Sequencing and first draft assembly of the genome of the flounder Paralichthys orbignyanus

GERMÁN BURGUENER; JORDI VIÑAS; PAULINO MARTÍNEZ; JUAN JOSE BOCCANFUSO; GUSTAVO M. SOMOZA; ADRIAN TURJANSKI; ALEJANDRO S. MECHALY

Mar del Plata

Congreso; IX Argentinian Congress of Bioinformatics and Computational Biology; 2018

The flounder (Paralichthys orbignyanus) is an economically important marine fish with aquaculture potential in Argentina due to its market value. In this study, we sequenced the whole genome using an Illumina paired-end sequencing platform and assembly. We started with four independent libraries (from male, female, a pool of males and a pool of females; with 150bp paired-end reads, mean insert length of 350bp and >35 X-fold coverage each). Each library was assembled separately using SOAPdenovo2 and the resulting contigs where scaffolded with SSPACE3, prior gap-filling with GapCloser. The assemblies showed a genome size of ~550 Mbp, both for male and female samples (41.35% of GC content, 0.11% of undetermined bases). An analysis of assemblies at the level of core genes (subset of 458 universally expressed KOG families) showed more than 98% of core genes present, with more than 78% of them having coverage greater than 50%. This indicates a fairly complete and accurate genome at the coding sequence level. A prediction of genes was made based on statistical predictors (geneid) and predictors based on sequences (exonerate, with a closely related species, Paralichthys olivaceus as reference), finding 25,231 protein coding genes, 445 tRNAs, 3 rRNAs and more than 1,500 non-coding RNAs of other types (including a complete spliceosome set and several types of snoRNA and miRNA). A genome map for this species will help in future studies of genes related to sex differentiation, puberty, food intake, reproduction and other important functions related to the culture of this fish.Supported by: ANPCyT (Agencia Nacional de Promoción Científica y Tecnológica) grant PICT-2014-0515.