Whole Genome Shotgun Sequencing and Denovo Assembly of the Atheriniform Fish Odontesthes bonariensis (Pejerrey)

DANIELA CAMPANELLA; JASON MILLER; GUSTAVO M. SOMOZA; JUAN I. FERNANDINO; GUILLERMO ORTÍ; ELISABET CALER

Santa Fé

Congreso; Sequencing, Finishing, and Analysis in the Future (SFAF).; 2013

Los Alamos National Laboratory

Odontesthes bonariensis, commonly known as pejerrey, inhabits freshwaterenvironments of the South American Pampas. The pejerrey is a popular sport fisheryspecies, with a long history of domestic and international introductions due to the highquality and market value of its flesh. Several efforts for its aquaculture have been madefor over a century in South America and Japan.A first draft of the pejerrey genome was obtained using whole genome shotgunsequencing of 3 Illumina libraries of 200, 300 (paired-end) and 3 K bp (mate-paired)insert size. Assembly of the 1 billion resulting reads was attempted using SOAPdenovoand AllPaths. The AllPaths assembly resulted in larger number of bases incorporated ina smaller number of scaffolds with higher N50. The SOAP assembly resulted in 147,183scaffolds, 32.5 X coverage and N50=32kb (contig N50=2,553 in 189,087 contigs). TheAllPaths assembly resulted in 31,274 scaffolds, 40 X coverage, and N50=61kb (contigN50=13kb in 148,185 contigs). The estimated genome size is 800 Mb.Preliminary assembly analyses showed a low repeat content, and long stretches of dinucleotiderepeats, characteristic of vertebrate microsatellites. Swimmer, a LINE familyof retrotransposons, originally described in medaka and desert pupfish, was alsoidentified. Preliminary alignments with medaka chromosomes showed high sequenceidentity and synteny: 21,562 medaka genes have orthologous genes in the pejerreygenome, revealing a great level of conservation despite 80M years of divergencebetween Atheriniformes (pejerrey) and Beloniformes (medaka).