First Draft Genome for Red Sea Bream of Family Sparidae.

Abstract

Reference genomes for all organisms on earth are now attainable owing to advances in genome sequencing technologies (Goodwin et al., 2016). Generally, species that contribute considerably to the economy or human welfare are sequenced and are considered more important than others. Furthermore, coastal indigenous people mainly depend on marine species for their food sources, which has resulted in the extinction of several marine species (Cisneros-Montemayor et al., 2016). Of these, an extinction risk assessment of marine fishes, mainly for sea breams (Family: Sparidae), has recently been conducted by way of a global extinction risk assessment from the dataset of the International Union for Conservation of Nature's Red List Process, which mentions that around 25 species are threatened/near-threatened according to their body weight (Comeros-Raynal et al., 2016). Another report clearly showed the benefit of worldwide aquaculture production, which contributed to 47% of total seafood production, and also highlighted the over-fishing of sea breams (FAO, 2018). The Republic of Korea is the fourth largest seafood producer in the world, producing 3.3 million tons in 2015 and exporting seafood worth $1.6 billion in 2016; therefore, aquaculture-associated research is fundamental for Korea. In the present study, the red sea bream (Pagrus major), which belongs to the family Sparidae, which comprises 35 genera, 132 species, and 10 subspecies (de la Herran et al., 2001; NCBI, 2018), was assessed. It is widely distributed in the coastal regions of Korea, Japan, China, and Taiwan (Blanco Gonzalez et al., 2015), commonly on rocky substrates, soft sand, and muddy bottoms. Species of this family are hermaphroditic and mature 4 years after birth, surviving for 10 or more years. This group of fishes is an important resource to better understand the genetics of sexual dimorphism. Another major factor affecting this species is microbial infections, which are dominant in the aquaculture industry and account for a considerable decline in aquaculture production (Nam et al., 2016; Sawayama et al., 2017). Few studies have analyzed the molecular markers associated with these problems. Recently, sexual dimorphism-related genes from the Sparus aurata genome have been profiled, including stage-specific expression (Pauletto et al., 2018), and three other studies have assessed molecular markers associated with microbial and environmental toxicity in the red sea bream (Iida et al., 2016; Hano et al., 2017; Sawayama et al., 2017). However, genome-wide molecular marker characterization is needed to conduct genome selection in breeding schemes (Lopez et al., 2014), which is not possible in P. major, owing to the absence of a reference genome. To the best of our knowledge, only two draft genomes (S. aurata and Spondyliosoma cantharus) are available for the entire Sparidae family, which is the largest clade in class Actinopteri (de la Herran et al., 2001), but there is no draft or reference genome sequence for the genus Pagrus. Therefore, we constructed a draft genome using contig level assembly, with a size of 829.3 Mb, employing the 90X PacBio sequence alone. Value of the Data This draft genome would be considerably useful for detailing the molecular characterization of various breeding-associated problems in species from the family Sparidae as well as other comparative genome mining applications.