Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023 Jan 19:8:31.
doi: 10.12688/wellcomeopenres.18856.1. eCollection 2023.

The genome sequence of the segmented worm, Sthenelais limicola (Ehlers, 1864)

Teresa Darbyshire  1 , Mitchell Brennan  2 , Sean McTierney  2 ; Marine Biological Association Genome Acquisition Lab; Darwin Tree of Life Barcoding collective; Wellcome Sanger Institute Tree of Life programme; Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective; Tree of Life Core Informatics collective; Darwin Tree of Life Consortium
Affiliations

The genome sequence of the segmented worm, Sthenelais limicola (Ehlers, 1864)

Teresa Darbyshire et al. Wellcome Open Res. .

Abstract

We present a genome assembly from an individual Sthenelais limicola (the segmented worm; Annelida; Polychaeta; Phyllodocida; Sigalionidae). The genome sequence is 1,131 megabases in span. Most of the assembly is scaffolded into nine chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.7 kilobases in length.

Keywords: Phyllodocida; Sthenelais limicola; chromosomal; genome sequence; segmented worm.

PubMed Disclaimer

Conflict of interest statement

No competing interests were disclosed.

Figures

Figure 1.
Figure 1.
Photographs of the Sthenelais limicola (wpSthLimi1) specimen used for genome sequencing showing the dorsum of the head ( A), mid body ( B) and tail ( C).
Figure 2.
Figure 2.. Genome assembly of Sthenelais limicola, wpSthLimi1.1: metrics.
The BlobToolKit Snailplot shows N50 metrics and BUSCO gene completeness. The main plot is divided into 1,000 size-ordered bins around the circumference with each bin representing 0.1% of the 1,131,150,536 bp assembly. The distribution of scaffold lengths is shown in dark grey with the plot radius scaled to the longest scaffold present in the assembly (161,876,864 bp, shown in red). Orange and pale-orange arcs show the N50 and N90 scaffold lengths (136,979,486 and 84,233,480 bp), respectively. The pale grey spiral shows the cumulative scaffold count on a log scale with white scale lines showing successive orders of magnitude. The blue and pale-blue area around the outside of the plot shows the distribution of GC, AT and N percentages in the same bins as the inner plot. A summary of complete, fragmented, duplicated and missing BUSCO genes in the metazoa_odb10 set is shown in the top right. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/wpSthLimi1.1/dataset/CALNXF01/snail.
Figure 3.
Figure 3.. Genome assembly of Sthenelais limicola, wpSthLimi1.1: GC coverage.
BlobToolKit GC-coverage plot. Scaffolds are coloured by phylum. Circles are sized in proportion to scaffold length. Histograms show the distribution of scaffold length sum along each axis. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/wpSthLimi1.1/dataset/CALNXF01/blob.
Figure 4.
Figure 4.. Genome assembly of Sthenelais limicola, wpSthLimi1.1: cumulative sequence.
BlobToolKit cumulative sequence plot. The grey line shows cumulative length for all scaffolds. Coloured lines show cumulative lengths of scaffolds assigned to each phylum using the buscogenes taxrule. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/wpSthLimi1.1/dataset/CALNXF01/cumulative.
Figure 5.
Figure 5.. Genome assembly of Sthenelais limicola, wpSthLimi1.1: Hi-C contact map.
Hi-C contact map of the wpSthLimi1.1 assembly, visualised using HiGlass. Chromosomes are shown in order of size from left to right and top to bottom. An interactive version of this figure may be viewed at https://genome-note-higlass.tol.sanger.ac.uk/l/?d=X-bn6mmVRHqGemal-zlDZA.
See this image and copyright information in PMC

References

    1. Allio R, Schomaker-Bastos A, Romiguier J, et al. : MitoFinder: Efficient automated large‐scale extraction of mitogenomic data in target enrichment phylogenomics. Mol Ecol Resour. 2020;20(4):892–905. 10.1111/1755-0998.13160 - DOI - PMC - PubMed
    1. Barnich R, Fiege D: The Aphroditoidea (Annelida: Polychaeta) of the Mediterranean Sea. Abhandlungen der Senckenbergischen Naturforschenden Gesellschaft, 2003;559:1–167. Reference Source
    1. Challis R, Richards E, Rajan J, et al. : BlobToolKit - interactive quality assessment of genome assemblies. G3 (Bethesda). 2020;10(4):1361–1374. 10.1534/g3.119.400908 - DOI - PMC - PubMed
    1. Chambers SJ, Muir AI: Polychaetes: British Chrysopetaloidea, Pisionoidea and Aphroditoidea. Synopses of the British Fauna (New Series). 1997;54:1–202. Reference Source
    1. Cheng H, Concepcion GT, Feng X, et al. : Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat Methods. 2021;18(2):170–175. 10.1038/s41592-020-01056-5 - DOI - PMC - PubMed

LinkOut - more resources