1
|
Villarreal F, Burguener GF, Sosa EJ, Stocchi N, Somoza GM, Turjanski AG, Blanco A, Viñas J, Mechaly AS. Genome sequencing and analysis of black flounder (Paralichthys orbignyanus) reveals new insights into Pleuronectiformes genomic size and structure. BMC Genomics 2024; 25:297. [PMID: 38509481 PMCID: PMC10956332 DOI: 10.1186/s12864-024-10081-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 02/02/2024] [Indexed: 03/22/2024] Open
Abstract
Black flounder (Paralichthys orbignyanus, Pleuronectiformes) is a commercially significant marine fish with promising aquaculture potential in Argentina. Despite extensive studies on Black flounder aquaculture, its limited genetic information available hampers the crucial role genetics plays in the development of this activity. In this study, we first employed Illumina sequencing technology to sequence the entire genome of Black flounder. Utilizing two independent libraries-one from a female and another from a male-with 150 bp paired-end reads, a mean insert length of 350 bp, and over 35 X-fold coverage, we achieved assemblies resulting in a genome size of ~ 538 Mbp. Analysis of the assemblies revealed that more than 98% of the core genes were present, with more than 78% of them having more than 50% coverage. This indicates a somehow complete and accurate genome at the coding sequence level. This genome contains 25,231 protein-coding genes, 445 tRNAs, 3 rRNAs, and more than 1,500 non-coding RNAs of other types. Black flounder, along with pufferfishes, seahorses, pipefishes, and anabantid fish, displays a smaller genome compared to most other teleost groups. In vertebrates, the number of transposable elements (TEs) is often correlated with genome size. However, it remains unclear whether the sizes of introns and exons also play a role in determining genome size. Hence, to elucidate the potential factors contributing to this reduced genome size, we conducted a comparative genomic analysis between Black flounder and other teleost orders to determine if the small genomic size could be explained by repetitive elements or gene features, including the whole genome genes and introns sizes. We show that the smaller genome size of flounders can be attributed to several factors, including changes in the number of repetitive elements, and decreased gene size, particularly due to lower amount of very large and small introns. Thus, these components appear to be involved in the genome reduction in Black flounder. Despite these insights, the full implications and potential benefits of genome reduction in Black flounder for reproduction and aquaculture remain incompletely understood, necessitating further research.
Collapse
Affiliation(s)
- Fernando Villarreal
- Facultad de Ciencias Exactas y Naturales, Instituto de Investigaciones Biológicas (IIB-CONICET-UNMdP), Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
| | - Germán F Burguener
- Plataforma de Bioinformática Argentina, Facultad de Ciencias Exactas y Naturales, Instituto de Cálculo, UBA, Pabellón 2, Ciudad Universitaria, Buenos Aires, Argentina
| | - Ezequiel J Sosa
- Plataforma de Bioinformática Argentina, Facultad de Ciencias Exactas y Naturales, Instituto de Cálculo, UBA, Pabellón 2, Ciudad Universitaria, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Ciudad Universitaria, Buenos Aires, Argentina
| | - Nicolas Stocchi
- Facultad de Ciencias Exactas y Naturales, Instituto de Investigaciones Biológicas (IIB-CONICET-UNMdP), Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
| | - Gustavo M Somoza
- Instituto Tecnológico de Chascomús (CONICET-UNSAM), Chascomús, Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (UNSAM), Buenos Aires, Argentina
| | - Adrián G Turjanski
- Plataforma de Bioinformática Argentina, Facultad de Ciencias Exactas y Naturales, Instituto de Cálculo, UBA, Pabellón 2, Ciudad Universitaria, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Ciudad Universitaria, Buenos Aires, Argentina
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Andrés Blanco
- Facultade de Veterinaria, Universidade de Santiago de Compostela, Santiago de Compostela, Lugo, Spain
- Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Campus Terra, Universidade de Santiago de Compostela, Lugo, Spain
| | - Jordi Viñas
- Laboratori d'Ictiologia Genètica, Departament de Biologia, Universitat de Girona, Maria Aurèlia Campmany, 40, Girona, Spain
| | - Alejandro S Mechaly
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC-CONICET), Mar del Plata, Argentina.
