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Non-synonymous variation and protein structure of candidate genes associated with selection in farm and wild populations of turbot (Scophthalmus maximus). Sci Rep 2023; 13:3019. [PMID: 36810752 PMCID: PMC9944912 DOI: 10.1038/s41598-023-29826-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 02/10/2023] [Indexed: 02/24/2023] Open
Abstract
Non-synonymous variation (NSV) of protein coding genes represents raw material for selection to improve adaptation to the diverse environmental scenarios in wild and livestock populations. Many aquatic species face variations in temperature, salinity and biological factors throughout their distribution range that is reflected by the presence of allelic clines or local adaptation. The turbot (Scophthalmus maximus) is a flatfish of great commercial value with a flourishing aquaculture which has promoted the development of genomic resources. In this study, we developed the first atlas of NSVs in the turbot genome by resequencing 10 individuals from Northeast Atlantic Ocean. More than 50,000 NSVs where detected in the ~ 21,500 coding genes of the turbot genome, and we selected 18 NSVs to be genotyped using a single Mass ARRAY multiplex on 13 wild populations and three turbot farms. We detected signals of divergent selection on several genes related to growth, circadian rhythms, osmoregulation and oxygen binding in the different scenarios evaluated. Furthermore, we explored the impact of NSVs identified on the 3D structure and functional relationship of the correspondent proteins. In summary, our study provides a strategy to identify NSVs in species with consistently annotated and assembled genomes to ascertain their role in adaptation.
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de la Herrán R, Hermida M, Rubiolo JA, Gómez-Garrido J, Cruz F, Robles F, Navajas-Pérez R, Blanco A, Villamayor PR, Torres D, Sánchez-Quinteiro P, Ramirez D, Rodríguez ME, Arias-Pérez A, Cross I, Duncan N, Martínez-Peña T, Riaza A, Millán A, De Rosa MC, Pirolli D, Gut M, Bouza C, Robledo D, Rebordinos L, Alioto T, Ruíz-Rejón C, Martínez P. A chromosome-level genome assembly enables the identification of the follicule stimulating hormone receptor as the master sex-determining gene in the flatfish Solea senegalensis. Mol Ecol Resour 2023; 23:886-904. [PMID: 36587276 DOI: 10.1111/1755-0998.13750] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 12/23/2022] [Accepted: 12/28/2022] [Indexed: 01/02/2023]
Abstract
Sex determination (SD) shows huge variation among fish and a high evolutionary rate, as illustrated by the Pleuronectiformes (flatfishes). This order is characterized by its adaptation to demersal life, compact genomes and diversity of SD mechanisms. Here, we assembled the Solea senegalensis genome, a flatfish of great commercial value, into 82 contigs (614 Mb) combining long- and short-read sequencing, which were next scaffolded using a highly dense genetic map (28,838 markers, 21 linkage groups), representing 98.9% of the assembly. Further, we established the correspondence between the assembly and the 21 chromosomes by using BAC-FISH. Whole genome resequencing of six males and six females enabled the identification of 41 single nucleotide polymorphism variants in the follicle stimulating hormone receptor (fshr) consistent with an XX/XY SD system. The observed sex association was validated in a broader independent sample, providing a novel molecular sexing tool. The fshr gene displayed differential expression between male and female gonads from 86 days post-fertilization, when the gonad is still an undifferentiated primordium, concomitant with the activation of amh and cyp19a1a, testis and ovary marker genes, respectively, in males and females. The Y-linked fshr allele, which included 24 nonsynonymous variants and showed a highly divergent 3D protein structure, was overexpressed in males compared to the X-linked allele at all stages of gonadal differentiation. We hypothesize a mechanism hampering the action of the follicle stimulating hormone driving the undifferentiated gonad toward testis.
