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

Chloe N Rabinowitz; Shannon D Brown; Sean M McAllister; Amanda K Winans; Julie E Keister; Matthew P Galaska

doi:10.1080/23802359.2023.2270206

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

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

Authors

Chloe N Rabinowitz¹, Shannon D Brown^{2

3}, Sean M McAllister^{2

3}, Amanda K Winans⁴, Julie E Keister⁴, Matthew P Galaska³

Affiliations

¹ School of Environmental and Forest Sciences, University of Washington, Seattle, WA, USA.
² Cooperative Institute for Climate, Ocean, & Ecosystem Studies, University of Washington, Seattle, WA, USA.
³ Pacific Marine Environmental Laboratory, National Oceanographic and Atmospheric Administration, Seattle, WA, USA.
⁴ School of Oceanography, University of Washington, Seattle, WA, USA.

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.

This work was authored as part of the Contributor’s official duties as an Employee of the United States Government and is therefore a work of the United States Government. In accordance with 17 U.S.C. 105, no copyright protection is available for such works under U.S. Law.

Grants and funding

This publication was partially funded by the Cooperative Institute for Climate, Ocean, & Ecosystem Studies (CICOES) under National Oceanic and Atmospheric Administration (NOAA) Cooperative Agreement NA20OAR4320271, Contribution No. 2022-1246. This is the NOAA Pacific Marine Environmental Laboratory (PMEL) Contribution No. 5455. Additional funding support for a summer internship was provided by the University of Washington (UW) EarthLab. Funding for collecting and identifying C. challengeri was provided through the Washington Ocean Acidification Center to Julie E. Keister. Moira Galbraith at the Fisheries and Oceans Canada Institute of Ocean Sciences provided valuable consultation on the identification of C. challengeri. This work is also supported by the University of Washington EarthLab.