- Fundación Para Investigaciones Biológicas Aplicadas (FIBA), Mar del Plata, Argentina.
| |
Collapse
|
2
|
Yang Y, Li H, Qian C. Analysis of the implementation effects of ecological restoration projects based on carbon storage and eco-environmental quality: A case study of the Yellow River Delta, China. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 340:117929. [PMID: 37086561 DOI: 10.1016/j.jenvman.2023.117929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 04/03/2023] [Accepted: 04/10/2023] [Indexed: 05/03/2023]
Abstract
As an important means to address global climate change and land-use/land-cover (LULC) change, ecological restoration projects (ERPs) have a large effect on carbon storage functions and eco-environmental quality. However, the various ERPs carried out in the Yellow River Delta region have important implications for ecological security strategies in China. Therefore, based on land-use data and remote sensing image data, with the help of ArcGIS and Google Earth Engine (GEE) platforms, this study uses the Integrated Valuation of Ecosystem Services and Trade-offs (InVEST) model, an improved remote sensing ecological index (RSEI) model and other methods to deeply examine the evolutionary trends of eco-environmental quality and carbon storage during the implementation of ERPs in the Yellow River Delta and selects key implementation areas for in-depth analysis to determine the implementation effects of ERPs. Our findings suggested that the RSEI and carbon storage levels in the study area had opposite evolutionary trends from 2001 to 2020. Among them, the RSEI showed a fluctuating upwards trend (0.4461 (2001) and 0.5185 (2020)), while the total carbon stock showed a fluctuating downwards trend (30.67 Tg (2001) and 26.40 Tg (2020)). However, from 2015 to 2020, the RSEI and carbon storage were at a relatively stable level, which indirectly indicated that the ERPs carried out during the period from 2015 to 2020 had achieved a good comprehensive implementation effect. In addition, the areas with better improvement effects from 2015 to 2020 were primarily located in the mouth of the Yellow River Delta (Areas C and D), and their RSEI and the total carbon stock showed a certain upwards trend. This research can promote the formulation of the management strategy of ERPs in the Yellow River Delta, which is of tremendous importance to the ecological environmental preservation and high-quality development of the Yellow River Basin.
Collapse
Affiliation(s)
- Yijia Yang
- Institute of Management Engineering, Qingdao University of Technology, Qingdao, 266525, China; College of Resources & Environment, Northeast Agricultural University, Harbin, 150030, China.
| | - Huiying Li
- Institute of Management Engineering, Qingdao University of Technology, Qingdao, 266525, China
| | - Cheng Qian
- Institute of Management Engineering, Qingdao University of Technology, Qingdao, 266525, China
| |
Collapse
|
3
|
Liu Z, Liu P, Cui T, Chen X, Wang B, Gao C, Wang Z, Li C, Yang N. Genome-wide identification and functional characterization of inhibitor of nuclear factor-κB (IκB) kinase (IKK) in turbot (Scophthalmus maximus). FISH & SHELLFISH IMMUNOLOGY 2023; 134:108619. [PMID: 36803778 DOI: 10.1016/j.fsi.2023.108619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 02/13/2023] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
The inhibitor of nuclear factor-κB (IκB) kinase (IKK) is involved in a variety of intracellular cell signaling pathways and is an important component of the NF-κB signaling pathway. IKK genes have been suggested to play important roles in the innate immune response to pathogen infection in both vertebrates and invertebrates. However, little information is available about IKK genes in turbot (Scophthalmus maximus). In this study, six IKK genes were identified including SmIKKα, SmIKKα2, SmIKKβ, SmIKKε, SmIKKγ, and SmTBK1. The IKK genes of turbot showed the highest identity and similarity with Cynoglossus semilaevis. Then, phylogenetic analysis showed that the IKK genes of turbot were most closely related to C. semilaevis. In addition, IKK genes were widely expressed in all the examined tissues. Meanwhile, the expression patterns of IKK genes were investigated by QRT-PCR after Vibrio anguillarum and Aeromonas salmonicida infection. The results showed that IKK genes had varying expression patterns in mucosal tissues after bacteria infection, indicating that they may play key roles in maintaining the integrity of the mucosal barrier. Subsequently, protein and protein interaction (PPI) network analysis showed that most proteins interacting with IKK genes were located in the NF-κB signaling pathway. Finally, the double luciferase report and overexpression experiments showed that SmIKKα/SmIKKα2/SmIKKβ involved in the activation of NF-κB in turbot. In summary, our results suggested that IKK genes of turbot played important roles in the innate immune response of teleost, and provide valuable information for further study of the function of IKK genes.