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Affiliation(s)
- Roberto de la Herrán
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Miguel Hermida
- Departamento de Zoología, Genética y Antropología Física; Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Juan Andres Rubiolo
- Departamento de Zoología, Genética y Antropología Física; Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Jèssica Gómez-Garrido
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona, Spain
| | - Fernando Cruz
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona, Spain
| | - Francisca Robles
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Rafael Navajas-Pérez
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Andres Blanco
- Departamento de Zoología, Genética y Antropología Física; Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Paula Rodriguez Villamayor
- Departamento de Zoología, Genética y Antropología Física; Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Dorinda Torres
- Departamento de Zoología, Genética y Antropología Física; Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Pablo Sánchez-Quinteiro
- Departamento de Anatomía, Producción Animal y Ciencias Clínicas Veterinarias Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Daniel Ramirez
- Departamento de Biomedicina, Biotecnología y Salud Pública CASEM - Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Cádiz, Spain
| | - Maria Esther Rodríguez
- Departamento de Biomedicina, Biotecnología y Salud Pública CASEM - Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Cádiz, Spain
| | - Alberto Arias-Pérez
- Departamento de Biomedicina, Biotecnología y Salud Pública CASEM - Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Cádiz, Spain
| | - Ismael Cross
- Departamento de Biomedicina, Biotecnología y Salud Pública CASEM - Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Cádiz, Spain
| | - Neil Duncan
- IRTA Sant Carles de la Rapita, Tarragona, Spain
| | | | - Ana Riaza
- Stolt Sea Farm SA, Departamento I+D, A Coruña, Spain
| | | | - M Cristina De Rosa
- Institute of Chemical Sciences and Technologies "Giulio Natta" (SCITEC) - CNR c/o Catholic University of Rome, Rome, Italy
| | - Davide Pirolli
- Institute of Chemical Sciences and Technologies "Giulio Natta" (SCITEC) - CNR c/o Catholic University of Rome, Rome, Italy
| | - Marta Gut
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona, Spain
| | - Carmen Bouza
- Departamento de Zoología, Genética y Antropología Física; Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Diego Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, UK
| | - Laureana Rebordinos
- Departamento de Biomedicina, Biotecnología y Salud Pública CASEM - Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Cádiz, Spain
| | - Tyler Alioto
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Carmelo Ruíz-Rejón
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Paulino Martínez
- Departamento de Zoología, Genética y Antropología Física; Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
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3
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Huang J, Chen W, Wang Q, Zhang Y, Liu Q, Yang D. Iso-Seq assembly and functional annotation of full-length transcriptome of turbot (Scophthalmus maximus) during bacterial infection. Mar Genomics 2022; 63:100954. [DOI: 10.1016/j.margen.2022.100954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 03/28/2022] [Accepted: 04/19/2022] [Indexed: 10/18/2022]
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Sandoval-Castillo J, Beheregaray LB, Wellenreuther M. Genomic prediction of growth in a commercially, recreationally, and culturally important marine resource, the Australian snapper (Chrysophrys auratus). G3 (BETHESDA, MD.) 2022; 12:jkac015. [PMID: 35100370 PMCID: PMC8896003 DOI: 10.1093/g3journal/jkac015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 01/07/2022] [Indexed: 06/14/2023]
Abstract
Growth is one of the most important traits of an organism. For exploited species, this trait has ecological and evolutionary consequences as well as economical and conservation significance. Rapid changes in growth rate associated with anthropogenic stressors have been reported for several marine fishes, but little is known about the genetic basis of growth traits in teleosts. We used reduced genome representation data and genome-wide association approaches to identify growth-related genetic variation in the commercially, recreationally, and culturally important Australian snapper (Chrysophrys auratus, Sparidae). Based on 17,490 high-quality single-nucleotide polymorphisms and 363 individuals representing extreme growth phenotypes from 15,000 fish of the same age and reared under identical conditions in a sea pen, we identified 100 unique candidates that were annotated to 51 proteins. We documented a complex polygenic nature of growth in the species that included several loci with small effects and a few loci with larger effects. Overall heritability was high (75.7%), reflected in the high accuracy of the genomic prediction for the phenotype (small vs large). Although the single-nucleotide polymorphisms were distributed across the genome, most candidates (60%) clustered on chromosome 16, which also explains the largest proportion of heritability (16.4%). This study demonstrates that reduced genome representation single-nucleotide polymorphisms and the right bioinformatic tools provide a cost-efficient approach to identify growth-related loci and to describe genomic architectures of complex quantitative traits. Our results help to inform captive aquaculture breeding programs and are of relevance to monitor growth-related evolutionary shifts in wild populations in response to anthropogenic pressures.
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Affiliation(s)
- Jonathan Sandoval-Castillo
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
| | - Luciano B Beheregaray
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
| | - Maren Wellenreuther
- School of Biological Sciences, The New Zealand Institute for Plant and Food Research Limited, Nelson 7010, New Zealand
- Seafood Production Group, The School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
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Development of EST-Molecular Markers from RNA Sequencing for Genetic Management and Identification of Growth Traits in Potato Grouper ( Epinephelus tukula). BIOLOGY 2021; 10:biology10010036. [PMID: 33430356 PMCID: PMC7825770 DOI: 10.3390/biology10010036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 12/25/2020] [Accepted: 01/05/2021] [Indexed: 12/16/2022]
Abstract
Simple Summary The potato grouper is a novel aquaculture species in Taiwan. Due to the lack of genetic information concerning this species, we have developed molecular markers based on transcriptome sequencing and further characterized their association with gene diversity and growth traits of this species. Ultimately, these markers could be utilized as accurate and efficient tools for genetic management and marker-assisted selection of potato grouper with distinct growth traits. Abstract The accuracy and efficiency of marker-assisted selection (MAS) has been proven for economically critical aquaculture species. The potato grouper (Epinephelus tukula), a novel cultured grouper species in Taiwan, shows large potential in aquaculture because of its fast growth rate among other groupers. Because of the lack of genetic information for the potato grouper, the first transcriptome and expressed sequence tag (EST)-derived simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers were developed. Initially, the transcriptome was obtained from seven cDNA libraries by using the Illumina platform. De novo transcriptome of the potato grouper yielded 51.34 Gb and 111,490 unigenes. The EST-derived SSR and SNP markers were applied in genetic management, in parentage analysis, and to discover the functional markers of economic traits. The F1 juveniles were identified as siblings from one pair of parents (80 broodstocks). Fast- and slow-growth individuals were analyzed using functional molecular markers and through their association with growth performance. The results revealed that two SNPs were correlated with growth traits. The transcriptome database obtained in this study and its derived SSR and SNP markers may be applied not only for MAS but also to maintain functional gene diversity in the novel cultured grouper.
