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Eaton KM, Krabbenhoft TJ, Backenstose NJC, Bernal MA. The chromosome-scale reference genome for the pinfish (Lagodon rhomboides) provides insights into their evolutionary and demographic history. G3 (BETHESDA, MD.) 2024; 14:jkae096. [PMID: 38739549 PMCID: PMC11228864 DOI: 10.1093/g3journal/jkae096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 03/18/2024] [Accepted: 05/06/2024] [Indexed: 05/16/2024]
Abstract
The pinfish (Lagodon rhomboides) is an ecologically, economically, and culturally relevant member of the family Sparidae, playing crucial roles in the marine food webs of the western Atlantic Ocean and Gulf of Mexico. Despite their high abundance and ecological importance, there is a scarcity of genomic resources for this species. We assembled and annotated a chromosome-scale genome for the pinfish, resulting in a highly contiguous 785 Mb assembly of 24 scaffolded chromosomes. The high-quality assembly contains 98.9% complete BUSCOs and shows strong synteny to other chromosome-scale genomes of fish in the family Sparidae, with a limited number of large-scale genomic rearrangements. Leveraging this new genomic resource, we found evidence of significant expansions of dietary gene families over the evolutionary history of the pinfish, which may be associated with an ontogenetic shift from carnivory to herbivory seen in this species. Estimates of historical patterns of population demography using this new reference genome identified several periods of population growth and contraction which were associated with ancient climatic shifts and sea level changes. This genome serves as a valuable reference for future studies of population genomics and differentiation and provides a much-needed genomic resource for this western Atlantic sparid.
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Affiliation(s)
- Katherine M Eaton
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Trevor J Krabbenhoft
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
- Research and Education in Energy, Environment, and Water (RENEW) Institute, University at Buffalo, Buffalo, NY 14260, USA
| | | | - Moisés A Bernal
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
- Smithsonian Tropical Research Institute (STRI), Panama City, 0843-03092, Panama
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2
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Kim JW, Kim J, Cho JY, Shin Y, Son H, Sathiyamoorthy S, Kim BS, Kim YO, Kang BC, Kong HJ. Association Between Muscle Growth and Transcription of a Mutant MSTN Gene in Olive Flounder (Paralichthys olivaceus). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024; 26:599-608. [PMID: 38683458 DOI: 10.1007/s10126-024-10322-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 04/22/2024] [Indexed: 05/01/2024]
Abstract
Myostatin (MSTN, also known as growth differentiation factor-8 (GDF-8)), a member of the transforming growth factor β (TGF-β) superfamily, functions as a negative regulator of skeletal muscle development and growth. However, it is also expressed in a wide range of tissues in fish and thus may have more diverse roles in this group than in mammals. In this study, we assessed the genome-wide transcriptional expression pattern associated with the CRISPR/Cas9-mutated MSTN gene in the olive flounder (Paralichthys olivaceus) in association with changes in cell proliferation and transportation processes. There were no differences in the hepatosomatic index, and the growth of male and female fish increased in the F1 progeny of the MSTN mutants. Furthermore, the histopathological analysis showed that myostatin editing resulted in a 41.24% increase in back muscle growth and 46.92% increase in belly muscle growth in male flounder compared with normal flounder, and a 16.01% increase in back muscle growth and 14.26% increase in belly muscle growth in female flounder compared with normal flounder. This study demonstrates that editing of the myostatin gene enhances muscle growth in olive flounder, with a notably more pronounced effect observed in males. Consequently, myostatin-edited male flounder could represent a valuable asset for the flounder aquaculture industry.
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Affiliation(s)
- Ju-Won Kim
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, 46083, Republic of Korea
| | - Julan Kim
- Genetics and Breeding Research Center, National Institute of Fisheries Science, Geoje, 53334, Republic of Korea
| | - Ja Young Cho
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, 46083, Republic of Korea
| | - Younhee Shin
- Research and Development Center, Insilicogen Inc., Yongin-si, 16954, Republic of Korea
| | - Hyojung Son
- Research and Development Center, Insilicogen Inc., Yongin-si, 16954, Republic of Korea
| | | | - Bo-Seong Kim
- Department of Aquatic Life Medicine, Kunsan National University, Gunsan, 54150, Republic of Korea
| | - Young-Ok Kim
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, 46083, Republic of Korea
| | | | - Hee Jeong Kong
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, 46083, Republic of Korea.
