian holobionts. GigaScience, 7(7). doi:10.1093/gigascience/giy075

Accessions (data included in GigaDB):

BioProject: PRJEB25185
BioProject: PRJEB23570
AE: E-MTAB-6535





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
E-MTAB-6535:Sample 1262591  Porites rus Description:RNA-seq of an adult Porites rus colony...
Life stage:adult
Analyte type:RNA
...
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Prus262591  Porites rus Description:Draft genome sequence of Porites rus
Life stage:adult
Analyte type:DNA
...
+
Prus_16S 496922  coral metagenome Description:16S amplicon analysis of the Porites r...
Life stage:adult
Analyte type:RNA
...
+
Displaying 1-3 of 3 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
transcriptome sequenceBAM1.8 GB2018-06-12
Expression dataEXCEL45.58 MB2018-06-12
Sequence assemblyFASTA980.94 MB2018-06-12
Sequence assemblyFASTA142.4 MB2018-06-12
Sequence readsFASTQ9.39 GB2018-06-12
Sequence readsFASTQ3.55 GB2018-06-12
Sequence readsFASTQ34 MB2018-06-12
Sequence readsFASTQ9.02 GB2018-06-12
Sequence readsFASTQ3.7 GB2018-06-12
Sequence readsFASTQ15.31 GB2018-06-12
Displaying 1-10 of 22 File(s).
Funding body Awardee Award ID Comments
German Academic Exchange Service Juan S Celis 91559856
Bundesministerium für Bildung und Forschung 031A533
Date Action
June 25, 2018 Dataset publish
June 25, 2018 File readme.txt updated
July 4, 2018 Manuscript Link added : 10.1093/gigascience/giy075