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Özcan Gökçek E, Işık R. Associations between genetic variants of the insulin-like growth factor I (IGF-I) gene and growth traits in European sea bass (Dicentrarchus labrax, L.). FISH PHYSIOLOGY AND BIOCHEMISTRY 2020; 46:1131-1138. [PMID: 32140978 DOI: 10.1007/s10695-020-00779-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 02/20/2020] [Indexed: 06/10/2023]
Abstract
The IGF-I is a significant peptide hormone to cell growth, development, reproduction, and metabolism of teleost fish. This study was conducted to investigate the IGF-I gene polymorphism and to reveal the association between the genotypes of IGF-I gene and growth traits in 80 harvest size European sea bass (Dicentrarchus labrax, L.) reared in İzmir region of Turkey. The 821 bp long exon 1 and 5' UTR regions of IGF-I gene were amplified, and PCR products were analyzed via DNA sequencing method. Two novel single nucleotide polymorphisms (SNPs) such as g.46672A > G and g.46749C > T in the 5' UTR region of IGF-I gene in the European sea bass were detected for the first time with this study. Associations between the genotypes of IGF-I g.46749C > T locus and body weight were found statistically significant (p < 0.05). The genotypes of IGF-I g.46749C > T and g.46672A > G loci were found significantly associated with total length (p < 0.05). However, both loci did not show significant associations with body width. The studied gene region sequences were entered to NCBI GenBank database with the accession numbers: MK621680-MK621682. Thus, these polymorphisms have a significant effect on the body weight and total length which could be useful for sea bass selection and breeding for marker-assisted selection (MAS) program.
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Affiliation(s)
- Emel Özcan Gökçek
- Faculty of Fisheries, Department of Aquaculture, Ege University, İzmir, Turkey.
| | - Raziye Işık
- Faculty of Agriculture, Department of Agricultural Biotechnology, Tekirdağ Namık Kemal University, Tekirdağ, Turkey
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7
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Aramburu O, Ceballos F, Casanova A, Le Moan A, Hemmer-Hansen J, Bekkevold D, Bouza C, Martínez P. Genomic Signatures After Five Generations of Intensive Selective Breeding: Runs of Homozygosity and Genetic Diversity in Representative Domestic and Wild Populations of Turbot ( Scophthalmus maximus). Front Genet 2020; 11:296. [PMID: 32346384 PMCID: PMC7169425 DOI: 10.3389/fgene.2020.00296] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 03/12/2020] [Indexed: 12/16/2022] Open
Abstract
Massive genotyping of single nucleotide polymorphisms (SNP) has opened opportunities for analyzing the way in which selection shapes genomes. Artificial or natural selection usually leaves genomic signatures associated with selective sweeps around the responsible locus. Strong selective sweeps are most often identified either by lower genetic diversity than the genomic average and/or islands of runs of homozygosity (ROHi). Here, we conducted an analysis of selective sweeps in turbot (Scophthalmus maximus) using two SNP datasets from a Northeastern Atlantic population (36 individuals) and a domestic broodstock (46 individuals). Twenty-six families (∼ 40 offspring per family) from this broodstock and three SNP datasets applying differing filtering criteria were used to adjust ROH calling parameters. The best-fitted genomic inbreeding estimate (FROH) was obtained by the sum of ROH longer than 1 Mb, called using a 21,615 SNP panel, a sliding window of 37 SNPs and one heterozygous SNP per window allowed. These parameters were used to obtain the ROHi distribution in the domestic and wild populations (49 and 0 ROHi, respectively). Regions with higher and lower genetic diversity within each population were obtained using sliding windows of 37 SNPs. Furthermore, those regions were mapped in the turbot genome against previously reported genetic markers associated with QTL (Quantitative Trait Loci) and outlier loci for domestic or natural selection to identify putative selective sweeps. Out of the 319 and 278 windows surpassing the suggestive pooled heterozygosity thresholds (ZHp) in the wild and domestic population, respectively, 78 and 54 were retained under more restrictive ZHp criteria. A total of 116 suggestive windows (representing 19 genomic regions) were linked to either QTL for production traits, or outliers for divergent or balancing selection. Twenty-four of them (representing 3 genomic regions) were retained under stricter ZHp thresholds. Eleven QTL/outlier markers were exclusively found in suggestive regions of the domestic broodstock, 7 in the wild population and one in both populations; one (broodstock) and two (wild) of those were found in significant regions retained under more restrictive ZHp criteria in the broodstock and the wild population, respectively. Genome mining and functional enrichment within regions associated with selective sweeps disclosed relevant genes and pathways related to aquaculture target traits, including growth and immune-related pathways, metabolism and response to hypoxia, which showcases how this genome atlas of genetic diversity can be a valuable resource to look for candidate genes related to natural or artificial selection in turbot populations.