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3
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Mitochondrial genomes reveal mid-Pleistocene population divergence, and post-glacial expansion, in Australasian snapper (Chrysophrys auratus). Heredity (Edinb) 2023; 130:30-39. [PMID: 36463371 DOI: 10.1038/s41437-022-00579-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 11/17/2022] [Accepted: 11/17/2022] [Indexed: 12/05/2022] Open
Abstract
Glacial cycles play important roles in determining the phylogeographic structure of terrestrial species, however, relatively little is known about their impacts on the distribution of marine biota. This study utilised modern (n = 350) and ancient (n = 26) mitochondrial genomes from Australasian snapper (Chrysophrys auratus) sampled in New Zealand to assess their demographic and phylogeographic history. We also tested for changes in genetic diversity using the up to 750-year-old mitochondrial genomes from pre-European archaeological sites to assess the potential impacts of human exploitation. Nucleotide diversity and haplotype diversity was high (π = 0.005, h = 0.972). There was no significant change in nucleotide diversity over the last 750 years (p = 0.343), with no detectable loss of diversity as a result of indigenous and industrial-scale fishing activity. While there was no evidence for contemporary population structure (AMOVA, p = 0.764), phylogeographic analyses identified two distinct mitochondrial clades that diverged approximately 650,000 years ago during the mid-Pleistocene, suggesting the species experienced barriers to gene flow when sea levels dropped over 120 m during previous glacial maxima. An exponential population increase was also observed around 8000 years ago consistent with a post-glacial expansion, which was likely facilitated by increased ocean temperatures and rising sea levels. This study demonstrates that glacial cycles likely played an important role in the demographic history of C. auratus and adds to our growing understanding of how dynamic climatic changes have influenced the evolution of coastal marine species.
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Karam Q, Kumar V, Shajan AB, Al-Nuaimi S, Sattari Z, El-Dakour S. De-novo genome assembly and annotation of sobaity seabream Sparidentex hasta. Front Genet 2022; 13:988488. [PMID: 36386818 PMCID: PMC9659893 DOI: 10.3389/fgene.2022.988488] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 10/06/2022] [Indexed: 11/30/2022] Open
Abstract
Sparidentex hasta (Valenciennes, 1830) of the Sparidae family, is an economically important fish species. However, the genomic studies on S. hasta are limited due to the absence of its complete genome. The goal of the current study was to sequence, assemble, and annotate the genome of S. hasta that will fuel further research related to this seabream. The assembled draft genome of S. hasta was 686 Mb with an N50 of 80 Kb. The draft genome contained approximately 22% repeats, and 41,201 genes coding for 44,555 transcripts. Furthermore, the assessment of the assembly completeness was estimated based on the detection of ∼93% BUSCOs at the protein level and alignment of >99% of the filtered reads to the assembled genome. Around 68% of the predicted proteins (n = 30,545) had significant BLAST matches, and 30,473 and 13,244 sequences were mapped to Gene Ontology annotations and different enzyme classes, respectively. The comparative genomics analysis indicated S. hasta to be closely related to Acanthopagrus latus. The current assembly provides a solid foundation for future population and conservation studies of S. hasta as well as for investigations of environmental adaptation in Sparidae family of fishes. Value of the Data: This draft genome of S. hasta would be very applicable for molecular characterization, gene expression studies, and to address various problems associated with pathogen-associated immune response, climate adaptability, and comparative genomics. The accessibility of the draft genome sequence would be useful in understanding the pathways and functions at the molecular level, which may further help in improving the economic value and their conservation.
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Affiliation(s)
- Qusaie Karam
- Crises Management and Decision Support Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait City, Kuwait
| | - Vinod Kumar
- Biotechnology Program, Environment and Life Sciences Research Center, Kuwait Institute ForScientific Research, Kuwait City, Kuwait
| | - Anisha B. Shajan
- Biotechnology Program, Environment and Life Sciences Research Center, Kuwait Institute ForScientific Research, Kuwait City, Kuwait
| | - Sabeeka Al-Nuaimi
- Crises Management and Decision Support Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait City, Kuwait
| | - Zainab Sattari
- Aquaculture Program, Environment and Life Sciences Research Center, Kuwait Institute ForScientific Research, Kuwait City, Kuwait
| | - Saleem El-Dakour
- Aquaculture Program, Environment and Life Sciences Research Center, Kuwait Institute ForScientific Research, Kuwait City, Kuwait
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Murashita K, Takakuwa F, Matsunari H, Yoshinaga H, Yamamoto T, Oku H, Furuita H. Effect of oral administration of a single bolus of six different protein sources on digestive physiology of red seabream Pagrus major juveniles. FISH PHYSIOLOGY AND BIOCHEMISTRY 2022; 48:939-954. [PMID: 35768739 DOI: 10.1007/s10695-022-01096-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 06/24/2022] [Indexed: 06/15/2023]
