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Sequencing Bait: Nuclear and Mitogenome Assembly of an Abundant Coastal Tropical and Subtropical Fish, Atherinomorus stipes

Abstract Genetic data from nonmodel species can inform ecology and physiology, giving insight into a species’ distribution and abundance as well as their responses to changing environments, all of which are important for species conservation and management. Moreover, reduced sequencing costs and improved long-read sequencing technology allows researchers to readily generate genomic resources for nonmodel species. Here, we apply Oxford Nanopore long-read sequencing and low-coverage (∼1x) whole genome short-read sequencing technology (Illumina) to assemble a genome and examine population genetics of an abundant tropical and subtropical fish, the hardhead silverside (Atherinomorus stipes). These fish are found in shallow coastal waters and are frequently included in ecological models because they serve as abundant prey for commercially and ecologically important species. Despite their importance in sub-tropical and tropical ecosystems, little is known about their population connectivity and genetic diversity. Our A. stipes genome assembly is about 1.2 Gb with comparable repetitive element content (∼47%), number of protein duplication events, and DNA methylation patterns to other teleost fish species. Among five sampled populations spanning 43 km of South Florida and the Florida Keys, we find little population structure suggesting high population connectivity.


Introduction
It is estimated that 2-40 billion gigabytes of genomic data are produced each year (Stephens et al. 2015). These data result from both decreasing sequencing costs and increasing accessibility of high-throughput genomic approaches and computational analysis tools (Cosart et al. 2011;Kumar et al. 2012;Picelli et al. 2014;Schlotterer et al. 2014;Fuentes-Pardo and Ruzzante 2017;Therkildsen and Palumbi 2017;Dudchenko et al. 2018;Puritz and Lotterhos 2018;Rice and Green 2019;Gatter et al. 2020;Pallares et al. 2020;Lou et al. 2021). When population-level indices are of interest rather than individual genotypes, low-coverage whole genome sequencing (lcWGS) can be nearly as cost effective as pool-seq approaches while retaining the ability to assess individuals. Similar to pool-seq and in contrast to reduced representation approaches (e.g., genotyping-by-sequencing [Elshire et al. 2011], RADseq [Davey and Blaxter 2010]), the lcWGS approach also surveys the entire genome. Thus, lcWGS can be advantageous over reduced representation methods for population-level queries in nonmodel species, including threatened or species of interest for conservation purposes.
One potential drawback of lcWGS is the need for a reference genome (Therkildsen and Palumbi 2017). Yet, with improved accuracy in third-generation sequencing technology, including Pacific Biosciences (PacBio) and Oxford Nanopore (ONT) sequencing, it is feasible and affordable to prepare a de novo genome or transcriptome for nonmodel organisms (Gatter et al. 2020;Faulk 2022). Incorporating short read data can additionally mitigate long read sequencing error rates [now approximately 13% for PacBio (Ardui et al. 2018) less than 5% for ONT (Dohm et al. 2020)] and improve final assembly quality (Michael et al. 2018;Shin et al. 2019;Warren et al. 2019;Gatter et al. 2020;Chen et al. 2021). Notably, ONT is portable and can be used to sequence novel samples in the field (e.g., Johnson et al. 2017;Leggett and Clark 2017). Several recent publications and improved coding resource accessibility provide new users with detailed analysis pipelines relying on free software for genome assembly and lcWGS data analyses, which can be readily adapted (Fuentes-Pardo and Ruzzante 2017;Therkildsen and Palumbi 2017;Lou et al. 2021).
Here, we apply ONT genome assembly and lcWGS to better understand the ecology and population genetics of an abundant tropical and subtropical fish, the hardhead silverside (Atherinomorus stipes). This species is often included in ecosystem models and ecological surveys (Ley et al. 1999;Vaslet et al. 2015) and may be impacted by anthropogenic habitat alterations (Hernández-Mendoza et al. 2022). They are prey for several piscivorous fishes and form large schools in shallow reefs, coastal mangroves, and seagrass meadows in west Atlantic waters from Bermuda to southern Florida and Brazil. Atherinomorus stipes predators such as snapper, barracuda, seabream (Hammerschlag et al. 2010) are commercially important for fisheries and tourism and are often targeted among fishing communities throughout the Caribbean (Schmitter-Soto and Herrera-Pavón 2019). Therefore, understanding A. stipes population distribution and connectivity can improve our ability to manage and model fishery-dependent ecosystems, which ultimately can aid in conservation management in this region.
Despite their large populations and ecological importance, very little is known about A. stipes population dynamics. Other Atherinidae species have demersal eggs that attach to nearby substrate using chorionic filaments, and it is likely that A. stipes also have demersal eggs, limiting embryonic dispersal (Takemura et al. 2004;Nash et al. 2017). It may be expected that little genetic structure exists among A. stipes populations due to their ubiquity, yet egg attachment to local substrate may limit early life stage dispersal and could drive population differentiation. Previously, a study using a single mitochondrial locus (nd2) found high haplotype divergence but no evidence of isolation by distance (IBD) among Belize cays and Florida Keys populations (Nash et al. 2017). However, because these conclusions are drawn from a single mitochondrial locus, they may not reflect nuclear genetic diversity patterns.
In this study, we use lcWGS to investigate genome-wide population structure of five A. stipes populations located throughout South Florida and the Florida Keys, USA. Additionally, we use ONT sequencing to assemble the nuclear genome and mitogenome for A. stipes, as this was previously not available. We examine genome composition statistics to validate the assembly and compare to fish species with published genomes. These data build on existing genomic resources for Atherinidae species and demonstrate the utility of lcWGS paired with third generation sequencing to examine nonmodel organism genetics.

