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

CAMPANELLA, D.; MILLER, J.; SOMOZA, G.M.; FERNANDINO, J.I.; ORTI, G; CALER, E.

Santa Fe, New Mexico

Congreso; 8th Annual Sequencing, Finishing, Analysis in the Future Meeting; 2013

Odontesthes bonariensis, commonly known as pejerrey, inhabits freshwater environments of the South American Pampas. The pejerrey is a popular sport fishery species, with a long history of domestic and international introductions due to the high quality and market value of its flesh. Several efforts for its aquaculture have been made for over a century in South America and Japan. A first draft of the pejerrey genome was obtained using whole genome shotgun sequencing 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 SOAPdenovo and AllPaths. The AllPaths assembly resulted in larger number of bases incorporated in a smaller number of scaffolds with higher N50. The SOAP assembly resulted in 147,183 scaffolds, 32.5 X coverage and N50=32kb (contig N50=2,553 in 189,087 contigs). The AllPaths assembly resulted in 31,274 scaffolds, 40 X coverage, and N50=61kb (contig N50=13kb in 148,185 contigs). The estimated genome size is 800 Mb.Preliminary assembly analyses showed a low repeat content, and long stretches of dinucleotide repeats, characteristic of vertebrate microsatellites. Swimmer, a LINE family of retrotransposons, originally described in medaka and desert pupfish, was also identified. Preliminary alignments with medaka chromosomes showed high sequence identity and synteny: 21,562 medaka genes have orthologous genes in the pejerrey genome, revealing a great level of conservation despite 80M years of divergence between Atheriniformes (pejerrey) and Beloniformes (medaka).