Abstract
To reveal direct effects of various protein sources on digestive physiology of red seabream, Pagrus major (38.5 ± 0.4 g), six different protein sources of fishmeal (FM), soybean meal (SBM), corn gluten meal (CGM), soy protein concentrate (SPC), poultry by-product meal (PBM), and poultry-feather meal (PFM) were orally administered to fish (2 mg protein/g body weight) and sampled at 1.5 h and 3 h after administration. Gallbladder weight of fish administered FM, PBM, and PFM decreased after administration (p < 0.0001), while no difference was observed in the other ingredients compared to a non-protein sham control group, indicating that animal protein sources could more strongly stimulate bile secretion than plant protein sources in red seabream. Trypsin and chymotrypsin activity in the intestinal content markedly increased by the FM, SBM, and PFM administration (p < 0.0001). Lipase and amylase activity was also increased by FM and SBM but also by CGM for lipase and by PBM and PFM for amylase (p < 0.0001). These indicate that stimulation effect of the secretion of digestive enzymes is largely different among the protein sources. This might be due to the absorptive capacity of the protein source since intestinal absorption parameter genes (anpep, cpa, ggt1, and atp1a2) also increased by the FM, SBM, PBM or PFM (p < 0.05). In addition to the secretion levels of bile and digestive enzymes, gene expression levels of bile related genes (cyp7a1, cyp8b1, and shp) and digestion-regulating genes (casr and cck) were increased by the FM, SBM, PFM, and/or PBM administration, suggesting that animal proteins and SBM could be potent digestive stimulants compared to CGM and SPC. This study first revealed that single protein sources directly influence digestive enzyme secretion and bile secretion in fish. Information about the direct effect of each single source on digestive physiology could help to design feed formulation with less fishmeal.
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Affiliation(s)
- Koji Murashita
- Physiological Function Division, Aquaculture Research Department, Fisheries Technology Institute, Japan Fisheries Research and Education Agency, 224-1 Hiruda, Tamaki, Mie, 519-0423, Japan.
| | - Fumiaki Takakuwa
- Uragami Station, Aquaculture Research Institute, Kindai University, 468-3, Uragami, Nachi-Katsuura, Higashimuro, Wakayama, 649-5145, Japan
| | - Hiroyuki Matsunari
- Physiological Function Division, Aquaculture Research Department, Fisheries Technology Institute, Japan Fisheries Research and Education Agency, 224-1 Hiruda, Tamaki, Mie, 519-0423, Japan
| | - Hazuki Yoshinaga
- Physiological Function Division, Aquaculture Research Department, Fisheries Technology Institute, Japan Fisheries Research and Education Agency, 224-1 Hiruda, Tamaki, Mie, 519-0423, Japan
| | - Takeshi Yamamoto
- Physiological Function Division, Aquaculture Research Department, Fisheries Technology Institute, Japan Fisheries Research and Education Agency, 224-1 Hiruda, Tamaki, Mie, 519-0423, Japan
| | - Hiromi Oku
- Physiological Function Division, Aquaculture Research Department, Fisheries Technology Institute, Japan Fisheries Research and Education Agency, 224-1 Hiruda, Tamaki, Mie, 519-0423, Japan
| | - Hirofumi Furuita
- Physiological Function Division, Aquaculture Research Department, Fisheries Technology Institute, Japan Fisheries Research and Education Agency, 224-1 Hiruda, Tamaki, Mie, 519-0423, Japan
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Sawayama E, Handa Y, Nakano K, Noguchi D, Takagi M, Akiba Y, Sanada S, Yoshizaki G, Usui H, Kawamoto K, Suzuki M, Asahina K. Identification of the causative gene of a transparent phenotype of juvenile red sea bream Pagrus major. Heredity (Edinb) 2021; 127:167-175. [PMID: 34175895 PMCID: PMC8322342 DOI: 10.1038/s41437-021-00448-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Deformities in cultured fish species may be genetic, and identifying causative genes is essential to expand production and maintain farmed animal welfare. We previously reported a genetic deformity in juvenile red sea bream, designated a transparent phenotype. To identify its causative gene, we conducted genome-wide linkage analysis and identified two single nucleotide polymorphisms (SNP) located on LG23 directly linked to the transparent phenotype. The scaffold on which the two SNPs were located contained two candidate genes, duox and duoxa, which are related to thyroid hormone synthesis. Four missense mutations were found in duox and one in duoxa, with that in duoxa showing perfect association with the transparent phenotype. The mutation of duoxa was suggested to affect the transmembrane structure and thyroid-related traits, including an enlarged thyroid gland and immature erythrocytes, and lower thyroxine (T4) concentrations were observed in the transparent phenotype. The transparent phenotype was rescued by T4 immersion. Loss-of-function of duoxa by CRISPR-Cas9 induced the transparent phenotype in zebrafish. Evidence suggests that the transparent phenotype of juvenile red sea bream is caused by the missense mutation of duoxa and that this mutation disrupts thyroid hormone synthesis. The newly identified missense mutation will contribute to effective selective breeding of red sea bream to purge the causative gene of the undesirable phenotype and improve seed production of red sea bream as well as provide basic information of the mechanisms of thyroid hormones and its related diseases in fish and humans.
