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

Abstract The jack silverside (Atherinopsis californiensis), also referred to as jacksmelt, is a neotropical silverside fish that inhabits nearshore shallow waters of the California Current Ecosystem in the Northeast Pacific Ocean, ranging from the coast of Oregon, USA, in the north to as far south as Baja California, Mexico. This fish is the sole member of its genus and is a commonly taken species when hook-and-line fishing in pelagic-neritic environments including bays, estuaries, kelp forests, and along sand beaches. Here we report the first complete mitochondrial genome of jack silverside consisting of 16,519 bp nucleotides and encoding 13 protein-coding regions, 12S and 16S rRNAs, 22 tRNAs, and an 841 bp D-loop control region. Phylogenetic analysis using all protein-coding genes of the complete mitogenome confirmed the inclusion of A. californiensis within subfamily Atherinopsinae of family Atherinopsidae, order Atheriniformes. This complete mitochondrial DNA genome will be of use for biodiversity assessments in the California Current ecosystem, while also providing a foundation for future mtDNA population genetic studies on this prominently caught species in shore- and pier-based recreational sport fishing.


Introduction
The jack silverside (Atherinopsis californiensis, Girard, 1854)also commonly referred to as 'jacksmelt'is a pelagic schooling fish that reaches up to $20 cm in length and lives for 9-10 years (Clark 1929). A. californiensis ranges from Yaquina Bay, Oregon in the Pacific Ocean to as far south as Bah ıa Magdalena, Baja California Sur, Mexico (De La Cruz-Ag€ uero et al. 1994). This species is generally considered to be omnivorous and consumes a broad range of food types (Barry et al. 1996;Horn et al. 2006;Higgins and Horn 2014). That versatility in diet allows both adult and juvenile A. californiensis to occupy a variety of open shallow water habitats, typically ranging in depths from approximately 1.5-15 m, from within and beyond the surf zone along sand beaches to estuaries and kelp forests (Horn 1979;Allen and Pondella 2006). With a nearshore distribution, A. californiensis is commonly caught by recreational sport anglers fishing from boats or shore (Ono 1982;Hill and Schneider 1999;Jarvis et al. 2004).

Materials
Here we report the first complete mitochondrion DNA genome for A. californiensis. Skeletal muscle tissue was dissected from an adult jack silverside ( Figure 1)

Methods
DNA was extracted from the skeletal muscle using the DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA), analyzed for quality and quantity both fluorometrically (Qubit 2.0 Fluorometer, Life Technologies, Carlsbad, CA) and by gel electrophoresis. DNA was then fragmented into a $350 bp library (Illumina Nextera DNA Flex Library Prep kit) and sequenced on the Illumina NovaSeq 6000 System (Novogene, Sacramento, CA) to generate $125 million 150 bp PE reads (GenBank BioSample no. SAMN27483993, Run Sequence Read Archive no. SRR18689888). Raw read quality was evaluated using FastQC version 0.11.9 (Andrews 2010). Raw 150 bp sequences were then assembled into a complete mitogenome using SMART2 (Alqahtani and Mandoiu 2020) using a partial sequence of the A. californiensis cytochrome b (cytb) gene (GenBank accession no. JQ282018; Bloom et al. 2012) as the 'seed sequence' for mitogenome assembly. SMART2 assembly generated a 16,519 bp nucleotide complete CONTACT Sean S. Lema slema@calpoly.edu Biological Sciences Department, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, CA, 93407, USA mitogenome from 400,000 of the raw 150PE sequences (median coverage depth: 26X). The complete mitogenome was subsequently confirmed in Galaxy version 21.09 (https:// usegalaxy.org/) by going back to the raw 150 bp reads and conducting a separate alignment of those reads to the mitogenome assembled from the SMART2 pipeline. For that confirmational assembly, sequencing adaptors were first trimmed from the raw reads using fastp (Chen et al. 2018), and the trimmed sequences were aligned to the SMART2-generated mitogenome using Bowtie2 (Langmead and Salzberg 2012). Trimmed sequences that aligned to the SMART2 mitogenome were then downloaded and reassembled in Sequencher version 5.4.6 software (GeneCodes Corp., Ann Arbor, MI) for final confirmation of the complete mitogenome sequence. The resulting mitogenome was annotated using MitoFish (Iwasaki et al. 2013;Sato et al. 2018).
To confirm evolutionary relationships of A. californiensis, a maximum-likelihood phylogenetic tree was constructed using all amino acid coding sequence (CDS) regions concatenated from the mitogenomes of A. californiensis and eleven other fishes of Order Atheriniformes. Sequences were aligned using Clustal X software (Larkin et al. 2007), and the tree was constructed using all sites with pairwise gap deletion in MEGA version 11 (Tamura et al. 2021). Percent confidence values for each node were calculated from 1000 bootstrap replicates. The tree was rooted using the complete mitogenome from the Northern Anchovy, Engraulis mordax (MH613715) (Lewis and Lema 2019).

Results
The 16,519 bp complete mitogenome of jack silverside (GenBank accession no. ON310810) contains 13 protein-coding genes, 22 tRNAs, and 12S and 16 rRNAs in the typical arrangement of mitochondrial genes for actinopterygian fishes (Table 1). Of the 13 protein-coding genes, only nd6 was encoded on the light strand (L-strand), and all others were found on the heavy strand (H-strand) (Figure 2). Similarly, eight of the tRNA genes (tRNA Gln , tRNA Ala , tRNA Asn , tRNA Cys , tRNA Tyr , tRNA Ser , tRNA Glu , and tRNA Pro ) were located on the L-strand, while the other 14 tRNAs and both rRNAs were positioned on the H-strand. Overall nucleotide composition of the mitogenome had a GC content of 46.63% composed of the following: A, 26.24%; T, 27.13%; G, 17.34%; and C, 29.29%.
Phylogenetic analysis of protein-coding genes confirmed that A. californiensis belongs to the clade of Neotropical silverside fishes of subfamily Atherinopsinae, family Atherinopsidae ( Figure 3). That phylogenetic arrangement corroborated the close relationship of A. californiensis to California grunion (Leuresthes tenuis) (Muñoz et al. 2020), which agrees with the relationship of A. californiensis to Leuresthes fishes observed previously using allozyme variation (Crabtree 1987).

Discussion and conclusion
Although A. californiensis has received little research attention due to the species not being a target of commercial fisheries,    A. californiensis is commonly caught in nearshore saltwater recreational sport fishing and is regularly consumed (Jarvis et al. 2004). The complete mitochondrial genome for A. californiensis reported here supports the evolutionary relationships of this species within subfamily Atherinopsinae, family Atherinopsidae, and provides a foundation for future assessments to fill a data gap on the population structure and genetic diversity of A. californiensis across its geographic range. Studies into how fishing and climate change are affecting marine fish biodiversity in the California Current Ecosystem are increasingly utilizing environmental DNA (eDNA) and other high throughput DNA sequencing approaches (e.g. Closek et al. 2019;Stat et al. 2019). The cytochrome oxidase I (coi) sequence from this new mitogenome and other sequences from A. californiensis (e.g. KM019227-KM019229) show >7% nucleotide sequence divergence compared to topsmelt silverside Atherinops affinis (OL806589-OL806590), the closest relative of A. californiensis, and $10% divergence with California grunion (L. tenuis, MN181432), indicating coi is a viable target for distinguishing these species in large-scale, DNA-based studies in the California Current Ecosystem.