Collapse
Affiliation(s)
- Zhe Liu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Peng Liu
- Yantai Marine Economic Research Institute, China
| | - Tong Cui
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xuan Chen
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Beibei Wang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Chengbin Gao
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Zhongyi Wang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Chao Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China.
| | - Ning Yang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China.
| |
Collapse
|
4
|
Identification of stress-related genes by co-expression network analysis based on the improved turbot genome. Sci Data 2022; 9:374. [PMID: 35768602 PMCID: PMC9243025 DOI: 10.1038/s41597-022-01458-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 06/07/2022] [Indexed: 02/07/2023] Open
Abstract
Turbot (Scophthalmus maximus), commercially important flatfish species, is widely cultivated in Europe and China. With the continuous expansion of the intensive breeding scale, turbot is exposed to various stresses, which greatly impedes the healthy development of turbot industry. Here, we present an improved high-quality chromosome-scale genome assembly of turbot using a combination of PacBio long-read and Illumina short-read sequencing technologies. The genome assembly spans 538.22 Mb comprising 27 contigs with a contig N50 size of 25.76 Mb. Annotation of the genome assembly identified 104.45 Mb repetitive sequences, 22,442 protein-coding genes and 3,345 ncRNAs. Moreover, a total of 345 stress responsive candidate genes were identified by gene co-expression network analysis based on 14 published stress-related RNA-seq datasets consisting of 165 samples. Significantly improved genome assembly and stress-related candidate gene pool will provide valuable resources for further research on turbot functional genome and stress response mechanism, as well as theoretical support for the development of molecular breeding technology for resistant turbot varieties. Measurement(s) | whole genome sequencing | Technology Type(s) | PacBio long-read and Illumina short-read sequencing technologies |
Collapse
|
5
|
Wang L, Zhang F, Chen Y, Wang S, Chen Z, Zhou Q, Chen S. Molecular cloning, expression analysis of the IgT gene and detection of IgT + B cells in the half-smooth tongue sole (Cynoglossus semilaevis). FISH & SHELLFISH IMMUNOLOGY 2022; 123:113-126. [PMID: 35218973 DOI: 10.1016/j.fsi.2022.02.051] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 02/02/2022] [Accepted: 02/22/2022] [Indexed: 06/14/2023]
Abstract
IgT is a specific Ig isotype in teleosts, which plays extremely important roles in the mucosal immunity of fish. In the present study, the membrane-bound and secretory IgT of the half-smooth tongue sole (Cynoglossus semilaevis) were identified for the first time. The V-D-J-C structure of two forms of csIgT are translated by the same Cτ gene, and the secretory tail and transmembrane domain were encoded through alternative splicing at the 3' end of the Cτ4. The CH regions of csIgT had high similarity with that of other flatfish (P. olivaceus and S. maximus). In healthy C. semilaevis, sIgT and mIgT were mainly expressed in mucus related tissues such as skin, intestine and gill. The transcript levels of sIgT and mIgT mRNA showed a significant induction in the immune-related tissues upon Vibrio Harveyi infection. A polyclonal rabbit anti-csIgT was successfully prepared using the csIgT heavy chain recombinant protein. Using this antibody, we detected the native IgT with the molecular mass at 220 kDa in skin total protein under non-reducing SDS-PAGE condition. Immunofluorescence analysis indicated that IgT+ B lymphocytes were intensively located in the skin, gill, intestine, and head kidney of C. semilaevis. These results suggest that IgT may participate in the immune response of C. semilaevis, which will facilitate the investigations of the immunoglobulins of marine fish.
