Genome sequencing and analysis of black flounder (Paralichthys orbignyanus) reveals new insights into Pleuronectiformes genomic size and structure

Abstract Black flounder (Paralichthys orbignyanus, Pleuronectiformes) is an economically important marine fish with aquaculture potential in Argentina. In this study, we sequenced the whole genome of this species using an Illumina sequencing technology. We started with two independent libraries (from one female and one male; each with 150 bp paired-end reads, a mean insert length of 350 bp, and > 35 X-fold coverage). The assemblies yielded a genome size of ~ 538 Mbp. Analysis of the assemblies at the core gene level revealed that more than 98% of the core genes were present, with more than 78% of them having more than 50% coverage. This indicates a somehow complete and accurate genome at the coding sequence level. This genome contains 25,231 protein-coding genes, 445 tRNAs, 3 rRNAs, and more than 1,500 non-coding RNAs of other types. On the other hand, in vertebrates the number of transposable elements (TEs) is related to genome size, but it remains unclear whether the size of introns and exons also plays a role. Therefore, the main objective of the present study was to determine whether the small genome size of Black flounder and other Pleuronectiformes is related to the size of their introns and exons. Indeed, Black flounder, along with pufferfishes, seahorses, pipefishes and anabantid fish appear to have smaller genomes than most other teleost groups. We performed a comparative genomic analysis between Black flounder and other teleost order, in order to determine if the small genomic size could be explained by gene features, including the whole genome genes and introns sizes. We show that the smaller genome size of flounders can be attributed to several factors, including changes in the number of repetitive elements, and decreased gene size, particularly due to lower amount of very large and small introns. Thus, these components appear to be involved in the genome reduction in Black flounder.