De novo genome assembly and annotation of Pacú (Piaractus mesopotamicus)

FLORENCIA MASCALI; VICTORIA POSNER; FELIPE DEL PAZO; JUAN RUBIOLO; PAULINO MARTINEZ; GABRIELA VANINA VILLANOVA

Simposio; ISCB-LA SoIBio BioNetMX 2020; 2020

Aquaculture, possibly the fastest growing food production sector, accounts today for almost 50% of the world's fish products destined for food. Pacú (Piaractus mesopotamicus) is the main product of fish farming production in Argentina. Despite the commercial importance of Pacú in Argentina, as well as in other countries, there is little genetic and genomic information about this species. Sustainable aquaculture from an environmental and economic point of view requires an understanding of the genetic basis of the traits that limit and/or improve crop development. Obtaining the genome for a given species of fish represents the starting point from which it is possible to make significant progress in the study of other areas of aquaculture such as reproduction, health, nutrition, behavior, physiology, larviculture, and molecular biology, among others. In this context, we carry out the de novo genome assembly of a male and a female reference genome for Pacú through Next-Generation Sequencing data. Genomic DNA was extracted from samples of specimens of both sexes. The preparation of Nextera Flex pair-end 600 bp libraries, as well as sequencing on a Novaseq 6000 equipment, were performed by the San Diego company Illumina. The reads quality was analyzed with FastQC program, and a pre-processing step of removing adapters and low quality bases was done with the program Trimmomatic. The final coverage was ~60X for each sex. The reads were assembled using the program VELVET. Both genomes are of ~1.2 Gb, with a 39.4 %GC. Female genome has 131388 contigs and a N50 of 22395, while the male genome has 205120 contigs with a N50 of 12026. Genome completeness was estimated using BUSCO, searching against the Actinopterygii database, resulting in 66% and 58% of completeness for females and males respectively. Regarding annotation, the AUGUSTUS program trained with Danio rerio data was used for ab initio gene prediction. More than 50000 genes were predicted for each genome, that were characterized by BLASTP against the non redundant database.This is the first draft genome available for Pacú, and constitutes a valuable tool to carry out other projects both in our group and in the scientific community, with perspectives sustainable and of improvement in the aquaculture production of this species.