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. 2023 Aug 1;8(8):809-814.
doi: 10.1080/23802359.2023.2241658. eCollection 2023.

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

Megan J Osborne  1 , Megan A Barela Hudgell  1 , Guilherme Caeiro-Dias  1 , Thomas F Turner  1
Affiliations

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

Megan J Osborne et al. Mitochondrial DNA B Resour. .

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: Gila Trout Spruce Creek lineage; Peppered Chub; mitogenomes.

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Conflict of interest statement

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

Figures

Figure 1.
Figure 1.
Photographs showing (A) Oncorhynchus gilae (photo credit: Thomas Kennedy, used with permission) and (B) Macrhybopsis tetranema (photo credit: Daniel Fenner, used with permission). Oncorhynchus gilae are characterized by having a stocky, golden-yellowish body, large spots on the adipose fin, numerous fine spots above the lateral line and large spots on the adipose fin (Behnke 2002).
Figure 2.
Figure 2.
Mitochondrial genome maps showing 13 protein coding genes, 2 ribosomal RNAs, 22 transfer RNAs and the control region (D-loop) for (A) Oncorhynchus gilae (GenBank: OQ301638) and (B) Macrhybopsis tetranema (GenBank: OQ301637) generated using the program proksee v. 6.0.2 (https://proksee.ca/) using the relative scale option. Plots of GC content and skew used a window size of 500 and reflect GC content/skew scores on a scale of 0 to 1 using a baseline of 0.5. Positive and negative skew are indicated by values above and below the midpoint respectively. Asterisks in the control region indicate the approximate location and number of repetitive elements. The order of mitochondrial genes is conserved between species.
Figure 3.
Figure 3.
Maximum likelihood trees constructed with the coding sequences of the mitochondrial genomes (A) from Oncorhynchus species including the Spruce Creek lineage of O. gilae (GenBank: OQ301638). Coho salmon (Oncorhynchus kisutch) was included as an outgroup. (B) a subset of cypriniform fishes, including M. tetranema (GenBank: OQ301637) new mitogenome. Roundnose minnow (Dionda episcopa) was included as an outgroup. Node support values were generated with 100 bootstrap replicates. Asterisks and light blue highlighting denote novel sequences presented in this study. GenBank accession numbers are provided near branch tips for all sequences used. References used for comparative analysis are provided in the Table 1.
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