Genome Assembly
Approximately 30x genome coverage was achieved using long-read nanopore sequences for primary assembly and short read Illumina sequences for polishing. The total genome assembly length is 1,210,410,840 bp (1.2 Gb) with an N50 of 422,115 bp and 41.03% GC content ( fig. 1). Although the assembly is not resolved to the chromosome level, contigs were generally large: the largest contig was 3,901,681 bp long and 82% of all contigs were less than 1 Mb in size. As a quality check, we used Benchmarking Universal Single-Copy Orthologs (BUSCO) scores to examine eukaryotic and Actinopterygii orthologous markers in the A. stipes genome (Simão et al. 2015). To compare GBE A. stipes genome completeness to other quality assemblies, we additionally calculated BUSCO scores using the Actinopterygii database for 30 fishes ( fig. 2; supplementary table S1, Supplementary Material online). The assembled A. stipes genome contains 98.0% of expected orthologs using the eukaryotic BUSCO database, and 96.8% of expected orthologs using the Actinopterygii database ( fig. 2; supplementary table S1, Supplementary Material online). For complete Actinopterygii and eukaryotic markers, less than 93% are single markers (not duplicated), which suggests few misaligned or duplicated segments among contigs. Our assembly is within the expected genome size range for teleost fishes and has comparable assembly completeness to other available fish genomes ( fig. 2; supplementary table S1, Supplementary Material online).