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Affiliation(s)
- Eitaro Sawayama
- grid.260969.20000 0001 2149 8846Department of Marine Science and Resources, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa Japan
| | | | | | - Daiki Noguchi
- Nippon Total Science, Inc., Fukuyama, Hiroshima Japan
| | - Motohiro Takagi
- grid.255464.40000 0001 1011 3808South Ehime Fisheries Research Center, Ehime University, Ehime, Japan
| | - Yosuke Akiba
- grid.412785.d0000 0001 0695 6482Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Shuwa Sanada
- grid.412785.d0000 0001 0695 6482Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Goro Yoshizaki
- grid.412785.d0000 0001 0695 6482Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Hayato Usui
- grid.260969.20000 0001 2149 8846Department of Marine Science and Resources, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa Japan
| | - Kenta Kawamoto
- grid.260969.20000 0001 2149 8846Department of Marine Science and Resources, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa Japan
| | - Miwa Suzuki
- grid.260969.20000 0001 2149 8846Department of Marine Science and Resources, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa Japan
| | - Kiyoshi Asahina
- grid.260969.20000 0001 2149 8846Department of Marine Science and Resources, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa Japan
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7
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Yu GE, Shin Y, Subramaniyam S, Kang SH, Lee SM, Cho C, Lee SS, Kim CK. Machine learning, transcriptome, and genotyping chip analyses provide insights into SNP markers identifying flower color in Platycodon grandiflorus. Sci Rep 2021; 11:8019. [PMID: 33850210 PMCID: PMC8044237 DOI: 10.1038/s41598-021-87281-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 03/24/2021] [Indexed: 11/27/2022] Open
Abstract
Bellflower is an edible ornamental gardening plant in Asia. For predicting the flower color in bellflower plants, a transcriptome-wide approach based on machine learning, transcriptome, and genotyping chip analyses was used to identify SNP markers. Six machine learning methods were deployed to explore the classification potential of the selected SNPs as features in two datasets, namely training (60 RNA-Seq samples) and validation (480 Fluidigm chip samples). SNP selection was performed in sequential order. Firstly, 96 SNPs were selected from the transcriptome-wide SNPs using the principal compound analysis (PCA). Then, 9 among 96 SNPs were later identified using the Random forest based feature selection method from the Fluidigm chip dataset. Among six machines, the random forest (RF) model produced higher classification performance than the other models. The 9 SNP marker candidates selected for classifying the flower color classification were verified using the genomic DNA PCR with Sanger sequencing. Our results suggest that this methodology could be used for future selection of breeding traits even though the plant accessions are highly heterogeneous.
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Affiliation(s)
- Go-Eun Yu
- Genomics Division, National Institute of Agricultural Sciences, Jeonju, 54874, Korea
| | - Younhee Shin
- Research and Development Center, Insilicogen Inc., Yongin-si 16954, Gyeonggi-do, Republic of Korea
| | | | - Sang-Ho Kang
- Genomics Division, National Institute of Agricultural Sciences, Jeonju, 54874, Korea
| | - Si-Myung Lee
- Genomics Division, National Institute of Agricultural Sciences, Jeonju, 54874, Korea
| | - Chuloh Cho
- Crop Foundation Research Division, National Institute of Crop Science, RDA, Wanju, 55365, Korea
| | - Seung-Sik Lee
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup, 56212, Korea
- Department of Radiation Science and Technology, University of Science and Technology, Daejeon, 34113, Korea
| | - Chang-Kug Kim
- Genomics Division, National Institute of Agricultural Sciences, Jeonju, 54874, Korea.
