Sequencing and characterization of the complete mitochondrial genome of the endangered Devils Hole pupfish Cyprinodon diabolis (Cyprinodontiformes: Cyprinodontidae)

Abstract

The Devils Hole pupfish ( Cyprinodon diabolis ) is an imperiled cypinodontid fish endemic to Devils Hole, a single groundwater-fed pool in western North America characterized by temperature and oxygen conditions lethal to most fishes. In this study, we obtained the 16,499 base pair (bp) mitochondrial DNA sequence of C. diabolis . The mitogenome encodes 13 polypeptides, 22 tRNAs, 12S and 18S rRNAs, and an 832 bp D-loop region, and has a nucleotide composition of A, 25.69%; T, 27.32%; G, 17.49%; and C, 29.50% (GC content: 46.99%). The availability of this mitogenome will facilitate evaluations of C. diabolis genetic structure for management and conservation of this iconic endangered species.

Complete mitochondrial genome of the Salt Creek pupfish, Cyprinodon salinus salinus: characterization and identification of single nucleotide polymorphisms (SNPs)

“…Phylogenetic analysis substantiates C. salinus salinus as monophyletic with other Death Valley region pupfishes Cyprinodon diabolis (KX061747), Cyprinodon nevadensis pectoralis (KP064222), and Cyprinodon nevadensis amargosae (KU883631) ( Figure 1 ). Notably, that phylogenetic analysis also revealed the White Sands pupfish ( Cyprinodon tularosa ) (KP013105) clustered between two independently sequenced C. variegatus mitogenomes, as was also observed by Lema, Wilson, et al ( 2016 ). Recent unpublished nuclear DNA analyses suggest possible genetic introgression of C. variegatus into C. tularosa (Black et al 2021 ), which may explain relationships of those taxa in Figure 1 .…”

“…C. variegatus mitogenomes, as was also observed by Lema, Wilson, et al (2016). Recent unpublished nuclear DNA analyses suggest possible genetic introgression of C. variegatus into C. tularosa (Black et al 2021), which may explain relationships of those taxa in Figure 1.…”

“…The four sequenced mitochondrial genomes of C. salinus salinus (GenBank accession nos. MW446237, MW446238, MW446239, and MW446240) are each 16,499 bp in length and contain 13 protein-coding genes, 22 tRNAs, 12S and 16S rRNAs, and a D-loop region of 842 bp, which follows the mitogenome arrangement of other Cyprinodon pupfishes (Keepers et al 2016 ; Barcelon and Lema 2016 ; Lema, Wilson, et al 2016 ). Phylogenetic analysis substantiates C. salinus salinus as monophyletic with other Death Valley region pupfishes Cyprinodon diabolis (KX061747), Cyprinodon nevadensis pectoralis (KP064222), and Cyprinodon nevadensis amargosae (KU883631) ( Figure 1 ).…”

Endocrine and metabolic impacts of warming aquatic habitats: differential responses between recently isolated populations of a eurythermal desert pupfish

“…In addition, we quantified heptic mRNA levels for the orphan nuclear receptors estrogen-related receptor α ( esrra ) and estrogen-related receptor γ ( esrrg ), which regulate mitochondrial gene expression and biogenesis, and gluconeogenesis, respectively (Villena et al ., 2007; Kim et al ., 2012). SYBR Green primers for atpase6/8 and cox2 were designed using the complete mitogenomes of the Death Valley pupfishes C. n. amargosae ( KU883631 ) and C. diabolis ( KX061747 ; Lema et al ., 2016), and primers for transcripts encoding all other proteins were designed to coding region sequences obtained from the C. n. pectoralis genome ( GCA_000776015 ). When possible, primers were designed to span an intron boundary.…”

The Endangered White Sands pupfish (Cyprinodon tularosa) genome reveals low diversity and heterogenous patterns of differentiation

“…The complete mtDNA sequence of C. tularosa was reconstructed using the cleaned Illumina paired-end reads. To help prevent the inadvertent incorporation of Nuclear Translocations (NUMTs) into the mtDNA assembly, we first used coalqc (v.0.1; Patil et al 2020) and samtools (v.1.17; to extract Illumina reads that aligned to the Devils Hole pupfish (C. diabolis ) mtDNA assembly (NC_030345.1; Lema et al 2016). The resulting bam file was then converted back to fastq file format with bedtools (v.2.29.0; Quinlan and Hall, 2010) and used alongside the C. diabolis full mitogenome as a backbone for the C. tularosa mtDNA genome assembly with mitobim (v.1.8;Hahn et al 2013).…”