Repeat Content and Genome Annotation
Using the Danio rerio database (http://www.repeatmasker. org/species/danRer.html) of known repetitive elements in RepeatMasker (Smit et al. 2013(Smit et al. -2015, we identified 18% of the A. stipes genome as repetitive. This is lower than the expected repetitive DNA proportion for vertebrates (30-60%) (Lander et al. 2001;Waterston and Pachter 2002;Gibbs et al. 2004;Mikkelsen et al. 2005;Kasahara et al. 2007), and D. rerio is known to have many unique repetitive element families (Howe et al. 2013). Therefore, to more accurately assess repeat content, we performed de novo novel repetitive element detection using RepeatModeler2 (Smit et al. 2013(Smit et al. -2015Flynn et al. 2020). With this approach, we detected 3,164 repeat families covering 47.78% of the genome (Table 1) with the largest group of classified elements being interspersed repeats (45.22%). Of the interspersed repeats, the most common were DNA transposons (19.5%) and retroelements (7.86%).
To assess ascertainment bias between genic and intergenic regions and compare predicted genic regions among fishes, we used AUGUSTUS gene annotation software (Stanke and Waack 2003;Keller et al. 2011). Using D. rerio FIG. 1.-Atherinomorus stipes genome assembly. Snail plot summary of genome assembly statistics. From inside to outside: the central purple spiral shows log scaled scaffold count with white scale lines marking changes in order of magnitude; dark gray segments represent scaffold length distribution with plot radius scaled to the longest scaffold (red line); the orange segment represents N50 scaffold length; the light orange segment represents N90 scaffold length; outer blue and light blue rings show GC and AT percentages along the genome. Benchmarking Universal Single Copy Ortholog (BUSCO) score for the Actinopterygii database is in the upper right corner. To summarize and visualize genome assembly statistics, we used the software 'assembly-stats' (https:// github.com/rjchallis/assembly-stats).
Genome Biol. Evol. 14(8) https://doi.org/10.1093/gbe/evac111 Advance Access publication 22 July 2022 trained models, AUGUSTUS gene annotation software identified 46.0% of the genome as genic versus intergenic regions with 89.8% of bases in genic regions having 10x or greater coverage. Genic regions were targeted for coding region and protein identification with 51,144 nucleotide coding genes and 51,142 amino acids detected. Within predicted coding regions (all but two genic regions), 288,543 exons were identified. Our four billion sequence reads were split equally between genic and intergenic regions with 48.6% landing within genic regions (no significant enrichment, 1.05-fold intergenic:genic). Of the 51,142 putative genes, orthofinder assigned 35,895 (70%) to an orthogroup (i.e., identified as duplicate). The magnitude of A. stipes specific gene duplication is comparable to other fish species (supplementary fig. S1, Supplementary Material online).

DNA Methylation
We used Megalodon (https://github.com/nanoporetech/ megalodon) to detect changes in raw nanopore sequencing signal at cytosine bases where methylation occurs in 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC) contexts. For these methylation analyses, flow cell runs were analyzed separately as technical replicates. For both runs, we examined sites with more than 10 reads and an average depth of 99.3 reads per site and found 5-mC DNA methylation of 78% and 5-mHC below 1%. Results were highly repeatable between runs despite subtle differences in sequencing statistics between runs (supplementary table S2, Supplementary Material online), as expected based on prior studies using Megalodon (Liu et al. 2021).

Mitogenome Assembly
We expected to have relatively high coverage of the mitochondrial DNA, which is about 16 kb in size, due to the high mitochondrial DNA to nuclear DNA ratio found in most animals. The assembled A. stipes mitogenome is circular with a total size of 16,553 bp, containing 22 tRNAs, seven nicotinamide adenine dinucleotide (NADH) subunits, four cytochrome oxidase (COX) subunits, two adenosine triphosphate (ATP) synthase subunits, and one D-loop  (Korneliussen et al. 2014). After filtering (supplemental file S1, Supplementary Material online), we used 266,731 single nucleotide polymorphisms (SNPs) to assess population connectivity among 75 individuals (N = 15 per population) with principal component analysis in PCAngsd (Meisner and Albrechtsen 2018). The first two principal components (PCs) explained 2.09% (PC1), and 0.92% (PC2) of variance among individuals ( fig. 4B). All populations clustered into a single group when using any of the first ten PCs examined, which together accounted for 10.32% of variance among individuals (supplementary fig. S2, Supplementary Material online).

