Amphimedon queenslandica (Sponge)



About the genome:


Overview

Sponges are an ancient group of animals that diverged from other metazoans over 600 million years ago. Here we present the draft genome sequence of Amphimedon queenslandica, a demosponge from the Great Barrier Reef, and show that it is remarkably similar to other animal genomes in content, structure and organization. Comparative analysis enabled by the sequencing of the sponge genome reveals genomic events linked to the origin and early evolution of animals, including the appearance, expansion and diversification of pan-metazoan transcription factor, signalling pathway and structural genes. This diverse of genes correlates with critical aspects of all metazoan body plans, and comprises cell cycle control and growth, development, somatic- and germ-cell specification, cell adhesion, innate immunity and allorecognition. Notably, many of the genes associated with the emergence of animals are also implicated in cancer, which arises from defects in basic processes associated with metazoan multicellularity.

Assembly and annotation

Amphimedon queenslandica is a hermaphroditic spermcast spawner, and cannot be readily inbred in the laboratory. Adult sponges also harbour many commensal microbes. To minimize allelic variation and microbial contamination we sequenced genomic DNA from multiple embryos and larvae from a single mother. This DNA contains four dominant parental haplotypes (~3% polymorphism), although a single brood may have multiple fathers. We used ~9-fold whole-genome Sanger shotgun coverage to produce a ~167-megabase-pair assembly that typically represents each locus once rather than splitting alleles and captures ~97% of the protein-coding gene content.

Statistics

Genome
The main genome assembly is approximately 167.1 Mb (13.2% gap)
Scaffold N50 (L50) = 310/119.9 KB
Contig N50 (L50) = 2526/11.7 KB
647 scaffolds are > 50kb in size, representing approximately 65.8% of the genome
Loci
29,600 total loci containing protein-coding transcripts

FAQ

How was the genome sequenced?

Amphimedon queenslandica is a hermaphroditic spermcast spawner, and cannot be readily inbred in the laboratory. Adult sponges also harbour many commensal microbes. To minimize allelic variation and microbial contamination we sequenced genomic DNA from multiple embryos and larvae from a single mother. This DNA contains four dominant parental haplotypes (~3% polymorphism), although a single brood may have multiple fathers. We used ~9-fold whole-genome Sanger shotgun coverage to produce a ~167-megabase-pair assembly that typically represents each locus once rather than splitting alleles and captures ~97% of the protein-coding gene content.

How was the assembly generated?

The Amphimedon genome was assembled using a custom approach developed for polymorphic genomes. In brief, passing reads are aligned in all pairwise combinations; clusters of overlapping reads are identified as likely derived from the same genomic locus; contigs are formed by local assemblies of clusters, which are subsequently ordered and oriented into scaffolds.

Reference Publication
Srivastava M, Simakov O, Chapman J, Fahey B, Gauthier ME, Mitros T, Richards GS, Conaco C, Dacre M, Hellsten U, Larroux C, Putnam NH, Stanke M, Adamska M, Darling A, Degnan SM, Oakley TH, Plachetzki DC, Zhai Y, Adamski M, Calcino A, Cummins SF, Goodstein DM, Harris C, Jackson DJ, Leys SP, Shu S, Woodcroft BJ, Vervoort M, Kosik KS, Manning G, Degnan BM, Rokhsar DS. The Amphimedon queenslandica genome and the evolution of animal complexity. Nature. 2010 Aug 5;466(7307):720-6. doi: 10.1038/nature09201. PubMed PMID: 20686567; PubMedCentral PMCID: PMC3130542.

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