Abstract
BackgroundMarine medaka (Oryzias melastigma) is considered as an important ecotoxicological indicator to study the biochemical, physiological and molecular responses of marine organisms towards increasing amount of pollutants in marine and estuarine waters.ResultsIn this study, we reported a high-quality and accurate de novo genome assembly of marine medaka through the integration of single-molecule sequencing, Illumina paired-end sequencing, and 10X Genomics linked-reads. The 844.17 Mb assembly is estimated to cover more than 98% of the genome and is more continuous with fewer gaps and errors than the previous genome assembly. Comparison of O. melastigma with closely related species showed significant expansion of gene families associated with DNA repair and ATP-binding cassette (ABC) transporter pathways. We identified 274 genes that appear to be under significant positive selection and are involved in DNA repair, cellular transportation processes, conservation and stability of the genome. The positive selection of genes and the considerable expansion in gene numbers, especially related to stimulus responses provide strong supports for adaptations of O. melastigma under varying environmental stresses.ConclusionsThe highly contiguous marine medaka genome and comparative genomic analyses will increase our understanding of the underlying mechanisms related to its extraordinary adaptation capability, leading towards acceleration in the ongoing and future investigations in marine ecotoxicology.
Highlights
Marine medaka (Oryzias melastigma) is considered as an important ecotoxicological indicator to study the biochemical, physiological and molecular responses of marine organisms towards increasing amount of pollutants in marine and estuarine waters
Marine medaka is considered as a model organism to illustrate the toxicological impacts on the marine ecosystem
We demonstrated the deployment of long-read sequence technology to generate high-quality, accurate and near to complete draft genome of marine medaka
Summary
Marine medaka (Oryzias melastigma) is considered as an important ecotoxicological indicator to study the biochemical, physiological and molecular responses of marine organisms towards increasing amount of pollutants in marine and estuarine waters. With the rapid development of global industrialization, pollutants, such as oil contaminations and heavy metals, released into the rivers and coastal waters increase every year [1,2,3]. Those pollutions have drawn extensive attention because they are toxic, non-biodegradable, easy to accumulate and they have drastic effects on living organisms and the ecosystem. Several fish species such as tilapia (Oreochromis niloticus) [9], rainbow trout (Oncorhynchus mykiss) [10], Japanese medaka (Oryzias latipes) [11] and zebrafish (Danio rerio) [12] have been widely used as model organisms to study the ecotoxicological impacts on freshwater ecosystems in laboratory experiments.
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