Characterization of the complete mitochondrial genomes of two Critically Endangered wedgefishes: Rhynchobatus djiddensis and Rhynchobatus australiae

Figures & data

Figure 1. Species reference images of (A) Rhynchobatus djiddensis (Photo by the South African Institute for Aquatic Biodiversity), the whitespotted wedgefish, with prominent black markings between eyes, large number of white spots and black pectoral marking surrounded by four or more white spots and (B) Rhynchobatus australiae (Photo by John Nevill), the bottlenose wedgefish, with bottle-shaped snout slightly constricted near tip, three white spots aligned over the pectoral marking (usually two spots below), a short line of well-demarcated white spots on the mid dorsal surface and no spots on the tail (TL = 137 cm).

Table 1. Whole mitogenomes from the order Rhinopristiformes used to infer the phylogenetic placement of R. djiddensis (ON065568) and R. australiae (ON065567).

Family	Species	Size (bp)	GenBank accession number	Reference
Glaucostegidae	Glaucostegus granulatus (Cuvier, 1829)	16,547	MN783017	Johri, Fellows, et al. (2020)
Pristidae	Anoxypristis cuspidata (Latham, 1794)	17,243	KP233202	Chen, Kyne, et al. (2016)
	Pristis clavata (Garman, 1906)	16,804	KF381507	Feutry et al. (2015)
	Pristis pectinata (Latham, 1794)	16,802	KP400584	Chen, Wiley, et al. (2016)
	Pristis pectinata (Latham, 1794)	16,803	MF682494	Díaz-Jaimes et al. (2018)
	Pristis pristis (Linnaeus, 1758)	16,912	MH005928	Kyne et al. (2018)
	Pristis zijsron (Bleeker, 1851)	16,804	MH005927	Direct submission
Rhinidae	Rhina ancylostoma (Bloch & Schneider, 1801)	17,217	KU721837	Si, Chen, et al. (2016)
	Rhynchobatus australiae (Whitley, 1939)	16,804	KU746824	Si, Ding, et al. (2016)
	Rhynchobatus australiae (Whitley, 1939)	16,805	ON065567	This study
	Rhynchobatus djiddensis (Forsskål, 1775)	16,799	ON065568	This study
	Rhynchobatus laevis (Bloch & Schneider, 1801)	16,560	MN988687	Johri, Tiwari, et al. (2020)
Rhinobatidae	Rhinobatos hynnicephalus (Richardson, 1846)	16,776	KF534708	Chen et al. (2015)
	Rhinobatos schlegelii (Müller & Henle, 1841)	16,780	KJ140136	Chen, Ai, et al. (2016)
Trygonorrhinidae	Zapteryx exasperata (Jordan & Gilbert, 1880)	17,310	KM370325	Castillo-Páez et al. (2014)

Those in bold are the mitogenomes from this study.

Figure 2. Gene maps of the Rhynchobatus djiddensis (ON065568) and Rhynchobatus australiae (ON065567) mitogenomes. The outermost circle genes are transcribed clockwise and the rest counter clockwise.

Figure 3. Maximum-likelihood phylogeny of five families from the order Rhinopristiformes based on the concatenated dataset of 13 protein-coding genes, with members of the families Rajidae and Arhynchobatidae included as outgroups. Numbers at nodes indicate bootstrap values. GenBank accession numbers are given adjacent to the species name, scale bar indicates groupings of species into families and the taxa in bold are the mitogenomes from this study.

Table 2. Single nucleotide polymorphisms (SNPs) found in 16 regions of the mitogenomes from this study; Rhynchobatus djiddensis (ON065568) and Rhynchobatus australiae (ON065567), and the online-available R. australiae sequence (KU746924).

Gene	Length (bp)	SNPs	Relative variation (%)
COX1	1557	53	3.404
COX2	691	18	2.605
COX3	786	25	3.181
NADH1	975	38	3.897
NADH2	1046	47	4.493
NADH3	351	9	2.564
NADH4L	297	11	3.704
NADH4	1381	38	2.752
NADH5	1851	75	4.052
NADH6	519	22	4.239
CYTB	1143	46	4.024
12S rRNA	967	7	0.724
16S rRNA	1690	24	1.420
ATP6	684	22	3.216
ATP8	168	5	2.976
Control region	1108	41	3.700

ATP: adenosine triphosphate; CO: cytochrome c oxidase subunit; CYTB: cytochrome b; NADH: nicotinamide adenine dehydrogenase subunit; rRNA: ribosomal ribonucleic acid.

