The complete mitochondrial genomes of two imperiled species endemic to the Southwestern United States: Peppered Chub (Macrhybopsis tetranema) and Gila Trout (Oncorhynchus gilae)

Abstract

Macrhybopsis tetranema and Oncorhynchus gilae are fish species endemic to the Southwestern United States. We present the complete mitochondrial genomes for these species. Each genome consisted of 13 protein-coding genes, two ribosomal (rRNA) genes, 22 transfer RNA (tRNA) genes, and the control region (D-loop). Mitogenome lengths were 16,916 base pairs (bp) for M. tetranema, and 16,976 bp for O. gilae. The GC content was 41% for M. tetranema and 46% for O. gilae. The relationships of M. tetranema and O. gilae were consistent with previous phylogenetic analyses.

Keywords:

• Peppered Chub
• Gila Trout Spruce Creek lineage
• mitogenomes

Acknowledgements

Samples were collected with permits from the New Mexico Department of Game and Fish (3015 to TFT and 3764 to Stephen Davenport [US. Fish and Wildlife Service]) and the US. Fish and Wildlife Service (TE38055-0). Samples were collected according to UNM IACUC protocol MSC10-100492-MCC. Images of Gila Trout and Peppered Chub were kindly provided by Thomas Kennedy (UNM) and Daniel Fenner (USFWS) respectively.

Ethical approval

This research project has been reviewed and approved by the UNM Institutional Animal Care and Use Committee (IACUC). All investigators in this study have attained animal-use certification regarding the ethical treatment of animals (D16-00565 A4023-01). Sample collection was conducted in accordance with the regulations of the International Union for Conservation of Nature (IUCN).

Authors’ contributions

All authors were involved in study design. MO isolated the DNA of O. gilae and M. tetranema. MO, MBH, and GCD conducted sequence analyses. MO, MBH, GCD and TT drafted and edited the manuscript and approve the study and this manuscript.

Disclosure statement

The authors report no conflicts of interest. The authors are solely responsible for the content and writing of the paper.

Data availability statement

The mitogenome sequence data that support the findings of this study are openly available at NCBI Genbank (https://www.ncbi.nlm.nih.gov/genbank/) under the accession no. OQ301638 for O. gilae and OQ301637 for M. tetranema. The associated sequencing data is available at NCBI Sequence Read Archive (SRA; https://www.ncbi.nlm.nih.gov/sra/). For O. gilae the associated BioProject, BioSample and SRA numbers are PRJNA941852, SAMN33611619 and SRR23721617, respectively; for M. tetranema the associated BioProject, BioSample and SRA numbers are PRJNA941280, SAMN33600811 and SRR24116728, respectively.

Additional information

Funding

The sequencing was carried by the DNA Technologies and Expression Analysis Core at the UC Davis Genome Center, supported by NIH Shared Instrumentation Grant 1S10OD010786-01. The material contributed by MBH is supported by the NSF Postdoctoral Research Fellowships in Biology Program under Grant No. NSF 21-614