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Affiliation(s)
- Oscar Aramburu
- Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, Lugo, Spain.,Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Francisco Ceballos
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, Johannesburg, South Africa
| | - Adrián Casanova
- Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, Lugo, Spain.,Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Alan Le Moan
- National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | - Jakob Hemmer-Hansen
- National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | - Dorte Bekkevold
- National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | - Carmen Bouza
- Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, Lugo, Spain.,Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Paulino Martínez
- Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, Lugo, Spain.,Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
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8
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Zhou Z, Han K, Wu Y, Bai H, Ke Q, Pu F, Wang Y, Xu P. Genome-Wide Association Study of Growth and Body-Shape-Related Traits in Large Yellow Croaker (Larimichthys crocea) Using ddRAD Sequencing. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:655-670. [PMID: 31332575 DOI: 10.1007/s10126-019-09910-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 06/26/2019] [Indexed: 06/10/2023]
Abstract
Large yellow croaker (Larimichthys crocea) is an economically important marine fish species of China. Due to overfishing and marine pollution, the wild stocks of this croaker have collapsed in the past decades. Meanwhile, the cultured croaker is facing the difficulties of reduced genetic diversity and low growth rate. To explore the molecular markers related to the growth traits of croaker and providing the related SNPs for the marker-assisted selection, we used double-digest restriction-site associated DNA (ddRAD) sequencing to dissect the genetic bases of growth traits in a cultured population and identify the SNPs that associated with important growth traits by GWAS. A total of 220 individuals were genotyped by ddRAD sequencing. After quality control, 27,227 SNPs were identified in 220 samples and used for GWAS analysis. We identified 13 genome-wide significant associated SNPs of growth traits on 8 chromosomes, and the beta P of these SNPs ranged from 0.01 to 0.86. Through the definition of candidate regions and gene annotation, candidate genes related to growth were identified, including important regulators such as fgf18, fgf1, nr3c1, cyp8b1, fabp2, cyp2r1, ppara, and ccm2l. We also identified SNPs and candidate genes that significantly associated with body shape, including bmp7, col1a1, col11a2, and col18a1, which are also economically important traits for large yellow croaker aquaculture. The results provided insights into the genetic basis of growth and body shape in large yellow croaker population and would provide reliable genetic markers for molecular marker-assisted selection in the future. Meanwhile, the result established a basis for our subsequent fine mapping and related gene study.
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Affiliation(s)
- Zhixiong Zhou
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352130, China
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Kunhuang Han
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352130, China
- Key Laboratory of Healthy Mariculture for the East China Sea, Fisheries College, Jimei University, Xiamen, 361021, China
| | - Yidi Wu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Huaqiang Bai
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Qiaozhen Ke
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352130, China
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Fei Pu
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352130, China
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Yilei Wang
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352130, China.
- Key Laboratory of Healthy Mariculture for the East China Sea, Fisheries College, Jimei University, Xiamen, 361021, China.
| | - Peng Xu
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352130, China.
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
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9
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The recognition of development-related genes in the testis and MAGs of time-series Harmonia axyridis adults using a time-series analysis by RNA-seq. Gene 2019; 693:52-60. [PMID: 30699331 DOI: 10.1016/j.gene.2019.01.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 01/13/2019] [Accepted: 01/22/2019] [Indexed: 11/20/2022]
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10
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Transcriptome Dynamics During Turbot Spermatogenesis Predicting the Potential Key Genes Regulating Male Germ Cell Proliferation and Maturation. Sci Rep 2018; 8:15825. [PMID: 30361543 PMCID: PMC6202422 DOI: 10.1038/s41598-018-34149-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 08/23/2018] [Indexed: 01/19/2023] Open
Abstract
Spermatogenesis is a dynamic developmental process in which spermatogonial stem cells proliferate, differentiate and mature into functional spermatozoa. These processes require an accurate gene regulation network. Here, we investigated the dynamic changes that occur during spermatogenesis through a combination of histological and transcriptome analyses of different developmental stages of the testis. We constructed 18 testis transcriptome libraries, and the average length, N50, and GC content of the unigenes were 1,795 bp; 3,240 bp and 49.25%, respectively. Differentially expressed genes (DEGs) that were related to germ cell proliferation and maturation, such as NANOS3, RARs, KIFs, steroid hormone synthesis-related genes and receptor genes, were identified between pairs of testis at different developmental stages. Gene ontology annotation and pathway analyses were conducted on DEGs with specific expression patterns involved in the regulation of spermatogenesis. Nine important pathways such as steroid hormone biosynthesis related to spermatogenesis were identified. A total of 21 modules that ranged from 49 to 7,448 genes were designed by a weighted gene co-expression network analysis. Furthermore, a total of 83 candidate miRNA were identified by computational methods. Our study provides the first transcriptomic evidence for differences in gene expression between different developmental stages of spermatogenesis in turbot (Scophthalmus maximus).
