Homarus gammarus (European lobster, reference) Assembly and Gene Annotation

About Homarus gammarus

Homarus gammarus, known as the European lobster, is a species of clawed lobster found in rocky substrate habitats from across the eastern Atlantic Ocean and throughout the Mediterranean Sea [1]. The species is closely related to the American lobster, H.americanus, which it occasionally hybridises with in the wild [2]. It may grow to a length of 60cm (24in) and a mass of 6 kilograms (13lb), and bears a conspicuous pair of claws. In life the lobsters are blue (sometimes dark navy), only becoming "lobster red" on cooking. Mating occurs in the summer, producing eggs which are carried by the females for up to a year before hatching into planktonic larvae. Homarus gammarus is a highly esteemed seafood, and is widely caught using baited lobster pots, mostly around the British Isles and France.

Picture credit: Public domain via Wikimedia Commons (Image source)

Taxonomy ID 6707

(Text adapted from Wikipedia.)

More information General information about this species can be found in Wikipedia

Prepublication data sharing

These data are released under Fort Lauderdale principles, as confirmed in the Toronto Statement [3]. Any use of this dataset must abide by the AquaLeap: Innovation in Genetics and Breeding to Advance UK Aquaculture Production Project data sharing principles. The data producers reserve the right to make the first publication of these data. If you are unsure if you are allowed to publish using this dataset, please contact Dr Eduarda Santos (e.santos@exeter.ac.uk) and Professor Jamie Stevens (j.r.stevens@exeter.ac.uk) to enquire.

LobsterGeneX

LobsterGeneX is a web application designed to visualise gene expression results from ten different tissue types (Eye, Gill, Nerve, Muscle, Heart, Hepatopancreas, Gut, Ovary, Testes, Juvenile) from the European lobster (Homarus gammarus). All results reserved; article in prep. (Paris et al.); See prepublication data sharing.

Assembly

The assembly presented here has been imported from INSDC and is linked to the assembly accession [GCA_958450375.1].

Genome assembly of the European lobster (Homarus gammarus) was produced by the University of Exeter in association with the AquaLEAP consortium [4]. Assembly was performed with Flye [5] using PacBio CLR data, polished with short-read paired-end Illumina Data.

The total length of the assembly is 1,761,786,531 bp contained within 4,133 scaffolds. The scaffold N50 value is 1,823,183, the scaffold L50 value is 274. The GC% content of the assembly is 42.5%.

Annotation

The annotation presented is derived from annotation submitted to INSDC with the assembly accession GCA_958450375.1.

Transcript models are supported by RNA-seq experimental evidence. Including publicly available illumina transcriptome data of genus:Homarus (n=107), genomic annotation also utilized forty transcriptomic libraries from multiple developmental and tissue specific samples of Homarus gammarus generated for this purpose PRJEB50279.

Gene model layering was supported with protein-to-genome alignment with experimentally verified proteins [PE evidence level 1, 2] obtained from Crustacea - (Uniprot, March 2022). The Ensembl Gene Annotation pipeline implemented transcript consensus filtration to remove unsupported alternate transcript isoforms.

Most ncRNAs are annotated by aligning genomic sequence against RFAM using BLASTN. Pseudogenes were calculated by examining genes with a large percentage of non-biological introns (introns of <10bp), where the gene was covered in repeats, or where the gene was single exon and evidence of a functional multi-exon paralog was found elsewhere in the genome. tRNAs are annotated as part of the raw compute process using tRNAscan-SE

lncRNAs were generated via RNA-seq data where no evidence of protein homology or protein domains could be found in the transcript.

For in-depth overview of the Ensembl Gene Annotation pipeline see detailed information here.

References

1. Jenkins, T. L., Ellis, C. D., Triantafyllidis, A., & Stevens, J. R. (2019). Single nucleotide polymorphisms reveal a genetic cline across the north-east Atlantic and enable powerful population assignment in the European lobster. Evolutionary Applications, 12(10), 1881–1899.
2. Ellis, C. D., Jenkins, T. L., Svanberg, L., Eriksson, S. P., & Stevens, J. R. (2020). Crossing the pond: genetic assignment detects lobster hybridisation. Scientific Reports, 10(1), 7781.
3. Toronto International Data Release Workshop Authors (2009). Prepublication data sharing. Nature, 461, 168-170, doi: 10.1038/461168a
4. Houston, R. D., Bean, T. P., Macqueen, D. J., Gundappa, M. K., Jin, Y. H., Jenkins, T. L., Selly, S. L. C., Martin, S. A. M., Stevens, J. R., Santos, E. M., Davie, A., & Robledo, D. (2020). Harnessing genomics to fast-track genetic improvement in aquaculture. Nature Reviews. Genetics, 21(7), 389–409.
5. Kolmogorov, M., Yuan, J., Lin, Y., & Pevzner, P. A. (2019). Assembly of long, error-prone reads using repeat graphs. Nature Biotechnology, 37(5), 540–546.