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

FERNANDO VILLARREAL; GERMÁN BURGUENER; EZEQUIEL SOZA; NICOLAS STOCCHI; GUSTAVO M. SOMOZA; ADRIAN TURJANSKI; ANDRES BLANCO; JORDI VIÑAS; ALEJANDRO S. MECHALY

Rosario

Congreso; XIII Argentine Congress of Bioinformatics and Computational Biology; 2023

Iberoamerican Society of Bioinformatics

BACKGROUNDBlack 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, revealing a small genome size of ~538 Mbp compared to most teleosts.Black flounder and Pleuronectiformes appear to have smaller genomes than most other teleost groups. Thus, the main objective of the present study was to determine whether the small genome size of Black flounder and other Pleuronectiformes can be explained by the amount of transposable elements (TEs) and other repetitive elements, as well as the size of introns and exons.RESULTSThe Black flounder's genome (libraries from one male and one female were used) was sequenced with > 35 X-fold coverage. 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 reasonably 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. Next, we performed a comparative genome analysis between Pleuronectiformes and other teleost orders to determine whether the small genome size can be explained by gene features, including whole genome genes and introns sizes, and as well as differential contents of repetitive elements. We show that the genome size shrinkage in flounder is indeed due to several factors, including changes in the number of repetitive elements (particularly TEs) and smaller gene size, mainly due to a reduced number of very large and small introns.Thus, these components appear to be involved in the reduction in Black flounder genome size.CONCLUSIONSBlack flounder genome's resolution is an important tool for future aquaculture strategies for this species. The reduction of its genome size compared to other teleost is achieved by a mechanisms that, combined, are novel compared to those from another teleost, in general, and Pleuronectiformes, in particular.