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11
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do Prado FD, Vera M, Hermida M, Bouza C, Pardo BG, Vilas R, Blanco A, Fernández C, Maroso F, Maes GE, Turan C, Volckaert FAM, Taggart JB, Carr A, Ogden R, Nielsen EE, Martínez P. Parallel evolution and adaptation to environmental factors in a marine flatfish: Implications for fisheries and aquaculture management of the turbot ( Scophthalmus maximus). Evol Appl 2018; 11:1322-1341. [PMID: 30151043 PMCID: PMC6099829 DOI: 10.1111/eva.12628] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 02/23/2018] [Indexed: 12/16/2022] Open
Abstract
Unraveling adaptive genetic variation represents, in addition to the estimate of population demographic parameters, a cornerstone for the management of aquatic natural living resources, which, in turn, represent the raw material for breeding programs. The turbot (Scophthalmus maximus) is a marine flatfish of high commercial value living on the European continental shelf. While wild populations are declining, aquaculture is flourishing in southern Europe. We evaluated the genetic structure of turbot throughout its natural distribution range (672 individuals; 20 populations) by analyzing allele frequency data from 755 single nucleotide polymorphism discovered and genotyped by double-digest RAD sequencing. The species was structured into four main regions: Baltic Sea, Atlantic Ocean, Adriatic Sea, and Black Sea, with subtle differentiation apparent at the distribution margins of the Atlantic region. Genetic diversity and effective population size estimates were highest in the Atlantic populations, the area of greatest occurrence, while turbot from other regions showed lower levels, reflecting geographical isolation and reduced abundance. Divergent selection was detected within and between the Atlantic Ocean and Baltic Sea regions, and also when comparing these two regions with the Black Sea. Evidence of parallel evolution was detected between the two low salinity regions, the Baltic and Black seas. Correlation between genetic and environmental variation indicated that temperature and salinity were probably the main environmental drivers of selection. Mining around the four genomic regions consistently inferred to be under selection identified candidate genes related to osmoregulation, growth, and resistance to diseases. The new insights are useful for the management of turbot fisheries and aquaculture by providing the baseline for evaluating the consequences of turbot releases from restocking and farming.
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Affiliation(s)
- Fernanda Dotti do Prado
- Department of Zoology, Genetics and Physical AnthropologyUniversity of Santiago de CompostelaLugoSpain
- CAPES FoundationMinistry of Education of BrazilBrasíliaBrazil
| | - Manuel Vera
- Department of Zoology, Genetics and Physical AnthropologyUniversity of Santiago de CompostelaLugoSpain
| | - Miguel Hermida
- Department of Zoology, Genetics and Physical AnthropologyUniversity of Santiago de CompostelaLugoSpain
| | - Carmen Bouza
- Department of Zoology, Genetics and Physical AnthropologyUniversity of Santiago de CompostelaLugoSpain
| | - Belén G. Pardo
- Department of Zoology, Genetics and Physical AnthropologyUniversity of Santiago de CompostelaLugoSpain
| | - Román Vilas
- Department of Zoology, Genetics and Physical AnthropologyUniversity of Santiago de CompostelaLugoSpain
| | - Andrés Blanco
- Department of Zoology, Genetics and Physical AnthropologyUniversity of Santiago de CompostelaLugoSpain
| | - Carlos Fernández
- Department of Zoology, Genetics and Physical AnthropologyUniversity of Santiago de CompostelaLugoSpain
| | - Francesco Maroso
- Department of Zoology, Genetics and Physical AnthropologyUniversity of Santiago de CompostelaLugoSpain
| | - Gregory E. Maes
- Laboratory of Biodiversity and Evolutionary GenomicsUniversity of LeuvenLeuvenBelgium
- Center for Human GeneticsUZ Leuven‐Genomics Core, KU LeuvenLeuvenBelgium
- Comparative Genomics CentreCollege of Science and EngineeringJames Cook UniversityTownsvilleQLDAustralia
| | - Cemal Turan
- Faculty of Marine Science and TechnologyIskenderun Technical UniversityIskenderunTurkey
| | - Filip A. M. Volckaert
- Laboratory of Biodiversity and Evolutionary GenomicsUniversity of LeuvenLeuvenBelgium
- Center for Human GeneticsUZ Leuven‐Genomics Core, KU LeuvenLeuvenBelgium
- Comparative Genomics CentreCollege of Science and EngineeringJames Cook UniversityTownsvilleQLDAustralia
| | | | | | - Rob Ogden
- Trace Wildlife Forensics NetworkRoyal Zoological Society of ScotlandEdinburghUK
| | - Einar Eg Nielsen
- National Institute of Aquatic ResourcesTechnical University of DenmarkSilkeborgDenmark
| | | | - Paulino Martínez
- Department of Zoology, Genetics and Physical AnthropologyUniversity of Santiago de CompostelaLugoSpain
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12
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Maroso F, Hermida M, Millán A, Blanco A, Saura M, Fernández A, Dalla Rovere G, Bargelloni L, Cabaleiro S, Villanueva B, Bouza C, Martínez P. Highly dense linkage maps from 31 full-sibling families of turbot (Scophthalmus maximus) provide insights into recombination patterns and chromosome rearrangements throughout a newly refined genome assembly. DNA Res 2018; 25:439-450. [PMID: 29897548 PMCID: PMC6105115 DOI: 10.1093/dnares/dsy015] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 05/05/2018] [Indexed: 12/26/2022] Open
Abstract
Highly dense linkage maps enable positioning thousands of landmarks useful for anchoring the whole genome and for analysing genome properties. Turbot is the most important cultured flatfish worldwide and breeding programs in the fifth generation of selection are targeted to improve growth rate, obtain disease resistant broodstock and understand sex determination to control sex ratio. Using a Restriction-site Associated DNA approach, we genotyped 18,214 single nucleotide polymorphism in 1,268 turbot individuals from 31 full-sibling families. Individual linkage maps were combined to obtain a male, female and species consensus maps. The turbot consensus map contained 11,845 markers distributed across 22 linkage groups representing a total normalised length of 3,753.9 cM. The turbot genome was anchored to this map, and scaffolds representing 96% of the assembly were ordered and oriented to obtain the expected 22 megascaffolds according to its karyotype. Recombination rate was lower in males, especially around centromeres, and pairwise comparison of 44 individual maps suggested chromosome polymorphism at specific genomic regions. Genome comparison across flatfish provided new evidence on karyotype reorganisations occurring across the evolution of this fish group.