Johri S, Fellows SR, Solanki J, Busch A, Livingston I, Mora MF, Tiwari A, Cantu VA, Goodman A, Morris MM, et al. 2020. Mitochondrial genome to aid species delimitation and effective conservation of the Sharpnose Guitarfish (Glaucostegus granulatus). Meta Gene. 24:100648.

 Web of Science ®Google Scholar

Chen X, Kyne PM, Pillans RD, Feutry P. 2016. Complete mitochondrial genome of the endangered narrow sawfish Anoxypristis cuspidata (Rajiformes: Pristidae). Mitochondrial DNA A DNA Mapp Seq Anal. 27(6):4172–4173.

 PubMedGoogle Scholar

Feutry P, Kyne PM, Grewe PM, Chen X, Liu M. 2015. Whole mitogenome of the endangered dwarf sawfish Pristis clavata (Rajiformes: Pristidae). Mitochondrial DNA. 26(2):329–330.

 PubMed Web of Science ®Google Scholar

Chen X, Wiley T, Kyne PM, Feutry P. 2016. Complete mitochondrial genome of the Critically Endangered smalltooth sawfish Pristis pectinata (Rajiformes: Pristidae). Mitochondrial DNA A DNA Mapp Seq Anal. 27(5):3331–3332.

 PubMedGoogle Scholar

Díaz-Jaimes P, Bonfil R, Palacios-Barreto P, Bolaño-Martinez N, Bayona-Vásquez NJ. 2018. Mitochondrial genome of the Critically Endangered smalltooth sawfish Pristis pectinata from Veracruz, Mexico. Conserv Genet Resour. 10(4):663–666.

 Web of Science ®Google Scholar

Kyne PM, Wang J-J, Xiang D, Chen X, Feutry P. 2018. The phylogenomic position of the Critically Endangered largetooth sawfish Pristis pristis (Rhinopristiformes, Pristidae), inferred from the complete mitochondrial genome. Mitochondrial DNA B Resour. 3(2):970–971.

 PubMed Web of Science ®Google Scholar

Si R, Chen H, Ai W, Chen X, Chen S. 2016. Complete mitochondrial genome and the phylogenetic position of the Bowmouth guitarfish Rhina ancylostoma (Rajiformes, Rhinobatidae). Mitochondrial DNA B Resour. 1(1):270–272.

 PubMed Web of Science ®Google Scholar

Si R, Ding W, Chen H, Chen X, Ai W. 2016. Complete mitochondrial genome and the phylogenetic position of the White-spotted guitarfish Rhynchobatus australiae (Rajiformes, Rhinobatidae). Mitochondrial DNA B Resour. 1(1):315–317.

 PubMed Web of Science ®Google Scholar

Johri S, Tiwari A, Kerr EN, Dinsdale EA. 2020. Mitochondrial genome of the smoothnose wedgefish Rhynchobatus laevis from the Western Indian Ocean. Mitochondrial DNA B Resour. 5(3):2083–2084.

 PubMed Web of Science ®Google Scholar

Chen X, Ai W, Shi X, Gao T. 2015. Mitochondrial genome of the ringstraked guitarfish Rhinobatos hynnicephalus (Elasmobranchii: Rajiformes). Mitochondrial DNA. 26(4):653–654.

 PubMed Web of Science ®Google Scholar

Chen X, Ai W, Xiang D, Pan L, Shi X. 2016. Complete mitogenome of the brown guitarfish Rhinobatos schlegelii (Rajiformes, Rhinobatidae). Mitochondrial DNA A DNA Mapp Seq Anal. 27(1):310–311.

 PubMedGoogle Scholar

Castillo-Páez A, del Río-Portilla MA, Oñate-González E, Rocha-Olivares A. 2014. The mitochondrial genome of the banded guitarfish, Zapteryx exasperata (Jordan and Gilbert, 1880), possesses a non-coding duplication remnant region. Mitochondrial DNA A DNA Mapp Seq Anal. 27(3):1–3.

 PubMedGoogle Scholar

Data availability statement

The genome sequence data that support the findings of this study are openly available in GenBank of NCBI (https://www.ncbi.nlm.nih.gov/) under the accession numbers ON065567–ON065568. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA886704, SRX17782697–SRX17782698, and SAMN31139799–SAMN31139800, respectively.