GENOMIC ANALYSIS AND VIRAL AND TRANSPOSON SEQUENCES IN AQUATIC ORGANISMS.  

Miguel Ángel del Río-Portilla*, Fabiola Lafarga-De La Cruz, Carmen Paniagua-Chávez, and Francisco J. García-De León.
Departamento de Acuicultura. Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE). Carretera Ensenada-Tijuana No. 3918, Zona Playitas, C.P. 22860, Ensenada, B.C. México
* mdelrio@cicese.edu.mx

The National Subsystem of Genetic Aquatic Resources (SUBNARGENA in Spanish) from Mexico is in charge to preserve and genetically characterize the germplasm of economically important aquatic organisms. Next Generation Sequencing (NGS) is the best way to obtain large number of genetic markers of non-model species. We have been able to obtain microsatellite and candidate sequences for single nucleotide polymorphism (SNP´s). However, when sequences are compared with the nucleotide database (GenBank) in some cases a particular sequence can be related with a viral o transposon sequence. In this paper, we show how the NGS and annotation procedures have helped us to find viral and transposon related sequences in aquatic organisms.

Total DNA was extracted from seven aquatic species: Porites panamensis, Strombus gigas, Panulirus interruptus, Artractosteus tropicus, Petenia splendida, Fundulus lima and Pterois volitans. Genomic DNA was partially sequenced by Illumina protocol at the University of Georgia. Contig assembling was carried out with the CLC Genomic Workbench 6.5 program and the obtained contigs were annotated with FastAnnotation program.

The average number of contigs was 141,534 (±82,323), but only 15.37% could be annotated. This was due to the lack of a reference genome of each species. From the annotated contigs 2.83% and 1.35% were related with transposons and virus respectively. These results suggest that, although, there are several transposons and viral related sequences in the genome of these species, the number of these sequences are similar to other metazoan organisms. Further discussion on this subject will be presented.