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Affiliation(s)
| | - M Hermida
- Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | | | - A Blanco
- Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - M Saura
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - A Fernández
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - G Dalla Rovere
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Padova, Italy
| | - L Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Padova, Italy
| | - S Cabaleiro
- Cluster de Acuicultura de Galicia (Punta do Couso), Aguiño-Ribeira, Spain
| | - B Villanueva
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - C Bouza
- Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - P Martínez
- Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
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13
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Schlicht K, Krattenmacher N, Lugert V, Schulz C, Thaller G, Tetens J. Genetic analysis of production traits in turbot (Scophthalmus maximus)
using random regression models based on molecular relatedness. J Anim Breed Genet 2018. [DOI: 10.1111/jbg.12337] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Kristina Schlicht
- Institute of Animal Breeding and Husbandry; Christian-Albrechts-University of Kiel; Kiel Germany
| | - Nina Krattenmacher
- Institute of Animal Breeding and Husbandry; Christian-Albrechts-University of Kiel; Kiel Germany
| | - Vincent Lugert
- Institute of Animal Breeding and Husbandry; Christian-Albrechts-University of Kiel; Kiel Germany
- College of the Marshall Islands; Majuro Marshall Islands
| | - Carsten Schulz
- Institute of Animal Breeding and Husbandry; Christian-Albrechts-University of Kiel; Kiel Germany
- GMA - Gesellschaft für Marine Aquakultur mbH; Büsum Germany
| | - Georg Thaller
- Institute of Animal Breeding and Husbandry; Christian-Albrechts-University of Kiel; Kiel Germany
| | - Jens Tetens
- Department of Animal Sciences; Functional Breeding Group; Georg-August-University Göttingen; Göttingen Germany
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14
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Taboada X, Rey M, Bouza C, Viñas A. Cytogenomic analysis of several repetitive DNA elements in turbot (Scophthalmus maximus). Gene 2018; 644:4-12. [PMID: 29246535 DOI: 10.1016/j.gene.2017.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 11/23/2017] [Accepted: 12/11/2017] [Indexed: 11/29/2022]
Abstract
Repetitive DNA plays a fundamental role in the organization, size and evolution of eukaryotic genomes. The sequencing of the turbot revealed a small and compact genome, as in all flatfish studied to date. The assembly of repetitive regions is still incomplete because it is difficult to correctly identify their position, number and array. The combination of classical cytogenetic techniques along with high quality sequencing is essential to increase the knowledge of the structure and composition of these sequences and, thus, of the structure and function of the whole genome. In this work, the in silico analysis of H1 histone, 5S rDNA, telomeric and Rex repetitive sequences, was compared to their chromosomal mapping by fluorescent in situ hybridization (FISH), providing a more comprehensive picture of these elements in the turbot genome. FISH assays confirmed the location of H1 in LG8; 5S rDNA in LG4 and LG6; telomeric sequences at the end of all chromosomes whereas Rex elements were dispersed along most chromosomes. The discrepancies found between both approaches could be related to the sequencing methodology applied in this species and also to the resolution limitations of the FISH technique. Turbot cytogenomic analyses have proven to add new chromosomal landmarks in the karyotype of this species, representing a powerful tool to investigate targeted genomic sequences or regions in the genetic and physical maps of this species.
