Amphimedon queenslandica Assembly and Gene Annotation

About Amphimedon queenslandica

Amphimedon queenslandica (formerly A. reniera) is a sponge, discovered in 1998 and formally described in 2006 [1]. Despite its recent identification, this native of Great Barrier Reef has already proved itself a useful subject for the study of the evolutionary origins of metazoan development [2,3], and is the first member of phylum Porifera to have had its genome sequenced.

Picture credit (Creative Commons BY 2.5): Wikimedia Commons 2007

Assembly

Genomic DNA was isolated from ~1,500 embryos and larvae obtained from the brood chambers of a single mother sponge and the genome was sequenced and assembled by the Joint Genome Institute in 2010. This ~167 Mb assembly was constructed from ~9x coverage Sanger shotgun sequencing and covers ~97% of the protein-coding regions. The genome has a scaffold N50 of 120kb and contig N50 of 11.2kb.

Annotation

Ensembl Metazoa displays the latest, v2.1 gene set [4]. The original gene set [3] is available as a separate track in the genome browser.

References

  1. A new species of Amphimedon (Porifera, Demospongiae, Haplosclerida, Niphatidae) from the Capricorn-Bunker Group of Islands, Great Barrier Reef, Australia: target species for the 'sponge genome project'.
    Hooper JNA and Van Soest RWM. 2006. Zootaxa. 1314:31-29.
  2. The demosponge Amphimedon queenslandica: reconstructing the ancestral metazoan genome and deciphering the origin of animal multicellularity.
    Degnan BM, Adamska M, Craigie A, Degnan SM, Fahey B, Gauthier M, Hooper JN, Larroux C, Leys SP, Lovas E et al. 2008. Cold Spring Harbor Protocols. 2008:pdb.emo108.
  3. The Amphimedon queenslandica genome and the evolution of animal complexity.
    Srivastava M, Simakov O, Chapman J, Fahey B, Gauthier ME, Mitros T, Richards GS, Conaco C, Dacre M, Hellsten U et al. 2010. Nature. 466:720-726.
  4. Deep developmental transcriptome sequencing uncovers numerous new genes and enhances gene annotation in the sponge Amphimedon queenslandica.
    Fernandez-Valverde SL, Calcino AD, Degnan BM. 2015. BMC Genomics. 16:387.

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyAqu1, INSDC Assembly GCA_000090795.1, Oct 2010
Database version90.1
Base Pairs166,679,601
Golden Path Length166,679,601
Genebuild byDegnan
Genebuild methodImport
Data sourceDegnan Lab

Gene counts

Coding genes43,615
Non coding genes130
Small non coding genes130
Gene transcripts43,745

About this species