A draft reference genome of the South African yellowtail, Seriola lalandi.

Jenkins, S. F.*, Rhode, C.

Department of Genetics, Stellenbosch, South Africa

Yellowtail (Seriola lalandi) is an emerging candidate for marine finfish aquaculture in South Africa due to declining wild population numbers and increasing consumer demand. Sustainable aquaculture production relies on the implementation of well-informed genetic management and improvement strategies for economically important traits. Understanding the genetic factors influencing complex traits is fundamental for the development of molecular selection strategies that can help overcome some of the challenges associated with traditional phenotypic selection, such as variability in production performance and long generation intervals. However, genomic resources for yellowtail are limited. To address this, a draft genome sequence of yellowtail was assembled and annotated. Both long and short-read DNA sequencing technologies were utilized for the initial de novo assembly, which was scaffolded into 24 pseudochromosomes, yielding an estimated size of 660 Mb and a BUSCO complete score of 98.5%. Annotation pipelines revealed that interspersed repeats, particularly DNA transposons and LTR elements, comprise 25% of the genome. Additionally, 21,796 genes were identified from RNA-seq and protein evidence. The resulting gene annotations were further used to identify single copy orthologs shared among Seriola species for phylogenetic tree construction and signatures of positive selection analysis. The results reaffirmed the evolutionary placement of yellowtail within the genus and provided valuable insights into genes and genetic mechanisms underlying yellowtail evolution, with potential applications for the genetic improvement of commercial stocks.