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Zhu KC, Zhang N, Liu BS, Guo L, Guo HY, Jiang SG, Zhang DC. A chromosome-level genome assembly of the yellowfin seabream (Acanthopagrus latus; Hottuyn, 1782) provides insights into its osmoregulation and sex reversal. Genomics 2021; 113:1617-1627. [PMID: 33839268 DOI: 10.1016/j.ygeno.2021.04.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 12/14/2020] [Accepted: 04/05/2021] [Indexed: 12/15/2022]
Abstract
The yellowfin seabream Acanthopagrus latus is the economically most important Sparidae fish in the northern South China Sea. As euryhaline fish, they are perfect model for investigating osmoregulatory mechanisms in teleosts. Moreover, the reproductive biology of hermaphrodites has long been intriguing; however, little information is known about the molecular pathways underlying their sex change. Here, we report a chromosome level reference genome of A. latus generated by employing the PacBio single molecule sequencing technique (SMRT) and high-throughput chromosome conformation capture (Hi-C) technologies. The draft genome of yellowfin seabream was 806 Mb, with 732 Mb scaffolds anchored on 24 chromosomes. The contig N50 and scaffold N50 were 2.6 Mb and 30.17 Mb, respectively. The assembly is of high integrity and includes 92.23% universal single-copy orthologues based on benchmarking universal single-copy orthologs (BUSCO) analysis. A total of 19,631 protein-coding genes were functionally annotated in the reference genome. Moreover, ARRDC3 and GSTA gene families which related to osmoregulation underwent an extensive expansion in two euryhaline sparids fish genomes compared to other teleost genomes. Moreover, integrating sex-specific transcriptome analyses, several genes related to the transforming growth factor beta (TGF-β) signalling pathway involved in sex differentiation and development. This genomic resource will not only be valuable for studying the osmoregulatory mechanisms in estuarine fish and sex determination in hermaphrodite vertebrate species, but also provide useful genomic tools for facilitating breeding of the yellowfin seabream.
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Affiliation(s)
- Ke-Cheng Zhu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, Guangdong Province, PR China; Tropical Aquaculture Research and Development Center, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Sanya 572018, China
| | - Nan Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, Guangdong Province, PR China; Southern Marine Science and Engineering Guangdong Laboratory(Guangzhou), 511458, Guangzhou, Guangdong Province, PR China; Tropical Aquaculture Research and Development Center, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Sanya 572018, China
| | - Bao-Suo Liu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, Guangdong Province, PR China; Tropical Aquaculture Research and Development Center, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Sanya 572018, China
| | - Liang Guo
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, Guangdong Province, PR China; Southern Marine Science and Engineering Guangdong Laboratory(Guangzhou), 511458, Guangzhou, Guangdong Province, PR China; Tropical Aquaculture Research and Development Center, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Sanya 572018, China
| | - Hua-Yang Guo
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, Guangdong Province, PR China; Tropical Aquaculture Research and Development Center, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Sanya 572018, China
| | - Shi-Gui Jiang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, Guangdong Province, PR China; Southern Marine Science and Engineering Guangdong Laboratory(Guangzhou), 511458, Guangzhou, Guangdong Province, PR China; Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, Guangdong Province, PR China; Sanya Tropical Fisheries Research Institute, Sanya, Hainan Province, China
| | - Dian-Chang Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, Guangdong Province, PR China; Southern Marine Science and Engineering Guangdong Laboratory(Guangzhou), 511458, Guangzhou, Guangdong Province, PR China; Tropical Aquaculture Research and Development Center, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Sanya 572018, China; Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, Guangdong Province, PR China; Sanya Tropical Fisheries Research Institute, Sanya, Hainan Province, China.
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9
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Lee JH, Jung M, Shin Y, Subramaniyam S, Kim IW, Seo M, Kim MA, Kim SH, Hwang J, Choi EH, Hwang UW, Hwang JS. Draft Genome of the Edible Oriental Insect Protaetia brevitarsis seulensis. Front Genet 2021; 11:593994. [PMID: 33519896 PMCID: PMC7838600 DOI: 10.3389/fgene.2020.593994] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 12/10/2020] [Indexed: 01/20/2023] Open
Affiliation(s)
- Joon Ha Lee
- Department of Agricultural Biology, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, South Korea
| | - Myunghee Jung
- Research and Development Center, Insilicogen Inc., Yongin, South Korea
| | - Younhee Shin
- Research and Development Center, Insilicogen Inc., Yongin, South Korea
| | | | - In-Woo Kim
- Department of Agricultural Biology, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, South Korea
| | - Minchul Seo
- Department of Agricultural Biology, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, South Korea
| | - Mi-Ae Kim
- Department of Agricultural Biology, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, South Korea
| | - Seong Hyun Kim
- Department of Agricultural Biology, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, South Korea
| | - Jihye Hwang
- Department of Biology Education, Teachers College and Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu, South Korea
| | - Eun Hwa Choi
- Department of Biology Education, Teachers College and Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu, South Korea
| | - Ui Wook Hwang
- Department of Biology Education, Teachers College and Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu, South Korea
| | - Jae Sam Hwang
- Department of Agricultural Biology, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, South Korea
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10
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Molecular Identification and mRNA Expression Profiles of Galectin-9 Gene in Red Sea Bream ( Pagrus major) Infected with Pathogens. Animals (Basel) 2021; 11:ani11010139. [PMID: 33440635 PMCID: PMC7827478 DOI: 10.3390/ani11010139] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 01/08/2021] [Accepted: 01/08/2021] [Indexed: 11/17/2022] Open
Abstract
Galectin (Gal) is a member of a family of β-galactoside-binding lectin. The members of this family play important roles in the recognition of carbohydrate ligands and in various other biological processes. In this study, we identified the gene encoding Gal-9 in Pagrus major (PmGal-9) and analyzed its expression in various tissues after pathogen challenge. Alignment analysis revealed that the two galactose-binding lectin domains of the deduced protein were highly conserved among all the teleosts. Phylogenetic analysis revealed that PmGal-9 is most closely related to the Gal-9 gene of gilthead sea bream. PmGal-9 was ubiquitously expressed in all tissues analyzed but was predominantly expressed in the spleen, head kidney, and intestine. After challenges with major microbial pathogens (Edwardsiella piscicida, Streptococcus iniae, or red sea bream iridovirus) of red sea bream, PmGal-9 mRNA expression was significantly regulated in most immune-related tissues. These results suggested that PmGal-9 not only plays an important role in the immune system of red sea bream but is also a possible inflammatory marker for pathogenic diseases.