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Affiliation(s)
- Xoana Taboada
- Departamento de Zoología, Genética y Antropología Física, Facultad de Biología, CIBUS, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Magalí Rey
- Departamento de Zoología, Genética y Antropología Física, Facultad de Biología, CIBUS, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Carmen Bouza
- Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Ana Viñas
- Departamento de Zoología, Genética y Antropología Física, Facultad de Biología, CIBUS, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
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15
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Li N, Zhou T, Geng X, Jin Y, Wang X, Liu S, Xu X, Gao D, Li Q, Liu Z. Identification of novel genes significantly affecting growth in catfish through GWAS analysis. Mol Genet Genomics 2017; 293:587-599. [PMID: 29230585 DOI: 10.1007/s00438-017-1406-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 12/07/2017] [Indexed: 12/01/2022]
Abstract
Growth is the most important economic trait in aquaculture. Improvements in growth-related traits can enhance production, reduce costs and time to produce market-size fish. Catfish is the major aquaculture species in the United States, accounting for 65% of the US finfish production. However, the genes underlying growth traits in catfish were not well studied. Currently, the majority of the US catfish industry uses hybrid catfish derived from channel catfish female mated with blue catfish male. Interestingly, channel catfish and blue catfish exhibit differences in growth-related traits, and therefore the backcross progenies provide an efficient system for QTL analysis. In this study, we conducted a genome-wide association study for catfish body weight using the 250 K SNP array with 556 backcross progenies generated from backcross of male F1 hybrid (female channel catfish × male blue catfish) with female channel catfish. A genomic region of approximately 1 Mb on linkage group 5 was found to be significantly associated with body weight. In addition, four suggestively associated QTL regions were identified on linkage groups 1, 2, 23 and 24. Most candidate genes in the associated regions are known to be involved in muscle growth and bone development, some of which were reported to be associated with obesity in humans and pigs, suggesting that the functions of these genes may be evolutionarily conserved in controlling growth. Additional fine mapping or functional studies should allow identification of the causal genes for fast growth in catfish, and elucidation of molecular mechanisms of regulation of growth in fish.
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Affiliation(s)
- Ning Li
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Tao Zhou
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Xin Geng
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Yulin Jin
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Xiaozhu Wang
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Shikai Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Xiaoyan Xu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA.,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, 201306, China
| | - Dongya Gao
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Qi Li
- The Shellfish Genetics and Breeding Laboratory, Fisheries College, Ocean University of China, Qingdao, 266003, Shandong, China
| | - Zhanjiang Liu
- Department of Biology, Syracuse University, Syracuse, NY, 13244, USA.
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16
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Veale AJ, Russello MA. Genomic Changes Associated with Reproductive and Migratory Ecotypes in Sockeye Salmon (Oncorhynchus nerka). Genome Biol Evol 2017; 9:2921-2939. [PMID: 29045601 PMCID: PMC5737441 DOI: 10.1093/gbe/evx215] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2017] [Indexed: 12/12/2022] Open
Abstract
Mechanisms underlying adaptive evolution can best be explored using paired populations displaying similar phenotypic divergence, illuminating the genomic changes associated with specific life history traits. Here, we used paired migratory [anadromous vs. resident (kokanee)] and reproductive [shore- vs. stream-spawning] ecotypes of sockeye salmon (Oncorhynchus nerka) sampled from seven lakes and two rivers spanning three catchments (Columbia, Fraser, and Skeena) in British Columbia, Canada to investigate the patterns and processes underlying their divergence. Restriction-site associated DNA sequencing was used to genotype this sampling at 7,347 single nucleotide polymorphisms, 334 of which were identified as outlier loci and candidates for divergent selection within at least one ecotype comparison. Sixty-eight of these outliers were present in two or more comparisons, with 33 detected across multiple catchments. Of particular note, one locus was detected as the most significant outlier between shore and stream-spawning ecotypes in multiple comparisons and across catchments (Columbia, Fraser, and Snake). We also detected several genomic islands of divergence, some shared among comparisons, potentially showing linked signals of differential selection. The single nucleotide polymorphisms and genomic regions identified in our study offer a range of mechanistic hypotheses associated with the genetic basis of O. nerka life history variation and provide novel tools for informing fisheries management.
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Affiliation(s)
- Andrew J. Veale
- Department of Biology, The University of British Columbia, Kelowna, British Columbia, Canada
- Present address: Department of Environmental and Animal Sciences, Unitec, 139 Carrington Rd, Auckland, New Zealand
| | - Michael A. Russello
- Department of Biology, The University of British Columbia, Kelowna, British Columbia, Canada
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17
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Robledo D, Rubiolo JA, Cabaleiro S, Martínez P, Bouza C. Differential gene expression and SNP association between fast- and slow-growing turbot (Scophthalmus maximus). Sci Rep 2017; 7:12105. [PMID: 28935875 PMCID: PMC5608734 DOI: 10.1038/s41598-017-12459-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 09/08/2017] [Indexed: 12/20/2022] Open
Abstract
Growth is among the most important traits for animal breeding. Understanding the mechanisms underlying growth differences between individuals can contribute to improving growth rates through more efficient breeding schemes. Here, we report a transcriptomic study in muscle and brain of fast- and slow-growing turbot (Scophthalmus maximus), a relevant flatfish in European and Asian aquaculture. Gene expression and allelic association between the two groups were explored. Up-regulation of the anaerobic glycolytic pathway in the muscle of fast-growing fish was observed, indicating a higher metabolic rate of white muscle. Brain expression differences were smaller and not associated with major growth-related genes, but with regulation of feeding-related sensory pathways. Further, SNP variants showing frequency differences between fast- and slow-growing fish pointed to genomic regions likely involved in growth regulation, and three of them were individually validated through SNP typing. Although different mechanisms appear to explain growth differences among families, general mechanisms seem also to be involved, and thus, results provide a set of useful candidate genes and markers to be evaluated for more efficient growth breeding programs and to perform comparative genomic studies of growth in fish and vertebrates.
