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 Oct 25;8(10):1128-1131.
doi: 10.1080/23802359.2023.2270206. eCollection 2023.

The complete mitochondrial genome of Cyphocaris challengeri (Amphipoda: Cyphocarididae)

Chloe N Rabinowitz  1 , Shannon D Brown  2   3 , Sean M McAllister  2   3 , Amanda K Winans  4 , Julie E Keister  4 , Matthew P Galaska  3
Affiliations

The complete mitochondrial genome of Cyphocaris challengeri (Amphipoda: Cyphocarididae)

Chloe N Rabinowitz et al. Mitochondrial DNA B Resour. .

Abstract

The amphipod Cyphocaris challengeri is a globally distributed, highly abundant species of zooplankton. Here, we report the complete mitochondrial genome of C. challengeri obtained using the Illumina sequencing platform from a specimen collected from Puget Sound, Washington. The mitogenome is a circular DNA molecule with a size of 14,338 bp and 26.7% GC content, with 13 protein-encoding genes, 2 rRNAs, and 22 tRNAs annotated. A maximum likelihood phylogenetic analysis including C. challengeri and all other available mitogenomes from Amphipoda places our mitogenome firmly within the Lysianassoidea superfamily, as expected. The newly described mitochondrial genome of C. challengeri fills a gap in valuable reference data for detecting this organism using molecular methods such as environmental DNA.

Keywords: Lysianassoidea; Mitogenome; mtDNA; next-generation sequencing.

PubMed Disclaimer

Conflict of interest statement

No potential conflict of interest was reported by the authors.

Figures

Figure 1.
Figure 1.
Photograph of the Cyphocaris challengeri specimen sequenced in this study. Scale bar 1 mm. Photo taken by C. Rabinowitz.
Figure 2.
Figure 2.
Circular mitogenome map of Cyphocaris challengeri. All annotated genes are indicated with their direction. Inner tract shows GC content with an 80 bp sliding window; high (51% GC) and low (5% GC) values are bounded by the gray rings.
Figure 3.
Figure 3.
Maximum likelihood phylogenetic tree of a concatenated alignment of all thirteen protein encoding genes available from Amphipoda mitogenomes. Cyphocaris challengeri label is highlighted in red. Branches are colored by superfamily. Bootstrap values are indicated at nodes with a solid dot (≥75% support), open dot (≥50%, <75% support), or no dot (<50% support).
See this image and copyright information in PMC

References

    1. Bernt M, Donath A, Jühling F, Externbrink F, Florentz C, Fritzsch G, Pütz J, Middendorf M, Stadler PF.. 2013. MITOS: improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol. 69(2):313–319. doi: 10.1016/j.ympev.2012.08.023. - DOI - PubMed
    1. Boeck A. 1871. Crustacea amphipoda borealia et arctica. Forhandlinger i Videnskabs-Selskabet i Christiana. 1870:83–280.
    1. Bolger AM, Lohse M, Usadel B.. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 30(15):2114–2120. doi: 10.1093/bioinformatics/btu170. - DOI - PMC - PubMed
    1. Bowman TE, McCain JC.. 1967. Variation and distribution of the pelagic amphipod Cyphocaris challengeri in the Northeast Pacific (Gammaridea: lysianassidae). Proceedings of the United States National Museum. 122(3588):1–14. doi: 10.5479/si.00963801.122-3588.1. - DOI
    1. Chevreux E. 1899. Sur deux espèces géantes d'amphipodes provenant des campagnes du yacht Princesse Alice. Bull Soc Zool France. 24:152–158. doi: 10.5962/bhl.part.24435. - DOI