Genome of a Giant (Trevally): Caranx ignobilis

Abstract

Caranx ignobilis, commonly known as the kingfish or giant trevally, is a large, reef-associated apex predator. It is a prized sportfish, targeted heavily throughout its tropical and subtropical range in the Indian and Pacific Oceans, and it has drawn significant interest in aquaculture due to an unusual tolerance for freshwater. In this study, we present a high-quality nuclear genome assembly of a C. ignobilis individual from Hawaiian waters, which have recently been shown to host a genetically distinct population. The assembly has a contig NG50 of 7.3Mbp and scaffold NG50 of 46.3Mbp. Twenty-five of the 203 scaffolds contain 90% of the genome. We also present the raw Pacific Biosciences continuous long-reads from which the assembly was created. A Hi-C dataset (Dovetail Genomics Omni-C) and Illumina-based RNA-seq from eight tissues are also presented; the latter of which can be particularly useful for annotation and studies of freshwater tolerance. Overall, this genome assembly and supporting data is a valuable tool for ecological and comparative genomics studies of kingfish and other carangoid fishes.

The genome of a giant (trevally): Caranx ignobilis

“…An overview of the methods used in this study is provided here. Where appropriate, additional details, such as the code of custom scripts and the commands used to run software tools, are provided in a file in GigaDB [16].…”

“…Science Framework [80]. Snapshots of the code and other results files are available in the GigaDB repository [16].…”

“…No significant computer programs were generated in this work. The commands used to generate these data are available as a shell script via the archived Bioinformatics Methods file in GigaDB [16]. Custom scripts referenced therein are available via GitHub.…”

“…Giant trevally (Caranx ignobilis) adult and juvenile.The quantitative morphological data for this illustration of C. ignobilis were obtained primarily from Smith-Vaniz (1999)[12]. These were evaluated by the artist who selected the specific values for meristic traits represented in the adult illustration, including the number of lateral-line scutes(32), the number of dorsal-fin rays(20) and spines(9), and the number of anal-fin rays(16) and spines (1*). Each value represents the centermost whole number in the corresponding range reported (within 1).…”