The genome size of gilthead sea bream (sparus aurata) reveals novel fish insights in gene duplication

Abstract

We report a draft genome assembly for the teleost gilthead sea bream (Sparus aurata), reconstructed by combination of short- and long-read high-throughput sequencing, and genetic linkage maps. The assembly comprised 5,039 scaffolds that span 1.24 Gb of the expected 1.59 Gb complete genome size, with 932 scaffolds (~732 Mb) anchored to 24 chromosomes. This sequencing strategy resulted in a high quality fish genome assembly, as supported by the high N50 (1.07 Mb) and lower L50 (227) values. These long and continuous reads allowed the annotation of a large number of coding genes (55,423), non-coding RNA genes (2,991) and 345 Mb of mobile genetic elements (MGEs). Synteny analysis revealed a high level of homology between gilthead sea bream genes. Phylogenomics relationships with other fish species were established to locate temporal speciation and to assign duplication events. A large degree of recent and lineage-specific gene duplications was found, that were mainly enriched in functions related to genome transposition, immune response and response to stimulus. These duplications and gene family expansions could be related in part to the activity of MGEs. This fact makes gilthead sea bream an interesting model for the study of gene repertoire expansion strategies complementary to fish whole genome duplication events. Transcriptional analyses across six different tissues (anterior and posterior intestine, skeletal muscle, liver, gills, spleen) indicated that gene duplication preferentially affected genes expressed in two or more tissues. These findings highlight the genomic complexity of this species and the importance of selective gene ; This work was financed by Spanish (Intramural-CSIC, 1201530E025; MICINN, BreamAquaINTECH, RTI2018-094128-B-I00) and European Union (AQUAEXCEL2020, 652831) projects. BS was supported by a predoctoral research fellowship (Doctorados industriales, DI-17-09134) from Spanish MINECO.