Discussion
We use ONT to rapidly assemble a high-quality genome (based on BUSCO completeness and N50) for a nonmodel organism without any existing genomic resources. Our pipeline relies on open-source software and includes repetitive element detection and classification, DNA methylation and hydroxymethylation quantification, genic region prediction and annotation, and orthologous protein region identification. Oxford nanopore technology is frequently used in metagenomics (Loit et al. 2019;Overholt et al. 2020;Kerkhof 2021) and for vertebrate genome assembly (Jansen et al. 2017;Tan et al. 2018;Dhar et al. 2019;Bian et al. 2020;Johnson et al. 2020;Xu et al. 2021). Here, we provide methods (supplemental file S1, Supplementary Material online), that use fairly low coverage (∼30x) combined ONT and Illumina sequencing for vertebrate genome assembly and genomic investigations. This is similar to assembly methods in Gatter et al. (2020) emphasizing how genomic resources can be readily produced for nonmodel organisms.

Atherinomorus stipes Genome
Despite relatively low coverage (∼30x), our genome assembly is of reasonable size and quality compared to other available fish genomes ( fig. 2; supplementary table S1, Supplementary Material online). The A. stipes assembly has a total size of approximately 1.2 Gb with 41% GC content and an N50 of 422,115 bp ( fig. 1). This is about twice the genome size of an available close relative, Atlantic silverside (M. menidia), which is roughly 620 Mb (Tigano et al. 2021), and similar in size to Atlantic killifish (Fundulus heteroclitus) and zebrafish (Danio rerio) ( fig. 2; supplementary table S1, Supplementary Material online). We also found protein duplications to be comparable in magnitude to those present among other fishes (supplementary fig. S1, Supplementary Material online), suggesting that there is not a lineage specific genome duplication contributing to genome size variation among species. Instead, we suggest that genome size variation is due to repeat content variation, which we identified to be 47.78%, ∼40% higher than the 17.73% detected in M. menidia and among the highest present in any fish (Yuan et al. 2018). This is reasonable as repetitive element content is known to increase with increasing genome size among fishes (Yuan et al. 2018) and other organisms (Lee and Kim 2014;Sessegolo et al. 2016;Blommaert et al. 2019). Notably, Atheriniformes are within the same clade as Cyprinidontiformes (Hughes et al. 2018), and available data on repetitive element content among cyprinodont fishes show similar genome size and repetitive element content as we have identified in A. stipes (Yuan et al. 2018).
For further comparison, we examined the A. stipes epigenome by identifying CpG sites with 5′-methylcytosine (5-mC) and 5′-hydroxymethylcytosine (5-mhC) modifications. Nanopore uniquely allows epigenetic modifications including DNA or RNA methylation in 5-mC and 5-mhC contexts to be detected from direct DNA and RNA sequencing, which is an improvement over other methods that cannot differentiate 5-mC and 5-mhC and leads to overestimation of 5-mC presence (Metzger and Schulte 2016;Wanner et al. 2021). With ∼15x genome coverage we identified an average DNA methylation among CpG sites of ∼78% 5-mC and ∼0.3% 5-mhC in two runs (supplementary table S2, Supplementary Material online). These 5-mC and 5-hmC values are similar to those found in zebrafish (78% 5-mC methylation and 2.3% 5-mhC) (de Mendoza et al. 2019) and are in the expected range for vertebrate genome 5-mC and 5-mhC values (Jabbari et al. 1997;Jiang et al. 2014;Keller et al. 2015;Colwell et al. 2018). To our knowledge, no prior studies have used Nanopore sequencing to examine DNA methylation in fish (Metzger and Schulte 2016). Nanopore sequencing may be beneficial in future studies examining DNA methylation to reduce time and cost by preventing the need for sample pre-treatment. These methods could be applied in fish to further study DNA methylation variation with habitat temperature (Varriale and Bernardi 2006), across generations or populations (Hu et al. 2021;Kelley et al. 2021), or in response to environmental stressors (Aluru et al. 2011). Due to the portability of Nanopore, investigations of epigenetic variation among otherwise genetically indistinguishable populations could enhance our understanding of species' environmental responses.

