A genomic investigation of the marine teleost tarakihi (Nemadactylus macropterus) provides insights into its genome evolution and population structure
Authors:   , Papa Yvan 
Published: January 2022

<p><b>Understanding the patterns of connectivity and stock structure of a fishery is an essential prerequisite for effective and sustainable management. Genetic markers can assist with the delineation of fish stock boundaries. The ongoing progress in high-throughput DNA sequencing technologies has transformed the field of genetics forward into genomics. Genome-wide marker sets allow for an unprecedented level of resolution for the investigation of population differentiation, levels of gene flow, and the functional loci associated with adaptation. They can provide significant insights into the evolutionary processes that influence populations and link these to environmental conditions. Equally important is the application of genetic information to improve population management decisions. However, genomic analyses have not yet been widely used for fisheries research in New Zealand.</b></p>
<p>Tarakihi (Nemadactylus macropterus) is a marine fish widely distributed around the inshore areas of New Zealand and the southern parts of Australia. It supports an important commercial fishery with annual landings in New Zealand averaging over 5,000 tonnes over the past 40 years. As with many other New Zealand fish, very little is known about its stock structure as well as the characteristics of its genome. Previous studies using low-resolution population genetic markers did not detect any significant level of population structure. Genome-wide markers now offer the opportunity to obtain a more complete picture of tarakihi population genetic variation. The aims of this thesis were to (1) study the evolution of the tarakihi genome and to (2) assess the population structure of tarakihi in New Zealand. This was achieved by producing the first tarakihi genome assembly, compare it with genomes of other fish species and analyse a population sample of tarakihi low-coverage genomes to test for genetic differentiation and identify presumably adaptive genetic variation.</p>
<p>This thesis presents an in-depth review of the studies that have been conducted on genetic stock structure of fishes in New Zealand and of the applications of genomics for fisheries management. This provides an important framework and establishes why there is a strong need to carry out population genomic research on New Zealand fisheries species.</p>
<p>A de novo genome sequence of tarakihi was assembled using high-molecular-weight DNA obtained from a vouchered specimen. DNA sequencing was performed using 92x high-quality Illumina short-reads and 122x Oxford Nanopore Technology long-reads. Two genome assembly algorithms were used. An assembly based on a trial run of low-coverage PacBio HiFi data from another specimen was also produced. The polished Illumina + Nanopore assembly performed in MaSuRCA with the Flye algorithm gave the best results. The final reference genome is 568 Mb long and comprised of 1,214 scaffolds with an N50 of 3.37 Mb. Genome completeness was high, with 97.8% of complete Actinopterygii BUSCOs retrieved. An additional 250 Gb of PacBio Sequel II Iso-Seq RNA reads were obtained from four tissue types to assist with gene annotation. Approximately 30.5% of the tarakihi genome was composed of repetitive elements and 20,169 protein-coding genes were annotated. Iso-Seq analysis found 91,313 unique transcripts and the most common alternative splicing event was intron retention. This highly contiguous genome assembly will be a valuable genomic resource to assist the study of population genomics and comparative genomics; its value is demonstrated in the subsequent analyses of this study.</p>
<p>The de novo short-read genomes of five additional New Zealand fish species were assembled: barracouta (Thyrsites atun), blue moki (Latridopsis ciliaris), butterfish (Odax pullus), kahawai (Arripis trutta), and king tarakihi (Nemadactylus n.sp.). One specimen of each species was sequenced for at least 33x coverage with paired-end Illumina short reads. The resulting draft genome assemblies ranged in size from 532 Mb (butterfish) to 714 Mb (barracouta), with the number of scaffolds ranging from 58,102 to 150,595, N50 from 10,031 to 30,942 bp, and BUSCO completeness scores from 70.2% to 89.1%. The tarakihi genome was added to the dataset for a comparative genomic analysis using all six species. While the proportion of repeat elements was highly correlated with genome size (R2 = 0.97, P < 0.01), most of the metrics for the genic features (e.g. number of exons or intron length) were significantly correlated with assembly contiguity (|R2| = 0.79–0.97). A phylogenomic tree of Percomorpha including eight additional high-quality fish genomes was reconstructed from sequences of shared gene families. Based on the branch-site model, evidence of positive selection was found in 65 genes in tarakihi and 209 genes in Latridae: most of these were involved in the ATP binding pathway and the integral structure of membranes. These results can be used to inform future studies when considering the strengths and weaknesses of scaffold-level assemblies for comparative genomics. This also provided useful insights into the evolutionary patterns and processes of genome evolution in bony fishes.</p>
<p>A population genomics analysis was conducted using 175 wild-caught tarakihi specimens obtained from around New Zealand and Tasmania (Australia) and an additional 12 king tarakihi specimens. All individuals were whole-genome sequenced for c. 12x coverage using Illumina short read data. A dataset of 7.5 million high-quality single-nucleotide polymorphisms (SNPs) was obtained. Variant filtering, FST-outlier analysis, and redundancy analysis (RDA) were used to evaluate population structure, presumably adaptive structure, and locus-environment association. King tarakihi displayed high levels of genetic divergence, differences in heterozygosity, and differences in linkage disequilibrium patterns that were all consistent with reproductive isolation from tarakihi from New Zealand and Tasmania. This provided additional evidence that king tarakihi is genetically distinct and a different species. While the tarakihi population sampled from Tasmania showed a significant level of neutral genetic differentiation from the New Zealand populations (FST = 0.0054–0.0073, P ≤ 0.05), there was no clear genetic sub-structuring that could be detected among New Zealand tarakihi samples (ФST < 0.001, P = 0.77). However, presumably adaptive variation based on outlier SNPs suggested fine-scale adaptive structure between locations around central New Zealand off the east (Wairarapa, Cape Campbell, and Hawke’s Bay) and the west coast (Tasman Bay/Golden Bay and Upper West Coast of South Island). Locus-environment association analysis found that 47 loci were correlated with mean depth temperature and projection of the RDA indicated that tarakihi in New Zealand are distributed following a North-South temperature cline. Taken together, these findings indicate that tarakihi are composed of one genetically panmictic stock in New Zealand, but the presence of presumably adaptive variation suggests that the latitudinal pattern of tarakihi migration could be influenced by water temperature or some other environmental feature with a distribution linked to temperature.</p>
<p>The tarakihi genome presented here is the first genome assembly for a species in the Cirrhitioidei superfamily and one of the first to be reported for a New Zealand fisheries species. This will provide a valuable genetic resource for analyses of genome-wide patterns of evolution. The additional five draft fish genomes establish the much-needed genomic resource for studies of the fishes of New Zealand and are available as reference genomes for population genomic studies. The results of the tarakihi population structure analysis can be used to support stock assessment models and improve fisheries management. Overall, the findings of this thesis research can be built upon with long-term temporal and spatial genomic sampling studies and incorporate the results as part of an integrative evidence-based approach to fisheries management. This will be a crucial step toward sustainable fisheries as wild-harvest resources face strong pressures from increasing commercial demands, a changing climate, and a marine ecosystem with an uncertain future.</p>