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11
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Kang SH, Pandey RP, Lee CM, Sim JS, Jeong JT, Choi BS, Jung M, Ginzburg D, Zhao K, Won SY, Oh TJ, Yu Y, Kim NH, Lee OR, Lee TH, Bashyal P, Kim TS, Lee WH, Hawkins C, Kim CK, Kim JS, Ahn BO, Rhee SY, Sohng JK. Genome-enabled discovery of anthraquinone biosynthesis in Senna tora. Nat Commun 2020; 11:5875. [PMID: 33208749 PMCID: PMC7674472 DOI: 10.1038/s41467-020-19681-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 10/22/2020] [Indexed: 02/06/2023] Open
Abstract
Senna tora is a widely used medicinal plant. Its health benefits have been attributed to the large quantity of anthraquinones, but how they are made in plants remains a mystery. To identify the genes responsible for plant anthraquinone biosynthesis, we reveal the genome sequence of S. tora at the chromosome level with 526 Mb (96%) assembled into 13 chromosomes. Comparison among related plant species shows that a chalcone synthase-like (CHS-L) gene family has lineage-specifically and rapidly expanded in S. tora. Combining genomics, transcriptomics, metabolomics, and biochemistry, we identify a CHS-L gene contributing to the biosynthesis of anthraquinones. The S. tora reference genome will accelerate the discovery of biologically active anthraquinone biosynthesis pathways in medicinal plants.
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Affiliation(s)
- Sang-Ho Kang
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea.
| | - Ramesh Prasad Pandey
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, Asan, 31460, Republic of Korea
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Chang-Muk Lee
- Metabolic Engineering Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Joon-Soo Sim
- Metabolic Engineering Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Jin-Tae Jeong
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science, RDA, Eumseong, 55365, Republic of Korea
| | - Beom-Soon Choi
- Phyzen Genomics Institute, Seongnam, 13488, Republic of Korea
| | - Myunghee Jung
- Department of Forest Science, College of Agriculture and Life Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Daniel Ginzburg
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Kangmei Zhao
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - So Youn Won
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Tae-Jin Oh
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, Asan, 31460, Republic of Korea
| | - Yeisoo Yu
- Phyzen Genomics Institute, Seongnam, 13488, Republic of Korea
- DNACARE Co. Ltd, Seoul, 06730, Republic of Korea
| | - Nam-Hoon Kim
- Phyzen Genomics Institute, Seongnam, 13488, Republic of Korea
| | - Ok Ran Lee
- Department of Applied Plant Science, College of Agriculture and Life Science, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Tae-Ho Lee
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Puspalata Bashyal
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, Asan, 31460, Republic of Korea
| | - Tae-Su Kim
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, Asan, 31460, Republic of Korea
| | - Woo-Haeng Lee
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, Asan, 31460, Republic of Korea
| | - Charles Hawkins
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Chang-Kug Kim
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Jung Sun Kim
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Byoung Ohg Ahn
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Seung Yon Rhee
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA.
| | - Jae Kyung Sohng
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, Asan, 31460, Republic of Korea.