Atherinomorus stipes Population Connectivity
The five A. stipes populations examined here are spread across 43 km of coastal habitat where salinity, anthropogenic influence, and temperature fluctuate widely ( fig. 4A). While higher salinity has previously been correlated with greater abundance for this species, it does not seem to influence genetic structure among these populations ( fig. 4B [Ley et al. 1999]). Despite distance and habitat variation, we do not observe population structure among these populations ( fig. 4B). Similar to previous observations using the mitochondrial locus nd2, IBD is not supported in this data set (Nash et al. 2017). Although it is likely these fish lay demersal eggs, this does not impact population connectivity. Instead, it appears gene flow is not restricted among these southeast Florida populations. This may be due to high migration and low-site fidelity, or larval distribution by currents, resulting in a single admixed population.
Insights into population structure and connectivity are important for fisheries modeling. Typically, fisheries incorporate species information based upon stock units, which are discrete populations (Ovenden et al. 2015). Incorporating genetic data in ecological and fisheries modeling can improve how a stock is defined in terms of population and community structure (Overcast et al. 2019). Additionally, genetic data can improve resolution of ecological factors, recruitment, connectivity, signatures of selection and adaptive response (Bernatchez et al. 2017). Atherinomorus stipes is often included in fisheries models in South Florida and the Florida Bay (Flaherty et al. 2013, Smith et al. 2021. With our lcWGS data we can conclude that among the sampled southeast Florida sites, A. stipes is not impacted by habitat fragmentation. The region represented in this study can be included as a single population stock, which was previously uncertain based on limited data. Overall, incorporating lcWGS allows for greater knowledge that has many applications for improving many fields, including fisheries management. Future studies encompassing more of A. stipes' range, throughout the Caribbean, Gulf of Mexico, and northeast coast of South America would further inform the degree of genetic connectivity among populations.

Conclusions
Our study builds on existing genomic resources for teleost fish and provides a novel genome for Atherinidae species. The A. stipes genome assembly is similar in completeness and quality to other available fish genomes, and future studies should consider its inclusion in comparative genomics work, especially among fishes. In addition, we show that A. stipes individuals sampled across this 43 km range do not exhibit significant population structure. As these fish are an important prey item for several economically important species, we suggest that future ecological models could consider A. stipes found across this spatial scale as a single interbreeding population with little fragmentation or structure. However, any conclusions about population structure outside of the range presented here would require further testing, which will be possible with the genomic resources developed here. Overall, we highlight the importance and simplicity of increasing genomic resources and genome sequence data in nonmodel organisms. Doing so, particularly for commercial fishery species, can increase understanding of threatened habitats and allow for improved modeling resolution and conservation practices.

Sample Collection
Fin clips from adult A. stipes individuals were collected from five populations in south Florida including: Crandon Park

Sequencing
Genomic DNA was shipped on ice to the University of Minnesota, prepared with the SQK-LSK-109 (run 1) or SQK-LSK-110 (run 2) kit, and sequenced on an in-house ONT MinION instrument. Each sequencing run used 2 ug of DNA as input and took place over 2 days with one wash (wash kit 004) and reloaded with DNA from the original library prep.
For population genetics analysis and whole genome polishing, an additional 76 samples (15 per population, ONT individual at 10X) were prepared for 150 bp paired end sequencing on an Illumina HiSeq3000 (Genewiz LLC, New Jersey, USA). Briefly, a recombinant Tn5 was used as in (Picelli et al. 2014) with 15 cycles of PCR amplification, similar to the Illumina Nextera XT DNA library preparation kit. Final libraries were size-selected to 300-700 bp fragments using SPRI magnetic beads. Dual barcodes for each individual and sequencing primers used for library preparation are available in supplementary table S4, Supplementary Material online.

Supplementary Material
Supplementary data are available at Genome Biology and Evolution online.