Genome assembly and isoform analysis of a highly heterozygous New Zealand fisheries species, the tarakihi (Nemadactylus macropterus)

Abstract

Although being some of the most valuable and heavily exploited wild organisms, few fisheries species have been studied at the whole-genome level. This is especially the case in New Zealand, where genomics resources are urgently needed to assist fisheries management attains its sustainability goals. Here we generated 55 Gb of short Illumina reads (92 coverage) and 73 Gb of long Nanopore reads (122) to produce the first genome assembly of the marine teleost tarakihi (Nemadactylus macropterus), a highly valuable fisheries species in New Zealand. An additional 300 Mb of Iso-Seq RNA reads were obtained from four tissue types of another specimen to assist in gene annotation. The final genome assembly was 568 Mb long and consisted of 1,214 scaffolds with an N50 of 3.37 Mb. The genome completeness was high, with 97.8% of complete Actinopterygii BUSCOs. Heterozygosity values estimated through k-mer counting (1.00%) and bi-allelic SNPs (0.64%) were high compared to the same values reported for other fishes. Repetitive elements covered 30.45% of the genome and 20,169 protein-coding genes were annotated. Iso-Seq analysis recovered 91,313 unique transcripts (isoforms) from 15,515 genes (mean ratio of 5.89 transcripts per gene), and the most common alternative splicing event was intron retention. This highly contiguous genome assembly along with the isoform-resolved transcriptome will provide a useful resource to assist the study of population genomics, as well as comparative eco-evolutionary studies in other teleost and related organisms.

Genomic stock structure of the marine teleost tarakihi (Nemadactylus macropterus) provides evidence of fine-scale adaptation and a temperature-associated cline amid panmixia

“…Trimmed and filtered paired reads were mapped to the tarakihi reference genome (1,214 scaffolds) assembled in a previous study (Papa et al, 2021c) by using the Burrows-Wheeler Alignment (BWA) method with bwa-kit v0.7.15 (Li and Durbin, 2009). In brief, a BWA index was created for the reference genome, as well as a SAM index with SAMtools v1.9 (Li et al, 2009).…”

“…SNP filtering for the neutral dataset was identical to the pruned dataset but with an additional step of filtering out potentially adaptive outliers (see below). The 250 longest scaffolds were retained because (1) they contained more than 90% of the total number of bases in the tarakihi reference genome (L90 = 219 (Papa et al, 2021c)), (2) for computational efficiency, and (3) because the default parameters used for the OutFLANK analysis (see below) were not optimal anymore to fit the F ST curve in some scaffolds past that number, which means they would have had to be manually tuned for the c. 1,000 remaining scaffolds. Chatham Islands, Fiordland and the juvenile TBGB samples were discarded at that stage because of their low number of samples (two, three, and five, respectively), which was considered too low to confidently predict population allele frequencies.…”

“…Loci that were strong candidates for local adaptation were selected by identifying the SNPs with scores ± 3.5 standard deviations from the mean score of each significant constrained axis. The position in the genome and putative associated function of the selected loci were obtained using the tarakihi reference genome assembly annotation produced in Papa et al (2021c).…”

Comparative genomics of tarakihi (Nemadactylus macropterus) and five New Zealand fish species: assembly contiguity affects the identification of genic features but not transposable elements

“…Repetitive elements in the five genomes were identified using the same method and tools as reported in Papa, Wellenreuther, et al (2021). During the repeat identification step, the Actinopterygii homology-based repeat library produced in Papa, Wellenreuther, et al (2021) was combined with each of the de novo repeat libraries produced separately for each species. Genome annotation was carried out with the MAKER v2.31.10 (Holt & Yandell, 2011) pipeline on the unmasked genomes.…”

“…To achieve this, the five new genomes were assembled using Illumina short read sequences. The high-coverage genome assembly and annotation of tarakihi produced in Papa, Wellenreuther, et al (2021) was combined with these five genomes to explore the diversity of repeat elements and genic features. High-quality genomic data from eight other fishes retrieved from Ensembl were then added to identify genes under positive selection in tarakihi and Latridae in a phylogenomic framework.…”