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12
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Kang SH, Pandey RP, Lee CM, Sim JS, Jeong JT, Choi BS, Jung M, Ginzburg D, Zhao K, Won SY, Oh TJ, Yu Y, Kim NH, Lee OR, Lee TH, Bashyal P, Kim TS, Lee WH, Hawkins C, Kim CK, Kim JS, Ahn BO, Rhee SY, Sohng JK. Genome-enabled discovery of anthraquinone biosynthesis in Senna tora. Nat Commun 2020. [PMID: 33208749 DOI: 10.1101/2020.04.27.063495] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023] Open
Abstract
Senna tora is a widely used medicinal plant. Its health benefits have been attributed to the large quantity of anthraquinones, but how they are made in plants remains a mystery. To identify the genes responsible for plant anthraquinone biosynthesis, we reveal the genome sequence of S. tora at the chromosome level with 526 Mb (96%) assembled into 13 chromosomes. Comparison among related plant species shows that a chalcone synthase-like (CHS-L) gene family has lineage-specifically and rapidly expanded in S. tora. Combining genomics, transcriptomics, metabolomics, and biochemistry, we identify a CHS-L gene contributing to the biosynthesis of anthraquinones. The S. tora reference genome will accelerate the discovery of biologically active anthraquinone biosynthesis pathways in medicinal plants.
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Affiliation(s)
- Sang-Ho Kang
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea.
| | - Ramesh Prasad Pandey
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, Asan, 31460, Republic of Korea
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Chang-Muk Lee
- Metabolic Engineering Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Joon-Soo Sim
- Metabolic Engineering Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Jin-Tae Jeong
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science, RDA, Eumseong, 55365, Republic of Korea
| | - Beom-Soon Choi
- Phyzen Genomics Institute, Seongnam, 13488, Republic of Korea
| | - Myunghee Jung
- Department of Forest Science, College of Agriculture and Life Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Daniel Ginzburg
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Kangmei Zhao
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - So Youn Won
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Tae-Jin Oh
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, Asan, 31460, Republic of Korea
| | - Yeisoo Yu
- Phyzen Genomics Institute, Seongnam, 13488, Republic of Korea
- DNACARE Co. Ltd, Seoul, 06730, Republic of Korea
| | - Nam-Hoon Kim
- Phyzen Genomics Institute, Seongnam, 13488, Republic of Korea
| | - Ok Ran Lee
- Department of Applied Plant Science, College of Agriculture and Life Science, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Tae-Ho Lee
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Puspalata Bashyal
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, Asan, 31460, Republic of Korea
| | - Tae-Su Kim
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, Asan, 31460, Republic of Korea
| | - Woo-Haeng Lee
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, Asan, 31460, Republic of Korea
| | - Charles Hawkins
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Chang-Kug Kim
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Jung Sun Kim
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Byoung Ohg Ahn
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Seung Yon Rhee
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA.
| | - Jae Kyung Sohng
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, Asan, 31460, Republic of Korea.
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13
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Expression of Heat Shock Proteins in Thermally Challenged Pacific Abalone Haliotis discus hannai. Genes (Basel) 2019; 11:genes11010022. [PMID: 31878084 PMCID: PMC7016835 DOI: 10.3390/genes11010022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 12/09/2019] [Accepted: 12/16/2019] [Indexed: 12/12/2022] Open
Abstract
Summer mortality, caused by thermal conditions, is the biggest threat to abalone aquaculture production industries. Various measures have been taken to mitigate this issue by adjusting the environment; however, the cellular processes of Pacific abalone (Haliotis discus hannai) have been overlooked due to the paucity of genetic information. The draft genome of H. discus hannai has recently been reported, prompting exploration of the genes responsible for thermal regulation in Pacific abalone. In this study, 413 proteins were systematically annotated as members of the heat shock protein (HSP) super families, and among them 26 HSP genes from four Pacific abalone tissues (hemocytes, gill, mantle, and muscle) were differentially expressed under cold and heat stress conditions. The co-expression network revealed that HSP expression patterns were tissue-specific and similar to those of other shellfish inhabiting intertidal zones. Finally, representative HSPs were selected at random and their expression patterns were identified by RNA sequencing and validated by qRT-PCR to assess expression significance. The HSPs expressed in hemocytes were highly similar in both analyses, suggesting that hemocytes could be more reliable samples for validating thermal condition markers compared to other tissues.
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Bivagina Pagrosomi Murray (1931) (Monogenea: Polyopisthocotylea), a Microcotylid Infecting the Gills of the Gilt-head Sea Bream Sparus Aurata (Sparidae) from the Red Sea: Morphology and Phylogeny. J Vet Res 2019; 63:345-352. [PMID: 31572814 PMCID: PMC6749742 DOI: 10.2478/jvetres-2019-0053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 08/12/2019] [Indexed: 11/28/2022] Open
Abstract
Introduction Monogenea is a class of ectoparasitic flatworms on the skin, gills, or fins of fish. Microcotylidae is a family of polyopisthocotylean monogeneans parasitising only marine fishes. This work describes and taxonomically determines a microcotylid polyopisthocotylean monogenean in an important fish in Saudi aquaculture. Material and Methods Thirty gilt-head sea bream captured alive from the Red Sea of Saudi Arabia were examined for monogenean infection. Worms were described morphologically and morphometrically by light microscopy and multiple sequence alignments and phylogenetic trees were also constructed after maximum likelihood analysis of the 28S rRNA sequences. Results Seventeen fish were infected by a monogenean parasite in the gill lamellae. It showed a bilobed anterior extremity, two rows of numerous unequal clamps of microcotylid type, and paired muscular vaginae crowned by differently sized spines. The vaginal number and its relative armature suggested the species’ affiliation to group D; the parasite possessed large, muscular vaginae with a full corona of spines over almost the entire width resembling Bivagina pagrosomi Murray (1931). The molecular analysis of the parasite 28s rRNA revealed 97% homology with B. pagrosomi (AJ577461.1). Conclusion The results confirmed the taxonomic status of the parasite recorded. On the basis of morphology and molecular data, we consider that several conclusions on the systematic status of microcotylids from Red Sea fishes in Saudi Arabia should be discussed.
