The genome of the marine medaka <i>Oryzias melastigma</i>

Kim, Hui-Su; Lee, Bo-Young; Han, Jeonghoon; Jeong, Chang‐Bum; Hwang, Dae‐Sik; Lee, Min Chul; Kang, Hye-Min; Kim, Duck-Hyun; Lee, Daehwan; Kim, Jaebum; Choi, Ik‐Young; Lee, Jae‐Seong

doi:10.1111/1755-0998.12769

Cited by 39 publications

(27 citation statements)

References 60 publications

(59 reference statements)

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“…For instance, Malmstrøm and colleagues [ 13 ] reported the genome of 66 teleost species, in which 48 genomes showed between 33 and 84% (complete and fragmented) of the genes present in the Actinopterygii library. A combination of short and long read provides, however, a higher detection of BUSCO scores, and should be pursued in the near future [ 29 , 30 , 31 , 32 ]. To further determine the genome completeness, we mapped the de novo assembled liver transcriptome against the genome with Blat [ 33 ].…”

Section: Methods Results and Discussionmentioning

confidence: 99%

“Out of the Can”: A Draft Genome Assembly, Liver Transcriptome, and Nutrigenomics of the European Sardine, Sardina pilchardus

Machado

Tørresen

Kabeya

et al. 2018

Genes

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Clupeiformes, such as sardines and herrings, represent an important share of worldwide fisheries. Among those, the European sardine (Sardina pilchardus, Walbaum 1792) exhibits significant commercial relevance. While the last decade showed a steady and sharp decline in capture levels, recent advances in culture husbandry represent promising research avenues. Yet, the complete absence of genomic resources from sardine imposes a severe bottleneck to understand its physiological and ecological requirements. We generated 69 Gbp of paired-end reads using Illumina HiSeq X Ten and assembled a draft genome assembly with an N50 scaffold length of 25,579 bp and BUSCO completeness of 82.1% (Actinopterygii). The estimated size of the genome ranges between 655 and 850 Mb. Additionally, we generated a relatively high-level liver transcriptome. To deliver a proof of principle of the value of this dataset, we established the presence and function of enzymes (Elovl2, Elovl5, and Fads2) that have pivotal roles in the biosynthesis of long chain polyunsaturated fatty acids, essential nutrients particularly abundant in oily fish such as sardines. Our study provides the first omics dataset from a valuable economic marine teleost species, the European sardine, representing an essential resource for their effective conservation, management, and sustainable exploitation.

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Section: Methods Results and Discussionmentioning

confidence: 99%

“Out of the Can”: A Draft Genome Assembly, Liver Transcriptome, and Nutrigenomics of the European Sardine, Sardina pilchardus

Machado

Tørresen

Kabeya

et al. 2018

Genes

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“…2 ), which mapped 90.7% (713 Mb) of the reference genome assembly sequence onto the genetic map ( Table 3 ). Although all SNP markers were extracted by the alignment of RAD sequences against the reference genome of marine medaka (Kim et al 2018), the number of anchored markers were lower than anticipated. Many markers in the LGs were excluded from the integrating process due to inconsistency between the genetic map and reference assembly, indicating possible errors in marker order and/or de novo assembly.…”

Section: Discussionmentioning

confidence: 98%

“…RAD-tag extraction and genotyping were performed with Stacks v.1.47 software (http://creskolab.uoregon.edu/stacks/) (Catchen et al 2011). The sequence reads were aligned to the available reference genome (GCF_002922805.1; Kim et al 2018 ) using GSnap (https://www.gvst.co.uk/gsnap.htm) with default parameters (-t 30 –n 1 –m 5 –i 2), which were converted to BAM files. All RAD-tags catalog from the parental samples were extracted by Stacks using the ref_map.pl pipeline with the parameters –m10 and -P 3 and genotyping was called by the parameters of minimum number of 5 reads to call a homozygous genotype, a minimum minor allele frequency of 0.1 to call a heterozygote, and a maximum minor allele frequency of 0.05 to call a homozygote.…”

Section: Methodsmentioning

confidence: 99%

Construction of High-Resolution RAD-Seq Based Linkage Map, Anchoring Reference Genome, and QTL Mapping of the Sex Chromosome in the Marine Medaka Oryzias melastigma