Collapse
Affiliation(s)
- Lei Wang
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao, 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Fumiao Zhang
- Shandong Normal University, Jinan, 250014, China
| | - Yadong Chen
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao, 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Shuangyan Wang
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao, 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Zhangfan Chen
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao, 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Qian Zhou
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao, 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Songlin Chen
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao, 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| |
Collapse
|
6
|
Guerrero-Cózar I, Gomez-Garrido J, Berbel C, Martinez-Blanch JF, Alioto T, Claros MG, Gagnaire PA, Manchado M. Chromosome anchoring in Senegalese sole (Solea senegalensis) reveals sex-associated markers and genome rearrangements in flatfish. Sci Rep 2021; 11:13460. [PMID: 34188074 PMCID: PMC8242048 DOI: 10.1038/s41598-021-92601-5] [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: 11/21/2020] [Accepted: 06/07/2021] [Indexed: 11/16/2022] Open
Abstract
The integration of physical and high-density genetic maps is a very useful approach to achieve chromosome-level genome assemblies. Here, the genome of a male Senegalese sole (Solea senegalensis) was de novo assembled and the contigs were anchored to a high-quality genetic map for chromosome-level scaffolding. Hybrid assembled genome was 609.3 Mb long and contained 3403 contigs with a N50 of 513 kb. The linkage map was constructed using 16,287 informative SNPs derived from ddRAD sequencing in 327 sole individuals from five families. Markers were assigned to 21 linkage groups with an average number of 21.9 markers per megabase. The anchoring of the physical to the genetic map positioned 1563 contigs into 21 pseudo-chromosomes covering 548.6 Mb. Comparison of genetic and physical distances indicated that the average genome-wide recombination rate was 0.23 cM/Mb and the female-to-male ratio 1.49 (female map length: 2,698.4 cM, male: 2,036.6 cM). Genomic recombination landscapes were different between sexes with crossovers mainly concentrated toward the telomeres in males while they were more uniformly distributed in females. A GWAS analysis using seven families identified 30 significant sex-associated SNP markers located in linkage group 18. The follicle-stimulating hormone receptor appeared as the most promising locus associated with sex within a region with very low recombination rates. An incomplete penetrance of sex markers with males as the heterogametic sex was determined. An interspecific comparison with other Pleuronectiformes genomes identified a high sequence similarity between homologous chromosomes, and several chromosomal rearrangements including a lineage-specific Robertsonian fusion in S. senegalensis.
Collapse
Affiliation(s)
- Israel Guerrero-Cózar
- IFAPA Centro El Toruño, Junta de Andalucía, Camino Tiro Pichón s/n, 11500 El Puerto de Santa María, Cádiz, Spain
| | - Jessica Gomez-Garrido
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
| | - Concha Berbel
- IFAPA Centro El Toruño, Junta de Andalucía, Camino Tiro Pichón s/n, 11500 El Puerto de Santa María, Cádiz, Spain
| | - Juan F Martinez-Blanch
- Biopolis S.L.-ADM, Parc Cientific Universidad De Valencia, Edif. 2, C/ Catedrático Agustín Escardino Benlloch, 9, 46980, Paterna, Spain
| | - Tyler Alioto
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
| | - M Gonzalo Claros
- Department of Molecular Biology and Biochemistry, Universidad de Málaga, 29071, Málaga, Spain
- CIBER de Enfermedades Raras (CIBERER), 29071, Málaga, Spain
- Institute of Biomedical Research in Málaga (IBIMA), IBIMA-RARE, 29010, Málaga, Spain
- Instituto de Hortofruticultura Subtropical Y Mediterránea (IHSM-UMA-CSIC), 29010, Málaga, Spain
| | | | - Manuel Manchado
- IFAPA Centro El Toruño, Junta de Andalucía, Camino Tiro Pichón s/n, 11500 El Puerto de Santa María, Cádiz, Spain.
- Crecimiento Azul, Centro IFAPA El Toruño, Unidad Asociada al CSIC, El Puerto de Santa María, Spain.
