The Demosponge Amphimedon queenslandica: Reconstructing the Ancestral Metazoan Genome and Deciphering the Origin of Animal Multicellularity

2008 ◽  
Vol 2008 (12) ◽  
pp. pdb.emo108-pdb.emo108 ◽  
Author(s):  
B. M. Degnan ◽  
M. Adamska ◽  
A. Craigie ◽  
S. M. Degnan ◽  
B. Fahey ◽  
...  
Keyword(s):  
Metazoan Genome ◽  
Amphimedon Queenslandica

scholarly journals Draft genome of Bugula neritina, a colonial animal packing powerful symbionts and potential medicines

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Mikhail Rayko ◽  
Aleksey Komissarov ◽  
Jason C. Kwan ◽  
Grace Lim-Fong ◽  
Adelaide C. Rhodes ◽  
...  
Keyword(s):  
De Novo ◽  
Draft Genome ◽  
Transcriptome Data ◽  
Biomedical Sciences ◽  
Bugula Neritina ◽  
Genome Sequences ◽  
Illumina Hiseq ◽  
Draft Assembly ◽  
Metazoan Genome ◽  
Animal Phyla

Abstract Many animal phyla have no representatives within the catalog of whole metazoan genome sequences. This dataset fills in one gap in the genome knowledge of animal phyla with a draft genome of Bugula neritina (phylum Bryozoa). Interest in this species spans ecology and biomedical sciences because B. neritina is the natural source of bioactive compounds called bryostatins. Here we present a draft assembly of the B. neritina genome obtained from PacBio and Illumina HiSeq data, as well as genes and proteins predicted de novo and verified using transcriptome data, along with the functional annotation. These sequences will permit a better understanding of host-symbiont interactions at the genomic level, and also contribute additional phylogenomic markers to evaluate Lophophorate or Lophotrochozoa phylogenetic relationships. The effort also fits well with plans to ultimately sequence all orders of the Metazoa.

scholarly journals The GPCR repertoire in the demosponge Amphimedon queenslandica: insights into the GPCR system at the early divergence of animals

2014 ◽  
Vol 14 (1) ◽  
Author(s):  
Arunkumar Krishnan ◽  
Rohit Dnyansagar ◽  
Markus Sällman Almén ◽  
Michael J Williams ◽  
Robert Fredriksson ◽  
...  
Keyword(s):  
Amphimedon Queenslandica

scholarly journals Are there systematic biases in RNA-seq data analysis? A case study for Amphimedon queenslandica sponge as a model object

2020 ◽  
Author(s):  
Sergey Feranchuk
Keyword(s):  
Functional Annotation ◽  
Rna Seq ◽  
Expression Levels ◽  
Model Object ◽  
Wide Range ◽  
Amphimedon Queenslandica ◽  
Systematic Biases ◽  
Series Of Experiments ◽  
Notch Pathways

AbstractBACKGROUNDThe performance of a functional annotation approach for RNA-seq bioinformatics pipelines was to be compared with the method where groups of genes are generated with no relation to ontologes. Three publicly available RNA-Seq experiments for Amphimedon queenslandica sponge were used for the designed comparison. One of these experiments was referred in the publication where stages of embryo development were compared for a wide range of animal species.METHODSThe expression levels were re-calculated here for three independent series of experiments. The functional annotation of differential expression levels was than conducted. This allow to compare an applicability of the two approaches, and to re-evaluate the interpretation provided in the mentioned publication.RESULTSIt was confirmed by the conventional approach that Wnt and Notch pathways do operate in a development of a sponge embryo. The method of annotation which uses unbounded grouping of genes was effective in an ability to separate development stages of sponge embryo. In addition, the published results were by a suggestion distorted by an artifact, caused by a positive feedback in the stage of data processing.

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’

Zootaxa ◽  
2006 ◽  
Vol 1314 (1) ◽  
pp. 31 ◽  
Author(s):  
JOHN N.A. HOOPER ◽  
ROB W.M. VAN SOEST
Keyword(s):  
New Species ◽  
Great Barrier Reef ◽  
New Caledonia ◽  
Genome Project ◽  
Tree Islands ◽  
Barrier Reef ◽  
Amphimedon Queenslandica ◽  
The Subject ◽  
Globally Distributed ◽  
A New Species

A new niphatid demosponge, Amphimedon queenslandica sp.nov., is described from Heron and One Tree Islands, southern Great Barrier Reef, Queensland, Australia. The new species is of particular significance as it is currently the subject of the first sponge genome project. The species is characterized within the globally distributed genus Amphimedon by its distinctive blue-green colour, and the combination of encrusting-lobate growth form, spongin-rich spiculofibres and feeble spicule size, The new species is compared and contrasted with known or suspected Amphimedon species of Australia and adjacent territories of Papua New Guinea, New Caledonia and Indonesia.

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