Lee

Kim

Choi

et al. 2019

Preprint

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Medaka (Oryzias spp.) is an important fish species in ecotoxicology and 31 considered as a model species due to its biological features including small body size and 32 short generation time. Since Japanese medaka Oryzias latipes is a freshwater species with 33 access to an excellent genome resources, the marine medaka Oryzias melastigma is also 34 applicable for marine ecotoxicology. In genome era, a high-density genetic linkage map is a 35 very useful resource in genomic research, providing a means for comparative genomic 36 analysis and verification of de novo genome assembly. In this study, we developed a high-37 density genetic linkage map for O. melastigma using restriction-site associated DNA 38 sequencing (RAD-seq). The genetic map consisted of 24 linkage groups with 2,481 RAD-tag 39 markers. The total map length was 1,784 cM with an average marker space of 0.72 cM. The 40 genetic map was integrated with the reference-assisted chromosome assembly (RACA) of O. 41 melastigma, which anchored 90.7% of the assembled sequence onto the linkage map. The 42 values of complete Benchmarking Universal Single-Copy Orthologs (BUSCO) were similar 43 to RACA assembly but N50 (23.74 Mb; total genome length 779.4 Mb; gap 5.29%) increased 44 to 29.99 Mb (total genome length 778.7 Mb; gap 5.2%). Using MapQTL analysis with a 45 single nucleotide polymorphism markers, we identified a major quantitative trait locus for sex 46 traits on the Om10. The integration of the genetic map with the reference genome of marine 47 medaka will serve as a good resource for studies in molecular toxicology, genomics, 48 CRISPR/Cas9, and epigenetics. 49 50 KEYWORDS Marine medaka, Oryzias melastigma, linkage map, reference genome, sex, 51 quantitative trait locus 52 3 Many fish species are useful for ecotoxicological research, as they indicate an early 53 warning of environmental contamination caused by various aquatic pollutants (Arellano-54 Aguilar et al. 2009). Recently, an increase in the contamination levels in estuaries and coastal 55 water due to anthropogenic pollutants emphasizes the needs for marine sentinel model fish 56 species. Medaka (Oryzias spp.) is an important fish species in ecotoxicology and considered a 57 model species, as its biological features include certain advantages such as small body size 58 and short generation time (Kim et al. 2016). Japanese medaka Oryzias latipes is important 59 and widely used model species for the studies of genetics, evolution, and ecotoxicological 60 study, with abundant genomic resources. Since O. latipes is a freshwater species, their 61 responses to environmental toxicants can be different in those of marine fish (Shi et al. 2008; 62

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“…Fortunately, plummeting cost and numerous advancements in sequencing technologies and bioinformatic algorithms have made assembling of highly sophisticated genomes possible with relatively low cost. Currently, one draft genome of O. melastigma has published based on a reference genome assistant assembling approach [25]. The published genome of O. melastigma was generated using Illumina reads from several libraries, including three paired-end libraries (PE400, PE500 and PE800) and four MP (mate-pair) libraries (MP2kb, MP5kb, MP10kb and MP20kb).…”

Section: Introductionmentioning

confidence: 99%

“…The published genome of O. melastigma was generated using Illumina reads from several libraries, including three paired-end libraries (PE400, PE500 and PE800) and four MP (mate-pair) libraries (MP2kb, MP5kb, MP10kb and MP20kb). Then scaffolds and pseudochromosomes were assembled based on alignment to the chromosomes of Japanese medaka (Oryzias latipes) genome [25]. However, studies have shown that the usage of short Illumina sequencing reads for wholegenome sequencing is a cost-efficient way, but it can also omit the most exciting and perhaps evolutionarily important genome regions [26].…”

Section: Introductionmentioning

confidence: 99%

Long-read sequencing and de novo genome assembly of marine medaka (Oryzias melastigma)

Liang

Saqib

et al. 2020

BMC Genomics

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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 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. 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.

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The genome of the marine medaka Oryzias melastigma

Cited by 39 publications

References 60 publications

“Out of the Can”: A Draft Genome Assembly, Liver Transcriptome, and Nutrigenomics of the European Sardine, Sardina pilchardus

“Out of the Can”: A Draft Genome Assembly, Liver Transcriptome, and Nutrigenomics of the European Sardine, Sardina pilchardus

Construction of High-Resolution RAD-Seq Based Linkage Map, Anchoring Reference Genome, and QTL Mapping of the Sex Chromosome in the Marine Medaka Oryzias melastigma

Long-read sequencing and de novo genome assembly of marine medaka (Oryzias melastigma)

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