Mitochondrial genome of the jack silverside, Atherinopsis californiensis (Atherinopsidae, Atheriniformes), a nearshore fish of the California Current Ecosystem

Figures & data

Figure 1. Photos of the jack silverside, Atherinopsis californiensis. (A) Jack silverside, commonly also called jacksmelt, belongs to the family of silversides (family Atherinopsidae) and not the taxon of ‘true’ smelts (family Osmeridae). Jack silverside are distinguished from another morphologically similar species – the topsmelt silverside (Atherinops affinis) – by the anterior edge of the anal fin (dotted line) being positioned between the posterior edge of the first dorsal fin and anterior boundary of the second dorsal fin (arrows). (B) Adult jack silverside showing the typical yellow color on the gill operculum, with positioning of the two dorsal fins stretched upright. Photos by Sean Lema.

Figure 2. Circular sketch map of the complete mitogenome of the jack silverside Atherinopsis californiensis. Positions of amino acid coding sequence (CDS) genes, rRNAs, and tRNAs are indicated, as is GC nucleotide composition variation. Visualization generated using the Proksee server (https://proksee.ca/), which utilizes GCView (Stothard and Wishart 2005) for circular genome drawing.

Table 1. Location and arrangement of genes on the mitogenome of A. californiensis.

Gene		Position^b			Codon
	Strand^a	From (bp)	To (bp)	Size (bp)	Start	Stop^c	# of amino acids	Intergenic spacer (bp)^d
tRNA^Phe	H	1	69	69
12S rRNA	H	70	1012	943
tRNA^Val	H	1013	1085	73
16S rRNA	H	1086	2779	1694
tRNA^Leu	H	2780	2853	74
ND1	H	2854	3828	975	ATG	TAG	325	4
tRNA^Ile	H	3833	3902	70
tRNA^Gln	L	(3902)	(3972)	71
tRNA^Met	H	3972	4040	69
ND2	H	4041	5085	1045	ATG	T-	349	0
tRNA^Trp	H	5086	5157	72
tRNA^Ala	L	(5159)	(5227)	69
tRNA^Asn	L	(5229)	(5301)	73
tRNA^c^ys	L	(5340)	(5405)	66
tRNA^Tyr	L	(5406)	(5475)	70
COI	H	5477	7027	1551	GTG	TAA	516	19
tRNA^Ser	L	(7047)	(7117)	71
tRNA^Asp	H	7121	7192	72
COII	H	7199	7889	691	ATG	T-	231	0
tRNA^Lys	H	7890	7963	74
ATPase8	H	7965	8132	168	ATG	TAA	56	−8
ATPase6	H	8123	8805	683	ATG	TA-	228	0
COIII	H	8806	9590	785	ATG	T-	262	0
tRNA^Gly	H	9591	9661	71
ND3	H	9662	10,010	349	ATG	T-	117	0
tRNA^Arg	H	10,011	10,079	69
ND4L	H	10,080	10,376	297	ATG	TAA	99	−5
ND4	H	10,370	11,750	1381	ATG	T-	461	0
tRNA^His	H	11,751	11,819	69
tRNA^Ser	H	11,820	11,887	68
tRNA^Leu	H	11,892	11,964	73
ND5	H	11,965	13,803	1839	ATG	TAA	613	−2
ND6	L	(13,800)	(14,321)	522	ATG	CAT	174	0
tRNA^Glu	L	(14,322)	(14,389)	68
Cyt b	H	14,394	15,534	1141	ATG	T-	381	0
tRNA^Thr	H	15,535	15,608	74
tRNA^Pro	L	(15,608)	(15,677)	70
D-loop	–	15,678	16,519	69

^aH and L indicate position on the heavy H or light (L) strand.

^bNucleotide (bp) positions in parentheses indicate encoded on complementary, light (L) strand.

^cCodons containing ‘-’ symbols indicate an incomplete stop codon.

^dValues correspond to the number of nucleotides separating this and the next gene or RNA. Negative numbers denote overlapping positions.

Figure 3. Consensus maximum-likelihood phylogenetic tree of the complete mitogenome of jack silverside Atherinopsis californiensis (GenBank accession no. ON310810; shown in grey box) and other fishes of Order Atheriniformes. GenBank accession numbers are provided in parentheses accompanying each taxon. The tree was rooted using the complete mitogenome from the Northern Anchovy, Engraulis mordax (Lewis and Lema 2019). Additional information on previously published complete mitogenomes for the following species used in this phylogenetic analysis can be found as follows: Odontesthes sp. (AB370894) (Setiamarga et al. 2008); Leuresthes tenuis (MN181432) (Muñoz et al. 2020); Chirostoma humboldtianum (KJ921739) (Barriga-Sosa et al. 2016); Menidia menidia (MH538888) (Lou et al. 2018); Hypoatherina tsurugae (AP004420) (Miya et al. 2003); Hyporhamphus limbatus (MH734934) (Lü et al. 2018); Hyporhamphus quoyi (MH714706) (Zhu et al. 2018), and Cichla ocellaris (KU878410) (Lin et al. 2017).

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Data availability

The mitochondrion genome sequence data that support the findings of this study are openly available in GenBank of the National Center for Biotechnology Information (NCBI) at https://www.ncbi.nlm.nih.gov/ under accession no. ON310810. Raw 150PE reads generated by the authors to assemble this mitogenome are available under GenBank BioProject no. PRJNA824876, BioSample no. SAMN27483993, and Run Sequence Read Archive no. SRR18689888.