Nematostella vectensis (Starlet sea anemone, CH2 x CH6) Assembly and Gene Annotation

About Nematostella vectensis

The starlet sea anemone, Nematostella vectensis, is a cnidarian, a phylum that also includes coral, jellyfish and hydras. N. vectensis has a tubular shape (length ranges from about 2 to 6 cm) with a bulbous area at the basal end (used to burrow into the mud) and an oral disk containing the mouth and two rings of tentacles at the top end. It has been observed in salt marshes around the coast of United Kingdom, East and West coasts of the USA, and Nova Scotia in Canada.

Nematostella vectensis can reproduce asexually all year round, and sexually during summer and autumn. Its sensitivity to hypoxia (low levels of oxygen) makes it a good indicator for pollution, and N. vectensis are the simplest organism with true tissues. These characteristics mean that the species is used in a variety of fields, including evolution, genomics, reproductive biology, developmental biology and ecology.

Picture credit: Southeastern Regional Taxonomic Center

Assembly

The genome of Nematostella vectensis was sequenced and assembled by the Joint Genome Institute (JGI) [1]. The genome assembly, constructed with the JGI assembler Jazz, includes approximately 7x WGS in small insert end-sequence coverage. After cleaning, 10,804 scaffolds were assembled, containing about 296 million base pairs (Mbp), and 356 Mbp of sequence.

Annotation

Gene models were predicted using ab initio and homology-based methods (FGENESH, FGENESH+ and GENEWISE). Since release 22 (March 2014), Ensembl Genomes has displayed the ENA gene set; this gene set is a subset of the original JGI gene set, therefore all genes contain a JGI cross reference. Between Ensembl Genomes release 21 and release 22, 203 protein-coding genes were removed, and 119 new pseudogenes were imported. Non-coding RNA genes were added using the Ensembl Genomes pipeline, and BLAST hits and protein features have been computed. Additional data is available at StellaBase [2].

References

1. Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization.
   Putnam NH, Srivastava M, Hellsten U, Dirks B, Chapman J, Salamov A, Terry A, Shapiro H, Lindquist E, Kapitonov VV et al. 2007. Science. 317:86-94.
2. Upgrades to StellaBase facilitate medical and genetic studies on the starlet sea anemone, Nematostella vectensis.
   Sullivan JC, Reitzel AM, Finnerty JR. 2008. Nucleic Acids Research. 36:D607-11.

More information

General information about this species can be found in Wikipedia.