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Nguinkal JA, Brunner RM, Verleih M, Rebl A, de Los Ríos-Pérez L, Schäfer N, Hadlich F, Stüeken M, Wittenburg D, Goldammer T. The First Highly Contiguous Genome Assembly of Pikeperch ( Sander lucioperca), an Emerging Aquaculture Species in Europe. Genes (Basel) 2019; 10:E708. [PMID: 31540274 PMCID: PMC6770990 DOI: 10.3390/genes10090708] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 08/27/2019] [Accepted: 09/08/2019] [Indexed: 01/14/2023] Open
Abstract
The pikeperch (Sander lucioperca) is a fresh and brackish water Percid fish natively inhabiting the northern hemisphere. This species is emerging as a promising candidate for intensive aquaculture production in Europe. Specific traits like cannibalism, growth rate and meat quality require genomics based understanding, for an optimal husbandry and domestication process. Still, the aquaculture community is lacking an annotated genome sequence to facilitate genome-wide studies on pikeperch. Here, we report the first highly contiguous draft genome assembly of Sander lucioperca. In total, 413 and 66 giga base pairs of DNA sequencing raw data were generated with the Illumina platform and PacBio Sequel System, respectively. The PacBio data were assembled into a final assembly size of ~900 Mb covering 89% of the 1,014 Mb estimated genome size. The draft genome consisted of 1966 contigs ordered into 1,313 scaffolds. The contig and scaffold N50 lengths are 3.0 Mb and 4.9 Mb, respectively. The identified repetitive structures accounted for 39% of the genome. We utilized homologies to other ray-finned fishes, and ab initio gene prediction methods to predict 21,249 protein-coding genes in the Sander lucioperca genome, of which 88% were functionally annotated by either sequence homology or protein domains and signatures search. The assembled genome spans 97.6% and 96.3% of Vertebrate and Actinopterygii single-copy orthologs, respectively. The outstanding mapping rate (99.9%) of genomic PE-reads on the assembly suggests an accurate and nearly complete genome reconstruction. This draft genome sequence is the first genomic resource for this promising aquaculture species. It will provide an impetus for genomic-based breeding studies targeting phenotypic and performance traits of captive pikeperch.
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Affiliation(s)
- Julien Alban Nguinkal
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
| | - Ronald Marco Brunner
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
| | - Marieke Verleih
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
| | - Alexander Rebl
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
| | - Lidia de Los Ríos-Pérez
- Institute of Genetics and Biometry, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
| | - Nadine Schäfer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
| | - Frieder Hadlich
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
| | - Marcus Stüeken
- State Research Center of Agriculture and Fisheries M-V, 17194 Hohen Wangelin, Germany.
| | - Dörte Wittenburg
- Institute of Genetics and Biometry, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
| | - Tom Goldammer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
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16
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Whole genome sequencing reveals the impact of recent artificial selection on red sea bream reared in fish farms. Sci Rep 2019; 9:6487. [PMID: 31019228 PMCID: PMC6482192 DOI: 10.1038/s41598-019-42988-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 04/10/2019] [Indexed: 01/17/2023] Open
Abstract
Red sea bream, a popular fish resource in Korea and Japan, is being bred in fish farms of the two countries. It is hypothesized that the genomes of red sea bream are influenced by decades of artificial selection. This study investigates the impact of artificial selection on genomes of red sea bream. Whole genome sequencing was conducted for 40 samples of red sea bream either from Ehime, Nagasaki and Tongyeong fish farms or from the wild. Population stratification based on whole genome data was investigated and the genomic regions of fish farm populations under selection were identified using XP-EHH and relative nucleotide diversity. Gene ontology analysis revealed that different functions were enriched in different fish farms. In conclusion, this study highlights the difference between independently cultured red sea bream populations by showing that influence of artificial selection acted upon completely different genes related to different functions including metabolic and developmental processes.
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