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Affiliation(s)
- Diego Robledo
- Departamento de Zooloxía, Xenética e Antropoloxía Física, Facultade de Veterinaria, Universidade de Santiago de Compostela, 27002, Lugo, Spain.,The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, United Kingdom
| | - Juan A Rubiolo
- Departamento de Zooloxía, Xenética e Antropoloxía Física, Facultade de Veterinaria, Universidade de Santiago de Compostela, 27002, Lugo, Spain
| | - Santiago Cabaleiro
- Cluster de Acuicultura de Galicia (Punta do Couso), Aguiño-Ribeira, 15695, Spain
| | - Paulino Martínez
- Departamento de Zooloxía, Xenética e Antropoloxía Física, Facultade de Veterinaria, Universidade de Santiago de Compostela, 27002, Lugo, Spain
| | - Carmen Bouza
- Departamento de Zooloxía, Xenética e Antropoloxía Física, Facultade de Veterinaria, Universidade de Santiago de Compostela, 27002, Lugo, Spain.
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18
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Robledo D, Hermida M, Rubiolo JA, Fernández C, Blanco A, Bouza C, Martínez P. Integrating genomic resources of flatfish (Pleuronectiformes) to boost aquaculture production. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2016; 21:41-55. [PMID: 28063346 DOI: 10.1016/j.cbd.2016.12.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 12/09/2016] [Accepted: 12/13/2016] [Indexed: 12/15/2022]
Abstract
Flatfish have a high market acceptance thus representing a profitable aquaculture production. The main farmed species is the turbot (Scophthalmus maximus) followed by Japanese flounder (Paralichthys olivaceous) and tongue sole (Cynoglossus semilaevis), but other species like Atlantic halibut (Hippoglossus hippoglossus), Senegalese sole (Solea senegalensis) and common sole (Solea solea) also register an important production and are very promising for farming. Important genomic resources are available for most of these species including whole genome sequencing projects, genetic maps and transcriptomes. In this work, we integrate all available genomic information of these species within a common framework, taking as reference the whole assembled genomes of turbot and tongue sole (>210× coverage). New insights related to the genetic basis of productive traits and new data useful to understand the evolutionary origin and diversification of this group were obtained. Despite a general 1:1 chromosome syntenic relationship between species, the comparison of turbot and tongue sole genomes showed huge intrachromosomic reorganizations. The integration of available mapping information supported specific chromosome fusions along flatfish evolution and facilitated the comparison between species of previously reported genetic associations for productive traits. When comparing transcriptomic resources of the six species, a common set of ~2500 othologues and ~150 common miRNAs were identified, and specific sets of putative missing genes were detected in flatfish transcriptomes, likely reflecting their evolutionary diversification.
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Affiliation(s)
- Diego Robledo
- Department of Zoology, Genetics and Physical Anthropology, Faculty of Biology (CIBUS), Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Miguel Hermida
- Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Juan A Rubiolo
- Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Carlos Fernández
- Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Andrés Blanco
- Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Carmen Bouza
- Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Paulino Martínez
- Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, 27002 Lugo, Spain.
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19
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Identification of Development-Related Genes in the Ovaries of Adult Harmonia axyridis (Pallas) Lady Beetles Using a Time- Series Analysis by RNA-seq. Sci Rep 2016; 6:39109. [PMID: 27966611 PMCID: PMC5155419 DOI: 10.1038/srep39109] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 11/17/2016] [Indexed: 01/10/2023] Open
Abstract
Adults of the lady beetle species Harmonia axyridis (Pallas) are bred artificially en masse for classic biological control, which requires egg-laying by the H. axyridis ovary. Development-related genes may impact the growth of the H. axyridis adult ovary but have not been reported. Here, we used integrative time-series RNA-seq analysis of the ovary in H. axyridis adults to detect development-related genes. A total of 28,558 unigenes were functionally annotated using seven types of databases to obtain an annotated unigene database for ovaries in H. axyridis adults. We also analysed differentially expressed genes (DEGs) between samples. Based on a combination of the results of this bioinformatics analysis with literature reports and gene expression level changes in four different stages, we focused on the development of oocyte reproductive stem cell and yolk formation process and identified 26 genes with high similarity to development-related genes. 20 DEGs were randomly chosen for quantitative real-time PCR (qRT-PCR) to validate the accuracy of the RNA-seq results. This study establishes a robust pipeline for the discovery of key genes using high-throughput sequencing and the identification of a class of development-related genes for characterization.
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