| |
Collapse
|
7
|
Rossi AR. Fish Cytogenetics: Present and Future. Genes (Basel) 2021; 12:genes12070983. [PMID: 34203124 PMCID: PMC8305243 DOI: 10.3390/genes12070983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 06/24/2021] [Indexed: 11/16/2022] Open
Affiliation(s)
- Anna Rita Rossi
- Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza-Università di Roma, Via Alfonso Borelli 50, 00161 Rome, Italy
| |
Collapse
|
8
|
Martínez P, Robledo D, Taboada X, Blanco A, Moser M, Maroso F, Hermida M, Gómez-Tato A, Álvarez-Blázquez B, Cabaleiro S, Piferrer F, Bouza C, Lien S, Viñas AM. A genome-wide association study, supported by a new chromosome-level genome assembly, suggests sox2 as a main driver of the undifferentiatiated ZZ/ZW sex determination of turbot (Scophthalmus maximus). Genomics 2021; 113:1705-1718. [PMID: 33838278 DOI: 10.1016/j.ygeno.2021.04.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/20/2021] [Accepted: 04/05/2021] [Indexed: 01/10/2023]
Abstract
BACKGROUND Understanding sex determination (SD) across taxa is a major challenge for evolutionary biology. The new genomic tools are paving the way to identify genomic features underlying SD in fish, a group frequently showing limited sex chromosome differentiation and high SD evolutionary turnover. Turbot (Scophthalmus maximus) is a commercially important flatfish with an undifferentiated ZW/ZZ SD system and remarkable sexual dimorphism. Here we describe a new long-read turbot genome assembly used to disentangle the genetic architecture of turbot SD by combining genomics and classical genetics approaches. RESULTS The new turbot genome assembly consists of 145 contigs (N50 = 22.9 Mb), 27 of them representing >95% of its estimated genome size. A genome wide association study (GWAS) identified a ~ 6.8 Mb region on chromosome 12 associated with sex in 69.4% of the 36 families analyzed. The highest associated markers flanked sox2, the only gene in the region showing differential expression between sexes before gonad differentiation. A single SNP showed consistent differences between Z and W chromosomes. The analysis of a broad sample of families suggested the presence of additional genetic and/or environmental factors on turbot SD. CONCLUSIONS The new chromosome-level turbot genome assembly, one of the most contiguous fish assemblies to date, facilitated the identification of sox2 as a consistent candidate gene putatively driving SD in this species. This chromosome SD system barely showed any signs of differentiation, and other factors beyond the main QTL seem to control SD in a certain proportion of families.
Collapse
Affiliation(s)
- Paulino Martínez
- Departament of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, Campus de Lugo, 27002 Lugo, Spain.
| | - Diego Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK.
| | - Xoana Taboada
- Departament of Zoology, Genetics and Physical Anthropology, Faculty of Biology, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Andrés Blanco
- Departament of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, Campus de Lugo, 27002 Lugo, Spain.
| | - Michel Moser
- Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway.
| | - Francesco Maroso
- Department of Life Science and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
| | - Miguel Hermida
- Departament of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, Campus de Lugo, 27002 Lugo, Spain.
| | - Antonio Gómez-Tato
- Departament of Mathematics, Faculty of Mathematics, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
| | - Blanca Álvarez-Blázquez
- Instituto Español de Oceanografía (IEO), Centro Oceanográfico de Vigo, Cabo Estay-Canido, 36280 Vigo, Spain.
| | - Santiago Cabaleiro
- Cluster de Acuicultura de Galicia (Punta do Couso), Aguiño-Ribeira, 15695 A Coruña, Spain.
| | - Francesc Piferrer
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), 08003 Barcelona, Spain.
| | - Carmen Bouza
- Departament of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, Campus de Lugo, 27002 Lugo, Spain.
| | - Sigbjørn Lien
- Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway.
| | - Ana M Viñas
- Departament of Zoology, Genetics and Physical Anthropology, Faculty of Biology, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
| |
Collapse
|
9
|
Development of whole-genome multiplex assays and construction of an integrated genetic map using SSR markers in Senegalese sole. Sci Rep 2020; 10:21905. [PMID: 33318526 PMCID: PMC7736592 DOI: 10.1038/s41598-020-78397-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 11/20/2020] [Indexed: 11/08/2022] Open
Abstract
The Senegalese sole (Solea senegalensis) is an economically important flatfish species. In this study, a genome draft was analyzed to identify microsatellite (SSR) markers for whole-genome genotyping. A subset of 224 contigs containing SSRs were preselected and validated by using a de novo female hybrid assembly. Overall, the SSR density in the genome was 886.7 markers per megabase of genomic sequences and the dinucleotide motif was the most abundant (52.4%). In silico comparison identified a set of 108 SSRs (with di-, tetra- or pentanucleotide motifs) widely distributed in the genome and suitable for primer design. A total of 106 markers were structured in thirteen multiplex PCR assays (with up to 10-plex) and the amplification conditions were optimized with a high-quality score. Main genetic diversity statistics and genotyping reliability were assessed. A subset of 40 high polymorphic markers were selected to optimize four supermultiplex PCRs (with up to 11-plex) for pedigree analysis. Theoretical exclusion probabilities and real parentage allocation tests using parent–offspring information confirmed their robustness and effectiveness for parental assignment. These new SSR markers were combined with previously published SSRs (in total 229 makers) to construct a new and improved integrated genetic map containing 21 linkage groups that matched with the expected number of chromosomes. Synteny analysis with respect to C. semilaevis provided new clues on chromosome evolution in flatfish and the formation of metacentric and submetacentric chromosomes in Senegalese sole.
Collapse
|