Strigamia maritima (Soil centipede) Assembly and Gene Annotation

About Strigamia maritima

Strigamia maritima is a coastal European centipede of the Geophilimorph order. Like all centipedes, it is predatory, using venomous forcipules (legs adapted into pincers) to eat worms and small marine invertebrates that have been washed onshore. S. maritima is an eyeless species, using antennae to hunt, and specimens have around 49 pairs of legs; the exact number of segments depends on both genetic and environmental factors, and varies on a latitudinal cline [1]. The variablility in segment number (some centipede species always have the same number of segments) makes S. maritima a useful model for arthropod development [2, 3].

S. maritima is the first myriapod genome to be sequenced, which makes it an interesting species in phylogenetic terms. The placement of myriapods (centipedes, millipedes and similar species) on the tree of life has been a subject of some debate, but a recent study [4] has myriapods as a sister group to pancrustacea (insects and crustaceans), with chelicerates (such as ticks and spiders) as an outgroup. Centipedes have a simple, possibly ancestral, bodyplan, so the genome sequence of S. maritima is an important reference for arthropod comparative genomics.

Picture credit: Carlo Brena

Assembly

The Strigamia maritima genome was sequenced with 454 Life Sciences technology at Baylor College of Medicine, in collaboration with with the Akam group at the University of Cambridge. The genome was assembled into 24,079 contigs and then 14,739 scaffolds using the CABOG pipeline [5].

Annotation

Gene models were generated with the MAKER pipeline; resources for MAKER included RNA-seq data (via the Cufflinks pipeline), similarity search with metazoan protein databases, and the ab initio gene predictors SNAP and Augustus. Non-coding RNA genes were added with the standard Ensembl Genomes RNA pipeline; BLAST hits, protein features, and cross-references have also been computed.

References

1. Segment number, body length, and latitude in geophilomorph centipedes: a converse-Bergmann pattern.
   Hayden L, Parkes G, Arthur W. 2012. Biological Journal of the Linnean Society. 107(1):16674.
2. The centipede Strigamia maritima: what it can tell us about the development and evolution of segmentation.
   Arthur W, Chipman AD. 2005. Bioessays. 27:653-660.
3. The embryonic development of the centipede Strigamia maritima.
   Brena C, Akam M. 2012. Dev. Biol.. 363:290-307.
4. A congruent solution to arthropod phylogeny: phylogenomics, microRNAs and morphology support monophyletic Mandibulata.
   Rota-Stabelli O, Campbell L, Brinkmann H, Edgecombe GD, Longhorn SJ, Peterson KJ, Pisani D, Philippe H, Telford MJ. 2011. Proceedings of the Royal Society B. 278:298-306.
5. The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima.
   Chipman AD et al.. 2014. PLoS Biology. 12:e1002005.

Other Alignments

Approximately 11000 community annotations are mapped to the genome (Example: JH430149: 27800-54000).