Long-read sequencing and de novo genome assembly of marine medaka ( Oryzias melastigma )
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RESEARCH ARTICLE
Open Access
Long-read sequencing and de novo genome assembly of marine medaka (Oryzias melastigma) Pingping Liang1, Hafiz Sohaib Ahmed Saqib2, Xiaomin Ni1,3 and Yingjia Shen1*
Abstract Background: 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. Results: In 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 linkedreads. 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. Conclusions: The 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. Keywords: de novo genome assembly, Marine ecotoxicology, Pacific biosciences SMRT sequencing, Transposable elements
Background 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 [1–3]. 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. Furthermore, the ecotoxicological impacts of pollutants are different on inhabiting * Correspondence: [email protected] 1 College of the Environment and Ecology, Xiamen University, Xiamen 361102, China Full list of author information is available at the end of the article
flora and fauna between seawater and freshwater ecosystems [4, 5]. Whereas, many characteristics of seawater are dramatically different from those of freshwater (i.e., ionic strength, buoyancy, salinity, density, dissolved oxygen and pH) [6, 7]. These differences modulate the impact of ecotoxicological features of pollutants, such as the packing fraction and size, the bioaccumulation of the pollutants, the distribution and composition of the pollutants in liquid and solid phases [8]. Thus, the rising level of anthropogenic pollutants in coastal and estuaries waters is a
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